--- _id: '5672' abstract: - lang: eng text: The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits. article_processing_charge: No author: - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine. 2018;215(12):2959-2961. doi:10.1084/jem.20181934 apa: Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934 chicago: Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934. ieee: A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018. ista: Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961. mla: Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:10.1084/jem.20181934. short: A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961. date_created: 2018-12-16T22:59:18Z date_published: 2018-11-20T00:00:00Z date_updated: 2023-09-11T14:12:06Z day: '20' ddc: - '570' department: - _id: MiSi doi: 10.1084/jem.20181934 external_id: isi: - '000451920600002' file: - access_level: open_access checksum: 687beea1d64c213f4cb9e3c29ec11a14 content_type: application/pdf creator: dernst date_created: 2019-02-06T08:49:52Z date_updated: 2020-07-14T12:47:09Z file_id: '5931' file_name: 2018_JournalExperMed_Reversat.pdf file_size: 1216437 relation: main_file file_date_updated: 2020-07-14T12:47:09Z has_accepted_license: '1' intvolume: ' 215' isi: 1 issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: 2959-2961 publication: Journal of Experimental Medicine publication_identifier: issn: - '00221007' publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: IgM's exit route tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 215 year: '2018' ... --- _id: '398' abstract: - lang: eng text: 'Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices.' article_processing_charge: No author: - first_name: Philippe full_name: Dodier, Philippe last_name: Dodier - first_name: Josa full_name: Frischer, Josa last_name: Frischer - first_name: Wei full_name: Wang, Wei last_name: Wang - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Ammar full_name: Mallouhi, Ammar last_name: Mallouhi - first_name: Wolfgang full_name: Serles, Wolfgang last_name: Serles - first_name: Andreas full_name: Gruber, Andreas last_name: Gruber - first_name: Engelbert full_name: Knosp, Engelbert last_name: Knosp - first_name: Gerhard full_name: Bavinzski, Gerhard last_name: Bavinzski citation: ama: Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096 apa: Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096 chicago: Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096. ieee: P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018. ista: Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578. mla: Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096. short: P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578. date_created: 2018-12-11T11:46:15Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-11T14:12:33Z day: '01' department: - _id: BeBi doi: 10.1016/j.wneu.2018.02.096 external_id: isi: - '000432942700070' intvolume: ' 13' isi: 1 language: - iso: eng month: '05' oa_version: None page: e568-e578 publication: World Neurosurgery publication_status: published publisher: Elsevier publist_id: '7431' quality_controlled: '1' scopus_import: '1' status: public title: Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13 year: '2018' ... --- _id: '458' abstract: - lang: eng text: We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem. acknowledgement: DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734] article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Alexander full_name: Bobenko, Alexander last_name: Bobenko citation: ama: Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292 apa: Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7292 chicago: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society. American Mathematical Society, 2018. https://doi.org/10.1090/tran/7292. ieee: A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions of the American Mathematical Society, vol. 370, no. 4. American Mathematical Society, pp. 2825–2854, 2018. ista: Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854. mla: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society, vol. 370, no. 4, American Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292. short: A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854. date_created: 2018-12-11T11:46:35Z date_published: 2018-04-01T00:00:00Z date_updated: 2023-09-11T14:19:12Z day: '01' department: - _id: HeEd doi: 10.1090/tran/7292 ec_funded: 1 external_id: isi: - '000423197800019' intvolume: ' 370' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.04637 month: '04' oa: 1 oa_version: Preprint page: 2825 - 2854 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Transactions of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '7363' quality_controlled: '1' scopus_import: '1' status: public title: Incircular nets and confocal conics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 370 year: '2018' ... --- _id: '426' abstract: - lang: eng text: Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality. acknowledgement: "Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n" article_processing_charge: No author: - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler orcid: 0000-0002-9547-2494 - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003 apa: Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003 chicago: Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology. Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003. ieee: S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier, pp. 284–290, 2018. ista: Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290. mla: Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90, doi:10.1016/j.jinsphys.2017.12.003. short: S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290. date_created: 2018-12-11T11:46:25Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-12T07:43:26Z day: '01' department: - _id: SyCr doi: 10.1016/j.jinsphys.2017.12.003 external_id: isi: - '000434751100034' intvolume: ' 107' isi: 1 language: - iso: eng month: '05' oa_version: None page: 284-290 publication: Journal of Insect Physiology publication_status: published publisher: Elsevier publist_id: '7397' quality_controlled: '1' scopus_import: '1' status: public title: Individual- and ejaculate-specific sperm traits in ant males type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 107 year: '2018' ... --- _id: '5788' abstract: - lang: eng text: In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games. alternative_title: - LNCS article_processing_charge: No author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - 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: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 citation: ama: 'Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2' apa: 'Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2' chicago: Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2. ieee: G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36. ista: Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36. mla: Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316, Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2. short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36. conference: end_date: 2018-12-17 location: Oxford, UK name: 14th International Conference on Web and Internet Economics, WINE start_date: 2018-12-15 date_created: 2018-12-30T22:59:14Z date_published: 2018-11-21T00:00:00Z date_updated: 2023-09-12T07:44:01Z day: '21' department: - _id: ToHe doi: 10.1007/978-3-030-04612-5_2 external_id: arxiv: - '1804.04372' isi: - '000865933000002' intvolume: ' 11316' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.04372 month: '11' oa: 1 oa_version: Preprint page: 21-36 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory publication_identifier: isbn: - '9783030046118' issn: - '03029743' publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Infinite-duration poorman-bidding games type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11316 year: '2018' ... --- _id: '150' abstract: - lang: eng text: A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1. article_processing_charge: No article_type: original author: - first_name: Robert full_name: Dick, Robert last_name: Dick - first_name: Kaneil K full_name: Zadrozny, Kaneil K last_name: Zadrozny - first_name: Chaoyi full_name: Xu, Chaoyi last_name: Xu - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Terri D full_name: Lyddon, Terri D last_name: Lyddon - first_name: Clifton L full_name: Ricana, Clifton L last_name: Ricana - first_name: Jonathan M full_name: Wagner, Jonathan M last_name: Wagner - first_name: Juan R full_name: Perilla, Juan R last_name: Perilla - first_name: Pornillos Barbie K full_name: Ganser, Pornillos Barbie K last_name: Ganser - first_name: Marc C full_name: Johnson, Marc C last_name: Johnson - first_name: Owen full_name: Pornillos, Owen last_name: Pornillos - first_name: Volker full_name: Vogt, Volker last_name: Vogt citation: ama: Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4 apa: Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4 chicago: Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4. ieee: R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,” Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018. ista: Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512. mla: Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:10.1038/s41586-018-0396-4. short: R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512. date_created: 2018-12-11T11:44:53Z date_published: 2018-08-29T00:00:00Z date_updated: 2023-09-12T07:44:37Z day: '29' department: - _id: FlSc doi: 10.1038/s41586-018-0396-4 external_id: isi: - '000442483400046' pmid: - '30158708' intvolume: ' 560' isi: 1 issue: '7719' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/ month: '08' oa: 1 oa_version: Submitted Version page: 509–512 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 publication_status: published publisher: Nature Publishing Group quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41586-018-0505-4 scopus_import: '1' status: public title: Inositol phosphates are assembly co-factors for HIV-1 type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 560 year: '2018' ... --- _id: '303' abstract: - lang: eng text: The theory of tropical series, that we develop here, firstly appeared in the study of the growth of pluriharmonic functions. Motivated by waves in sandpile models we introduce a dynamic on the set of tropical series, and it is experimentally observed that this dynamic obeys a power law. So, this paper serves as a compilation of results we need for other articles and also introduces several objects interesting by themselves. acknowledgement: The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility grant 168647. Support from the Basic Research Program of the National Research University Higher School of Economics is gratefully acknowledged. The second author, Mikhail Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science Foundation as well as by the National Center of Competence in Research SwissMAP of the Swiss National Science Foundation. article_processing_charge: No author: - first_name: Nikita full_name: Kalinin, Nikita last_name: Kalinin - first_name: Mikhail full_name: Shkolnikov, Mikhail id: 35084A62-F248-11E8-B48F-1D18A9856A87 last_name: Shkolnikov orcid: 0000-0002-4310-178X citation: ama: Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849. doi:10.3934/dcds.2018120 apa: Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. AIMS. https://doi.org/10.3934/dcds.2018120 chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120. ieee: N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6. AIMS, pp. 2827–2849, 2018. ista: Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849. mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120. short: N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series A 38 (2018) 2827–2849. date_created: 2018-12-11T11:45:43Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-12T07:45:37Z day: '01' department: - _id: TaHa doi: 10.3934/dcds.2018120 external_id: arxiv: - '1706.03062' isi: - '000438818400007' intvolume: ' 38' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.03062 month: '06' oa: 1 oa_version: Submitted Version page: 2827 - 2849 publication: Discrete and Continuous Dynamical Systems- Series A publication_status: published publisher: AIMS publist_id: '7576' quality_controlled: '1' scopus_import: '1' status: public title: Introduction to tropical series and wave dynamic on them type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 38 year: '2018' ... --- _id: '14202' abstract: - lang: eng text: "Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions." article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Gideon full_name: Dresdner, Gideon last_name: Dresdner - first_name: Rajiv full_name: Khanna, Rajiv last_name: Khanna - first_name: Isabel full_name: Valera, Isabel last_name: Valera - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch citation: ama: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: Advances in Neural Information Processing Systems. Vol 31. Neural Information Processing Systems Foundation; 2018.' apa: 'Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018). Boosting black box variational inference. In Advances in Neural Information Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.' chicago: Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural Information Processing Systems, Vol. 31. Neural Information Processing Systems Foundation, 2018. ieee: F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 31. ista: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.' mla: Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances in Neural Information Processing Systems, vol. 31, Neural Information Processing Systems Foundation, 2018. short: F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018. conference: end_date: 2018-12-08 location: Montreal, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2018-12-03 date_created: 2023-08-22T14:15:40Z date_published: 2018-06-06T00:00:00Z date_updated: 2023-09-13T07:38:24Z day: '06' department: - _id: FrLo extern: '1' external_id: arxiv: - '1806.02185' intvolume: ' 31' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.02185 month: '06' oa: 1 oa_version: Preprint publication: Advances in Neural Information Processing Systems publication_identifier: eissn: - 1049-5258 isbn: - '9781510884472' publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' scopus_import: '1' status: public title: Boosting black box variational inference type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2018' ... --- _id: '14201' abstract: - lang: eng text: "Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties." alternative_title: - PMLR article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Rajiv full_name: Khanna, Rajiv last_name: Khanna - first_name: Joydeep full_name: Ghosh, Joydeep last_name: Ghosh - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch citation: ama: 'Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.' apa: 'Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.' chicago: 'Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018.' ieee: 'F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.' ista: 'Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.' mla: 'Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.' short: F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472. conference: end_date: 2018-04-11 location: Playa Blanca, Lanzarote name: 'AISTATS: Conference on Artificial Intelligence and Statistics' start_date: 2018-04-09 date_created: 2023-08-22T14:15:20Z date_published: 2018-04-15T00:00:00Z date_updated: 2023-09-13T07:52:40Z day: '15' department: - _id: FrLo extern: '1' external_id: arxiv: - '1708.01733' intvolume: ' 84' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.01733 month: '04' oa: 1 oa_version: Preprint page: 464-472 publication: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: 'Boosting variational inference: An optimization perspective' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 84 year: '2018' ... --- _id: '14198' abstract: - lang: eng text: "High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data." article_processing_charge: No author: - first_name: Vincent full_name: Fortuin, Vincent last_name: Fortuin - first_name: Matthias full_name: Hüser, Matthias last_name: Hüser - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Heiko full_name: Strathmann, Heiko last_name: Strathmann - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch citation: ama: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.' apa: 'Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.' chicago: 'Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.' ieee: 'V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.' ista: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: 'Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.' short: V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018. conference: end_date: 2019-05-09 location: New Orleans, LA, United States name: 'ICLR: International Conference on Learning Representations' start_date: 2019-05-06 date_created: 2023-08-22T14:12:48Z date_published: 2018-06-06T00:00:00Z date_updated: 2023-09-13T06:35:12Z day: '06' department: - _id: FrLo extern: '1' external_id: arxiv: - '1806.02199' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.02199 month: '06' oa: 1 oa_version: Preprint publication: International Conference on Learning Representations publication_status: published quality_controlled: '1' status: public title: 'SOM-VAE: Interpretable discrete representation learning on time series' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '14203' abstract: - lang: eng text: We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework. alternative_title: - PMLR article_processing_charge: No author: - first_name: Alp full_name: Yurtsever, Alp last_name: Yurtsever - first_name: Olivier full_name: Fercoq, Olivier last_name: Fercoq - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Volkan full_name: Cevher, Volkan last_name: Cevher citation: ama: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736.' apa: 'Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.' chicago: Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018. ieee: A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736. ista: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.' mla: Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36. short: A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736. conference: end_date: 2018-07-15 location: Stockholm, Sweden name: 'ICML: International Conference on Machine Learning' start_date: 2018-07-10 date_created: 2023-08-22T14:16:01Z date_published: 2018-07-15T00:00:00Z date_updated: 2023-09-13T08:13:39Z day: '15' department: - _id: FrLo extern: '1' external_id: arxiv: - '1804.08544' intvolume: ' 80' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.08544 month: '07' oa: 1 oa_version: Preprint page: 5727-5736 publication: Proceedings of the 35th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: A conditional gradient framework for composite convex minimization with applications to semidefinite programming type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2018' ... --- _id: '282' abstract: - lang: eng text: Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci. article_processing_charge: No author: - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018 apa: Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018 chicago: Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018. ieee: H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018. ista: Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303. mla: Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018. short: H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303. date_created: 2018-12-11T11:45:36Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-13T08:22:32Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.118.301018 external_id: isi: - '000440014100020' intvolume: ' 209' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/early/2017/11/30/227082 month: '08' oa: 1 oa_version: Submitted Version page: 1279 - 1303 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '7617' quality_controlled: '1' scopus_import: '1' status: public title: Introgression of a block of genome under infinitesimal selection type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 209 year: '2018' ... --- _id: '108' abstract: - lang: eng text: Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \'collision graph\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes. alternative_title: - ISIT Proceedings article_processing_charge: No author: - first_name: Marciej full_name: Obremski, Marciej last_name: Obremski - first_name: Maciej full_name: Skorski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skorski citation: ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654' apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654' chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654. ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.' ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.' mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654. short: M. Obremski, M. Skórski, in:, IEEE, 2018. conference: end_date: 2018-06-22 location: Vail, CO, USA name: 'ISIT: International Symposium on Information Theory' start_date: '2018-06-17 ' date_created: 2018-12-11T11:44:40Z date_published: 2018-08-16T00:00:00Z date_updated: 2023-09-13T08:23:18Z day: '16' department: - _id: KrPi doi: 10.1109/ISIT.2018.8437654 external_id: isi: - '000448139300368' intvolume: ' 2018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/507 month: '08' oa: 1 oa_version: Submitted Version publication_status: published publisher: IEEE publist_id: '7946' quality_controlled: '1' scopus_import: '1' status: public title: Inverted leftover hash lemma type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018 year: '2018' ... --- _id: '14204' abstract: - lang: eng text: Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives. alternative_title: - PMLR article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Anant full_name: Raj, Anant last_name: Raj - first_name: Sai Praneeth full_name: Karimireddy, Sai Praneeth last_name: Karimireddy - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Sebastian U. full_name: Stich, Sebastian U. last_name: Stich - first_name: Martin full_name: Jaggi, Martin last_name: Jaggi citation: ama: 'Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.' apa: Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press. chicago: Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018. ieee: F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207. ista: Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207. mla: Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207. short: F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207. date_created: 2023-08-22T14:16:25Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-09-13T08:19:05Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '1803.09539' intvolume: ' 80' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.09539 month: '07' oa: 1 oa_version: Preprint page: 3198-3207 publication: Proceedings of the 35th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: On matching pursuit and coordinate descent type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2018' ... --- _id: '160' abstract: - lang: eng text: We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: 'Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5' apa: 'Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5' chicago: Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5. ieee: 'B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.' ista: 'Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.' mla: Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5. short: B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102. conference: end_date: 2018-07-17 location: Oxford, UK name: 'CAV: Computer Aided Verification' start_date: 2018-07-14 date_created: 2018-12-11T11:44:57Z date_published: 2018-07-18T00:00:00Z date_updated: 2023-09-13T08:45:09Z day: '18' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-96145-3_5 external_id: isi: - '000491481600005' file: - access_level: open_access checksum: c64fff560fe5a7532ec10626ad1c215e content_type: application/pdf creator: dernst date_created: 2018-12-17T12:52:12Z date_updated: 2020-07-14T12:45:04Z file_id: '5705' file_name: 2018_LNCS_Kragl.pdf file_size: 1603844 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 10981' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '07' oa: 1 oa_version: Published Version page: 79 - 102 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '7761' quality_controlled: '1' related_material: record: - id: '8332' relation: dissertation_contains status: public scopus_import: '1' status: public title: Layered Concurrent Programs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10981 year: '2018' ... --- _id: '280' abstract: - lang: eng text: Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span. acknowledgement: We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.). article_processing_charge: No author: - first_name: Zhen full_name: Gao, Zhen last_name: Gao - first_name: Anna full_name: Daneva, Anna last_name: Daneva - first_name: Yuliya full_name: Salanenka, Yuliya id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87 last_name: Salanenka - first_name: Matthias full_name: Van Durme, Matthias last_name: Van Durme - first_name: Marlies full_name: Huysmans, Marlies last_name: Huysmans - first_name: Zongcheng full_name: Lin, Zongcheng last_name: Lin - first_name: Freya full_name: De Winter, Freya last_name: De Winter - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Mansour full_name: Karimi, Mansour last_name: Karimi - first_name: Jan full_name: Van De Velde, Jan last_name: Van De Velde - first_name: Klaas full_name: Vandepoele, Klaas last_name: Vandepoele - first_name: Davy full_name: Van De Walle, Davy last_name: Van De Walle - first_name: Koen full_name: Dewettinck, Koen last_name: Dewettinck - first_name: Bart full_name: Lambrecht, Bart last_name: Lambrecht - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack citation: ama: Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7 apa: Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7 chicago: Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7. ieee: Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018. ista: Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375. mla: Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7. short: Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375. date_created: 2018-12-11T11:45:35Z date_published: 2018-05-28T00:00:00Z date_updated: 2023-09-13T08:24:17Z day: '28' department: - _id: JiFr doi: 10.1038/s41477-018-0160-7 external_id: isi: - '000435571000017' intvolume: ' 4' isi: 1 issue: '6' language: - iso: eng month: '05' oa_version: None page: 365 - 375 publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '7619' quality_controlled: '1' scopus_import: '1' status: public title: KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 4 year: '2018' ... --- _id: '503' abstract: - lang: eng text: Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry. acknowledged_ssus: - _id: Bio acknowledgement: "We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n" article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008 apa: Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008 chicago: Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008. ieee: K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018. ista: Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52. mla: Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008. short: K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52. date_created: 2018-12-11T11:46:50Z date_published: 2018-02-20T00:00:00Z date_updated: 2023-09-13T08:24:51Z day: '20' department: - _id: CaGu doi: 10.1016/j.jbiotec.2018.01.008 external_id: isi: - '000425715100006' intvolume: ' 268' isi: 1 language: - iso: eng month: '02' oa_version: None page: 40 - 52 publication: Journal of Biotechnology publication_status: published publisher: Elsevier publist_id: '7317' quality_controlled: '1' scopus_import: '1' status: public title: Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 268 year: '2018' ... --- _id: '82' abstract: - lang: eng text: In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”. article_number: '2005971' article_processing_charge: Yes author: - first_name: Waqas full_name: Chaudhry, Waqas last_name: Chaudhry - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Nilang full_name: Shah, Nilang last_name: Shah - first_name: Howard full_name: Weiss, Howard last_name: Weiss - first_name: Ingrid full_name: Mccall, Ingrid last_name: Mccall - first_name: Justin full_name: Meyer, Justin last_name: Meyer - first_name: Animesh full_name: Gupta, Animesh last_name: Gupta - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Bruce full_name: Levin, Bruce last_name: Levin citation: ama: Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971 apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971 chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971. ieee: W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018. ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971. mla: Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971. short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018). date_created: 2018-12-11T11:44:32Z date_published: 2018-08-16T00:00:00Z date_updated: 2023-09-13T08:45:41Z day: '16' ddc: - '570' department: - _id: CaGu doi: 10.1371/journal.pbio.2005971 external_id: isi: - '000443383300024' file: - access_level: open_access checksum: 527076f78265cd4ea192cd1569851587 content_type: application/pdf creator: dernst date_created: 2018-12-17T12:55:31Z date_updated: 2020-07-14T12:48:10Z file_id: '5706' file_name: 2018_Plos_Chaudhry.pdf file_size: 4007095 relation: main_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '7972' quality_controlled: '1' related_material: record: - id: '9810' relation: research_data status: public scopus_import: '1' status: public title: Leaky resistance and the conditions for the existence of lytic bacteriophage tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 16 year: '2018' ... --- _id: '4' abstract: - lang: eng text: We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body. article_number: '89' article_processing_charge: No author: - first_name: Nobuyuki full_name: Umetani, Nobuyuki last_name: Umetani - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325 apa: Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325 chicago: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325. ieee: N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018. ista: Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89. mla: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325. short: N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018). date_created: 2018-12-11T11:44:06Z date_published: 2018-08-04T00:00:00Z date_updated: 2023-09-13T08:46:15Z day: '04' ddc: - '003' - '004' department: - _id: BeBi doi: 10.1145/3197517.3201325 ec_funded: 1 external_id: isi: - '000448185000050' file: - access_level: open_access checksum: 7a2243668f215821bc6aecad0320079a content_type: application/pdf creator: system date_created: 2018-12-12T10:16:28Z date_updated: 2020-07-14T12:46:22Z file_id: '5216' file_name: IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf file_size: 22803163 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Trans. Graph. publication_status: published publisher: ACM publist_id: '8053' pubrep_id: '1049' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/ scopus_import: '1' status: public title: Learning three-dimensional flow for interactive aerodynamic design type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '183' abstract: - lang: eng text: 'Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.' acknowledgement: This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway. alternative_title: - HSCC Proceedings article_processing_charge: No author: - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Niveditha full_name: Manjunath, Niveditha last_name: Manjunath - first_name: Dejan full_name: Nickovic, Dejan last_name: Nickovic citation: ama: 'Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:10.1145/3178126.3178131' apa: 'Bartocci, E., Ferrere, T., Manjunath, N., & Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. https://doi.org/10.1145/3178126.3178131' chicago: Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. https://doi.org/10.1145/3178126.3178131. ieee: 'E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206.' ista: 'Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206.' mla: Bartocci, Ezio, et al. Localizing Faults in Simulink/Stateflow Models with STL. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:10.1145/3178126.3178131. short: E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206. conference: end_date: 2018-04-13 location: Porto, Portugal name: 'HSCC: Hybrid Systems: Computation and Control' start_date: 2018-04-11 date_created: 2018-12-11T11:45:04Z date_published: 2018-04-11T00:00:00Z date_updated: 2023-09-13T08:48:46Z day: '11' department: - _id: ToHe doi: 10.1145/3178126.3178131 external_id: isi: - '000474781600022' isi: 1 language: - iso: eng month: '04' oa_version: None page: 197 - 206 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Association for Computing Machinery, Inc publist_id: '7738' quality_controlled: '1' scopus_import: '1' status: public title: Localizing faults in simulink/stateflow models with STL type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '566' abstract: - lang: eng text: "We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n" article_processing_charge: No article_type: original author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302 apa: Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular law. Annals Applied Probability . Institute of Mathematical Statistics. https://doi.org/10.1214/17-AAP1302 chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/17-AAP1302. ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018. ista: Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203. mla: Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:10.1214/17-AAP1302. short: J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203. date_created: 2018-12-11T11:47:13Z date_published: 2018-03-03T00:00:00Z date_updated: 2023-09-13T08:47:52Z day: '03' department: - _id: LaEr doi: 10.1214/17-AAP1302 ec_funded: 1 external_id: arxiv: - '1612.07776 ' isi: - '000431721800005' intvolume: ' 28' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://arxiv.org/abs/1612.07776 ' month: '03' oa: 1 oa_version: Preprint page: 148-203 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: 'Annals Applied Probability ' publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: '1' status: public title: Local inhomogeneous circular law type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 28 year: '2018' ... --- _id: '106' abstract: - lang: eng text: The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below. article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Anton full_name: Petrunin, Anton last_name: Petrunin citation: ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5 apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5 chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5. ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018. ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31. mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5. short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31. date_created: 2018-12-11T11:44:40Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-13T08:49:16Z day: '01' department: - _id: HeEd doi: 10.1007/s00283-018-9795-5 external_id: arxiv: - '1702.05172' isi: - '000444141200005' intvolume: ' 40' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.05172 month: '09' oa: 1 oa_version: Preprint page: 26 - 31 publication: Mathematical Intelligencer publication_status: published publisher: Springer publist_id: '7948' quality_controlled: '1' scopus_import: '1' status: public title: Long geodesics on convex surfaces type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2018' ... --- _id: '9810' article_processing_charge: No author: - first_name: Waqas full_name: Chaudhry, Waqas last_name: Chaudhry - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Nilang full_name: Shah, Nilang last_name: Shah - first_name: Howard full_name: Weiss, Howard last_name: Weiss - first_name: Ingrid full_name: Mccall, Ingrid last_name: Mccall - first_name: Justin full_name: Meyer, Justin last_name: Meyer - first_name: Animesh full_name: Gupta, Animesh last_name: Gupta - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Bruce full_name: Levin, Bruce last_name: Levin citation: ama: Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008 apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008 chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008. ieee: W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018. ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008. mla: Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008. short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018). date_created: 2021-08-06T12:43:44Z date_published: 2018-08-16T00:00:00Z date_updated: 2023-09-13T08:45:41Z day: '16' department: - _id: CaGu doi: 10.1371/journal.pbio.2005971.s008 month: '08' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '82' relation: used_in_publication status: public status: public title: Numerical data used in figures type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '275' abstract: - lang: eng text: Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments. acknowledgement: M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT). article_processing_charge: No author: - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Louise full_name: Johnson, Louise last_name: Johnson - first_name: Dario full_name: Leone, Dario last_name: Leone - first_name: Peter full_name: Májek, Peter last_name: Májek - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 - first_name: Daniel full_name: Senfter, Daniel last_name: Senfter - first_name: Nora full_name: Bukosza, Nora last_name: Bukosza - first_name: Helga full_name: Schachner, Helga last_name: Schachner - first_name: Gabriele full_name: Asfour, Gabriele last_name: Asfour - first_name: Brigitte full_name: Langer, Brigitte last_name: Langer - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Katja full_name: Parapatics, Katja last_name: Parapatics - first_name: Young full_name: Hong, Young last_name: Hong - first_name: Keiryn full_name: Bennett, Keiryn last_name: Bennett - first_name: Renate full_name: Kain, Renate last_name: Kain - first_name: Michael full_name: Detmar, Michael last_name: Detmar - 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: David full_name: Jackson, David last_name: Jackson - first_name: Dontscho full_name: Kerjaschki, Dontscho last_name: Kerjaschki citation: ama: Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051 apa: Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051 chicago: Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051. ieee: M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018. ista: Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221. mla: Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051. short: M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221. date_created: 2018-12-11T11:45:33Z date_published: 2018-04-12T00:00:00Z date_updated: 2023-09-13T08:51:29Z day: '12' ddc: - '570' department: - _id: MiSi - _id: Bio doi: 10.1083/jcb.201612051 ec_funded: 1 external_id: isi: - '000438077800026' pmid: - '29650776' file: - access_level: open_access checksum: 9c7eba51a35c62da8c13f98120b64df4 content_type: application/pdf creator: dernst date_created: 2018-12-17T12:50:07Z date_updated: 2020-07-14T12:45:45Z file_id: '5704' file_name: 2018_JournalCellBiology_Brown.pdf file_size: 2252043 relation: main_file file_date_updated: 2020-07-14T12:45:45Z has_accepted_license: '1' intvolume: ' 217' isi: 1 issue: '6' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 2205 - 2221 pmid: 1 project: - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '7627' quality_controlled: '1' scopus_import: '1' status: public title: Lymphatic exosomes promote dendritic cell migration along guidance cues tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 217 year: '2018' ... --- _id: '158' abstract: - lang: eng text: 'The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development.' acknowledgement: This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.; article_processing_charge: No author: - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Chulmin full_name: Park, Chulmin last_name: Park - first_name: Carla full_name: Gutièrrez, Carla last_name: Gutièrrez - first_name: Barbara full_name: Wójcikowska, Barbara last_name: Wójcikowska - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Junyi full_name: Chen, Junyi last_name: Chen - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Thomas full_name: Dresselhaus, Thomas last_name: Dresselhaus - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Thomas full_name: Laux, Thomas last_name: Laux citation: ama: Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z apa: Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z chicago: Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z. ieee: H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018. ista: Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553. mla: Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z. short: H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553. date_created: 2018-12-11T11:44:56Z date_published: 2018-07-16T00:00:00Z date_updated: 2023-09-13T08:53:28Z day: '16' department: - _id: JiFr doi: 10.1038/s41477-018-0204-z ec_funded: 1 external_id: isi: - '000443861300011' pmid: - '30013211' intvolume: ' 4' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30013211 month: '07' oa: 1 oa_version: Submitted Version page: 548 - 553 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '7763' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/ scopus_import: '1' status: public title: Maternal auxin supply contributes to early embryo patterning in Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 4 year: '2018' ... --- _id: '152' abstract: - lang: eng text: Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context. article_processing_charge: No article_type: original author: - first_name: Karol full_name: Fiedorczuk, Karol id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0 last_name: Fiedorczuk - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006 apa: Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006 chicago: Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006. ieee: K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018. ista: Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867. mla: Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006. short: K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867. date_created: 2018-12-11T11:44:54Z date_published: 2018-07-26T00:00:00Z date_updated: 2023-09-13T08:51:56Z day: '26' ddc: - '572' department: - _id: LeSa doi: 10.1016/j.tcb.2018.06.006 external_id: isi: - '000445118200007' file: - access_level: open_access checksum: ef6d2b4e1fd63948539639242610bfa6 content_type: application/pdf creator: lsazanov date_created: 2019-11-07T12:55:20Z date_updated: 2020-07-14T12:45:00Z file_id: '6994' file_name: SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf file_size: 2185385 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 28' isi: 1 issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Submitted Version page: 835 - 867 publication: Trends in Cell Biology publication_status: published publisher: Elsevier publist_id: '7769' quality_controlled: '1' scopus_import: '1' status: public title: Mammalian mitochondrial complex I structure and disease causing mutations tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 28 year: '2018' ... --- _id: '310' abstract: - lang: eng text: A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvorák, Wolfgang last_name: Dvorák - 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: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151' apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151' chicago: 'Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.' ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356.' ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.' mla: 'Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.' short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356. conference: end_date: 2018-01-10 location: New Orleans, Louisiana, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2018-01-07 date_created: 2018-12-11T11:45:45Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-13T08:50:16Z day: '01' department: - _id: KrCh doi: 10.1137/1.9781611975031.151 ec_funded: 1 external_id: arxiv: - '1711.09148' isi: - '000483921200152' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.09148 month: '01' oa: 1 oa_version: Preprint page: 2341 - 2356 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_status: published publisher: ACM publist_id: '7555' quality_controlled: '1' scopus_import: '1' status: public title: 'Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '436' abstract: - lang: eng text: There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits. article_number: '060601 ' article_processing_charge: No author: - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Matteo full_name: Aquilina, Matteo last_name: Aquilina - first_name: André full_name: Xuereb, André last_name: Xuereb citation: ama: Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601 apa: Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601 chicago: Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601. ieee: S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018. ista: Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601. mla: Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601. short: S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018). date_created: 2018-12-11T11:46:28Z date_published: 2018-02-07T00:00:00Z date_updated: 2023-09-13T08:52:27Z day: '07' department: - _id: JoFi doi: 10.1103/PhysRevLett.120.060601 ec_funded: 1 external_id: arxiv: - '1706.09051' isi: - '000424382100004' intvolume: ' 120' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.09051 month: '02' oa: 1 oa_version: Preprint project: - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7387' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/ scopus_import: '1' status: public title: Manipulating the flow of thermal noise in quantum devices type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 120 year: '2018' ... --- _id: '5858' abstract: - lang: eng text: Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights. article_number: '20180600' article_processing_charge: No author: - first_name: Sabrina full_name: Hross, Sabrina last_name: Hross - first_name: Fabian J. full_name: Theis, Fabian J. last_name: Theis - 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: Jan full_name: Hasenauer, Jan last_name: Hasenauer citation: ama: Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600 apa: Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600 chicago: Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600. ieee: S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018. ista: Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600. mla: Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600. short: S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018). date_created: 2019-01-20T22:59:18Z date_published: 2018-12-05T00:00:00Z date_updated: 2023-09-13T08:55:05Z day: '05' ddc: - '570' department: - _id: MiSi doi: 10.1098/rsif.2018.0600 external_id: isi: - '000456783800011' file: - access_level: open_access checksum: 56eb4308a15b7190bff938fab1f780e8 content_type: application/pdf creator: dernst date_created: 2019-02-05T14:46:44Z date_updated: 2020-07-14T12:47:13Z file_id: '5925' file_name: 2018_Interface_Hross.pdf file_size: 1464288 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '149' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Journal of the Royal Society Interface publication_identifier: issn: - '17425689' publication_status: published publisher: Royal Society Publishing quality_controlled: '1' scopus_import: '1' status: public title: Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 15 year: '2018' ... --- _id: '16' abstract: - lang: eng text: We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives. acknowledgement: This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145). article_number: '103303' article_processing_charge: No article_type: original author: - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 - first_name: Victor full_name: Steinberg, Victor last_name: Steinberg citation: ama: Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303 apa: Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303 chicago: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303. ieee: A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018. ista: Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303. mla: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303. short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018). date_created: 2018-12-11T11:44:10Z date_published: 2018-10-16T00:00:00Z date_updated: 2023-09-13T08:57:05Z day: '16' ddc: - '532' department: - _id: BjHo doi: 10.1103/PhysRevFluids.3.103303 ec_funded: 1 external_id: isi: - '000447469200001' file: - access_level: open_access checksum: 7fc0a2322214d1c04debef36d5bf2e8a content_type: application/pdf creator: system date_created: 2018-12-12T10:13:56Z date_updated: 2020-07-14T12:45:04Z file_id: '5043' file_name: IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf file_size: 1838431 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 3' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Fluids publication_status: published publisher: American Physical Society publist_id: '8039' pubrep_id: '1062' quality_controlled: '1' scopus_import: '1' status: public title: Mixing layer instability and vorticity amplification in a creeping viscoelastic flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 3 year: '2018' ... --- _id: '43' abstract: - lang: eng text: 'The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.' acknowledgement: J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541. article_processing_charge: No author: - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Eva full_name: Kisdi, Eva last_name: Kisdi - first_name: Jani full_name: Anttila, Jani last_name: Anttila citation: ama: Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115 apa: Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115 chicago: Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115. ieee: J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018. ista: Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695. mla: Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115. short: J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695. date_created: 2018-12-11T11:44:19Z date_published: 2018-10-02T00:00:00Z date_updated: 2023-09-13T08:57:38Z day: '02' ddc: - '570' - '577' department: - _id: DaAl doi: 10.1073/pnas.1721061115 ec_funded: 1 external_id: isi: - '000447491300057' file: - access_level: open_access checksum: df7ac544a587c06b75692653b9fabd18 content_type: application/pdf creator: dernst date_created: 2019-04-09T08:02:50Z date_updated: 2020-07-14T12:46:26Z file_id: '6258' file_name: 2018_PNAS_Rybicki.pdf file_size: 4070777 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 115' isi: 1 issue: '42' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 10690 - 10695 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '8011' pubrep_id: '1063' quality_controlled: '1' scopus_import: '1' status: public title: Model of bacterial toxin-dependent pathogenesis explains infective dose type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '13' abstract: - lang: eng text: We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery. article_number: '136' article_processing_charge: No author: - first_name: Thomas full_name: Alderighi, Thomas last_name: Alderighi - first_name: Luigi full_name: Malomo, Luigi last_name: Malomo - first_name: Daniela full_name: Giorgi, Daniela last_name: Giorgi - first_name: Nico full_name: Pietroni, Nico last_name: Pietroni - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Paolo full_name: Cignoni, Paolo last_name: Cignoni citation: ama: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381' apa: 'Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381' chicago: 'Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.' ieee: 'T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.' ista: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.' mla: 'Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.' short: T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018). date_created: 2018-12-11T11:44:09Z date_published: 2018-08-04T00:00:00Z date_updated: 2023-09-13T08:56:07Z day: '04' ddc: - '004' department: - _id: BeBi doi: 10.1145/3197517.3201381 ec_funded: 1 external_id: isi: - '000448185000097' file: - access_level: open_access checksum: 61d46273dca4de626accef1d17a0aaad content_type: application/pdf creator: system date_created: 2018-12-12T10:18:52Z date_updated: 2020-07-14T12:44:43Z file_id: '5374' file_name: IST-2018-1038-v1+1_metamolds_authorversion.pdf file_size: 91939066 relation: main_file file_date_updated: 2020-07-14T12:44:43Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Trans. Graph. publication_status: published publisher: ACM publist_id: '8043' pubrep_id: '1038' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/metamolds-molding-a-mold/ scopus_import: '1' status: public title: 'Metamolds: Computational design of silicone molds' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '137' abstract: - lang: eng text: Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli. article_processing_charge: No article_type: original author: - first_name: William full_name: Zhang, William last_name: Zhang - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Joshua full_name: Mitchell, Joshua last_name: Mitchell - first_name: Jason full_name: Whitfield, Jason last_name: Whitfield - first_name: Andreas full_name: Wulff, Andreas last_name: Wulff - first_name: Vanessa full_name: Vongsouthi, Vanessa last_name: Vongsouthi - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Polina full_name: Gulakova, Polina last_name: Gulakova - first_name: Daniel full_name: Minge, Daniel last_name: Minge - first_name: Björn full_name: Breithausen, Björn last_name: Breithausen - first_name: Susanne full_name: Schoch, Susanne last_name: Schoch - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Colin full_name: Jackson, Colin last_name: Jackson - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger citation: ama: Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2 apa: Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2 chicago: Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2. ieee: W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018. ista: Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869. mla: Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2. short: W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869. date_created: 2018-12-11T11:44:49Z date_published: 2018-07-30T00:00:00Z date_updated: 2023-09-13T08:58:05Z day: '30' department: - _id: HaJa doi: 10.1038/s41589-018-0108-2 external_id: isi: - '000442174500013' pmid: - '30061718 ' intvolume: ' 14' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30061718 month: '07' oa: 1 oa_version: Submitted Version page: 861 - 869 pmid: 1 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '7786' quality_controlled: '1' scopus_import: '1' status: public title: Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '153' abstract: - lang: eng text: Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters. article_processing_charge: No author: - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004' apa: Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91). Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004 chicago: Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91. Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004. ieee: J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91. ista: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.' mla: Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004. short: J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91. date_created: 2018-12-11T11:44:54Z date_published: 2018-07-27T00:00:00Z date_updated: 2023-09-13T08:56:35Z day: '27' department: - _id: MiSi - _id: NanoFab doi: 10.1016/bs.mcb.2018.07.004 external_id: isi: - '000452412300006' pmid: - '30165964' intvolume: ' 147' isi: 1 language: - iso: eng month: '07' oa_version: None page: 79 - 91 pmid: 1 publication: Methods in Cell Biology publication_identifier: issn: - 0091679X publication_status: published publisher: Academic Press publist_id: '7768' quality_controlled: '1' scopus_import: '1' status: public title: Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 147 year: '2018' ... --- _id: '54' abstract: - lang: eng text: During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics. acknowledgement: Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants. article_processing_charge: No article_type: review author: - first_name: Diana C full_name: Nunes Pinheiro, Diana C id: 2E839F16-F248-11E8-B48F-1D18A9856A87 last_name: Nunes Pinheiro orcid: 0000-0003-4333-7503 - first_name: Yohanns full_name: Bellaïche, Yohanns last_name: Bellaïche citation: ama: Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19. doi:10.1016/j.devcel.2018.09.014 apa: Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014 chicago: Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014. ieee: D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” Developmental Cell, vol. 47, no. 1. Cell Press, pp. 3–19, 2018. ista: Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19. mla: Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014. short: D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19. date_created: 2018-12-11T11:44:23Z date_published: 2018-10-08T00:00:00Z date_updated: 2023-09-13T08:54:38Z day: '08' department: - _id: CaHe doi: 10.1016/j.devcel.2018.09.014 external_id: isi: - '000446579900002' intvolume: ' 47' isi: 1 issue: '1' language: - iso: eng main_file_link: - url: https://doi.org/10.1016/j.devcel.2018.09.014 month: '10' oa_version: Published Version page: 3 - 19 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '8000' quality_controlled: '1' scopus_import: '1' status: public title: Mechanical force-driven adherents junction remodeling and epithelial dynamics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 47 year: '2018' ... --- _id: '276' abstract: - lang: eng text: Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo. acknowledgement: This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. article_number: e0198330 article_processing_charge: No article_type: original author: - first_name: Corina full_name: Frick, Corina last_name: Frick - first_name: Philip full_name: Dettinger, Philip last_name: Dettinger - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Annaïse full_name: Jauch, Annaïse last_name: Jauch - first_name: Christoph full_name: Berger, Christoph last_name: Berger - first_name: Mike full_name: Recher, Mike last_name: Recher - first_name: Timm full_name: Schroeder, Timm last_name: Schroeder - first_name: Matthias full_name: Mehling, Matthias last_name: Mehling citation: ama: Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330 apa: Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330 chicago: Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0198330. ieee: C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science, 2018. ista: Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330. mla: Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:10.1371/journal.pone.0198330. short: C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018). date_created: 2018-12-11T11:45:34Z date_published: 2018-06-07T00:00:00Z date_updated: 2023-09-13T09:00:15Z day: '07' ddc: - '570' department: - _id: MiSi doi: 10.1371/journal.pone.0198330 external_id: isi: - '000434384900031' file: - access_level: open_access checksum: 95fc5dc3938b3ad3b7697d10c83cc143 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:10:32Z date_updated: 2020-07-14T12:45:45Z file_id: '5709' file_name: 2018_Plos_Frick.pdf file_size: 7682167 relation: main_file file_date_updated: 2020-07-14T12:45:45Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '7626' quality_controlled: '1' scopus_import: '1' status: public title: Nano-scale microfluidics to study 3D chemotaxis at the single cell level tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13 year: '2018' ... --- _id: '283' abstract: - lang: eng text: Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors. article_number: '8754' article_processing_charge: No author: - first_name: Rosa Maria full_name: Ceinos, Rosa Maria last_name: Ceinos - first_name: Elena full_name: Frigato, Elena last_name: Frigato - first_name: Cristina full_name: Pagano, Cristina last_name: Pagano - first_name: Nadine full_name: Frohlich, Nadine last_name: Frohlich - first_name: Pietro full_name: Negrini, Pietro last_name: Negrini - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: Daniela full_name: Vallone, Daniela last_name: Vallone - first_name: Silvia full_name: Fuselli, Silvia last_name: Fuselli - first_name: Cristiano full_name: Bertolucci, Cristiano last_name: Bertolucci - first_name: Nicholas S full_name: Foulkes, Nicholas S last_name: Foulkes citation: ama: Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-27080-2 apa: Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-27080-2 chicago: Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-27080-2. ieee: R. M. Ceinos et al., “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018. ista: Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754. mla: Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2. short: R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018). date_created: 2018-12-11T11:45:36Z date_published: 2018-06-08T00:00:00Z date_updated: 2023-09-13T08:59:27Z day: '08' ddc: - '570' department: - _id: EvBe doi: 10.1038/s41598-018-27080-2 external_id: isi: - '000434640800008' file: - access_level: open_access checksum: 9c3942d772f84f3df032ffde0ed9a8ea content_type: application/pdf creator: dernst date_created: 2018-12-17T13:04:46Z date_updated: 2020-07-14T12:45:49Z file_id: '5707' file_name: 2018_ScientificReports_Ceinos.pdf file_size: 1855324 relation: main_file file_date_updated: 2020-07-14T12:45:49Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '7616' quality_controlled: '1' scopus_import: '1' status: public title: Mutations in blind cavefish target the light regulated circadian clock gene period 2 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '81' abstract: - lang: eng text: We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring, alternative_title: - LNCS article_processing_charge: No author: - first_name: Adrian full_name: Elgyütt, Adrian id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87 last_name: Elgyütt - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4' apa: 'Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4' chicago: Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4. ieee: 'A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.' ista: 'Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.' mla: Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4. short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70. conference: end_date: 2018-09-06 location: Beijing, China name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2018-09-04 date_created: 2018-12-11T11:44:31Z date_published: 2018-08-26T00:00:00Z date_updated: 2023-09-13T08:58:34Z day: '26' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-00151-3_4 external_id: isi: - '000884993200004' file: - access_level: open_access checksum: e5d81c9b50a6bd9d8a2c16953aad7e23 content_type: application/pdf creator: dernst date_created: 2020-10-09T06:24:21Z date_updated: 2020-10-09T06:24:21Z file_id: '8638' file_name: 2018_LNCS_Elgyuett.pdf file_size: 537219 relation: main_file success: 1 file_date_updated: 2020-10-09T06:24:21Z has_accepted_license: '1' intvolume: ' 11022' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 53 - 70 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '7973' quality_controlled: '1' scopus_import: '1' status: public title: Monitoring temporal logic with clock variables type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11022 year: '2018' ... --- _id: '76' abstract: - lang: eng text: 'Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.' article_processing_charge: Yes (via OA deal) author: - first_name: Christoph full_name: Lenzen, Christoph last_name: Lenzen - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 citation: ama: Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6 apa: Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6 chicago: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6. ieee: C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018. ista: Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing. mla: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6. short: C. Lenzen, J. Rybicki, Distributed Computing (2018). date_created: 2018-12-11T11:44:30Z date_published: 2018-09-12T00:00:00Z date_updated: 2023-09-13T09:01:06Z day: '12' ddc: - '000' department: - _id: DaAl doi: 10.1007/s00446-018-0342-6 external_id: isi: - '000475627800005' file: - access_level: open_access checksum: 872db70bba9b401500abe3c6ae2f1a61 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:21:22Z date_updated: 2020-07-14T12:48:01Z file_id: '5711' file_name: 2018_DistributedComputing_Lenzen.pdf file_size: 799337 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Distributed Computing publication_status: published publisher: Springer publist_id: '7978' quality_controlled: '1' scopus_import: '1' status: public title: Near-optimal self-stabilising counting and firing squads tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '530' abstract: - lang: eng text: Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: ama: 'Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014' apa: 'Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014' chicago: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.' ieee: 'H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.' ista: 'Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.' mla: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.' short: 'H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.' date_created: 2018-12-11T11:46:59Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-13T08:59:00Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.comgeo.2017.06.014 ec_funded: 1 external_id: isi: - '000415778300010' file: - access_level: open_access checksum: 1c8d58cd489a66cd3e2064c1141c8c5e content_type: application/pdf creator: dernst date_created: 2019-02-12T06:47:52Z date_updated: 2020-07-14T12:46:38Z file_id: '5953' file_name: 2018_Edelsbrunner.pdf file_size: 708357 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 68' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Preprint page: 119 - 133 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '7289' quality_controlled: '1' scopus_import: '1' status: public title: 'Multiple covers with balls I: Inclusion–exclusion' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 68 year: '2018' ... --- _id: '307' abstract: - lang: eng text: 'Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. ' acknowledgement: The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE). article_number: ' 043812 ' article_processing_charge: No article_type: original author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alexander full_name: Makarov, Alexander last_name: Makarov - first_name: Vladimir full_name: Yudson, Vladimir last_name: Yudson citation: ama: Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812 apa: Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812 chicago: Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812. ieee: E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018. ista: Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812. mla: Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812. short: E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018). date_created: 2018-12-11T11:45:44Z date_published: 2018-04-09T00:00:00Z date_updated: 2023-09-13T09:00:41Z day: '09' department: - _id: JoFi doi: 10.1103/PhysRevA.97.043812 external_id: arxiv: - '1712.10127' isi: - '000429454000015' intvolume: ' 97' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.10127 month: '04' oa: 1 oa_version: Submitted Version publication: ' Physical Review A - Atomic, Molecular, and Optical Physics' publication_status: published publisher: American Physical Society publist_id: '7572' quality_controlled: '1' scopus_import: '1' status: public title: Nanoscopy of pairs of atoms by fluorescence in a magnetic field type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 97 year: '2018' ... --- _id: '279' abstract: - lang: eng text: 'Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.' article_number: '67' article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0 apa: Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0 chicago: Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0. ieee: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018. ista: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67. mla: Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0. short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018). date_created: 2018-12-11T11:45:35Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:32Z day: '31' ddc: - '570' department: - _id: FyKo doi: 10.1186/s13059-018-1434-0 ec_funded: 1 external_id: isi: - '000433986200001' file: - access_level: open_access checksum: f3e4922486bd9bf1483271bdbed394a7 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:05:01Z date_updated: 2020-07-14T12:45:47Z file_id: '5708' file_name: 2018_GenomeBiology_Zapata.pdf file_size: 1414722 relation: main_file file_date_updated: 2020-07-14T12:45:47Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Genome Biology publication_status: published publisher: BioMed Central publist_id: '7620' quality_controlled: '1' related_material: record: - id: '9811' relation: research_data status: public - id: '9812' relation: research_data status: public scopus_import: '1' status: public title: Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '145' abstract: - lang: eng text: Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins. acknowledgement: We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A). article_number: e98044 article_processing_charge: No article_type: original author: - first_name: Sven M full_name: Truckenbrodt, Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - first_name: Abhiyan full_name: Viplav, Abhiyan last_name: Viplav - first_name: Sebsatian full_name: Jähne, Sebsatian last_name: Jähne - first_name: Angela full_name: Vogts, Angela last_name: Vogts - first_name: Annette full_name: Denker, Annette last_name: Denker - first_name: Hanna full_name: Wildhagen, Hanna last_name: Wildhagen - first_name: Eugenio full_name: Fornasiero, Eugenio last_name: Fornasiero - first_name: Silvio full_name: Rizzoli, Silvio last_name: Rizzoli citation: ama: Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044 apa: Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044 chicago: Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044. ieee: S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018. ista: Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044. mla: Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044. short: S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018). date_created: 2018-12-11T11:44:52Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-13T09:02:48Z day: '01' ddc: - '570' department: - _id: JoDa doi: 10.15252/embj.201798044 external_id: isi: - '000440416900005' pmid: - '29950309' file: - access_level: open_access checksum: a540feb6c9af6aefc78de531461a8835 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:17:29Z date_updated: 2020-07-14T12:44:56Z file_id: '5710' file_name: 2018_EMBO_Truckenbrodt.pdf file_size: 2846470 relation: main_file file_date_updated: 2020-07-14T12:44:56Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: The EMBO Journal publication_identifier: issn: - 0261-4189 publication_status: published publisher: Wiley publist_id: '7778' quality_controlled: '1' scopus_import: '1' status: public title: Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '462' abstract: - lang: eng text: 'AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. ' acknowledgement: 'This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ' article_processing_charge: No article_type: original author: - first_name: Ligang full_name: Fan, Ligang last_name: Fan - first_name: Lei full_name: Zhao, Lei last_name: Zhao - first_name: Wei full_name: Hu, Wei last_name: Hu - first_name: Weina full_name: Li, Weina last_name: Li - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jinbo full_name: Shen, Jinbo last_name: Shen - first_name: Liwen full_name: Jiang, Liwen last_name: Jiang - first_name: Quan full_name: Qiu, Quan last_name: Qiu citation: ama: Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153 apa: Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153 chicago: Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153. ieee: L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018. ista: Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864. mla: Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153. short: L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864. date_created: 2018-12-11T11:46:36Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-13T09:03:18Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/pce.13153 external_id: isi: - '000426870500012' pmid: - '29360148' file: - access_level: open_access checksum: 6a20f843565f962cb20281cdf5e40914 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:22:22Z date_updated: 2020-07-14T12:46:32Z file_id: '7042' file_name: 2018_PlantCellEnv_Fan.pdf file_size: 1937976 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 41' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '05' oa: 1 oa_version: Submitted Version page: 850 - 864 pmid: 1 publication: Plant, Cell and Environment publication_status: published publisher: Wiley-Blackwell publist_id: '7359' quality_controlled: '1' scopus_import: '1' status: public title: NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 41 year: '2018' ... --- _id: '519' abstract: - lang: eng text: 'This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. ' acknowledgement: S.Altmeyer is a Serra Húnter Fellow article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 citation: ama: Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073 apa: Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073 chicago: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073. ieee: S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018. ista: Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441. mla: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073. short: S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441. date_created: 2018-12-11T11:46:56Z date_published: 2018-04-15T00:00:00Z date_updated: 2023-09-13T09:03:44Z day: '15' ddc: - '530' department: - _id: BjHo doi: 10.1016/j.jmmm.2017.12.073 external_id: isi: - '000425547700061' file: - access_level: open_access checksum: 431f5cd4a628d7ca21161f82b14ccb4f content_type: application/pdf creator: dernst date_created: 2020-05-14T14:41:17Z date_updated: 2020-07-14T12:46:37Z file_id: '7838' file_name: 2018_Magnetism_Altmeyer.pdf file_size: 17309535 relation: main_file file_date_updated: 2020-07-14T12:46:37Z has_accepted_license: '1' intvolume: ' 452' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 427 - 441 publication: Journal of Magnetism and Magnetic Materials publication_status: published publisher: Elsevier publist_id: '7297' quality_controlled: '1' scopus_import: '1' status: public title: Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 452 year: '2018' ... --- _id: '5679' abstract: - lang: eng text: We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Mingzhang full_name: Huang, Mingzhang last_name: Huang - first_name: Hongfei full_name: Fu, Hongfei last_name: Fu - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11' apa: 'Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11' chicago: Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11. ieee: M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201. ista: Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201. mla: Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11. short: M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201. conference: end_date: 2018-12-06 location: Wellington, New Zealand name: 16th Asian Symposium on Programming Languages and Systems, APLAS start_date: 2018-12-02 date_created: 2018-12-16T22:59:20Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-09-13T09:02:22Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-030-02768-1_11 editor: - first_name: Sukyoung full_name: Ryu, Sukyoung last_name: Ryu external_id: arxiv: - '1806.06683' isi: - '000916310900011' intvolume: ' 11275' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1806.06683 month: '12' oa: 1 oa_version: Preprint page: 181-201 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_identifier: isbn: - '9783030027674' issn: - '03029743' publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: New approaches for almost-sure termination of probabilistic programs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11275 year: '2018' ... --- _id: '546' abstract: - lang: eng text: The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies. article_processing_charge: No author: - first_name: Roberto full_name: Sacco, Roberto id: 42C9F57E-F248-11E8-B48F-1D18A9856A87 last_name: Sacco - first_name: Emanuele full_name: Cacci, Emanuele last_name: Cacci - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005 apa: Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005 chicago: Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005. ieee: R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018. ista: Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138. mla: Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005. short: R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138. date_created: 2018-12-11T11:47:06Z date_published: 2018-02-01T00:00:00Z date_updated: 2023-09-13T09:01:56Z day: '01' department: - _id: GaNo doi: 10.1016/j.conb.2017.12.005 external_id: isi: - '000427101600018' intvolume: ' 48' isi: 1 issue: '2' language: - iso: eng month: '02' oa_version: None page: 131 - 138 publication: Current Opinion in Neurobiology publication_status: published publisher: Elsevier publist_id: '7268' quality_controlled: '1' scopus_import: '1' status: public title: Neural stem cells in neuropsychiatric disorders type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 48 year: '2018' ... --- _id: '9812' abstract: - lang: eng text: This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb) article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1' apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1' chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.' ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.' ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.' mla: 'Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.' short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018). date_created: 2021-08-06T12:58:25Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:31Z day: '31' department: - _id: FyKo doi: 10.6084/m9.figshare.6401414.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.6401414.v1 month: '05' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '279' relation: used_in_publication status: public status: public title: 'Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '9811' abstract: - lang: eng text: This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb) article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1' apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1' chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.' ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.' ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.' mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.' short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018). date_created: 2021-08-06T12:53:49Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:31Z day: '31' department: - _id: FyKo doi: 10.6084/m9.figshare.6401390.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.6401390.v1 month: '05' oa: 1 oa_version: Preprint publisher: Springer Nature related_material: record: - id: '279' relation: used_in_publication status: public status: public title: 'Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '20' abstract: - lang: eng text: 'Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.' acknowledgement: This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19). article_processing_charge: No article_type: original author: - first_name: Juan full_name: Higareda Almaraz, Juan last_name: Higareda Almaraz - first_name: Michael full_name: Karbiener, Michael last_name: Karbiener - first_name: Maude full_name: Giroud, Maude last_name: Giroud - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Teresa full_name: Gerhalter, Teresa last_name: Gerhalter - first_name: Stephan full_name: Herzig, Stephan last_name: Herzig - first_name: Marcel full_name: Scheideler, Marcel last_name: Scheideler citation: ama: Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0 apa: Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0 chicago: Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0. ieee: J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018. ista: Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1). mla: Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0. short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018). date_created: 2018-12-11T11:44:12Z date_published: 2018-11-03T00:00:00Z date_updated: 2023-09-13T09:10:47Z day: '03' ddc: - '570' department: - _id: SiHi doi: 10.1186/s12864-018-5173-0 external_id: isi: - '000450976700002' file: - access_level: open_access checksum: a56516e734dab589dc7f3e1915973b4d content_type: application/pdf creator: dernst date_created: 2018-12-17T14:52:57Z date_updated: 2020-07-14T12:45:23Z file_id: '5712' file_name: 2018_BMCGenomics_Higareda.pdf file_size: 4629784 relation: main_file file_date_updated: 2020-07-14T12:45:23Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: BMC Genomics publication_identifier: issn: - 1471-2164 publication_status: published publisher: BioMed Central publist_id: '8035' quality_controlled: '1' related_material: record: - id: '9807' relation: research_data status: public - id: '9808' relation: research_data status: public scopus_import: '1' status: public title: Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ...