--- _id: '5878' abstract: - lang: eng text: We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al. article_number: '013122' article_processing_charge: No article_type: original author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Marc full_name: Fleury, Marc last_name: Fleury citation: ama: 'Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279' apa: 'Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/1.5058279' chicago: 'Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279.' ieee: 'N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1. AIP Publishing, 2019.' ista: 'Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.' mla: 'Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.' short: 'N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).' date_created: 2019-01-23T08:35:09Z date_published: 2019-01-22T00:00:00Z date_updated: 2023-08-25T10:16:11Z day: '22' department: - _id: BjHo doi: 10.1063/1.5058279 external_id: arxiv: - '1812.09011' isi: - '000457409100028' intvolume: ' 29' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1812.09011 month: '01' oa: 1 oa_version: Preprint publication: 'Chaos: An Interdisciplinary Journal of Nonlinear Science' publication_identifier: eissn: - 1089-7682 issn: - 1054-1500 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: link: - relation: erratum url: https://aip.scitation.org/doi/abs/10.1063/1.5097157 scopus_import: '1' status: public title: State space geometry of the chaotic pilot-wave hydrodynamics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 29 year: '2019' ... --- _id: '6343' abstract: - lang: eng text: Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA. acknowledgement: The author acknowledges support from IST Austria and the Austrian Science Fund (FWF). article_processing_charge: No article_type: original author: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018 apa: Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018 chicago: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018. ieee: F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” Current Opinion in Structural Biology, vol. 58, no. 10. Elsevier, pp. 1–9, 2019. ista: Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9. mla: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018. short: F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9. date_created: 2019-04-19T11:19:13Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-25T10:13:31Z day: '01' department: - _id: FlSc doi: 10.1016/j.sbi.2019.03.018 external_id: isi: - '000494891800004' intvolume: ' 58' isi: 1 issue: '10' language: - iso: eng month: '10' oa_version: None page: 1-9 publication: Current Opinion in Structural Biology publication_identifier: issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 58 year: '2019' ... --- _id: '6428' abstract: - lang: eng text: 'Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.' article_processing_charge: No author: - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Alexandre full_name: Donzé, Alexandre last_name: Donzé - first_name: Hisahiro full_name: Ito, Hisahiro last_name: Ito - first_name: James full_name: Kapinski, James last_name: Kapinski citation: ama: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800' apa: 'Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800' chicago: 'Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.' ieee: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.' ista: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.' mla: 'Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.' short: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.' conference: end_date: 2019-04-18 location: Montreal, Canada name: 'HSCC: Hybrid Systems Computation and Control' start_date: 2019-04-16 date_created: 2019-05-13T08:13:46Z date_published: 2019-04-16T00:00:00Z date_updated: 2023-08-25T10:19:23Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1145/3302504.3311800 external_id: isi: - '000516713900007' file: - access_level: open_access checksum: b8e967081e051d1c55ca5d18fb187890 content_type: application/pdf creator: dernst date_created: 2020-10-08T17:25:45Z date_updated: 2020-10-08T17:25:45Z file_id: '8633' file_name: 2019_ACM_Ferrere.pdf file_size: 1055421 relation: main_file success: 1 file_date_updated: 2020-10-08T17:25:45Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 57-66 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 'Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control' publication_identifier: isbn: - '9781450362825' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Interface-aware signal temporal logic type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '6442' abstract: - lang: eng text: This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples. acknowledged_ssus: - _id: ScienComp article_number: '130' article_processing_charge: No author: - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002 apa: Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002 chicago: Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002. ieee: C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019. ista: Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130. mla: Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002. short: C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019). date_created: 2019-05-14T07:04:06Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-25T10:18:46Z day: '01' ddc: - '000' - '005' department: - _id: ChWo doi: 10.1145/3306346.3323002 ec_funded: 1 external_id: isi: - '000475740600104' file: - access_level: open_access checksum: 1b737dfe3e051aba8f3f4ab1dceda673 content_type: application/pdf creator: dernst date_created: 2019-05-14T07:03:55Z date_updated: 2020-07-14T12:47:30Z file_id: '6443' file_name: 2019_ACM_Schreck.pdf file_size: 44328918 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACM Transactions on Graphics publication_status: published publisher: ACM quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/ scopus_import: '1' status: public title: Fundamental solutions for water wave animation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '6413' abstract: - lang: eng text: Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase. article_processing_charge: No article_type: original author: - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Carlos full_name: Plana, Carlos last_name: Plana - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027 apa: Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027 chicago: Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027. ieee: B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019. ista: Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24. mla: Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027. short: B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24. date_created: 2019-05-13T07:58:35Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-25T10:19:55Z day: '01' department: - _id: BjHo doi: 10.1016/j.ijmultiphaseflow.2019.04.027 external_id: arxiv: - '1902.07351' isi: - '000474496000002' intvolume: ' 117' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07351 month: '08' oa: 1 oa_version: Preprint page: 14-24 publication: International Journal of Multiphase Flow publication_identifier: issn: - '03019322' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Phase-field simulation of core-annular pipe flow type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 117 year: '2019' ... --- _id: '6419' abstract: - lang: eng text: Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible. article_number: e1008079 article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079. ieee: V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079. mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019). date_created: 2019-05-13T07:58:38Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:37Z day: '10' ddc: - '570' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079 ec_funded: 1 external_id: isi: - '000466866000029' file: - access_level: open_access checksum: cf3889c8a8a16053dacf9c3776cbe217 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:26:08Z date_updated: 2020-07-14T12:47:30Z file_id: '6445' file_name: 2019_PLOSGenetics_Pokusaeva.pdf file_size: 3726017 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: PLoS Genetics publication_identifier: eissn: - '15537404' publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9789' relation: research_data status: public - id: '9790' relation: research_data status: public - id: '9797' relation: research_data status: public scopus_import: '1' status: public title: An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6412' abstract: - lang: eng text: Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates. article_number: '1931' article_processing_charge: No author: - first_name: Hagar F. full_name: Moussa, Hagar F. last_name: Moussa - first_name: Daniel full_name: Bsteh, Daniel last_name: Bsteh - first_name: Ramesh full_name: Yelagandula, Ramesh last_name: Yelagandula - first_name: Carina full_name: Pribitzer, Carina last_name: Pribitzer - first_name: Karin full_name: Stecher, Karin last_name: Stecher - first_name: Katarina full_name: Bartalska, Katarina id: 4D883232-F248-11E8-B48F-1D18A9856A87 last_name: Bartalska - first_name: Luca full_name: Michetti, Luca last_name: Michetti - first_name: Jingkui full_name: Wang, Jingkui last_name: Wang - first_name: Jorge A. full_name: Zepeda-Martinez, Jorge A. last_name: Zepeda-Martinez - first_name: Ulrich full_name: Elling, Ulrich last_name: Elling - first_name: Jacob I. full_name: Stuckey, Jacob I. last_name: Stuckey - first_name: Lindsey I. full_name: James, Lindsey I. last_name: James - first_name: Stephen V. full_name: Frye, Stephen V. last_name: Frye - first_name: Oliver full_name: Bell, Oliver last_name: Bell citation: ama: Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6 apa: Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6 chicago: Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6. ieee: H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019. ista: Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931. mla: Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6. short: H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019). date_created: 2019-05-13T07:58:35Z date_published: 2019-04-29T00:00:00Z date_updated: 2023-08-25T10:31:56Z day: '29' ddc: - '570' department: - _id: SaSi doi: 10.1038/s41467-019-09628-6 external_id: isi: - '000466118700002' file: - access_level: open_access checksum: 6550a328335396c856db4cbdda7d2994 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:45:51Z date_updated: 2020-07-14T12:47:29Z file_id: '6448' file_name: 2019_NatureComm_Moussa.pdf file_size: 1223647 relation: main_file file_date_updated: 2020-07-14T12:47:29Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6415' abstract: - lang: eng text: Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Cremer S. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011 apa: Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011 chicago: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011. ieee: S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019. ista: Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68. mla: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011. short: S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68. date_created: 2019-05-13T07:58:36Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-25T10:31:31Z day: '01' department: - _id: SyCr doi: 10.1016/j.cois.2019.03.011 external_id: isi: - '000477666000012' intvolume: ' 33' isi: 1 language: - iso: eng month: '06' oa_version: None page: 63-68 publication: Current Opinion in Insect Science publication_identifier: eissn: - '22145753' issn: - '22145745' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Pathogens and disease defense of invasive ants type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2019' ... --- _id: '9790' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011. ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011. mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T08:50:15Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s011 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: A statistical summary of segment libraries and sequencing results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9797' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011. ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011. mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T11:08:20Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s011 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: A statistical summary of segment libraries and sequencing results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9789' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010. ieee: V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library of Science, 10.1371/journal.pgen.1008079.s010. mla: Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T08:38:50Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s010 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: Multiple alignment of His3 orthologues type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6462' abstract: - lang: eng text: A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles. 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: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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: Bettina full_name: Konighofer, Bettina last_name: Konighofer - first_name: Stefan full_name: Pranger, Stefan last_name: Pranger citation: ama: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649. doi:10.1007/978-3-030-25540-4_36' apa: 'Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., & Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36' chicago: Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In 31st International Conference on Computer-Aided Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36. ieee: G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in 31st International Conference on Computer-Aided Verification, New York, NY, United States, 2019, vol. 11561, pp. 630–649. ista: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.' mla: Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36. short: G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649. conference: end_date: 2019-07-18 location: New York, NY, United States name: 'CAV: Computer Aided Verification' start_date: 2019-07-13 date_created: 2019-05-16T11:22:30Z date_published: 2019-07-12T00:00:00Z date_updated: 2023-08-25T10:33:27Z day: '12' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-030-25540-4_36 external_id: isi: - '000491468000036' file: - access_level: open_access checksum: c231579f2485c6fd4df17c9443a4d80b content_type: application/pdf creator: dernst date_created: 2019-08-14T09:35:24Z date_updated: 2020-07-14T12:47:31Z file_id: '6816' file_name: 2019_CAV_Avni.pdf file_size: 659766 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 11561' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 630-649 project: - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory - _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: 31st International Conference on Computer-Aided Verification publication_identifier: isbn: - '9783030255398' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Run-time optimization for learned controllers through quantitative games 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11561 year: '2019' ... --- _id: '6477' abstract: - lang: eng text: 'Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions.' article_number: '021001' article_processing_charge: No article_type: original author: - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin - first_name: Ehud full_name: Altman, Ehud last_name: Altman - first_name: Immanuel full_name: Bloch, Immanuel last_name: Bloch - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: 'Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2). doi:10.1103/revmodphys.91.021001' apa: 'Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001' chicago: 'Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001.' ieee: 'D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” Reviews of Modern Physics, vol. 91, no. 2. American Physical Society, 2019.' ista: 'Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.' mla: 'Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:10.1103/revmodphys.91.021001.' short: D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019). date_created: 2019-05-23T07:38:43Z date_published: 2019-05-22T00:00:00Z date_updated: 2023-08-25T10:37:56Z day: '22' ddc: - '530' department: - _id: MaSe doi: 10.1103/revmodphys.91.021001 external_id: arxiv: - '1804.11065' isi: - '000469046900001' file: - access_level: open_access checksum: 4aec0e6662b09f6e0f828cd30ff2c3a6 content_type: application/pdf creator: mserbyn date_created: 2019-05-23T07:39:05Z date_updated: 2020-07-14T12:47:31Z file_id: '6478' file_name: RevModPhys.91.021001.pdf file_size: 1695677 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 91' isi: 1 issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Reviews of Modern Physics publication_identifier: eissn: - 0034-6861 issn: - 1539-0756 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Colloquium: Many-body localization, thermalization, and entanglement' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 91 year: '2019' ... --- _id: '6466' abstract: - lang: eng text: "One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates." article_processing_charge: No author: - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 citation: ama: Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048 apa: Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048 chicago: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048. ieee: D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019. ista: Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581. mla: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048. short: D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581. date_created: 2019-05-19T21:59:15Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-25T10:37:30Z day: '01' ddc: - '580' - '576' department: - _id: NiBa doi: 10.1111/mec.15048 external_id: isi: - '000474808300001' file: - access_level: open_access checksum: 521e3aff3e9263ddf2ffbfe0b6157715 content_type: application/pdf creator: dernst date_created: 2019-05-20T11:49:06Z date_updated: 2020-07-14T12:47:31Z file_id: '6472' file_name: 2019_MolecularEcology_Field.pdf file_size: 367711 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 28' isi: 1 issue: '7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1579-1581 publication: Molecular ecology publication_identifier: eissn: - 1365294X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Breaking down barriers in morning glories 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 28 year: '2019' ... --- _id: '6465' abstract: - lang: eng text: Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells. article_number: '2013' article_processing_charge: No author: - first_name: Hélène full_name: Chassin, Hélène last_name: Chassin - first_name: Marius full_name: Müller, Marius last_name: Müller - first_name: Marcel full_name: Tigges, Marcel last_name: Tigges - first_name: Leo full_name: Scheller, Leo last_name: Scheller - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Martin full_name: Fussenegger, Martin last_name: Fussenegger citation: ama: Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09974-5 apa: Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5 chicago: Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5. ieee: H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019. ista: Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013. mla: Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:10.1038/s41467-019-09974-5. short: H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019). date_created: 2019-05-19T21:59:14Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-08-25T10:33:51Z day: '01' ddc: - '570' department: - _id: CaGu doi: 10.1038/s41467-019-09974-5 external_id: isi: - '000466338600006' file: - access_level: open_access checksum: e214d3e4f8c81e35981583c4569b51b8 content_type: application/pdf creator: dernst date_created: 2019-05-20T07:33:54Z date_updated: 2020-07-14T12:47:31Z file_id: '6471' file_name: 2019_NatureComm_Chassin.pdf file_size: 1191827 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-023-36111-0 scopus_import: '1' status: public title: A modular degron library for synthetic circuits in mammalian cells 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6467' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_number: '0881' article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881 apa: Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881 chicago: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881. ieee: C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019. ista: Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881. mla: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881. short: C. Fraisse, J.J. Welch, Biology Letters 15 (2019). date_created: 2019-05-19T21:59:15Z date_published: 2019-04-03T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '03' department: - _id: BeVi - _id: NiBa doi: 10.1098/rsbl.2018.0881 ec_funded: 1 external_id: isi: - '000465405300010' pmid: - '31014191' intvolume: ' 15' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rsbl.2018.0881 month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Biology Letters publication_identifier: eissn: - 1744957X issn: - '17449561' publication_status: published publisher: Royal Society of London quality_controlled: '1' related_material: link: - relation: supplementary_material url: https://dx.doi.org/10.6084/m9.figshare.c.4461008 record: - id: '9798' relation: research_data status: public - id: '9799' relation: research_data status: public scopus_import: '1' status: public title: The distribution of epistasis on simple fitness landscapes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6470' abstract: - lang: eng text: 'Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. ' article_processing_charge: No article_type: original author: - first_name: Tímea full_name: Éltes, Tímea last_name: Éltes - first_name: Miklos full_name: Szoboszlay, Miklos last_name: Szoboszlay - first_name: Margit Katalin full_name: Szigeti, Margit Katalin id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87 last_name: Szigeti orcid: 0000-0001-9500-8758 - first_name: Zoltan full_name: Nusser, Zoltan last_name: Nusser citation: ama: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681 apa: Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. Wiley. https://doi.org/10.1113/JP277681 chicago: Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681. ieee: T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019. ista: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947. mla: Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681. short: T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947. date_created: 2019-05-19T21:59:17Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-25T10:34:15Z day: '01' department: - _id: GaNo doi: 10.1113/JP277681 external_id: isi: - '000470780400013' pmid: - '31006863' intvolume: ' 597' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1113/JP277681 month: '06' oa: 1 oa_version: Published Version page: 2925–2947 pmid: 1 publication: Journal of Physiology publication_identifier: eissn: - '14697793' issn: - '00223751' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 597 year: '2019' ... --- _id: '6493' abstract: - lang: eng text: We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements. alternative_title: - LNCS article_processing_charge: No author: - first_name: Miriam full_name: Garcia Soto, Miriam id: 4B3207F6-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Soto orcid: 0000−0003−2936−5719 - 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: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Luka full_name: Zeleznik, Luka id: 3ADCA2E4-F248-11E8-B48F-1D18A9856A87 last_name: Zeleznik citation: ama: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16' apa: 'Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16' chicago: Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16. ieee: M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314. ista: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.' mla: Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16. short: M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314. conference: end_date: 2019-07-18 location: New York City, NY, USA name: 'CAV: Computer-Aided Verification' start_date: 2019-07-15 date_created: 2019-05-27T07:09:53Z date_published: 2019-07-12T00:00:00Z date_updated: 2023-08-25T10:40:41Z day: '12' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-25540-4_16 ec_funded: 1 external_id: isi: - '000491468000016' file: - access_level: open_access checksum: 1f1d61b83a151031745ef70a501da3d6 content_type: application/pdf creator: dernst date_created: 2019-08-14T11:05:30Z date_updated: 2020-07-14T12:47:32Z file_id: '6817' file_name: 2019_CAV_GarciaSoto.pdf file_size: 674795 relation: main_file file_date_updated: 2020-07-14T12:47:32Z has_accepted_license: '1' intvolume: ' 11561' isi: 1 keyword: - Synthesis - Linear hybrid automaton - Membership language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 297-314 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 31st International Conference on Computer-Aided Verification publication_identifier: isbn: - '9783030255398' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Membership-based synthesis of linear hybrid automata 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11561 year: '2019' ... --- _id: '6485' abstract: - lang: eng text: Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations. article_processing_charge: No author: - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Roman full_name: Elizarov, Roman last_name: Elizarov citation: ama: Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000 apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels for programming via communicating sequential processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming (pp. 417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000' chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels for Programming via Communicating Sequential Processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming. ACM Press, 2019. https://doi.org/10.1145/3293883.3297000. ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming via communicating sequential processes. ACM Press, 2019, pp. 417–418. ista: Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM Press,p. mla: Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000. short: N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM Press, 2019. conference: end_date: 2019-02-20 location: Washington, NY, United States name: 'PPoPP: Principles and Practice of Parallel Programming' start_date: 2019-02-16 date_created: 2019-05-24T10:09:12Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-08-25T10:41:20Z day: '01' department: - _id: DaAl doi: 10.1145/3293883.3297000 external_id: isi: - '000587604600044' isi: 1 language: - iso: eng month: '02' oa_version: None page: 417-418 publication: Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming publication_identifier: isbn: - '9781450362252' publication_status: published publisher: ACM Press quality_controlled: '1' status: public title: Lock-free channels for programming via communicating sequential processes type: conference_poster user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '6504' abstract: - lang: eng text: "Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response." article_processing_charge: No article_type: original author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: P full_name: He, P last_name: He - first_name: X full_name: Ma, X last_name: Ma - first_name: Z full_name: Yang, Z last_name: Yang - first_name: C full_name: Pang, C last_name: Pang - first_name: J full_name: Yu, J last_name: Yu - first_name: G full_name: Wang, G last_name: Wang - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: G full_name: Xiao, G last_name: Xiao citation: ama: Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932 apa: Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932 chicago: Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932. ieee: Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019. ista: Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774. mla: Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932. short: Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774. date_created: 2019-05-28T14:33:26Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-28T08:40:13Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.15932 external_id: isi: - '000487184200024' pmid: - '31111487' file: - access_level: open_access checksum: 6488243334538f5c39099a701cbf76b9 content_type: application/pdf creator: dernst date_created: 2020-10-14T08:59:33Z date_updated: 2020-10-14T08:59:33Z file_id: '8661' file_name: 2019_NewPhytologist_Zhang_accepted.pdf file_size: 1099061 relation: main_file success: 1 file_date_updated: 2020-10-14T08:59:33Z has_accepted_license: '1' intvolume: ' 224' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 761-774 pmid: 1 publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646x publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Auxin-mediated statolith production for root gravitropism type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 224 year: '2019' ... --- _id: '6506' abstract: - lang: eng text: How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele. article_processing_charge: No article_type: original author: - first_name: Lianet full_name: Noda-García, Lianet last_name: Noda-García - first_name: Dan full_name: Davidi, Dan last_name: Davidi - first_name: Elisa full_name: Korenblum, Elisa last_name: Korenblum - first_name: Assaf full_name: Elazar, Assaf last_name: Elazar - first_name: Ekaterina full_name: Putintseva, Ekaterina id: 2EF67C84-F248-11E8-B48F-1D18A9856A87 last_name: Putintseva - first_name: Asaph full_name: Aharoni, Asaph last_name: Aharoni - first_name: Dan S. full_name: Tawfik, Dan S. last_name: Tawfik citation: ama: Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y apa: Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y chicago: Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y. ieee: L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019. ista: Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230. mla: Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y. short: L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230. date_created: 2019-05-29T13:03:30Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-28T08:39:47Z day: '01' department: - _id: FyKo doi: 10.1038/s41564-019-0412-y external_id: isi: - '000480348200017' intvolume: ' 4' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/340828v2 month: '07' oa: 1 oa_version: Preprint page: 1221–1230 publication: Nature Microbiology publication_identifier: issn: - 2058-5276 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Chance and pleiotropy dominate genetic diversity in complex bacterial environments type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 4 year: '2019' ... --- _id: '6521' abstract: - lang: eng text: Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies. article_number: '134310' article_processing_charge: No article_type: original author: - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 - first_name: Rouven full_name: Schulz, Rouven id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87 last_name: Schulz orcid: 0000-0001-5297-733X - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: 'Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 2019;707. doi:10.1016/j.neulet.2019.134310' apa: 'Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310' chicago: 'Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.' ieee: 'M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience Letters, vol. 707. Elsevier, 2019.' ista: 'Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310.' mla: 'Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310, Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.' short: M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019). date_created: 2019-06-05T13:16:24Z date_published: 2019-08-10T00:00:00Z date_updated: 2023-08-28T09:30:57Z day: '10' ddc: - '570' department: - _id: SaSi doi: 10.1016/j.neulet.2019.134310 ec_funded: 1 external_id: isi: - '000486094600037' pmid: - '31158432' file: - access_level: open_access checksum: 553c9dbd39727fbed55ee991c51ca4d1 content_type: application/pdf creator: dernst date_created: 2019-06-08T11:44:20Z date_updated: 2020-07-14T12:47:33Z file_id: '6551' file_name: 2019_Neuroscience_Maes.pdf file_size: 1779287 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 707' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 25D4A630-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715571' name: Microglia action towards neuronal circuit formation and function in health and disease - _id: 267F75D8-B435-11E9-9278-68D0E5697425 name: Modulating microglia through G protein-coupled receptor (GPCR) signaling publication: Neuroscience Letters publication_identifier: issn: - 0304-3940 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 707 year: '2019' ... --- _id: '6513' abstract: - lang: eng text: Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property. article_processing_charge: No article_type: original author: - first_name: Jordi full_name: Guiu, Jordi last_name: Guiu - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Shiro full_name: Yui, Shiro last_name: Yui - first_name: Samuel full_name: Demharter, Samuel last_name: Demharter - first_name: Svetlana full_name: Ulyanchenko, Svetlana last_name: Ulyanchenko - first_name: Martti full_name: Maimets, Martti last_name: Maimets - first_name: Anne full_name: Jørgensen, Anne last_name: Jørgensen - first_name: Signe full_name: Perlman, Signe last_name: Perlman - first_name: Lene full_name: Lundvall, Lene last_name: Lundvall - first_name: Linn Salto full_name: Mamsen, Linn Salto last_name: Mamsen - first_name: Agnete full_name: Larsen, Agnete last_name: Larsen - first_name: Rasmus H. full_name: Olesen, Rasmus H. last_name: Olesen - first_name: Claus Yding full_name: Andersen, Claus Yding last_name: Andersen - first_name: Lea Langhoff full_name: Thuesen, Lea Langhoff last_name: Thuesen - first_name: Kristine Juul full_name: Hare, Kristine Juul last_name: Hare - first_name: Tune H. full_name: Pers, Tune H. last_name: Pers - first_name: Konstantin full_name: Khodosevich, Konstantin last_name: Khodosevich - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons - first_name: Kim B. full_name: Jensen, Kim B. last_name: Jensen citation: ama: Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5 apa: Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5 chicago: Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5. ieee: J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019. ista: Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111. mla: Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5. short: J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111. date_created: 2019-06-02T21:59:14Z date_published: 2019-06-06T00:00:00Z date_updated: 2023-08-28T09:30:23Z day: '06' department: - _id: EdHa doi: 10.1038/s41586-019-1212-5 external_id: isi: - '000470149000048' pmid: - '31092921' intvolume: ' 570' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928 month: '06' oa: 1 oa_version: Submitted Version page: 107-111 pmid: 1 publication: Nature publication_identifier: eissn: - '14764687' issn: - '00280836' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Tracing the origin of adult intestinal stem cells type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 570 year: '2019' ... --- _id: '6564' abstract: - lang: eng text: Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology. article_processing_charge: No article_type: original author: - first_name: Alexandra-Madelaine full_name: Tichy, Alexandra-Madelaine id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87 last_name: Tichy - first_name: Elliot J. full_name: Gerrard, Elliot J. last_name: Gerrard - first_name: Julien M.D. full_name: Legrand, Julien M.D. last_name: Legrand - first_name: Robin M. full_name: Hobbs, Robin M. last_name: Hobbs - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033 apa: Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033 chicago: Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033. ieee: A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” Journal of Molecular Biology, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019. ista: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055. mla: Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:10.1016/j.jmb.2019.05.033. short: A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055. date_created: 2019-06-16T21:59:14Z date_published: 2019-08-09T00:00:00Z date_updated: 2023-08-28T09:39:22Z day: '09' department: - _id: HaJa doi: 10.1016/j.jmb.2019.05.033 external_id: isi: - '000482872100002' intvolume: ' 431' isi: 1 issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: http://www.biorxiv.org/content/10.1101/583369v1 month: '08' oa: 1 oa_version: Preprint page: 3046-3055 publication: Journal of Molecular Biology publication_identifier: eissn: - '10898638' issn: - '00222836' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 431 year: '2019' ... --- _id: '6552' abstract: - lang: eng text: 'When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body''s physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). ' article_processing_charge: No article_type: original author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463. doi:10.1016/j.cub.2019.03.035 apa: Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.03.035 chicago: Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.03.035. ieee: S. Cremer, “Social immunity in insects,” Current Biology, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019. ista: Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463. mla: Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035. short: S. Cremer, Current Biology 29 (2019) R458–R463. date_created: 2019-06-09T21:59:10Z date_published: 2019-06-03T00:00:00Z date_updated: 2023-08-28T09:38:00Z day: '03' department: - _id: SyCr doi: 10.1016/j.cub.2019.03.035 external_id: isi: - '000470902000023' pmid: - '31163158' intvolume: ' 29' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2019.03.035 month: '06' oa: 1 oa_version: Published Version page: R458-R463 pmid: 1 publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Social immunity in insects type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 29 year: '2019' ... --- _id: '6511' abstract: - lang: eng text: Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N). article_processing_charge: No author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. Annals of Probability. 2019;47(3):1270-1334. doi:10.1214/18-AOP1284 apa: Bao, Z., Erdös, L., & Schnelli, K. (2019). Local single ring theorem on optimal scale. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1284 chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1284. ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” Annals of Probability, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019. ista: Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334. mla: Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:10.1214/18-AOP1284. short: Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334. date_created: 2019-06-02T21:59:13Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-08-28T09:32:29Z day: '01' department: - _id: LaEr doi: 10.1214/18-AOP1284 ec_funded: 1 external_id: arxiv: - '1612.05920' isi: - '000466616100003' intvolume: ' 47' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.05920 month: '05' oa: 1 oa_version: Preprint page: 1270-1334 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Annals of Probability publication_identifier: issn: - '00911798' publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Local single ring theorem on optimal scale type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 47 year: '2019' ... --- _id: '6559' abstract: - lang: eng text: Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology. article_processing_charge: No article_type: original author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons citation: ama: Hannezo EB, Simons BD. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 2019;60:99-105. doi:10.1016/j.ceb.2019.04.008 apa: Hannezo, E. B., & Simons, B. D. (2019). Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.04.008 chicago: Hannezo, Edouard B, and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.04.008. ieee: E. B. Hannezo and B. D. Simons, “Multiscale dynamics of branching morphogenesis,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 99–105, 2019. ista: Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 60, 99–105. mla: Hannezo, Edouard B., and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 99–105, doi:10.1016/j.ceb.2019.04.008. short: E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105. date_created: 2019-06-16T21:59:12Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-28T09:38:57Z day: '01' department: - _id: EdHa doi: 10.1016/j.ceb.2019.04.008 external_id: isi: - '000486545800014' pmid: - '31181348' intvolume: ' 60' isi: 1 language: - iso: eng month: '10' oa_version: None page: 99-105 pmid: 1 publication: Current Opinion in Cell Biology publication_identifier: eissn: - '18790410' issn: - '09550674' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Multiscale dynamics of branching morphogenesis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 60 year: '2019' ... --- _id: '6566' abstract: - lang: eng text: Methodologies that involve the use of nanoparticles as “artificial atoms” to rationally build materials in a bottom-up fashion are particularly well-suited to control the matter at the nanoscale. Colloidal synthetic routes allow for an exquisite control over such “artificial atoms” in terms of size, shape, and crystal phase as well as core and surface compositions. We present here a bottom-up approach to produce Pb–Ag–K–S–Te nanocomposites, which is a highly promising system for thermoelectric energy conversion. First, we developed a high-yield and scalable colloidal synthesis route to uniform lead sulfide (PbS) nanorods, whose tips are made of silver sulfide (Ag2S). We then took advantage of the large surface-to-volume ratio to introduce a p-type dopant (K) by replacing native organic ligands with K2Te. Upon thermal consolidation, K2Te-surface modified PbS–Ag2S nanorods yield p-type doped nanocomposites with PbTe and PbS as major phases and Ag2S and Ag2Te as embedded nanoinclusions. Thermoelectric characterization of such consolidated nanosolids showed a high thermoelectric figure-of-merit of 1 at 620 K. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Roger full_name: Hasler, Roger last_name: Hasler - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Oleksandr full_name: Dobrozhan, Oleksandr last_name: Dobrozhan - first_name: Olga full_name: Nazarenko, Olga last_name: Nazarenko - first_name: María de la full_name: Mata, María de la last_name: Mata - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Maksym V. full_name: Kovalenko, Maksym V. last_name: Kovalenko citation: ama: Ibáñez M, Genç A, Hasler R, et al. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 2019;13(6):6572-6580. doi:10.1021/acsnano.9b00346 apa: Ibáñez, M., Genç, A., Hasler, R., Liu, Y., Dobrozhan, O., Nazarenko, O., … Kovalenko, M. V. (2019). Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.9b00346 chicago: Ibáñez, Maria, Aziz Genç, Roger Hasler, Yu Liu, Oleksandr Dobrozhan, Olga Nazarenko, María de la Mata, Jordi Arbiol, Andreu Cabot, and Maksym V. Kovalenko. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano. American Chemical Society, 2019. https://doi.org/10.1021/acsnano.9b00346. ieee: M. Ibáñez et al., “Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks,” ACS Nano, vol. 13, no. 6. American Chemical Society, pp. 6572–6580, 2019. ista: Ibáñez M, Genç A, Hasler R, Liu Y, Dobrozhan O, Nazarenko O, Mata M de la, Arbiol J, Cabot A, Kovalenko MV. 2019. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 13(6), 6572–6580. mla: Ibáñez, Maria, et al. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano, vol. 13, no. 6, American Chemical Society, 2019, pp. 6572–80, doi:10.1021/acsnano.9b00346. short: M. Ibáñez, A. Genç, R. Hasler, Y. Liu, O. Dobrozhan, O. Nazarenko, M. de la Mata, J. Arbiol, A. Cabot, M.V. Kovalenko, ACS Nano 13 (2019) 6572–6580. date_created: 2019-06-18T13:54:34Z date_published: 2019-06-25T00:00:00Z date_updated: 2023-08-28T12:20:53Z day: '25' ddc: - '540' department: - _id: MaIb doi: 10.1021/acsnano.9b00346 ec_funded: 1 external_id: isi: - '000473248300043' pmid: - '31185159' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-07-16T14:17:09Z date_updated: 2020-07-14T12:47:33Z file_id: '6644' file_name: 2019_ACSNano_Ibanez.pdf file_size: 8628690 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '6' keyword: - colloidal nanoparticles - asymmetric nanoparticles - inorganic ligands - heterostructures - catalyst assisted growth - nanocomposites - thermoelectrics language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 6572-6580 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: ACS Nano publication_identifier: eissn: - 1936-086X issn: - 1936-0851 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2019' ... --- _id: '6607' abstract: - lang: eng text: Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically. article_number: '9139' article_processing_charge: No author: - first_name: Chi Huu full_name: Nguyen, Chi Huu last_name: Nguyen - first_name: Tobias full_name: Glüxam, Tobias last_name: Glüxam - first_name: Angela full_name: Schlerka, Angela last_name: Schlerka - first_name: Katharina full_name: Bauer, Katharina id: 2ED6B14C-F248-11E8-B48F-1D18A9856A87 last_name: Bauer - first_name: Alexander M. full_name: Grandits, Alexander M. last_name: Grandits - first_name: Hubert full_name: Hackl, Hubert last_name: Hackl - first_name: Oliver full_name: Dovey, Oliver last_name: Dovey - first_name: Sabine full_name: Zöchbauer-Müller, Sabine last_name: Zöchbauer-Müller - first_name: Jonathan L. full_name: Cooper, Jonathan L. last_name: Cooper - first_name: George S. full_name: Vassiliou, George S. last_name: Vassiliou - first_name: Dagmar full_name: Stoiber, Dagmar last_name: Stoiber - first_name: Rotraud full_name: Wieser, Rotraud last_name: Wieser - first_name: Gerwin full_name: Heller, Gerwin last_name: Heller citation: ama: Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-45579-0 apa: Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-019-45579-0 chicago: Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-019-45579-0. ieee: C. H. Nguyen et al., “SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019. ista: Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 9(1), 9139. mla: Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports, vol. 9, no. 1, 9139, Nature Publishing Group, 2019, doi:10.1038/s41598-019-45579-0. short: C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O. Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser, G. Heller, Scientific Reports 9 (2019). date_created: 2019-07-07T21:59:19Z date_published: 2019-06-24T00:00:00Z date_updated: 2023-08-28T12:26:51Z day: '24' ddc: - '576' department: - _id: PreCl doi: 10.1038/s41598-019-45579-0 external_id: isi: - '000472597400042' file: - access_level: open_access checksum: 3283522fffadf4b5fc8c7adfe3ba4564 content_type: application/pdf creator: kschuh date_created: 2019-07-08T15:15:28Z date_updated: 2020-07-14T12:47:34Z file_id: '6623' file_name: nature_2019_Nguyen.pdf file_size: 2017352 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 9' 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 quality_controlled: '1' scopus_import: '1' status: public title: SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '6609' abstract: - lang: eng text: Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons. acknowledged_ssus: - _id: NanoFab 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: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Dylan full_name: Lewis, Dylan last_name: Lewis - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation from micromechanical motion. Nature. 2019;570:480-483. doi:10.1038/s41586-019-1320-2 apa: Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G. M., & Fink, J. M. (2019). Stationary entangled radiation from micromechanical motion. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-019-1320-2 chicago: Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from Micromechanical Motion.” Nature. Nature Publishing Group, 2019. https://doi.org/10.1038/s41586-019-1320-2. ieee: S. Barzanjeh et al., “Stationary entangled radiation from micromechanical motion,” Nature, vol. 570. Nature Publishing Group, pp. 480–483, 2019. ista: Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM. 2019. Stationary entangled radiation from micromechanical motion. Nature. 570, 480–483. mla: Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical Motion.” Nature, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:10.1038/s41586-019-1320-2. short: S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M. Fink, Nature 570 (2019) 480–483. date_created: 2019-07-07T21:59:20Z date_published: 2019-06-27T00:00:00Z date_updated: 2023-08-28T12:29:56Z day: '27' department: - _id: JoFi doi: 10.1038/s41586-019-1320-2 ec_funded: 1 external_id: arxiv: - '1809.05865' isi: - '000472860000042' intvolume: ' 570' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.05865 month: '06' oa: 1 oa_version: Preprint page: 480-483 project: - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _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' - _id: 2671EB66-B435-11E9-9278-68D0E5697425 name: Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies publication: Nature publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Stationary entangled radiation from micromechanical motion type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 570 year: '2019' ... --- _id: '6596' abstract: - lang: eng text: It is well known that many problems in image recovery, signal processing, and machine learning can be modeled as finding zeros of the sum of maximal monotone and Lipschitz continuous monotone operators. Many papers have studied forward-backward splitting methods for finding zeros of the sum of two monotone operators in Hilbert spaces. Most of the proposed splitting methods in the literature have been proposed for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert spaces. In this paper, we consider splitting methods for finding zeros of the sum of maximal monotone operators and Lipschitz continuous monotone operators in Banach spaces. We obtain weak and strong convergence results for the zeros of the sum of maximal monotone and Lipschitz continuous monotone operators in Banach spaces. Many already studied problems in the literature can be considered as special cases of this paper. article_number: '138' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 citation: ama: Shehu Y. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 2019;74(4). doi:10.1007/s00025-019-1061-4 apa: Shehu, Y. (2019). Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. Springer. https://doi.org/10.1007/s00025-019-1061-4 chicago: Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics. Springer, 2019. https://doi.org/10.1007/s00025-019-1061-4. ieee: Y. Shehu, “Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces,” Results in Mathematics, vol. 74, no. 4. Springer, 2019. ista: Shehu Y. 2019. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 74(4), 138. mla: Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics, vol. 74, no. 4, 138, Springer, 2019, doi:10.1007/s00025-019-1061-4. short: Y. Shehu, Results in Mathematics 74 (2019). date_created: 2019-06-29T10:11:30Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-28T12:26:22Z day: '01' ddc: - '000' department: - _id: VlKo doi: 10.1007/s00025-019-1061-4 ec_funded: 1 external_id: arxiv: - '2101.09068' isi: - '000473237500002' file: - access_level: open_access checksum: c6d18cb1e16fc0c36a0e0f30b4ebbc2d content_type: application/pdf creator: kschuh date_created: 2019-07-03T15:20:40Z date_updated: 2020-07-14T12:47:34Z file_id: '6605' file_name: Springer_2019_Shehu.pdf file_size: 466942 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 74' isi: 1 issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Results in Mathematics publication_identifier: eissn: - 1420-9012 issn: - 1422-6383 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 74 year: '2019' ... --- _id: '6601' abstract: - lang: eng text: There is increasing evidence that both mechanical and biochemical signals play important roles in development and disease. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. This feedback occurs at the molecular level via mechanosensation but can also arise as an emergent property of the system at the cellular and tissue level. In recent years, dynamic changes in tissue geometry, flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical feedback loops in multiple processes. Here, we review recent experimental and theoretical advances in understanding how these feedbacks function in development and disease. article_processing_charge: No article_type: review author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development and disease. Cell. 2019;178(1):12-25. doi:10.1016/j.cell.2019.05.052 apa: Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Mechanochemical feedback loops in development and disease. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.05.052 chicago: Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.05.052. ieee: E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in development and disease,” Cell, vol. 178, no. 1. Elsevier, pp. 12–25, 2019. ista: Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25. mla: Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell, vol. 178, no. 1, Elsevier, 2019, pp. 12–25, doi:10.1016/j.cell.2019.05.052. short: E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25. date_created: 2019-06-30T21:59:11Z date_published: 2019-07-27T00:00:00Z date_updated: 2023-08-28T12:25:21Z day: '27' department: - _id: CaHe - _id: EdHa doi: 10.1016/j.cell.2019.05.052 ec_funded: 1 external_id: isi: - '000473002700005' pmid: - '31251912' intvolume: ' 178' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2019.05.052 month: '07' oa: 1 oa_version: Published Version page: 12-25 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 268294B6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31639 name: Active mechano-chemical description of the cell cytoskeleton publication: Cell publication_identifier: issn: - '00928674' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Mechanochemical feedback loops in development and disease type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 178 year: '2019' ... --- _id: '6617' abstract: - lang: eng text: 'The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Fischer JL. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 2019;234(2):635–726. doi:10.1007/s00205-019-01400-w apa: Fischer, J. L. (2019). The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-019-01400-w chicago: Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis. Springer, 2019. https://doi.org/10.1007/s00205-019-01400-w. ieee: J. L. Fischer, “The choice of representative volumes in the approximation of effective properties of random materials,” Archive for Rational Mechanics and Analysis, vol. 234, no. 2. Springer, pp. 635–726, 2019. ista: Fischer JL. 2019. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 234(2), 635–726. mla: Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis, vol. 234, no. 2, Springer, 2019, pp. 635–726, doi:10.1007/s00205-019-01400-w. short: J.L. Fischer, Archive for Rational Mechanics and Analysis 234 (2019) 635–726. date_created: 2019-07-07T21:59:23Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-28T12:31:21Z day: '01' ddc: - '500' department: - _id: JuFi doi: 10.1007/s00205-019-01400-w external_id: arxiv: - '1807.00834' isi: - '000482386000006' file: - access_level: open_access checksum: 4cff75fa6addb0770991ad9c474ab404 content_type: application/pdf creator: kschuh date_created: 2019-07-08T15:56:47Z date_updated: 2020-07-14T12:47:34Z file_id: '6626' file_name: Springer_2019_Fischer.pdf file_size: 1377659 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 234' isi: 1 issue: '2' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 635–726 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: The choice of representative volumes in the approximation of effective properties of random materials 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 234 year: '2019' ... --- _id: '6611' abstract: - lang: eng text: 'Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.' acknowledged_ssus: - _id: Bio article_number: '222' article_processing_charge: No author: - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Glanc M, Fendrych M, Friml J. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 2019;9(6). doi:10.3390/biom9060222 apa: Glanc, M., Fendrych, M., & Friml, J. (2019). PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. MDPI. https://doi.org/10.3390/biom9060222 chicago: Glanc, Matous, Matyas Fendrych, and Jiří Friml. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules. MDPI, 2019. https://doi.org/10.3390/biom9060222. ieee: M. Glanc, M. Fendrych, and J. Friml, “PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton,” Biomolecules, vol. 9, no. 6. MDPI, 2019. ista: Glanc M, Fendrych M, Friml J. 2019. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 9(6), 222. mla: Glanc, Matous, et al. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules, vol. 9, no. 6, 222, MDPI, 2019, doi:10.3390/biom9060222. short: M. Glanc, M. Fendrych, J. Friml, Biomolecules 9 (2019). date_created: 2019-07-07T21:59:21Z date_published: 2019-06-07T00:00:00Z date_updated: 2023-08-28T12:30:24Z day: '07' ddc: - '580' department: - _id: JiFr doi: 10.3390/biom9060222 ec_funded: 1 external_id: isi: - '000475301500018' pmid: - '31181636' file: - access_level: open_access checksum: 1ce1bd36038fe5381057a1bcc6760083 content_type: application/pdf creator: kschuh date_created: 2019-07-08T15:46:32Z date_updated: 2020-07-14T12:47:34Z file_id: '6625' file_name: biomolecules-2019-Matous.pdf file_size: 1066773 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Biomolecules publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '6620' abstract: - lang: eng text: "This paper establishes an asymptotic formula with a power-saving error term for the number of rational points of bounded height on the singular cubic surface of ℙ3ℚ given by the following equation \U0001D4650(\U0001D46521+\U0001D46522)−\U0001D46533=0 in agreement with the Manin-Peyre conjectures.\r\n" article_processing_charge: No article_type: original author: - first_name: Régis full_name: De La Bretèche, Régis last_name: De La Bretèche - first_name: Kevin N full_name: Destagnol, Kevin N id: 44DDECBC-F248-11E8-B48F-1D18A9856A87 last_name: Destagnol - first_name: Jianya full_name: Liu, Jianya last_name: Liu - first_name: Jie full_name: Wu, Jie last_name: Wu - first_name: Yongqiang full_name: Zhao, Yongqiang last_name: Zhao citation: ama: De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. On a certain non-split cubic surface. Science China Mathematics. 2019;62(12):2435–2446. doi:10.1007/s11425-018-9543-8 apa: De La Bretèche, R., Destagnol, K. N., Liu, J., Wu, J., & Zhao, Y. (2019). On a certain non-split cubic surface. Science China Mathematics. Springer. https://doi.org/10.1007/s11425-018-9543-8 chicago: De La Bretèche, Régis, Kevin N Destagnol, Jianya Liu, Jie Wu, and Yongqiang Zhao. “On a Certain Non-Split Cubic Surface.” Science China Mathematics. Springer, 2019. https://doi.org/10.1007/s11425-018-9543-8. ieee: R. De La Bretèche, K. N. Destagnol, J. Liu, J. Wu, and Y. Zhao, “On a certain non-split cubic surface,” Science China Mathematics, vol. 62, no. 12. Springer, pp. 2435–2446, 2019. ista: De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. 2019. On a certain non-split cubic surface. Science China Mathematics. 62(12), 2435–2446. mla: De La Bretèche, Régis, et al. “On a Certain Non-Split Cubic Surface.” Science China Mathematics, vol. 62, no. 12, Springer, 2019, pp. 2435–2446, doi:10.1007/s11425-018-9543-8. short: R. De La Bretèche, K.N. Destagnol, J. Liu, J. Wu, Y. Zhao, Science China Mathematics 62 (2019) 2435–2446. date_created: 2019-07-07T21:59:25Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-28T12:32:20Z day: '01' department: - _id: TiBr doi: 10.1007/s11425-018-9543-8 external_id: arxiv: - '1709.09476' isi: - '000509102200001' intvolume: ' 62' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.09476 month: '12' oa: 1 oa_version: Preprint page: 2435–2446 publication: Science China Mathematics publication_identifier: issn: - '16747283' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: On a certain non-split cubic surface type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 62 year: '2019' ... --- _id: '6637' abstract: - lang: eng text: The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations. acknowledgement: The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: 'Martin ' full_name: 'Krejca, Martin ' last_name: Krejca - first_name: Per Kristian full_name: Lehre, Per Kristian last_name: Lehre - first_name: Timo full_name: Kötzing, Timo last_name: Kötzing citation: ama: 'Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784' apa: 'Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784' chicago: 'Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784.' ieee: 'B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.' ista: 'Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.' mla: 'Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.' short: B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374. date_created: 2019-07-14T21:59:20Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-29T06:31:14Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1111/evo.13784 ec_funded: 1 external_id: isi: - '000474031600001' file: - access_level: open_access checksum: 9831ca65def2d62498c7b08338b6d237 content_type: application/pdf creator: apreinsp date_created: 2019-07-16T06:08:31Z date_updated: 2020-07-14T12:47:34Z file_id: '6643' file_name: 2019_Evolution_TrubenovaBarbora.pdf file_size: 815416 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 73' isi: 1 issue: '7' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: 1356-1374 project: - _id: 25AEDD42-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '704172' name: Rate of Adaptation in Changing Environment - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Evolution publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Surfing on the seascape: Adaptation in a changing environment' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 73 year: '2019' ... --- _id: '6634' abstract: - lang: eng text: In this paper we prove several new results around Gromov's waist theorem. We give a simple proof of Vaaler's theorem on sections of the unit cube using the Borsuk-Ulam-Crofton technique, consider waists of real and complex projective spaces, flat tori, convex bodies in Euclidean space; and establish waist-type results in terms of the Hausdorff measure. 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: Alfredo full_name: Hubard, Alfredo last_name: Hubard - first_name: Roman full_name: Karasev, Roman last_name: Karasev citation: ama: Akopyan A, Hubard A, Karasev R. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 2019;53(2):457-490. doi:10.12775/TMNA.2019.008 apa: Akopyan, A., Hubard, A., & Karasev, R. (2019). Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism. https://doi.org/10.12775/TMNA.2019.008 chicago: Akopyan, Arseniy, Alfredo Hubard, and Roman Karasev. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism, 2019. https://doi.org/10.12775/TMNA.2019.008. ieee: A. Akopyan, A. Hubard, and R. Karasev, “Lower and upper bounds for the waists of different spaces,” Topological Methods in Nonlinear Analysis, vol. 53, no. 2. Akademicka Platforma Czasopism, pp. 457–490, 2019. ista: Akopyan A, Hubard A, Karasev R. 2019. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 53(2), 457–490. mla: Akopyan, Arseniy, et al. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis, vol. 53, no. 2, Akademicka Platforma Czasopism, 2019, pp. 457–90, doi:10.12775/TMNA.2019.008. short: A. Akopyan, A. Hubard, R. Karasev, Topological Methods in Nonlinear Analysis 53 (2019) 457–490. date_created: 2019-07-14T21:59:19Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-29T06:32:48Z day: '01' department: - _id: HeEd doi: 10.12775/TMNA.2019.008 ec_funded: 1 external_id: arxiv: - '1612.06926' isi: - '000472541600004' intvolume: ' 53' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.06926 month: '06' oa: 1 oa_version: Preprint page: 457-490 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Topological Methods in Nonlinear Analysis publication_status: published publisher: Akademicka Platforma Czasopism quality_controlled: '1' scopus_import: '1' status: public title: Lower and upper bounds for the waists of different spaces type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 53 year: '2019' ... --- _id: '6638' abstract: - lang: eng text: The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one. article_processing_charge: No author: - first_name: 'André ' full_name: 'Silva, André ' last_name: Silva - first_name: Alan M full_name: Arroyo Guevara, Alan M id: 3207FDC6-F248-11E8-B48F-1D18A9856A87 last_name: Arroyo Guevara orcid: 0000-0003-2401-8670 - first_name: Bruce full_name: Richter, Bruce last_name: Richter - first_name: Orlando full_name: Lee, Orlando last_name: Lee citation: ama: Silva A, Arroyo Guevara AM, Richter B, Lee O. Graphs with at most one crossing. Discrete Mathematics. 2019;342(11):3201-3207. doi:10.1016/j.disc.2019.06.031 apa: Silva, A., Arroyo Guevara, A. M., Richter, B., & Lee, O. (2019). Graphs with at most one crossing. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2019.06.031 chicago: Silva, André , Alan M Arroyo Guevara, Bruce Richter, and Orlando Lee. “Graphs with at Most One Crossing.” Discrete Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.disc.2019.06.031. ieee: A. Silva, A. M. Arroyo Guevara, B. Richter, and O. Lee, “Graphs with at most one crossing,” Discrete Mathematics, vol. 342, no. 11. Elsevier, pp. 3201–3207, 2019. ista: Silva A, Arroyo Guevara AM, Richter B, Lee O. 2019. Graphs with at most one crossing. Discrete Mathematics. 342(11), 3201–3207. mla: Silva, André, et al. “Graphs with at Most One Crossing.” Discrete Mathematics, vol. 342, no. 11, Elsevier, 2019, pp. 3201–07, doi:10.1016/j.disc.2019.06.031. short: A. Silva, A.M. Arroyo Guevara, B. Richter, O. Lee, Discrete Mathematics 342 (2019) 3201–3207. date_created: 2019-07-14T21:59:20Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-29T06:31:41Z day: '01' department: - _id: UlWa doi: 10.1016/j.disc.2019.06.031 ec_funded: 1 external_id: arxiv: - '1901.09955' isi: - '000486358100025' intvolume: ' 342' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1901.09955 month: '11' oa: 1 oa_version: Preprint page: 3201-3207 project: - _id: 26366136-B435-11E9-9278-68D0E5697425 name: Reglas de Conectividad funcional en el hipocampo - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Discrete Mathematics publication_identifier: issn: - 0012-365X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Graphs with at most one crossing type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 342 year: '2019' ... --- _id: '6631' abstract: - lang: eng text: The spatiotemporal organization of cell divisions constitutes an integral part in the development of multicellular organisms, and mis-regulation of cell divisions can lead to severe developmental defects. Cell divisions have an important morphogenetic function in development by regulating growth and shape acquisition of developing tissues, and, conversely, tissue morphogenesis is known to affect both the rate and orientation of cell divisions. Moreover, cell divisions are associated with an extensive reorganization of the cytoskeleton and adhesion apparatus in the dividing cells that in turn can affect large-scale tissue rheological properties. Thus, the interplay between cell divisions and tissue morphogenesis plays a key role in embryo and tissue morphogenesis. article_processing_charge: No author: - first_name: Benoit G full_name: Godard, Benoit G id: 33280250-F248-11E8-B48F-1D18A9856A87 last_name: Godard - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Godard BG, Heisenberg C-PJ. Cell division and tissue mechanics. Current Opinion in Cell Biology. 2019;60:114-120. doi:10.1016/j.ceb.2019.05.007 apa: Godard, B. G., & Heisenberg, C.-P. J. (2019). Cell division and tissue mechanics. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.05.007 chicago: Godard, Benoit G, and Carl-Philipp J Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.05.007. ieee: B. G. Godard and C.-P. J. Heisenberg, “Cell division and tissue mechanics,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 114–120, 2019. ista: Godard BG, Heisenberg C-PJ. 2019. Cell division and tissue mechanics. Current Opinion in Cell Biology. 60, 114–120. mla: Godard, Benoit G., and Carl-Philipp J. Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 114–20, doi:10.1016/j.ceb.2019.05.007. short: B.G. Godard, C.-P.J. Heisenberg, Current Opinion in Cell Biology 60 (2019) 114–120. date_created: 2019-07-14T21:59:17Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-29T06:33:14Z day: '01' department: - _id: CaHe doi: 10.1016/j.ceb.2019.05.007 external_id: isi: - '000486545800016' intvolume: ' 60' isi: 1 language: - iso: eng month: '10' oa_version: None page: 114-120 publication: Current Opinion in Cell Biology publication_identifier: issn: - 0955-0674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cell division and tissue mechanics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 60 year: '2019' ... --- _id: '6660' abstract: - lang: eng text: "Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance.\r\n\r\nIn this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers." article_number: '111' article_processing_charge: No author: - first_name: Denis full_name: Sumin, Denis last_name: Sumin - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Tobias full_name: Rittig, Tobias last_name: Rittig - first_name: Vahid full_name: Babaei, Vahid last_name: Babaei - first_name: Thomas full_name: Nindel, Thomas last_name: Nindel - first_name: Alexander full_name: Wilkie, Alexander last_name: Wilkie - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Jaroslav full_name: Křivánek, Jaroslav last_name: Křivánek - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski citation: ama: Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992 apa: Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski, K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322992 chicago: Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel, Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992. ieee: D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019. ista: Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 38(4), 111. mla: Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992. short: D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk, B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019). date_created: 2019-07-22T07:22:28Z date_published: 2019-07-04T00:00:00Z date_updated: 2023-08-29T06:40:49Z day: '04' ddc: - '000' department: - _id: BeBi doi: 10.1145/3306346.3322992 ec_funded: 1 external_id: isi: - '000475740600085' file: - access_level: open_access checksum: 43c2019d6b48ed9c56e31686c4c2d1f5 content_type: application/pdf creator: dernst date_created: 2019-07-24T07:36:08Z date_updated: 2020-07-14T12:47:36Z file_id: '6669' file_name: 2019_ACM_Sumin_AuthorVersion.pdf file_size: 10109800 relation: main_file - access_level: open_access checksum: f80f365a04e35855fa467ea7ab26b16c content_type: application/zip creator: dernst date_created: 2019-10-11T06:51:07Z date_updated: 2020-07-14T12:47:36Z file_id: '6938' file_name: sumin19geometry-aware-suppl.zip file_size: 11051245 relation: supplementary_material file_date_updated: 2020-07-14T12:47:36Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Geometry-aware scattering compensation for 3D printing type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '6658' abstract: - lang: eng text: 'New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. ' article_processing_charge: No author: - first_name: Julia full_name: Raices, Julia id: 3EE67F22-F248-11E8-B48F-1D18A9856A87 last_name: Raices - first_name: Paulo full_name: Otto, Paulo last_name: Otto - first_name: Maria full_name: Vibranovski, Maria last_name: Vibranovski citation: ama: Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118 apa: Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. Genome Research. CSH Press. https://doi.org/10.1101/gr.238824.118 chicago: Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research. CSH Press, 2019. https://doi.org/10.1101/gr.238824.118. ieee: J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” Genome Research, vol. 29, no. 7. CSH Press, pp. 1115–1122, 2019. ista: Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122. mla: Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:10.1101/gr.238824.118. short: J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122. date_created: 2019-07-21T21:59:15Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-29T06:35:05Z day: '01' ddc: - '576' department: - _id: BeVi doi: 10.1101/gr.238824.118 external_id: isi: - '000473730600007' file: - access_level: open_access checksum: 4636f03a6750f90b88bf2bc3eb9d71ae content_type: application/pdf creator: apreinsp date_created: 2019-07-24T08:05:56Z date_updated: 2020-07-14T12:47:35Z file_id: '6670' file_name: 2019_GenomeResearch_Raices.pdf file_size: 2319022 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '7' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '07' oa: 1 oa_version: Published Version page: 1115-1122 publication: Genome Research publication_status: published publisher: CSH Press quality_controlled: '1' scopus_import: '1' status: public title: Haploid selection drives new gene male germline expression 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 29 year: '2019' ... --- _id: '6650' abstract: - lang: eng text: We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry. article_number: '110' 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: 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 - first_name: Nico full_name: Pietroni, Nico last_name: Pietroni citation: ama: Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware design of composite molds. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981 apa: Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni, N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322981 chicago: Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981. ieee: T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni, “Volume-aware design of composite molds,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019. ista: Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware design of composite molds. ACM Transactions on Graphics. 38(4), 110. mla: Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981. short: T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (2019). date_created: 2019-07-19T06:18:15Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-29T06:35:52Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1145/3306346.3322981 ec_funded: 1 external_id: isi: - '000475740600084' file: - access_level: open_access checksum: b4562af94672b44d2a501046427412af content_type: application/pdf creator: dernst date_created: 2019-07-19T06:18:53Z date_updated: 2020-07-14T12:47:35Z file_id: '6651' file_name: 2019_ACM_Alderighi_AuthorVersion.pdf file_size: 74316182 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: published publisher: ACM quality_controlled: '1' related_material: link: - description: YouTube Video relation: supplementary_material url: https://youtu.be/SO349S8-x_w scopus_import: '1' status: public title: Volume-aware design of composite molds type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '6717' abstract: - lang: eng text: With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple. article_number: '1171' article_processing_charge: Yes (via OA deal) author: - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Stephen T. full_name: Abedon, Stephen T. last_name: Abedon citation: ama: 'Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10. doi:10.3389/fmicb.2019.01171' apa: 'Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2019.01171' chicago: 'Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.' ieee: 'C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10. Frontiers, 2019.' ista: 'Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.' mla: 'Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology, vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.' short: C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019). date_created: 2019-07-28T21:59:18Z date_published: 2019-06-03T00:00:00Z date_updated: 2023-08-29T06:41:20Z day: '03' ddc: - '570' department: - _id: CaGu doi: 10.3389/fmicb.2019.01171 external_id: isi: - '000470131200001' file: - access_level: open_access checksum: 317a06067e9a8e717bb55f23e0d77ba7 content_type: application/pdf creator: apreinsp date_created: 2019-07-29T07:51:54Z date_updated: 2020-07-14T12:47:38Z file_id: '6722' file_name: 2019_Frontiers_Igler.pdf file_size: 246151 relation: main_file file_date_updated: 2020-07-14T12:47:38Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture (DOC Fellowship) publication: Frontiers in Microbiology publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6680' abstract: - lang: eng text: This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed. article_processing_charge: Yes (via OA deal) author: - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: ama: Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812 apa: Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812 chicago: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812. ieee: H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019. ista: Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745. mla: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812. short: H. Sachdeva, Evolution 73 (2019) 1729–1745. date_created: 2019-07-25T09:08:28Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-08-29T06:43:58Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1111/evo.13812 external_id: isi: - '000481300600001' file: - access_level: open_access checksum: 772ce7035965153959b946a1033de1ca content_type: application/pdf creator: kschuh date_created: 2019-09-17T10:56:27Z date_updated: 2020-07-14T12:47:37Z file_id: '6881' file_name: 2019_Evolution_Sachdeva.pdf file_size: 937573 relation: main_file file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' intvolume: ' 73' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1729-1745 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9802' relation: research_data status: public scopus_import: '1' status: public title: Effect of partial selfing and polygenic selection on establishment in a new habitat 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 73 year: '2019' ... --- _id: '6710' abstract: - lang: eng text: Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Cossard, Guillaume last_name: Cossard - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: 'John ' full_name: 'Pannell, John ' last_name: Pannell citation: ama: Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 2019;123(7):1119-1131. doi:10.1093/aob/mcy183 apa: Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183 chicago: Cossard, Guillaume, Melissa A Toups, and John Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183. ieee: G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019. ista: Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131. mla: Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183. short: G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131. date_created: 2019-07-28T21:59:15Z date_published: 2019-06-04T00:00:00Z date_updated: 2023-08-29T06:42:22Z day: '04' department: - _id: BeVi doi: 10.1093/aob/mcy183 external_id: isi: - '000493043500004' pmid: - '30289430' intvolume: ' 123' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/aob/mcy183 month: '06' oa: 1 oa_version: Published Version page: 1119-1131 pmid: 1 publication: Annals of botany publication_identifier: eissn: - 1095-8290 issn: - 0305-7364 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 123 year: '2019' ... --- _id: '9804' abstract: - lang: eng text: Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response. article_processing_charge: No author: - first_name: João Pl full_name: Castro, João Pl last_name: Castro - first_name: Michelle N. full_name: Yancoskie, Michelle N. last_name: Yancoskie - first_name: Marta full_name: Marchini, Marta last_name: Marchini - first_name: Stefanie full_name: Belohlavy, Stefanie id: 43FE426A-F248-11E8-B48F-1D18A9856A87 last_name: Belohlavy orcid: 0000-0002-9849-498X - first_name: Layla full_name: Hiramatsu, Layla last_name: Hiramatsu - first_name: Marek full_name: Kučka, Marek last_name: Kučka - first_name: William H. full_name: Beluch, William H. last_name: Beluch - first_name: Ronald full_name: Naumann, Ronald last_name: Naumann - first_name: Isabella full_name: Skuplik, Isabella last_name: Skuplik - first_name: John full_name: Cobb, John last_name: Cobb - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Campbell full_name: Rolian, Campbell last_name: Rolian - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan citation: ama: 'Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk' apa: 'Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk' chicago: 'Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk.' ieee: 'J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.' ista: 'Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.' mla: 'Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.' short: J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019). date_created: 2021-08-06T11:52:54Z date_published: 2019-06-06T00:00:00Z date_updated: 2023-08-29T06:41:51Z day: '06' department: - _id: NiBa doi: 10.5061/dryad.0q2h6tk main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.0q2h6tk month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '6713' relation: used_in_publication status: public status: public title: 'Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9802' abstract: - lang: eng text: This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed. article_processing_charge: No author: - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: ama: 'Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900' apa: 'Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900' chicago: 'Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900.' ieee: 'H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.' ista: 'Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.' mla: 'Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.' short: H. Sachdeva, (2019). date_created: 2021-08-06T11:45:11Z date_published: 2019-07-16T00:00:00Z date_updated: 2023-08-29T06:43:57Z day: '16' department: - _id: NiBa doi: 10.5061/dryad.8tp0900 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.8tp0900 month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '6680' relation: used_in_publication status: public status: public title: 'Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6756' abstract: - lang: eng text: "We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over \U0001D54A2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models." article_number: A163 article_processing_charge: No article_type: original author: - first_name: Pratyush full_name: Pranav, Pratyush last_name: Pranav - first_name: Robert J. full_name: Adler, Robert J. last_name: Adler - first_name: Thomas full_name: Buchert, Thomas last_name: Buchert - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Bernard J.T. full_name: Jones, Bernard J.T. last_name: Jones - first_name: Armin full_name: Schwartzman, Armin last_name: Schwartzman - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner - first_name: Rien full_name: Van De Weygaert, Rien last_name: Van De Weygaert citation: ama: Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 2019;627. doi:10.1051/0004-6361/201834916 apa: Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman, A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834916 chicago: Pranav, Pratyush, Robert J. Adler, Thomas Buchert, Herbert Edelsbrunner, Bernard J.T. Jones, Armin Schwartzman, Hubert Wagner, and Rien Van De Weygaert. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834916. ieee: P. Pranav et al., “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” Astronomy and Astrophysics, vol. 627. EDP Sciences, 2019. ista: Pranav P, Adler RJ, Buchert T, Edelsbrunner H, Jones BJT, Schwartzman A, Wagner H, Van De Weygaert R. 2019. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 627, A163. mla: Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics, vol. 627, A163, EDP Sciences, 2019, doi:10.1051/0004-6361/201834916. short: P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman, H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019). date_created: 2019-08-04T21:59:18Z date_published: 2019-07-17T00:00:00Z date_updated: 2023-08-29T07:01:48Z day: '17' ddc: - '520' - '530' department: - _id: HeEd doi: 10.1051/0004-6361/201834916 external_id: arxiv: - '1812.07678' isi: - '000475839300003' file: - access_level: open_access checksum: 83b9209ed9eefbdcefd89019c5a97805 content_type: application/pdf creator: dernst date_created: 2019-08-05T08:08:59Z date_updated: 2020-07-14T12:47:39Z file_id: '6766' file_name: 2019_AstronomyAstrophysics_Pranav.pdf file_size: 14420451 relation: main_file file_date_updated: 2020-07-14T12:47:39Z has_accepted_license: '1' intvolume: ' 627' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 265683E4-B435-11E9-9278-68D0E5697425 grant_number: M62909-18-1-2038 name: Toward Computational Information Topology - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Astronomy and Astrophysics publication_identifier: eissn: - '14320746' issn: - '00046361' publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: Unexpected topology of the temperature fluctuations in the cosmic microwave background 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 627 year: '2019' ... --- _id: '6755' abstract: - lang: eng text: 'Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.' acknowledged_ssus: - _id: CampIT article_processing_charge: No article_type: original author: - first_name: Marion A L full_name: Picard, Marion A L id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: David full_name: Roquis, David last_name: Roquis - first_name: Ingo full_name: Bulla, Ingo last_name: Bulla - first_name: Ronaldo C. full_name: Augusto, Ronaldo C. last_name: Augusto - first_name: Nathalie full_name: Arancibia, Nathalie last_name: Arancibia - first_name: Christoph full_name: Grunau, Christoph last_name: Grunau - first_name: Jérôme full_name: Boissier, Jérôme last_name: Boissier - first_name: Céline full_name: Cosseau, Céline last_name: Cosseau citation: ama: 'Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133' apa: 'Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford Academic Press. https://doi.org/10.1093/gbe/evz133' chicago: 'Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford Academic Press, 2019. https://doi.org/10.1093/gbe/evz133.' ieee: 'M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford Academic Press, pp. 1909–1922, 2019.' ista: 'Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.' mla: 'Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford Academic Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.' short: M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922. date_created: 2019-08-04T21:59:18Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-29T06:53:58Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evz133 external_id: isi: - '000484039500018' pmid: - '31273378' file: - access_level: open_access checksum: f9e8f6863a406dcc5a36b2be001c138c content_type: application/pdf creator: dernst date_created: 2019-08-05T07:55:02Z date_updated: 2020-07-14T12:47:39Z file_id: '6765' file_name: 2019_GenomeBiology_Picard.pdf file_size: 580205 relation: main_file file_date_updated: 2020-07-14T12:47:39Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1909-1922 pmid: 1 publication: Genome biology and evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford Academic Press quality_controlled: '1' scopus_import: '1' status: public title: 'Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2019' ... --- _id: '6752' abstract: - lang: eng text: 'Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players.' article_number: '31' 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: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev citation: ama: Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. Journal of the ACM. 2019;66(4). doi:10.1145/3340295 apa: Avni, G., Henzinger, T. A., & Chonev, V. K. (2019). Infinite-duration bidding games. Journal of the ACM. ACM. https://doi.org/10.1145/3340295 chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3340295. ieee: G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” Journal of the ACM, vol. 66, no. 4. ACM, 2019. ista: Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31. mla: Avni, Guy, et al. “Infinite-Duration Bidding Games.” Journal of the ACM, vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295. short: G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019). date_created: 2019-08-04T21:59:16Z date_published: 2019-07-16T00:00:00Z date_updated: 2023-08-29T07:02:13Z day: '16' department: - _id: ToHe doi: 10.1145/3340295 external_id: arxiv: - '1705.01433' isi: - '000487714900008' intvolume: ' 66' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.01433 month: '07' oa: 1 oa_version: Preprint project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-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: Journal of the ACM publication_identifier: eissn: - 1557735X issn: - '00045411' publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '950' relation: earlier_version status: public scopus_import: '1' status: public title: Infinite-duration bidding games type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 66 year: '2019' ... --- _id: '7010' abstract: - lang: eng text: Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines. article_number: 110760V article_processing_charge: No author: - first_name: Heather S. full_name: Davies, Heather S. last_name: Davies - first_name: Natalia S. full_name: Baranova, Natalia S. id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Nouha full_name: El Amri, Nouha last_name: El Amri - first_name: Liliane full_name: Coche-Guérente, Liliane last_name: Coche-Guérente - first_name: Claude full_name: Verdier, Claude last_name: Verdier - first_name: Lionel full_name: Bureau, Lionel last_name: Bureau - first_name: Ralf P. full_name: Richter, Ralf P. last_name: Richter - first_name: Delphine full_name: Débarre, Delphine last_name: Débarre citation: ama: 'Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: Advances in Microscopic Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058' apa: 'Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In Advances in Microscopic Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058' chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In Advances in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058. ieee: H. S. Davies et al., “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in Advances in Microscopic Imaging II, Munich, Germany, 2019, vol. 11076. ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. Advances in Microscopic Imaging II. European Conferences on Biomedical Optics vol. 11076, 110760V. mla: Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” Advances in Microscopic Imaging II, vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058. short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE, 2019. conference: end_date: 2019-06-27 location: Munich, Germany name: European Conferences on Biomedical Optics start_date: 2019-06-26 date_created: 2019-11-12T15:10:18Z date_published: 2019-07-22T00:00:00Z date_updated: 2023-08-29T06:54:38Z day: '22' department: - _id: MaLo doi: 10.1117/12.2527058 external_id: isi: - '000535353000023' intvolume: ' 11076' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf month: '07' oa: 1 oa_version: Published Version publication: Advances in Microscopic Imaging II publication_identifier: isbn: - '9781510628458' issn: - 1605-7422 publication_status: published publisher: SPIE quality_controlled: '1' scopus_import: '1' status: public title: Blood cell-vessel wall interactions probed by reflection interference contrast microscopy type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11076 year: '2019' ... --- _id: '6763' abstract: - lang: eng text: "When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.\r\nWe show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics." article_processing_charge: No article_type: original author: - first_name: Hamza K. full_name: Khattak, Hamza K. last_name: Khattak - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Aaron D. full_name: Slepkov, Aaron D. last_name: Slepkov citation: ama: Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 2019;15(29):5804-5809. doi:10.1039/c9sm00756c apa: Khattak, H. K., Waitukaitis, S. R., & Slepkov, A. D. (2019). Microwave induced mechanical activation of hydrogel dimers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c9sm00756c chicago: Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c9sm00756c. ieee: H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical activation of hydrogel dimers,” Soft Matter, vol. 15, no. 29. Royal Society of Chemistry, pp. 5804–5809, 2019. ista: Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809. mla: Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter, vol. 15, no. 29, Royal Society of Chemistry, 2019, pp. 5804–09, doi:10.1039/c9sm00756c. short: H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809. date_created: 2019-08-04T21:59:21Z date_published: 2019-07-15T00:00:00Z date_updated: 2023-08-29T06:53:34Z day: '15' department: - _id: ScWa doi: 10.1039/c9sm00756c external_id: isi: - '000476909200002' pmid: - '31305853' intvolume: ' 15' isi: 1 issue: '29' language: - iso: eng month: '07' oa_version: None page: 5804-5809 pmid: 1 publication: Soft Matter publication_identifier: eissn: - '17446848' issn: - 1744683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Microwave induced mechanical activation of hydrogel dimers type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6784' abstract: - lang: eng text: Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems. article_number: e1007168 article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - 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: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168 apa: Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168 chicago: Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168. ieee: J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019. ista: Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168. mla: Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168. short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019). date_created: 2019-08-11T21:59:19Z date_published: 2019-07-02T00:00:00Z date_updated: 2023-08-29T07:10:06Z day: '02' ddc: - '570' department: - _id: CaGu - _id: GaTk doi: 10.1371/journal.pcbi.1007168 external_id: isi: - '000481577700032' file: - access_level: open_access checksum: 7ded4721b41c2a0fc66a1c634540416a content_type: application/pdf creator: dernst date_created: 2019-08-12T12:27:26Z date_updated: 2020-07-14T12:47:40Z file_id: '6803' file_name: 2019_PlosComputBiology_Ruess.pdf file_size: 2200003 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level - _id: 251BCBEC-B435-11E9-9278-68D0E5697425 grant_number: RGY0079/2011 name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9786' relation: research_data status: public scopus_import: '1' status: public title: Molecular noise of innate immunity shapes bacteria-phage ecologies 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6778' abstract: - lang: eng text: "An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips\r\nalong with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land." article_number: '3480' article_processing_charge: No article_type: original author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: G full_name: Xiao, G last_name: Xiao - first_name: X full_name: Wang, X last_name: Wang - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. Nature Communications. 2019;10. doi:10.1038/s41467-019-11471-8 apa: Zhang, Y., Xiao, G., Wang, X., Zhang, X., & Friml, J. (2019). Evolution of fast root gravitropism in seed plants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11471-8 chicago: Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11471-8. ieee: Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root gravitropism in seed plants,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480. mla: Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications, vol. 10, 3480, Springer Nature, 2019, doi:10.1038/s41467-019-11471-8. short: Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019). date_created: 2019-08-09T08:46:26Z date_published: 2019-08-02T00:00:00Z date_updated: 2023-08-29T07:02:44Z day: '02' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-019-11471-8 ec_funded: 1 external_id: isi: - '000478576500012' pmid: - '31375675' file: - access_level: open_access checksum: d2c654fdb97f33078f606fe0c298bf6e content_type: application/pdf creator: dernst date_created: 2019-08-12T07:09:20Z date_updated: 2020-07-14T12:47:40Z file_id: '6798' file_name: 2019_NatureComm_Zhang.pdf file_size: 6406141 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/ scopus_import: '1' status: public title: Evolution of fast root gravitropism in seed plants 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6821' abstract: - lang: eng text: To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined. article_processing_charge: No article_type: original author: - first_name: Miranda R. full_name: Yourick, Miranda R. last_name: Yourick - first_name: Benjamin A. full_name: Sandkam, Benjamin A. last_name: Sandkam - first_name: William J full_name: Gammerdinger, William J id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87 last_name: Gammerdinger orcid: 0000-0001-9638-1220 - first_name: Daniel full_name: Escobar-Camacho, Daniel last_name: Escobar-Camacho - first_name: Sri Pratima full_name: Nandamuri, Sri Pratima last_name: Nandamuri - first_name: Frances E. full_name: Clark, Frances E. last_name: Clark - first_name: Brendan full_name: Joyce, Brendan last_name: Joyce - first_name: Matthew A. full_name: Conte, Matthew A. last_name: Conte - first_name: Thomas D. full_name: Kocher, Thomas D. last_name: Kocher - first_name: Karen L. full_name: Carleton, Karen L. last_name: Carleton citation: ama: Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 2019;19(6):1447-1460. doi:10.1111/1755-0998.13062 apa: Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri, S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13062 chicago: Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources. Wiley, 2019. https://doi.org/10.1111/1755-0998.13062. ieee: M. R. Yourick et al., “Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses,” Molecular Ecology Resources, vol. 19, no. 6. Wiley, pp. 1447–1460, 2019. ista: Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 19(6), 1447–1460. mla: Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources, vol. 19, no. 6, Wiley, 2019, pp. 1447–60, doi:10.1111/1755-0998.13062. short: M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri, F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology Resources 19 (2019) 1447–1460. date_created: 2019-08-18T22:00:41Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-29T07:10:44Z day: '01' department: - _id: BeVi doi: 10.1111/1755-0998.13062 external_id: isi: - '000480196800001' pmid: - '31325910' intvolume: ' 19' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727 month: '11' oa: 1 oa_version: Submitted Version page: 1447-1460 pmid: 1 publication: Molecular Ecology Resources publication_identifier: eissn: - 1755-0998 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2019' ... --- _id: '6788' abstract: - lang: eng text: We consider the Nelson model with ultraviolet cutoff, which describes the interaction between non-relativistic particles and a positive or zero mass quantized scalar field. We take the non-relativistic particles to obey Fermi statistics and discuss the time evolution in a mean-field limit of many fermions. In this case, the limit is known to be also a semiclassical limit. We prove convergence in terms of reduced density matrices of the many-body state to a tensor product of a Slater determinant with semiclassical structure and a coherent state, which evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: Sören P full_name: Petrat, Sören P id: 40AC02DC-F248-11E8-B48F-1D18A9856A87 last_name: Petrat orcid: 0000-0002-9166-5889 citation: ama: Leopold NK, Petrat SP. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 2019;20(10):3471–3508. doi:10.1007/s00023-019-00828-w apa: Leopold, N. K., & Petrat, S. P. (2019). Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-019-00828-w chicago: Leopold, Nikolai K, and Sören P Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” Annales Henri Poincare. Springer Nature, 2019. https://doi.org/10.1007/s00023-019-00828-w. ieee: N. K. Leopold and S. P. Petrat, “Mean-field dynamics for the Nelson model with fermions,” Annales Henri Poincare, vol. 20, no. 10. Springer Nature, pp. 3471–3508, 2019. ista: Leopold NK, Petrat SP. 2019. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 20(10), 3471–3508. mla: Leopold, Nikolai K., and Sören P. Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” Annales Henri Poincare, vol. 20, no. 10, Springer Nature, 2019, pp. 3471–3508, doi:10.1007/s00023-019-00828-w. short: N.K. Leopold, S.P. Petrat, Annales Henri Poincare 20 (2019) 3471–3508. date_created: 2019-08-11T21:59:21Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-29T07:09:06Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00023-019-00828-w ec_funded: 1 external_id: arxiv: - '1807.06781' isi: - '000487036900008' file: - access_level: open_access checksum: b6dbf0d837d809293d449adf77138904 content_type: application/pdf creator: dernst date_created: 2019-08-12T12:05:58Z date_updated: 2020-07-14T12:47:40Z file_id: '6801' file_name: 2019_AnnalesHenriPoincare_Leopold.pdf file_size: 681139 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 3471–3508 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Annales Henri Poincare publication_identifier: eissn: - 1424-0661 issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mean-field dynamics for the Nelson model with fermions 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '6795' abstract: - lang: eng text: The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations. article_processing_charge: No article_type: original author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager citation: ama: Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484 apa: Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484 chicago: Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484. ieee: B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019. ista: Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608. mla: Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484. short: B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608. date_created: 2019-08-11T21:59:24Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-08-29T07:03:10Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1002/ece3.5484 ec_funded: 1 external_id: isi: - '000479973400001' file: - access_level: open_access checksum: adcb70af4901977d95b8747eeee01bd7 content_type: application/pdf creator: dernst date_created: 2019-08-12T07:30:30Z date_updated: 2020-07-14T12:47:40Z file_id: '6799' file_name: 2019_EcologyEvolution_Trubenova.pdf file_size: 2839636 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '17' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 9597-9608 project: - _id: 25AEDD42-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '704172' name: Rate of Adaptation in Changing Environment publication: Ecology and Evolution publication_identifier: eissn: - '20457758' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Green beards in the light of indirect genetic effects 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '6793' abstract: - lang: eng text: The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry. article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Ivan full_name: Izmestiev, Ivan last_name: Izmestiev citation: ama: Akopyan A, Izmestiev I. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 2019;51(5):765-775. doi:10.1112/blms.12276 apa: Akopyan, A., & Izmestiev, I. (2019). The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12276 chicago: Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society. London Mathematical Society, 2019. https://doi.org/10.1112/blms.12276. ieee: A. Akopyan and I. Izmestiev, “The Regge symmetry, confocal conics, and the Schläfli formula,” Bulletin of the London Mathematical Society, vol. 51, no. 5. London Mathematical Society, pp. 765–775, 2019. ista: Akopyan A, Izmestiev I. 2019. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 51(5), 765–775. mla: Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society, vol. 51, no. 5, London Mathematical Society, 2019, pp. 765–75, doi:10.1112/blms.12276. short: A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51 (2019) 765–775. date_created: 2019-08-11T21:59:23Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-29T07:08:34Z day: '01' department: - _id: HeEd doi: 10.1112/blms.12276 ec_funded: 1 external_id: arxiv: - '1903.04929' isi: - '000478560200001' intvolume: ' 51' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.04929 month: '10' oa: 1 oa_version: Preprint page: 765-775 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended publication: Bulletin of the London Mathematical Society publication_identifier: eissn: - '14692120' issn: - '00246093' publication_status: published publisher: London Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: The Regge symmetry, confocal conics, and the Schläfli formula type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 51 year: '2019' ... --- _id: '9786' article_processing_charge: No author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - 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: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001 apa: Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001 chicago: Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001. ieee: J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019. ista: Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public Library of Science, 10.1371/journal.pcbi.1007168.s001. mla: Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001. short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019). date_created: 2021-08-06T08:23:43Z date_published: 2019-07-02T00:00:00Z date_updated: 2023-08-29T07:10:05Z day: '02' department: - _id: CaGu - _id: GaTk doi: 10.1371/journal.pcbi.1007168.s001 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6784' relation: used_in_publication status: public status: public title: Supporting text and results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6831' abstract: - lang: eng text: "* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David last_name: Field orcid: 0000-0002-4014-8478 - first_name: Spencer C.H. full_name: Barrett, Spencer C.H. last_name: Barrett citation: ama: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050' apa: 'Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050' chicago: 'Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.' ieee: 'G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.' ista: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120.' mla: 'Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.' short: G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120. date_created: 2019-08-25T22:00:51Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-29T07:17:07Z day: '01' ddc: - '570' department: - _id: NiBa - _id: BeVi doi: 10.1111/nph.16050 ec_funded: 1 external_id: isi: - '000481376500001' file: - access_level: open_access checksum: 6370e7567d96b7b562e77d8b89653f80 content_type: application/pdf creator: apreinsp date_created: 2019-08-27T12:44:54Z date_updated: 2020-07-14T12:47:42Z file_id: '6833' file_name: 2019_NewPhytologist_Puixeu.pdf file_size: 2314016 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 224' isi: 1 issue: '3' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1108-1120 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: New Phytologist publication_identifier: eissn: - 1469-8137 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9803' relation: research_data status: public - id: '14058' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 224 year: '2019' ... --- _id: '6824' abstract: - lang: eng text: Platelets are small anucleate cellular fragments that are released by megakaryocytes and safeguard vascular integrity through a process termed ‘haemostasis’. However, platelets have important roles beyond haemostasis as they contribute to the initiation and coordination of intravascular immune responses. They continuously monitor blood vessel integrity and tightly coordinate vascular trafficking and functions of multiple cell types. In this way platelets act as ‘patrolling officers of the vascular highway’ that help to establish effective immune responses to infections and cancer. Here we discuss the distinct biological features of platelets that allow them to shape immune responses to pathogens and tumour cells, highlighting the parallels between these responses. article_processing_charge: No article_type: original author: - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg citation: ama: 'Gärtner FR, Massberg S. Patrolling the vascular borders: Platelets in immunity to infection and cancer. Nature Reviews Immunology. 2019;19(12):747–760. doi:10.1038/s41577-019-0202-z' apa: 'Gärtner, F. R., & Massberg, S. (2019). Patrolling the vascular borders: Platelets in immunity to infection and cancer. Nature Reviews Immunology. Springer Nature. https://doi.org/10.1038/s41577-019-0202-z' chicago: 'Gärtner, Florian R, and Steffen Massberg. “Patrolling the Vascular Borders: Platelets in Immunity to Infection and Cancer.” Nature Reviews Immunology. Springer Nature, 2019. https://doi.org/10.1038/s41577-019-0202-z.' ieee: 'F. R. Gärtner and S. Massberg, “Patrolling the vascular borders: Platelets in immunity to infection and cancer,” Nature Reviews Immunology, vol. 19, no. 12. Springer Nature, pp. 747–760, 2019.' ista: 'Gärtner FR, Massberg S. 2019. Patrolling the vascular borders: Platelets in immunity to infection and cancer. Nature Reviews Immunology. 19(12), 747–760.' mla: 'Gärtner, Florian R., and Steffen Massberg. “Patrolling the Vascular Borders: Platelets in Immunity to Infection and Cancer.” Nature Reviews Immunology, vol. 19, no. 12, Springer Nature, 2019, pp. 747–760, doi:10.1038/s41577-019-0202-z.' short: F.R. Gärtner, S. Massberg, Nature Reviews Immunology 19 (2019) 747–760. date_created: 2019-08-20T17:24:32Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-29T07:16:14Z day: '01' department: - _id: MiSi doi: 10.1038/s41577-019-0202-z ec_funded: 1 external_id: isi: - '000499090600011' pmid: - '31409920' intvolume: ' 19' isi: 1 issue: '12' language: - iso: eng month: '12' oa_version: None page: 747–760 pmid: 1 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Nature Reviews Immunology publication_identifier: eissn: - 1474-1741 issn: - 1474-1733 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Patrolling the vascular borders: Platelets in immunity to infection and cancer' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2019' ... --- _id: '6832' abstract: - lang: eng text: Steady-state turnover is a hallmark of epithelial tissues throughout adult life. Intestinal epithelial turnover is marked by continuous cell migration, which is assumed to be driven by mitotic pressure from the crypts. However, the balance of forces in renewal remains ill-defined. Combining biophysical modeling and quantitative three-dimensional tissue imaging with genetic and physical manipulations, we revealed the existence of an actin-related protein 2/3 complex–dependent active migratory force, which explains quantitatively the profiles of cell speed, density, and tissue tension along the villi. Cells migrate collectively with minimal rearrangements while displaying dual—apicobasal and front-back—polarity characterized by actin-rich basal protrusions oriented in the direction of migration. We propose that active migration is a critical component of gut epithelial turnover. article_processing_charge: No author: - first_name: Denis full_name: Krndija, Denis last_name: Krndija - first_name: Fatima El full_name: Marjou, Fatima El last_name: Marjou - first_name: Boris full_name: Guirao, Boris last_name: Guirao - first_name: Sophie full_name: Richon, Sophie last_name: Richon - first_name: Olivier full_name: Leroy, Olivier last_name: Leroy - first_name: Yohanns full_name: Bellaiche, Yohanns last_name: Bellaiche - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Danijela Matic full_name: Vignjevic, Danijela Matic last_name: Vignjevic citation: ama: Krndija D, Marjou FE, Guirao B, et al. Active cell migration is critical for steady-state epithelial turnover in the gut. Science. 2019;365(6454):705-710. doi:10.1126/science.aau3429 apa: Krndija, D., Marjou, F. E., Guirao, B., Richon, S., Leroy, O., Bellaiche, Y., … Vignjevic, D. M. (2019). Active cell migration is critical for steady-state epithelial turnover in the gut. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aau3429 chicago: Krndija, Denis, Fatima El Marjou, Boris Guirao, Sophie Richon, Olivier Leroy, Yohanns Bellaiche, Edouard B Hannezo, and Danijela Matic Vignjevic. “Active Cell Migration Is Critical for Steady-State Epithelial Turnover in the Gut.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aau3429. ieee: D. Krndija et al., “Active cell migration is critical for steady-state epithelial turnover in the gut,” Science, vol. 365, no. 6454. American Association for the Advancement of Science, pp. 705–710, 2019. ista: Krndija D, Marjou FE, Guirao B, Richon S, Leroy O, Bellaiche Y, Hannezo EB, Vignjevic DM. 2019. Active cell migration is critical for steady-state epithelial turnover in the gut. Science. 365(6454), 705–710. mla: Krndija, Denis, et al. “Active Cell Migration Is Critical for Steady-State Epithelial Turnover in the Gut.” Science, vol. 365, no. 6454, American Association for the Advancement of Science, 2019, pp. 705–10, doi:10.1126/science.aau3429. short: D. Krndija, F.E. Marjou, B. Guirao, S. Richon, O. Leroy, Y. Bellaiche, E.B. Hannezo, D.M. Vignjevic, Science 365 (2019) 705–710. date_created: 2019-08-25T22:00:51Z date_published: 2019-08-16T00:00:00Z date_updated: 2023-08-29T07:16:40Z day: '16' department: - _id: EdHa doi: 10.1126/science.aau3429 external_id: isi: - '000481688700050' pmid: - '31416964' intvolume: ' 365' isi: 1 issue: '6454' language: - iso: eng month: '08' oa_version: None page: 705-710 pmid: 1 publication: Science publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Active cell migration is critical for steady-state epithelial turnover in the gut type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 365 year: '2019' ... --- _id: '6818' abstract: - lang: eng text: Indigoidine is a blue natural pigment, which can be efficiently synthetized in E. coli. In addition to its antioxidant and antimicrobial activities indigoidine due to its stability and deep blue color can find an application as an industrial, environmentally friendly dye. Moreover, similarly to its counterpart regular indigo dye, due to its molecular structure, indigoidine is an organic semiconductor. Fully conjugated aromatic moiety and intermolecular hydrogen bonding of indigoidine result in an unusually narrow bandgap for such a small molecule. This, in its turn, result is tight molecular packing in the solid state and opens a path for a wide range of application in organic and bio-electronics, such as electrochemical and field effect transistors, organic solar cells, light and bio-sensors etc. article_number: '107768' article_processing_charge: No article_type: original author: - first_name: Cigdem full_name: Yumusak, Cigdem last_name: Yumusak - first_name: Anna Jancik full_name: Prochazkova, Anna Jancik last_name: Prochazkova - first_name: Dogukan H full_name: Apaydin, Dogukan H id: 2FF891BC-F248-11E8-B48F-1D18A9856A87 last_name: Apaydin orcid: 0000-0002-1075-8857 - first_name: Hathaichanok full_name: Seelajaroen, Hathaichanok last_name: Seelajaroen - first_name: Niyazi Serdar full_name: Sariciftci, Niyazi Serdar last_name: Sariciftci - first_name: Martin full_name: Weiter, Martin last_name: Weiter - first_name: Jozef full_name: Krajcovic, Jozef last_name: Krajcovic - first_name: Yong full_name: Qin, Yong last_name: Qin - first_name: Wei full_name: Zhang, Wei last_name: Zhang - first_name: Jixun full_name: Zhan, Jixun last_name: Zhan - first_name: Alexander full_name: Kovalenko, Alexander last_name: Kovalenko citation: ama: Yumusak C, Prochazkova AJ, Apaydin DH, et al. Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. 2019;171. doi:10.1016/j.dyepig.2019.107768 apa: Yumusak, C., Prochazkova, A. J., Apaydin, D. H., Seelajaroen, H., Sariciftci, N. S., Weiter, M., … Kovalenko, A. (2019). Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. Elsevier. https://doi.org/10.1016/j.dyepig.2019.107768 chicago: Yumusak, Cigdem, Anna Jancik Prochazkova, Dogukan H Apaydin, Hathaichanok Seelajaroen, Niyazi Serdar Sariciftci, Martin Weiter, Jozef Krajcovic, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” Dyes and Pigments. Elsevier, 2019. https://doi.org/10.1016/j.dyepig.2019.107768. ieee: C. Yumusak et al., “Indigoidine - Biosynthesized organic semiconductor,” Dyes and Pigments, vol. 171. Elsevier, 2019. ista: Yumusak C, Prochazkova AJ, Apaydin DH, Seelajaroen H, Sariciftci NS, Weiter M, Krajcovic J, Qin Y, Zhang W, Zhan J, Kovalenko A. 2019. Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. 171, 107768. mla: Yumusak, Cigdem, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” Dyes and Pigments, vol. 171, 107768, Elsevier, 2019, doi:10.1016/j.dyepig.2019.107768. short: C. Yumusak, A.J. Prochazkova, D.H. Apaydin, H. Seelajaroen, N.S. Sariciftci, M. Weiter, J. Krajcovic, Y. Qin, W. Zhang, J. Zhan, A. Kovalenko, Dyes and Pigments 171 (2019). date_created: 2019-08-18T22:00:39Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-29T07:11:09Z day: '01' department: - _id: MaIb doi: 10.1016/j.dyepig.2019.107768 external_id: isi: - '000484870700099' intvolume: ' 171' isi: 1 language: - iso: eng month: '12' oa_version: None publication: Dyes and Pigments publication_identifier: issn: - 0143-7208 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Indigoidine - Biosynthesized organic semiconductor type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 171 year: '2019' ... --- _id: '6828' abstract: - lang: eng text: In this paper we construct a family of exact functors from the category of Whittaker modules of the simple complex Lie algebra of type to the category of finite-dimensional modules of the graded affine Hecke algebra of type . Using results of Backelin [2] and of Arakawa-Suzuki [1], we prove that these functors map standard modules to standard modules (or zero) and simple modules to simple modules (or zero). Moreover, we show that each simple module of the graded affine Hecke algebra appears as the image of a simple Whittaker module. Since the Whittaker category contains the BGG category as a full subcategory, our results generalize results of Arakawa-Suzuki [1], which in turn generalize Schur-Weyl duality between finite-dimensional representations of and representations of the symmetric group . article_processing_charge: No article_type: original author: - first_name: Adam full_name: Brown, Adam id: 70B7FDF6-608D-11E9-9333-8535E6697425 last_name: Brown citation: ama: Brown A. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 2019;538:261-289. doi:10.1016/j.jalgebra.2019.07.027 apa: Brown, A. (2019). Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2019.07.027 chicago: Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra. Elsevier, 2019. https://doi.org/10.1016/j.jalgebra.2019.07.027. ieee: A. Brown, “Arakawa-Suzuki functors for Whittaker modules,” Journal of Algebra, vol. 538. Elsevier, pp. 261–289, 2019. ista: Brown A. 2019. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 538, 261–289. mla: Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra, vol. 538, Elsevier, 2019, pp. 261–89, doi:10.1016/j.jalgebra.2019.07.027. short: A. Brown, Journal of Algebra 538 (2019) 261–289. date_created: 2019-08-22T07:54:13Z date_published: 2019-11-15T00:00:00Z date_updated: 2023-08-29T07:11:47Z day: '15' department: - _id: HeEd doi: 10.1016/j.jalgebra.2019.07.027 external_id: arxiv: - '1805.04676' isi: - '000487176300011' intvolume: ' 538' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.04676 month: '11' oa: 1 oa_version: Preprint page: 261-289 publication: Journal of Algebra publication_identifier: issn: - 0021-8693 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Arakawa-Suzuki functors for Whittaker modules type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 538 year: '2019' ... --- _id: '9803' abstract: - lang: eng text: Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle. article_processing_charge: No author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David last_name: Field - first_name: Spencer C.H. full_name: Barrett, Spencer C.H. last_name: Barrett citation: ama: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9' apa: 'Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9' chicago: 'Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.' ieee: 'G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019.' ista: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.' mla: 'Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.' short: G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019). date_created: 2021-08-06T11:48:42Z date_published: 2019-07-22T00:00:00Z date_updated: 2023-08-29T07:17:07Z day: '22' department: - _id: NiBa - _id: BeVi doi: 10.5061/dryad.n1701c9 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.n1701c9 month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '14058' relation: used_in_publication status: public - id: '6831' relation: used_in_publication status: public status: public title: 'Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6836' abstract: - lang: eng text: Direct reciprocity is a powerful mechanism for the evolution of cooperation on the basis of repeated interactions1,2,3,4. It requires that interacting individuals are sufficiently equal, such that everyone faces similar consequences when they cooperate or defect. Yet inequality is ubiquitous among humans5,6 and is generally considered to undermine cooperation and welfare7,8,9,10. Most previous models of reciprocity do not include inequality11,12,13,14,15. These models assume that individuals are the same in all relevant aspects. Here we introduce a general framework to study direct reciprocity among unequal individuals. Our model allows for multiple sources of inequality. Subjects can differ in their endowments, their productivities and in how much they benefit from public goods. We find that extreme inequality prevents cooperation. But if subjects differ in productivity, some endowment inequality can be necessary for cooperation to prevail. Our mathematical predictions are supported by a behavioural experiment in which we vary the endowments and productivities of the subjects. We observe that overall welfare is maximized when the two sources of heterogeneity are aligned, such that more productive individuals receive higher endowments. By contrast, when endowments and productivities are misaligned, cooperation quickly breaks down. Our findings have implications for policy-makers concerned with equity, efficiency and the provisioning of public goods. article_processing_charge: No article_type: letter_note author: - first_name: Oliver P. full_name: Hauser, Oliver P. last_name: Hauser - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Hauser OP, Hilbe C, Chatterjee K, Nowak MA. Social dilemmas among unequals. Nature. 2019;572(7770):524-527. doi:10.1038/s41586-019-1488-5 apa: Hauser, O. P., Hilbe, C., Chatterjee, K., & Nowak, M. A. (2019). Social dilemmas among unequals. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1488-5 chicago: Hauser, Oliver P., Christian Hilbe, Krishnendu Chatterjee, and Martin A. Nowak. “Social Dilemmas among Unequals.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1488-5. ieee: O. P. Hauser, C. Hilbe, K. Chatterjee, and M. A. Nowak, “Social dilemmas among unequals,” Nature, vol. 572, no. 7770. Springer Nature, pp. 524–527, 2019. ista: Hauser OP, Hilbe C, Chatterjee K, Nowak MA. 2019. Social dilemmas among unequals. Nature. 572(7770), 524–527. mla: Hauser, Oliver P., et al. “Social Dilemmas among Unequals.” Nature, vol. 572, no. 7770, Springer Nature, 2019, pp. 524–27, doi:10.1038/s41586-019-1488-5. short: O.P. Hauser, C. Hilbe, K. Chatterjee, M.A. Nowak, Nature 572 (2019) 524–527. date_created: 2019-09-01T22:00:56Z date_published: 2019-08-22T00:00:00Z date_updated: 2023-08-29T07:42:54Z day: '22' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41586-019-1488-5 ec_funded: 1 external_id: isi: - '000482219600045' file: - access_level: open_access checksum: a6e0e3168bf62de624e7772cdfaeb26f content_type: application/pdf creator: dernst date_created: 2020-05-14T10:00:32Z date_updated: 2020-07-14T12:47:42Z file_id: '7828' file_name: 2019_Nature_Hauser.pdf file_size: 18577756 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 572' isi: 1 issue: '7770' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 524-527 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature publication_identifier: eissn: - '14764687' issn: - '00280836' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/too-much-inequality-impedes-support-for-public-goods-according-to-research-published-in-nature/ scopus_import: '1' status: public title: Social dilemmas among unequals type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 572 year: '2019' ... --- _id: '6844' abstract: - lang: eng text: Studying the progression of the proliferative and differentiative patterns of neural stem cells at the individual cell level is crucial to the understanding of cortex development and how the disruption of such patterns can lead to malformations and neurodevelopmental diseases. However, our understanding of the precise lineage progression programme at single-cell resolution is still incomplete due to the technical variations in lineage- tracing approaches. One of the key challenges involves developing a robust theoretical framework in which we can integrate experimental observations and introduce correction factors to obtain a reliable and representative description of the temporal modulation of proliferation and differentiation. In order to obtain more conclusive insights, we carry out virtual clonal analysis using mathematical modelling and compare our results against experimental data. Using a dataset obtained with Mosaic Analysis with Double Markers, we illustrate how the theoretical description can be exploited to interpret and reconcile the disparity between virtual and experimental results. article_processing_charge: No article_type: original author: - first_name: Noemi full_name: Picco, Noemi last_name: Picco - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Julio full_name: Rodarte, Julio id: 3C70A038-F248-11E8-B48F-1D18A9856A87 last_name: Rodarte - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Zoltán full_name: Molnár, Zoltán last_name: Molnár - first_name: Philip K. full_name: Maini, Philip K. last_name: Maini - first_name: Thomas E. full_name: Woolley, Thomas E. last_name: Woolley citation: ama: Picco N, Hippenmeyer S, Rodarte J, et al. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 2019;235(3):686-696. doi:10.1111/joa.13001 apa: Picco, N., Hippenmeyer, S., Rodarte, J., Streicher, C., Molnár, Z., Maini, P. K., & Woolley, T. E. (2019). A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. Wiley. https://doi.org/10.1111/joa.13001 chicago: Picco, Noemi, Simon Hippenmeyer, Julio Rodarte, Carmen Streicher, Zoltán Molnár, Philip K. Maini, and Thomas E. Woolley. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” Journal of Anatomy. Wiley, 2019. https://doi.org/10.1111/joa.13001. ieee: N. Picco et al., “A mathematical insight into cell labelling experiments for clonal analysis,” Journal of Anatomy, vol. 235, no. 3. Wiley, pp. 686–696, 2019. ista: Picco N, Hippenmeyer S, Rodarte J, Streicher C, Molnár Z, Maini PK, Woolley TE. 2019. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 235(3), 686–696. mla: Picco, Noemi, et al. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” Journal of Anatomy, vol. 235, no. 3, Wiley, 2019, pp. 686–96, doi:10.1111/joa.13001. short: N. Picco, S. Hippenmeyer, J. Rodarte, C. Streicher, Z. Molnár, P.K. Maini, T.E. Woolley, Journal of Anatomy 235 (2019) 686–696. date_created: 2019-09-02T11:57:28Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-08-29T07:19:39Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1111/joa.13001 ec_funded: 1 external_id: isi: - '000482426800017' file: - access_level: open_access checksum: 160f960844b204057f20896e0e1f8ee7 content_type: application/pdf creator: dernst date_created: 2019-09-02T12:05:18Z date_updated: 2020-07-14T12:47:42Z file_id: '6845' file_name: 2019_JournalAnatomy_Picco.pdf file_size: 1192994 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 235' isi: 1 issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 686-696 project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Journal of Anatomy publication_identifier: eissn: - 1469-7580 issn: - 0021-8782 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: A mathematical insight into cell labelling experiments for clonal analysis 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 235 year: '2019' ... --- _id: '6855' abstract: - lang: eng text: Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance. article_processing_charge: No author: - first_name: Guy full_name: Sella, Guy last_name: Sella - 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: Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 2019;20:461-493. doi:10.1146/annurev-genom-083115-022316 apa: Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316 chicago: Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316. ieee: G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” Annual Review of Genomics and Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019. ista: Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493. mla: Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316. short: G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493. date_created: 2019-09-07T14:28:29Z date_published: 2019-07-05T00:00:00Z date_updated: 2023-08-29T07:49:38Z day: '05' ddc: - '576' department: - _id: NiBa doi: 10.1146/annurev-genom-083115-022316 external_id: isi: - '000485148400020' pmid: - '31283361' file: - access_level: open_access checksum: 23d3978cf4739a89ce2c3e779f9305ca content_type: application/pdf creator: dernst date_created: 2019-09-09T07:22:12Z date_updated: 2020-07-14T12:47:42Z file_id: '6862' file_name: 2019_AnnualReview_Sella.pdf file_size: 411491 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 20' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 461-493 pmid: 1 publication: Annual Review of Genomics and Human Genetics publication_identifier: eissn: - 1545-293X issn: - 1527-8204 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Thinking about the evolution of complex traits in the era of genome-wide association studies 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '6840' abstract: - lang: eng text: "We discuss thermodynamic properties of harmonically trapped\r\nimperfect quantum gases. The spatial inhomogeneity of these systems imposes\r\na redefinition of the mean-field interparticle potential energy as compared\r\nto the homogeneous case. In our approach, it takes the form a\r\n2N2 ωd, where\r\nN is the number of particles, ω—the harmonic trap frequency, d—system’s\r\ndimensionality, and a is a parameter characterizing the interparticle interaction.\r\nWe provide arguments that this model corresponds to the limiting case of\r\na long-ranged interparticle potential of vanishingly small amplitude. This\r\nconclusion is drawn from a computation similar to the well-known Kac scaling\r\nprocedure, which is presented here in a form adapted to the case of an isotropic\r\nharmonic trap. We show that within the model, the imperfect gas of trapped\r\nrepulsive bosons undergoes the Bose–Einstein condensation provided d > 1.\r\nThe main result of our analysis is that in d = 1 the gas of attractive imperfect\r\nfermions with a = −aF < 0 is thermodynamically equivalent to the gas of\r\nrepulsive bosons with a = aB > 0 provided the parameters aF and aB fulfill\r\nthe relation aB + aF = \x1F. This result supplements similar recent conclusion\r\nabout thermodynamic equivalence of two-dimensional (2D) uniform imperfect\r\nrepulsive Bose and attractive Fermi gases." article_number: '063101' article_processing_charge: No author: - first_name: Krzysztof full_name: Mysliwy, Krzysztof id: 316457FC-F248-11E8-B48F-1D18A9856A87 last_name: Mysliwy - first_name: Marek full_name: Napiórkowski, Marek last_name: Napiórkowski citation: ama: 'Mysliwy K, Napiórkowski M. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab190d' apa: 'Mysliwy, K., & Napiórkowski, M. (2019). Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab190d' chicago: 'Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab190d.' ieee: 'K. Mysliwy and M. Napiórkowski, “Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019.' ista: 'Mysliwy K, Napiórkowski M. 2019. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063101.' mla: 'Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6, 063101, IOP Publishing, 2019, doi:10.1088/1742-5468/ab190d.' short: 'K. Mysliwy, M. Napiórkowski, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).' date_created: 2019-09-01T22:00:59Z date_published: 2019-06-13T00:00:00Z date_updated: 2023-08-29T07:19:13Z day: '13' department: - _id: RoSe doi: 10.1088/1742-5468/ab190d ec_funded: 1 external_id: arxiv: - '1810.02209' isi: - '000471650100001' intvolume: ' 2019' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.02209 month: '06' oa: 1 oa_version: Preprint project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: 'Journal of Statistical Mechanics: Theory and Experiment' publication_identifier: eissn: - 1742-5468 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 2019 year: '2019' ... --- _id: '6843' abstract: - lang: eng text: The aim of this short paper is to offer a complete characterization of all (not necessarily surjective) isometric embeddings of the Wasserstein space Wp(X), where S is a countable discrete metric space and 0Journal of Mathematical Analysis and Applications. 2019;480(2). doi:10.1016/j.jmaa.2019.123435 apa: Gehér, G. P., Titkos, T., & Virosztek, D. (2019). On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. Elsevier. https://doi.org/10.1016/j.jmaa.2019.123435 chicago: Gehér, György Pál, Tamás Titkos, and Daniel Virosztek. “On Isometric Embeddings of Wasserstein Spaces – the Discrete Case.” Journal of Mathematical Analysis and Applications. Elsevier, 2019. https://doi.org/10.1016/j.jmaa.2019.123435. ieee: G. P. Gehér, T. Titkos, and D. Virosztek, “On isometric embeddings of Wasserstein spaces – the discrete case,” Journal of Mathematical Analysis and Applications, vol. 480, no. 2. Elsevier, 2019. ista: Gehér GP, Titkos T, Virosztek D. 2019. On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. 480(2), 123435. mla: Gehér, György Pál, et al. “On Isometric Embeddings of Wasserstein Spaces – the Discrete Case.” Journal of Mathematical Analysis and Applications, vol. 480, no. 2, 123435, Elsevier, 2019, doi:10.1016/j.jmaa.2019.123435. short: G.P. Gehér, T. Titkos, D. Virosztek, Journal of Mathematical Analysis and Applications 480 (2019). date_created: 2019-09-01T22:01:01Z date_published: 2019-12-15T00:00:00Z date_updated: 2023-08-29T07:18:50Z day: '15' department: - _id: LaEr doi: 10.1016/j.jmaa.2019.123435 ec_funded: 1 external_id: arxiv: - '1809.01101' isi: - '000486563900031' intvolume: ' 480' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.01101 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Mathematical Analysis and Applications publication_identifier: eissn: - '10960813' issn: - 0022247X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: On isometric embeddings of Wasserstein spaces – the discrete case type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 480 year: '2019' ... --- _id: '6835' abstract: - lang: eng text: We derive the Hasse principle and weak approximation for fibrations of certain varieties in the spirit of work by Colliot-Thélène–Sansuc and Harpaz–Skorobogatov–Wittenberg. Our varieties are defined through polynomials in many variables and part of our work is devoted to establishing Schinzel's hypothesis for polynomials of this kind. This last part is achieved by using arguments behind Birch's well-known result regarding the Hasse principle for complete intersections with the notable difference that we prove our result in 50% fewer variables than in the classical Birch setting. We also study the problem of square-free values of an integer polynomial with 66.6% fewer variables than in the Birch setting. article_number: '102794' article_processing_charge: No article_type: original author: - first_name: Kevin N full_name: Destagnol, Kevin N id: 44DDECBC-F248-11E8-B48F-1D18A9856A87 last_name: Destagnol - first_name: Efthymios full_name: Sofos, Efthymios last_name: Sofos citation: ama: Destagnol KN, Sofos E. Rational points and prime values of polynomials in moderately many variables. Bulletin des Sciences Mathematiques. 2019;156(11). doi:10.1016/j.bulsci.2019.102794 apa: Destagnol, K. N., & Sofos, E. (2019). Rational points and prime values of polynomials in moderately many variables. Bulletin Des Sciences Mathematiques. Elsevier. https://doi.org/10.1016/j.bulsci.2019.102794 chicago: Destagnol, Kevin N, and Efthymios Sofos. “Rational Points and Prime Values of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques. Elsevier, 2019. https://doi.org/10.1016/j.bulsci.2019.102794. ieee: K. N. Destagnol and E. Sofos, “Rational points and prime values of polynomials in moderately many variables,” Bulletin des Sciences Mathematiques, vol. 156, no. 11. Elsevier, 2019. ista: Destagnol KN, Sofos E. 2019. Rational points and prime values of polynomials in moderately many variables. Bulletin des Sciences Mathematiques. 156(11), 102794. mla: Destagnol, Kevin N., and Efthymios Sofos. “Rational Points and Prime Values of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques, vol. 156, no. 11, 102794, Elsevier, 2019, doi:10.1016/j.bulsci.2019.102794. short: K.N. Destagnol, E. Sofos, Bulletin Des Sciences Mathematiques 156 (2019). date_created: 2019-09-01T22:00:55Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-29T07:18:02Z day: '01' department: - _id: TiBr doi: 10.1016/j.bulsci.2019.102794 external_id: arxiv: - '1801.03082' isi: - '000496342100002' intvolume: ' 156' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.03082 month: '11' oa: 1 oa_version: Preprint publication: Bulletin des Sciences Mathematiques publication_identifier: issn: - 0007-4497 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Rational points and prime values of polynomials in moderately many variables type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 156 year: '2019' ... --- _id: '6837' abstract: - lang: eng text: Migrasomes are a recently discovered type of extracellular vesicles that are characteristically generated along retraction fibers in migrating cells. Two studies now show how migrasomes are formed and how they function in the physiologically relevant context of the developing zebrafish embryo. article_processing_charge: No author: - first_name: Ste full_name: Tavano, Ste id: 2F162F0C-F248-11E8-B48F-1D18A9856A87 last_name: Tavano orcid: 0000-0001-9970-7804 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Tavano S, Heisenberg C-PJ. Migrasomes take center stage. Nature Cell Biology. 2019;21(8):918-920. doi:10.1038/s41556-019-0369-3 apa: Tavano, S., & Heisenberg, C.-P. J. (2019). Migrasomes take center stage. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0369-3 chicago: Tavano, Ste, and Carl-Philipp J Heisenberg. “Migrasomes Take Center Stage.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0369-3. ieee: S. Tavano and C.-P. J. Heisenberg, “Migrasomes take center stage,” Nature Cell Biology, vol. 21, no. 8. Springer Nature, pp. 918–920, 2019. ista: Tavano S, Heisenberg C-PJ. 2019. Migrasomes take center stage. Nature Cell Biology. 21(8), 918–920. mla: Tavano, Ste, and Carl-Philipp J. Heisenberg. “Migrasomes Take Center Stage.” Nature Cell Biology, vol. 21, no. 8, Springer Nature, 2019, pp. 918–20, doi:10.1038/s41556-019-0369-3. short: S. Tavano, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 918–920. date_created: 2019-09-01T22:00:57Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-29T07:42:20Z day: '01' department: - _id: CaHe doi: 10.1038/s41556-019-0369-3 external_id: isi: - '000478029000003' pmid: - '31371826' intvolume: ' 21' isi: 1 issue: '8' language: - iso: eng month: '08' oa_version: None page: 918-920 pmid: 1 publication: Nature Cell Biology publication_identifier: eissn: - 1476-4679 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Migrasomes take center stage type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2019' ... --- _id: '6867' abstract: - lang: eng text: A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories. article_number: '12625' article_processing_charge: No author: - first_name: M. full_name: Fenu, M. last_name: Fenu - first_name: T. full_name: Bettermann, T. last_name: Bettermann - first_name: C. full_name: Vogl, C. last_name: Vogl - first_name: Nasser full_name: Darwish-Miranda, Nasser id: 39CD9926-F248-11E8-B48F-1D18A9856A87 last_name: Darwish-Miranda orcid: 0000-0002-8821-8236 - first_name: J. full_name: Schramel, J. last_name: Schramel - first_name: F. full_name: Jenner, F. last_name: Jenner - first_name: I. full_name: Ribitsch, I. last_name: Ribitsch citation: ama: Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-48930-7 apa: Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7 chicago: Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7. ieee: M. Fenu et al., “A novel magnet-based scratch method for standardisation of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019. ista: Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625. mla: Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:10.1038/s41598-019-48930-7. short: M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019). date_created: 2019-09-15T22:00:42Z date_published: 2019-09-02T00:00:00Z date_updated: 2023-08-29T07:55:15Z day: '02' ddc: - '570' department: - _id: Bio doi: 10.1038/s41598-019-48930-7 external_id: isi: - '000483697800007' pmid: - '31477739' file: - access_level: open_access checksum: 9cfd986d4108e288cc72276ef047ab0c content_type: application/pdf creator: dernst date_created: 2019-09-16T12:42:40Z date_updated: 2020-07-14T12:47:42Z file_id: '6879' file_name: 2019_ScientificReports_Fenu.pdf file_size: 3523795 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A novel magnet-based scratch method for standardisation of wound-healing assays 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '6859' abstract: - lang: eng text: V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation across theplasma membrane using the rotary-catalysis mechanism. They belong to the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthasesin overall architecture. We solved cryo–electron microscopy structures of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs, in three rotationalstates and two substates. These structures indicate substantial flexibility betweenV1and Voin a working enzyme, which results from mechanical competition between centralshaft rotation and resistance from the peripheral stalks. We also describedetails of adenosine diphosphate inhibition release, V1-Votorque transmission, andproton translocation, which are relevant for the entire V-type ATPase family. acknowledged_ssus: - _id: ScienComp article_number: eaaw9144 article_processing_charge: No author: - first_name: Long full_name: Zhou, Long id: 3E751364-F248-11E8-B48F-1D18A9856A87 last_name: Zhou orcid: 0000-0002-1864-8951 - 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: Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. 2019;365(6455). doi:10.1126/science.aaw9144 apa: Zhou, L., & Sazanov, L. A. (2019). Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. AAAS. https://doi.org/10.1126/science.aaw9144 chicago: Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” Science. AAAS, 2019. https://doi.org/10.1126/science.aaw9144. ieee: L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase,” Science, vol. 365, no. 6455. AAAS, 2019. ista: Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144. mla: Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” Science, vol. 365, no. 6455, eaaw9144, AAAS, 2019, doi:10.1126/science.aaw9144. short: L. Zhou, L.A. Sazanov, Science 365 (2019). date_created: 2019-09-07T19:04:45Z date_published: 2019-08-23T00:00:00Z date_updated: 2023-08-29T07:52:02Z day: '23' department: - _id: LeSa doi: 10.1126/science.aaw9144 external_id: isi: - '000482464000043' pmid: - '31439765' intvolume: ' 365' isi: 1 issue: '6455' language: - iso: eng month: '08' oa_version: None pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/ scopus_import: '1' status: public title: Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 365 year: '2019' ... --- _id: '6858' article_processing_charge: No article_type: review author: - 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: Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113 apa: Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113 chicago: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113. ieee: N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019. ista: Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292. mla: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113. short: N.H. Barton, National Science Review 6 (2019) 291–292. date_created: 2019-09-07T14:43:02Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-29T07:51:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1093/nsr/nwy113 external_id: isi: - '000467957400025' file: - access_level: open_access checksum: 571d60fa21a568607d1fd04e119da88c content_type: application/pdf creator: dernst date_created: 2020-10-02T09:16:44Z date_updated: 2020-10-02T09:16:44Z file_id: '8595' file_name: 2019_NSR_Barton.pdf file_size: 106463 relation: main_file success: 1 file_date_updated: 2020-10-02T09:16:44Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '2' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 291-292 publication: National Science Review publication_identifier: eissn: - 2053-714X issn: - 2095-5138 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Is speciation driven by cycles of mixing and isolation? 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 6 year: '2019' ... --- _id: '6868' abstract: - lang: eng text: "Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control electrical rhythmicity and excitability in the heart and brain, but the function of HCN channels at the subcellular level in axons remains poorly understood. Here, we show that the action potential conduction velocity in both myelinated and unmyelinated central axons can be bidirectionally modulated by a HCN channel blocker, cyclic adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar mossy fiber boutons show that HCN channels ensure reliable high-frequency firing and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration 13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2 channels control conduction velocity primarily by altering the resting membrane potential\r\nand are associated with significant metabolic costs. These results suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity to finely tune energy consumption and temporal delays across axons in the brain." article_number: e42766 article_processing_charge: No article_type: original author: - first_name: Niklas full_name: Byczkowicz, Niklas last_name: Byczkowicz - first_name: Abdelmoneim full_name: Eshra, Abdelmoneim last_name: Eshra - first_name: Jacqueline-Claire full_name: Montanaro-Punzengruber, Jacqueline-Claire id: 3786AB44-F248-11E8-B48F-1D18A9856A87 last_name: Montanaro-Punzengruber - first_name: Andrea full_name: Trevisiol, Andrea last_name: Trevisiol - first_name: Johannes full_name: Hirrlinger, Johannes last_name: Hirrlinger - first_name: Maarten Hp full_name: Kole, Maarten Hp last_name: Kole - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Stefan full_name: Hallermann, Stefan last_name: Hallermann citation: ama: Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, et al. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 2019;8. doi:10.7554/eLife.42766 apa: Byczkowicz, N., Eshra, A., Montanaro-Punzengruber, J.-C., Trevisiol, A., Hirrlinger, J., Kole, M. H., … Hallermann, S. (2019). HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42766 chicago: Byczkowicz, Niklas, Abdelmoneim Eshra, Jacqueline-Claire Montanaro-Punzengruber, Andrea Trevisiol, Johannes Hirrlinger, Maarten Hp Kole, Ryuichi Shigemoto, and Stefan Hallermann. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42766. ieee: N. Byczkowicz et al., “HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, Trevisiol A, Hirrlinger J, Kole MH, Shigemoto R, Hallermann S. 2019. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 8, e42766. mla: Byczkowicz, Niklas, et al. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” ELife, vol. 8, e42766, eLife Sciences Publications, 2019, doi:10.7554/eLife.42766. short: N. Byczkowicz, A. Eshra, J.-C. Montanaro-Punzengruber, A. Trevisiol, J. Hirrlinger, M.H. Kole, R. Shigemoto, S. Hallermann, ELife 8 (2019). date_created: 2019-09-15T22:00:43Z date_published: 2019-09-09T00:00:00Z date_updated: 2023-08-30T06:17:06Z day: '09' ddc: - '570' department: - _id: RySh doi: 10.7554/eLife.42766 external_id: isi: - '000485663900001' file: - access_level: open_access checksum: c350b7861ef0fb537cae8a3232aec016 content_type: application/pdf creator: dernst date_created: 2019-09-16T13:14:33Z date_updated: 2020-07-14T12:47:42Z file_id: '6880' file_name: 2019_eLife_Byczkowicz.pdf file_size: 4008137 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2019' ... --- _id: '6897' abstract: - lang: eng text: The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738)." article_number: dev175919 article_processing_charge: No article_type: original author: - first_name: Qiang full_name: Zhu, Qiang id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87 last_name: Zhu - first_name: Marçal full_name: Gallemi, Marçal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi orcid: 0000-0003-4675-6893 - first_name: Jiří full_name: Pospíšil, Jiří last_name: Pospíšil - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 2019;146(17). doi:10.1242/dev.175919 apa: Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., & Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. The Company of Biologists. https://doi.org/10.1242/dev.175919 chicago: Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.175919. ieee: Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” Development, vol. 146, no. 17. The Company of Biologists, 2019. ista: Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919. mla: Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” Development, vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:10.1242/dev.175919. short: Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019). date_created: 2019-09-22T22:00:36Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:19:04Z day: '12' department: - _id: EvBe doi: 10.1242/dev.175919 ec_funded: 1 external_id: isi: - '000486297400011' pmid: - '31391194' intvolume: ' 146' isi: 1 issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1242/dev.175919 month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Development publication_identifier: eissn: - '14779129' publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 146 year: '2019' ... --- _id: '6896' abstract: - lang: eng text: "Until recently, a great amount of brain studies have been conducted in human post mortem tissues, cell lines and model organisms. These researches provided useful insights regarding cell-cell interactions occurring in the brain. However, such approaches suffer from technical limitations and inaccurate modeling of the tissue 3D cytoarchitecture. Importantly, they might lack a human genetic background essential for disease modeling. With the development of protocols to generate human cerebral organoids, we are now closer to reproducing the early stages of human brain development in vitro. As a result, more relevant cell-cell interaction studies can be conducted.\r\n\r\nIn this review, we discuss the advantages of 3D cultures over 2D in modulating brain cell-cell interactions during physiological and pathological development, as well as the progress made in developing organoids in which neurons, macroglia, microglia and vascularization are present. Finally, we debate the limitations of those models and possible future directions." article_number: '146458' article_processing_charge: No article_type: original author: - first_name: Bárbara full_name: Oliveira, Bárbara id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87 last_name: Oliveira - first_name: Aysan Çerağ full_name: Yahya, Aysan Çerağ id: 365A65F8-F248-11E8-B48F-1D18A9856A87 last_name: Yahya - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Oliveira B, Yahya AÇ, Novarino G. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. 2019;1724. doi:10.1016/j.brainres.2019.146458 apa: Oliveira, B., Yahya, A. Ç., & Novarino, G. (2019). Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. Elsevier. https://doi.org/10.1016/j.brainres.2019.146458 chicago: Oliveira, Bárbara, Aysan Çerağ Yahya, and Gaia Novarino. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” Brain Research. Elsevier, 2019. https://doi.org/10.1016/j.brainres.2019.146458. ieee: B. Oliveira, A. Ç. Yahya, and G. Novarino, “Modeling cell-cell interactions in the brain using cerebral organoids,” Brain Research, vol. 1724. Elsevier, 2019. ista: Oliveira B, Yahya AÇ, Novarino G. 2019. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. 1724, 146458. mla: Oliveira, Bárbara, et al. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” Brain Research, vol. 1724, 146458, Elsevier, 2019, doi:10.1016/j.brainres.2019.146458. short: B. Oliveira, A.Ç. Yahya, G. Novarino, Brain Research 1724 (2019). date_created: 2019-09-22T22:00:35Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-30T06:19:49Z day: '01' department: - _id: GaNo doi: 10.1016/j.brainres.2019.146458 external_id: isi: - '000491646600033' pmid: - '31521639' intvolume: ' 1724' isi: 1 language: - iso: eng month: '12' oa_version: None pmid: 1 publication: Brain Research publication_identifier: eissn: - '18726240' issn: - '00068993' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Modeling cell-cell interactions in the brain using cerebral organoids type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 1724 year: '2019' ... --- _id: '9731' abstract: - lang: eng text: OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb) article_processing_charge: No author: - first_name: Olga full_name: Sigalova, Olga last_name: Sigalova - first_name: Andrei full_name: Chaplin, Andrei last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel full_name: Shelyakin, Pavel last_name: Shelyakin - first_name: Vsevolod full_name: Filaretov, Vsevolod last_name: Filaretov - first_name: Evgeny full_name: Akkuratov, Evgeny last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1 apa: Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1 chicago: Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1. ieee: O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808772.v1. mla: Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1. short: O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-07-27T14:09:11Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808772.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808772.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9783' abstract: - lang: eng text: Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1. ieee: O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1. mla: Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-06T07:59:56Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808760.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808760.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9897' abstract: - lang: eng text: Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808850.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808850.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 20 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808850.v1. ieee: O. M. Sigalova et al., “Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808850.v1. mla: Sigalova, Olga M., et al. Additional File 20 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808850.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T07:58:15Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808850.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808850.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9890' abstract: - lang: eng text: Distribution of OGs with mosaic phyletic patterns across species (complete genomes only). (CSV 7 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808802.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808802.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808802.v1. ieee: O. M. Sigalova et al., “Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808802.v1. mla: Sigalova, Olga M., et al. Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808802.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-11T14:26:40Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808802.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808802.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9892' abstract: - lang: eng text: Distribution of OGs with mosaic phyletic patterns across species (all genomes). (CSV 10 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V full_name: Chaplin, Andrei V last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808814.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808814.v1 chicago: Sigalova, Olga M., Andrei V Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808814.v1. ieee: O. M. Sigalova et al., “Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808814.v1. mla: Sigalova, Olga M., et al. Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808814.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T07:11:53Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808814.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808814.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9893' abstract: - lang: eng text: Summary of peripheral genesa phyletic patterns and tree concordance. (CSV 26 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808820.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808820.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808820.v1. ieee: O. M. Sigalova et al., “Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808820.v1. mla: Sigalova, Olga M., et al. Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808820.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T07:20:10Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808820.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808820.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9894' abstract: - lang: eng text: Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808826.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808826.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 18 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808826.v1. ieee: O. M. Sigalova et al., “Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808826.v1. mla: Sigalova, Olga M., et al. Additional File 18 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808826.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T07:25:07Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808826.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808826.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9895' abstract: - lang: eng text: Additional information on proteins from OG1. (CSV 30 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808835.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808835.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808835.v1. ieee: O. M. Sigalova et al., “Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808835.v1. mla: Sigalova, Olga M., et al. Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808835.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T07:44:52Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808835.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808835.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9896' abstract: - lang: eng text: Summary of the analysed genomes. (CSV 24 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808841.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808841.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808841.v1. ieee: O. M. Sigalova et al., “Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808841.v1. mla: Sigalova, Olga M., et al. Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808841.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T07:50:53Z date_published: 2019-09-02T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '02' department: - _id: FyKo doi: 10.6084/m9.figshare.9808841.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808841.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6899' abstract: - lang: eng text: Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed. article_processing_charge: No author: - first_name: Dorothee full_name: Bornhorst, Dorothee last_name: Bornhorst - first_name: Peng full_name: Xia, Peng id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87 last_name: Xia orcid: 0000-0002-5419-7756 - first_name: Hiroyuki full_name: Nakajima, Hiroyuki last_name: Nakajima - first_name: Chaitanya full_name: Dingare, Chaitanya last_name: Dingare - first_name: Wiebke full_name: Herzog, Wiebke last_name: Herzog - first_name: Virginie full_name: Lecaudey, Virginie last_name: Lecaudey - first_name: Naoki full_name: Mochizuki, Naoki last_name: Mochizuki - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Deborah full_name: Yelon, Deborah last_name: Yelon - first_name: Salim full_name: Abdelilah-Seyfried, Salim last_name: Abdelilah-Seyfried citation: ama: Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 2019;10(1):4113. doi:10.1038/s41467-019-12068-x apa: Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-019-12068-x chicago: Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications. Nature Publishing Group, 2019. https://doi.org/10.1038/s41467-019-12068-x. ieee: D. Bornhorst et al., “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” Nature communications, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019. ista: Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113. mla: Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:10.1038/s41467-019-12068-x. short: D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113. date_created: 2019-09-22T22:00:37Z date_published: 2019-09-11T00:00:00Z date_updated: 2023-08-30T06:21:23Z day: '11' ddc: - '570' department: - _id: CaHe doi: 10.1038/s41467-019-12068-x external_id: isi: - '000485216800009' pmid: - '31511517' file: - access_level: open_access checksum: 62c2512712e16d27c1797d318d14ba9f content_type: application/pdf creator: kschuh date_created: 2019-10-01T11:18:50Z date_updated: 2020-07-14T12:47:44Z file_id: '6926' file_name: 2019_Nature_Bornhorst.pdf file_size: 3905793 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '4113' pmid: 1 publication: Nature communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6898' abstract: - lang: eng text: "Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity." article_number: '710' article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-019-6059-5 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics. BioMed Central, 2019. https://doi.org/10.1186/s12864-019-6059-5. ieee: O. M. Sigalova et al., “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” BMC Genomics, vol. 20, no. 1. BioMed Central, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710. mla: Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics, vol. 20, no. 1, 710, BioMed Central, 2019, doi:10.1186/s12864-019-6059-5. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019). date_created: 2019-09-22T22:00:36Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' ddc: - '570' department: - _id: FyKo doi: 10.1186/s12864-019-6059-5 external_id: isi: - '000485256100001' file: - access_level: open_access checksum: b798773c5823012d31c812c9f7975da2 content_type: application/pdf creator: kschuh date_created: 2019-10-01T10:33:17Z date_updated: 2020-07-14T12:47:44Z file_id: '6924' file_name: 2019_BioMed_Sigalova.pdf file_size: 4157175 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: BMC Genomics publication_identifier: eissn: - '14712164' publication_status: published publisher: BioMed Central quality_controlled: '1' related_material: record: - id: '9731' relation: research_data status: public - id: '9783' relation: research_data status: public - id: '9890' relation: research_data status: public - id: '9892' relation: research_data status: public - id: '9893' relation: research_data status: public - id: '9894' relation: research_data status: public - id: '9895' relation: research_data status: public - id: '9896' relation: research_data status: public - id: '9897' relation: research_data status: public - id: '9898' relation: research_data status: public - id: '9899' relation: research_data status: public - id: '9900' relation: research_data status: public - id: '9901' relation: research_data status: public scopus_import: '1' status: public title: Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '6920' article_processing_charge: No article_type: original author: - first_name: Christina full_name: Artner, Christina id: 45DF286A-F248-11E8-B48F-1D18A9856A87 last_name: Artner - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 2019;12(10):1312-1314. doi:10.1016/j.molp.2019.09.003 apa: Artner, C., & Benková, E. (2019). Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2019.09.003 chicago: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant. Cell Press, 2019. https://doi.org/10.1016/j.molp.2019.09.003. ieee: C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth regulation,” Molecular Plant, vol. 12, no. 10. Cell Press, pp. 1312–1314, 2019. ista: Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 12(10), 1312–1314. mla: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant, vol. 12, no. 10, Cell Press, 2019, pp. 1312–14, doi:10.1016/j.molp.2019.09.003. short: C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314. date_created: 2019-09-30T10:00:40Z date_published: 2019-10-07T00:00:00Z date_updated: 2023-08-30T06:55:02Z day: '07' department: - _id: EvBe doi: 10.1016/j.molp.2019.09.003 external_id: isi: - '000489132500002' pmid: - '31541740' intvolume: ' 12' isi: 1 issue: '10' language: - iso: eng month: '10' oa_version: None page: 1312-1314 pmid: 1 project: - _id: 2685A872-B435-11E9-9278-68D0E5697425 name: Hormonal regulation of plant adaptive responses to environmental signals publication: Molecular Plant publication_identifier: issn: - 1674-2052 - 1752-9867 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Ethylene and cytokinin - partners in root growth regulation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2019' ... --- _id: '9898' abstract: - lang: eng text: All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808859.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808859.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1. ieee: O. M. Sigalova et al., “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808859.v1. mla: Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T08:10:23Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808859.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808859.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9901' abstract: - lang: eng text: Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1. ieee: O. M. Sigalova et al., “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808907.v1. mla: Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T10:54:03Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808907.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808907.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9899' abstract: - lang: eng text: Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808865.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808865.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808865.v1. ieee: O. M. Sigalova et al., “Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808865.v1. mla: Sigalova, Olga M., et al. Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808865.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T08:18:09Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808865.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808865.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9900' abstract: - lang: eng text: Pan-genome statistics by species. (CSV 3 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808886.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1. ieee: O. M. Sigalova et al., “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808886.v1. mla: Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T08:44:49Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808886.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808886.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6936' abstract: - lang: eng text: "A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n" article_processing_charge: No article_type: original author: - first_name: Otso full_name: Ovaskainen, Otso last_name: Ovaskainen - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Nerea full_name: Abrego, Nerea last_name: Abrego citation: ama: Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444 apa: Ovaskainen, O., Rybicki, J., & Abrego, N. (2019). What can observational data reveal about metacommunity processes? Ecography. Wiley. https://doi.org/10.1111/ecog.04444 chicago: Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444. ieee: O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal about metacommunity processes?,” Ecography, vol. 42, no. 11. Wiley, pp. 1877–1886, 2019. ista: Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal about metacommunity processes? Ecography. 42(11), 1877–1886. mla: Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444. short: O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886. date_created: 2019-10-08T13:01:24Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-30T06:57:25Z day: '01' ddc: - '577' department: - _id: DaAl doi: 10.1111/ecog.04444 ec_funded: 1 external_id: isi: - '000486348700001' file: - access_level: open_access checksum: 6c9fbbd5ea8ce10ae93e55ad560a7bf9 content_type: application/pdf creator: jrybicki date_created: 2019-10-08T13:07:44Z date_updated: 2020-07-14T12:47:45Z file_id: '6937' file_name: ecog.04444.pdf file_size: 1682718 relation: main_file file_date_updated: 2020-07-14T12:47:45Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1877-1886 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Ecography publication_identifier: eissn: - 1600-0587 issn: - 0906-7590 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: What can observational data reveal about metacommunity processes? 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 42 year: '2019' ... --- _id: '6857' abstract: - lang: eng text: "Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop." article_number: '1900151' article_processing_charge: No article_type: original author: - first_name: B full_name: Giese, B last_name: Giese - first_name: J L full_name: Friess, J L last_name: Friess - first_name: 'M F ' full_name: 'Schetelig, M F ' last_name: Schetelig - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Philip full_name: Messer, Philip last_name: Messer - first_name: Florence full_name: Debarre, Florence last_name: Debarre - first_name: H full_name: Meimberg, H last_name: Meimberg - first_name: N full_name: Windbichler, N last_name: Windbichler - first_name: C full_name: Boete, C last_name: Boete citation: ama: 'Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151' apa: 'Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151' chicago: 'Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151.' ieee: 'B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.' ista: 'Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.' mla: 'Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.' short: B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019). date_created: 2019-09-07T14:40:03Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-30T06:56:26Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1002/bies.201900151 external_id: isi: - '000489502000001' file: - access_level: open_access checksum: 8cc7551bff70b2658f8d5630f228ee12 content_type: application/pdf creator: dernst date_created: 2019-10-11T06:59:26Z date_updated: 2020-07-14T12:47:42Z file_id: '6939' file_name: 2019_BioEssays_Giese.pdf file_size: 193248 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: BioEssays publication_identifier: eissn: - 1521-1878 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 41 year: '2019' ... --- _id: '6890' abstract: - lang: eng text: Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods. article_processing_charge: No author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: 'Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008' apa: Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function (Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008 chicago: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008. ieee: M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in Complementary Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159. ista: 'Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.' mla: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008. short: M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159. date_created: 2019-09-18T08:15:37Z date_published: 2019-08-27T00:00:00Z date_updated: 2023-08-30T06:56:00Z day: '27' department: - _id: FlSc doi: 10.1016/bs.aivir.2019.07.008 editor: - first_name: Félix A. full_name: Rey, Félix A. last_name: Rey external_id: isi: - '000501594500006' pmid: - ' 31522703' intvolume: ' 105' isi: 1 language: - iso: eng month: '08' oa_version: None page: 117-159 pmid: 1 publication: Complementary Strategies to Study Virus Structure and Function publication_identifier: isbn: - '9780128184561' issn: - 0065-3527 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' series_title: Advances in Virus Research status: public title: Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging type: book_chapter user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 105 year: '2019' ... --- _id: '6940' abstract: - lang: eng text: "We study the effect of a linear tunneling coupling between two-dimensional systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the one-body correlation functions are algebraically decaying and the other with\r\nexponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law\r\ndecay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent. We provide a picture of the phase diagram using a renormalization group approach." acknowledgement: "We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1 - 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021 Joint Project “Strongly interacting systems in confined geometries” is gratefully acknowledged." article_number: '100601' article_processing_charge: No article_type: original author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Nicolò full_name: Defenu, Nicolò last_name: Defenu - first_name: István full_name: Nándori, István last_name: Nándori - first_name: Luca full_name: Salasnich, Luca last_name: Salasnich - first_name: Andrea full_name: Trombettoni, Andrea last_name: Trombettoni citation: ama: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 2019;123(10). doi:10.1103/physrevlett.123.100601 apa: Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019). Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601 chicago: Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601. ieee: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models,” Physical Review Letters, vol. 123, no. 10. American Physical Society, 2019. ista: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 123(10), 100601. mla: Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American Physical Society, 2019, doi:10.1103/physrevlett.123.100601. short: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019). date_created: 2019-10-14T06:31:13Z date_published: 2019-09-06T00:00:00Z date_updated: 2023-08-30T06:57:53Z day: '06' department: - _id: MiLe doi: 10.1103/physrevlett.123.100601 external_id: arxiv: - '1907.06253' isi: - '000483587200004' intvolume: ' 123' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.06253 month: '09' oa: 1 oa_version: Preprint project: - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News auf IST Website relation: press_release url: https://ist.ac.at/en/news/new-form-of-magnetism-found/ scopus_import: '1' status: public title: Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 123 year: '2019' ... --- _id: '6919' article_number: eaaw6490 article_processing_charge: No author: - first_name: Chao full_name: Qi, Chao last_name: Qi - first_name: Giulio Di full_name: Minin, Giulio Di last_name: Minin - first_name: Irene full_name: Vercellino, Irene id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87 last_name: Vercellino orcid: 0000-0001-5618-3449 - first_name: Anton full_name: Wutz, Anton last_name: Wutz - first_name: Volodymyr M. full_name: Korkhov, Volodymyr M. last_name: Korkhov citation: ama: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw6490 apa: Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019). Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490 chicago: Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw6490. ieee: C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019. ista: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490. mla: Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490. short: C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (2019). date_created: 2019-09-29T22:00:45Z date_published: 2019-09-18T00:00:00Z date_updated: 2023-08-30T06:55:31Z day: '18' ddc: - '570' department: - _id: LeSa doi: 10.1126/sciadv.aaw6490 external_id: isi: - '000491128800062' file: - access_level: open_access checksum: b2256c9117655bc15f621ba0babf219f content_type: application/pdf creator: kschuh date_created: 2019-10-02T11:13:54Z date_updated: 2020-07-14T12:47:44Z file_id: '6928' file_name: 2019_AAAS_Qi.pdf file_size: 1236101 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: eissn: - '23752548' publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Structural basis of sterol recognition by human hedgehog receptor PTCH1 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2019' ... --- _id: '6983' abstract: - lang: eng text: Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver. article_number: '2153' article_processing_charge: No article_type: original author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 - first_name: H full_name: Rajakaruna, H last_name: Rajakaruna - first_name: IA full_name: Cockburn, IA last_name: Cockburn - first_name: VV full_name: Ganusov, VV last_name: Ganusov citation: ama: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153 apa: Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153 chicago: Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153. ieee: R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers, 2019. ista: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153. mla: Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153. short: R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019). date_created: 2019-11-04T15:50:06Z date_published: 2019-09-20T00:00:00Z date_updated: 2023-08-30T07:18:23Z day: '20' ddc: - '570' department: - _id: BeVi doi: 10.3389/fimmu.2019.02153 external_id: isi: - '000487187000001' pmid: - '31616407' file: - access_level: open_access checksum: 68d1708f7aa412544159b498ef17a6b9 content_type: application/pdf creator: dernst date_created: 2019-11-04T15:54:00Z date_updated: 2020-07-14T12:47:46Z file_id: '6984' file_name: 2019_FrontiersImmonology_Kelemen.pdf file_size: 2083061 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Immunology publication_identifier: issn: - 1664-3224 publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ...