--- _id: '8283' abstract: - lang: eng text: 'Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. ' acknowledgement: 'We would like to thank the reviewers for their helpful comments on the original manuscript. ' article_number: '5272' article_processing_charge: No article_type: original author: - first_name: Huihuang full_name: Chen, Huihuang last_name: Chen - first_name: Linyi full_name: Lai, Linyi last_name: Lai - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Liping full_name: Liu, Liping last_name: Liu - first_name: Bello Hassan full_name: Jakada, Bello Hassan last_name: Jakada - first_name: Youmei full_name: Huang, Youmei last_name: Huang - first_name: Qing full_name: He, Qing last_name: He - first_name: Mengnan full_name: Chai, Mengnan last_name: Chai - first_name: Xiaoping full_name: Niu, Xiaoping last_name: Niu - first_name: Yuan full_name: Qin, Yuan last_name: Qin citation: ama: Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727 apa: Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727 chicago: Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727. ieee: H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020. ista: Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272. mla: Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727. short: H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020). date_created: 2020-08-24T06:24:03Z date_published: 2020-08-10T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '10' ddc: - '570' department: - _id: JiFr doi: 10.3390/ijms21165727 external_id: isi: - '000565090300001' pmid: - '32785037' file: - access_level: open_access checksum: 03b039244e6ae80580385fd9f577e2b2 content_type: application/pdf creator: cziletti date_created: 2020-08-25T09:53:50Z date_updated: 2020-08-25T09:53:50Z file_id: '8292' file_name: 2020_IntMolecSciences_Chen.pdf file_size: 5718755 relation: main_file success: 1 file_date_updated: 2020-08-25T09:53:50Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '16' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: International Journal of Molecular Sciences publication_identifier: eissn: - '14220067' issn: - '16616596' publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public scopus_import: '1' status: public title: AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling 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: 21 year: '2020' ... --- _id: '8139' abstract: - lang: eng text: 'Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.' acknowledged_ssus: - _id: EM-Fac - _id: Bio acknowledgement: "This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. " article_number: jcs248062 article_processing_charge: No article_type: original author: - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: G full_name: Vert, G last_name: Vert - first_name: SY full_name: Bednarek, SY last_name: Bednarek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062 apa: Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062 chicago: Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062. ieee: A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020. ista: Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062. mla: Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062. short: A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020). date_created: 2020-07-21T08:58:19Z date_published: 2020-08-06T00:00:00Z date_updated: 2023-12-01T13:51:07Z day: '06' ddc: - '575' department: - _id: JiFr - _id: EM-Fac doi: 10.1242/jcs.248062 ec_funded: 1 external_id: isi: - '000561047900021' pmid: - '32616560' file: - access_level: open_access checksum: 2d11f79a0b4e0a380fb002b933da331a content_type: application/pdf creator: ajohnson date_created: 2020-11-26T17:12:51Z date_updated: 2021-08-08T22:30:03Z embargo: 2021-08-07 file_id: '8815' file_name: 2020 - Johnson - JSC - plant CME toolbox.pdf file_size: 15150403 relation: main_file file_date_updated: 2021-08-08T22:30:03Z has_accepted_license: '1' intvolume: ' 133' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' related_material: record: - id: '14510' relation: dissertation_contains status: public scopus_import: '1' status: public title: Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 133 year: '2020' ... --- _id: '9160' abstract: - lang: eng text: Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development. acknowledgement: H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared. article_number: '100048' article_processing_charge: No article_type: original author: - first_name: Hana full_name: Semeradova, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semeradova - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: 'Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048' apa: 'Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048' chicago: 'Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.' ieee: 'H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.' ista: 'Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.' mla: 'Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048.' short: H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020). date_created: 2021-02-18T10:18:43Z date_published: 2020-05-11T00:00:00Z date_updated: 2024-03-27T23:30:46Z day: '11' ddc: - '580' department: - _id: EvBe doi: 10.1016/j.xplc.2020.100048 external_id: isi: - '000654052800010' pmid: - '33367243' file: - access_level: open_access checksum: 785b266d82a94b007cf40dbbe7c4847e content_type: application/pdf creator: dernst date_created: 2021-02-18T10:23:59Z date_updated: 2021-02-18T10:23:59Z file_id: '9161' file_name: 2020_PlantComm_Semeradova.pdf file_size: 840289 relation: main_file success: 1 file_date_updated: 2021-02-18T10:23:59Z has_accepted_license: '1' intvolume: ' 1' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis. - _id: 253E54C8-B435-11E9-9278-68D0E5697425 grant_number: ALTF710-2016 name: Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants publication: Plant Communications publication_identifier: issn: - 2590-3462 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '10135' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways' 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: 1 year: '2020' ... --- _id: '10877' abstract: - lang: eng text: 'This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with piecewise constant dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been applied to solve five different benchmark problems in the category for piecewise constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL. Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results probably provide the most complete assessment of tools for the safety verification of continuous and hybrid systems with piecewise constant dynamics up to this date.' acknowledgement: "The authors gratefully acknowledge \fnancial support by the European Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported by the National Natural Science\r\nFoundation of China (No.61572249)." alternative_title: - EPiC Series in Computing article_processing_charge: No author: - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Alessandro full_name: Abate, Alessandro last_name: Abate - first_name: Dieky full_name: Adzkiya, Dieky last_name: Adzkiya - first_name: Anna full_name: Becchi, Anna last_name: Becchi - first_name: Lei full_name: Bu, Lei last_name: Bu - first_name: Alessandro full_name: Cimatti, Alessandro last_name: Cimatti - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Alberto full_name: Griggio, Alberto last_name: Griggio - first_name: Sergio full_name: Mover, Sergio last_name: Mover - first_name: Muhammad Syifa'ul full_name: Mufid, Muhammad Syifa'ul last_name: Mufid - first_name: Idriss full_name: Riouak, Idriss last_name: Riouak - first_name: Stefano full_name: Tonetta, Stefano last_name: Tonetta - first_name: Enea full_name: Zaffanella, Enea last_name: Zaffanella citation: ama: 'Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In: Frehse G, Althoff M, eds. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. Vol 61. EasyChair; 2019:1-13. doi:10.29007/rjwn' apa: 'Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella, E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In G. Frehse & M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems (Vol. 61, pp. 1–13). Montreal, Canada: EasyChair. https://doi.org/10.29007/rjwn' chicago: 'Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” In ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, 61:1–13. EasyChair, 2019. https://doi.org/10.29007/rjwn.' ieee: 'G. Frehse et al., “ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics,” in ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, Montreal, Canada, 2019, vol. 61, pp. 1–13.' ista: 'Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series in Computing, vol. 61, 1–13.' mla: 'Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, vol. 61, EasyChair, 2019, pp. 1–13, doi:10.29007/rjwn.' short: G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe, A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G. Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13. conference: end_date: 2019-04-15 location: Montreal, Canada name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems' start_date: 2019-04-15 date_created: 2022-03-18T12:29:23Z date_published: 2019-05-25T00:00:00Z date_updated: 2022-05-17T07:09:47Z day: '25' ddc: - '000' department: - _id: ToHe doi: 10.29007/rjwn editor: - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Matthias full_name: Althoff, Matthias last_name: Althoff file: - access_level: open_access checksum: 4b92e333db7b4e2349501a804dfede69 content_type: application/pdf creator: dernst date_created: 2022-05-17T06:55:49Z date_updated: 2022-05-17T06:55:49Z file_id: '11391' file_name: 2019_EPiCs_Frehse.pdf file_size: 346415 relation: main_file success: 1 file_date_updated: 2022-05-17T06:55:49Z has_accepted_license: '1' intvolume: ' 61' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1-13 publication: ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems publication_identifier: issn: - 2398-7340 publication_status: published publisher: EasyChair quality_controlled: '1' scopus_import: '1' status: public title: 'ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2019' ... --- _id: '441' article_processing_charge: No article_type: original author: - first_name: Nikita full_name: Kalinin, Nikita last_name: Kalinin - first_name: Mikhail full_name: Shkolnikov, Mikhail id: 35084A62-F248-11E8-B48F-1D18A9856A87 last_name: Shkolnikov orcid: 0000-0002-4310-178X citation: ama: Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 2019;5(3):909–928. doi:10.1007/s40879-018-0218-0 apa: Kalinin, N., & Shkolnikov, M. (2019). Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-018-0218-0 chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40879-018-0218-0. ieee: N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part of SL(2,Z),” European Journal of Mathematics, vol. 5, no. 3. Springer Nature, pp. 909–928, 2019. ista: Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 5(3), 909–928. mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics, vol. 5, no. 3, Springer Nature, 2019, pp. 909–928, doi:10.1007/s40879-018-0218-0. short: N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928. date_created: 2018-12-11T11:46:29Z date_published: 2019-09-15T00:00:00Z date_updated: 2021-01-12T07:56:46Z day: '15' department: - _id: TaHa doi: 10.1007/s40879-018-0218-0 ec_funded: 1 external_id: arxiv: - '1711.02089' intvolume: ' 5' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.02089 month: '09' oa: 1 oa_version: Preprint page: 909–928 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: European Journal of Mathematics publication_identifier: eissn: - 2199-6768 issn: - 2199-675X publication_status: published publisher: Springer Nature publist_id: '7382' quality_controlled: '1' scopus_import: 1 status: public title: Tropical formulae for summation over a part of SL(2,Z) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 5 year: '2019' ... --- _id: '5793' abstract: - lang: eng text: The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis. alternative_title: - MIMB author: - first_name: Yoichi full_name: Asaoka, Yoichi last_name: Asaoka - first_name: Hitoshi full_name: Morita, Hitoshi last_name: Morita - first_name: Hiroko full_name: Furumoto, Hiroko last_name: Furumoto - 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: Makoto full_name: Furutani-Seiki, Makoto last_name: Furutani-Seiki citation: ama: 'Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:10.1007/978-1-4939-8910-2_14' apa: Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181). Springer. https://doi.org/10.1007/978-1-4939-8910-2_14 chicago: Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14. ieee: Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181. ista: 'Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.' mla: Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14. short: Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181. date_created: 2019-01-06T22:59:11Z date_published: 2019-01-01T00:00:00Z date_updated: 2021-01-12T08:03:30Z day: '01' department: - _id: CaHe doi: 10.1007/978-1-4939-8910-2_14 editor: - first_name: Alexander full_name: Hergovich, Alexander last_name: Hergovich intvolume: ' 1893' language: - iso: eng month: '01' oa_version: None page: 167-181 publication: The hippo pathway publication_identifier: isbn: - 978-1-4939-8909-6 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: 1 series_title: Methods in Molecular Biology status: public title: Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1893 year: '2019' ... --- _id: '5887' abstract: - lang: eng text: 'Cryptographic security is usually defined as a guarantee that holds except when a bad event with negligible probability occurs, and nothing is guaranteed in that bad case. However, in settings where such failure can happen with substantial probability, one needs to provide guarantees even for the bad case. A typical example is where a (possibly weak) password is used instead of a secure cryptographic key to protect a session, the bad event being that the adversary correctly guesses the password. In a situation with multiple such sessions, a per-session guarantee is desired: any session for which the password has not been guessed remains secure, independently of whether other sessions have been compromised. A new formalism for stating such gracefully degrading security guarantees is introduced and applied to analyze the examples of password-based message authentication and password-based encryption. While a natural per-message guarantee is achieved for authentication, the situation of password-based encryption is more delicate: a per-session confidentiality guarantee only holds against attackers for which the distribution of password-guessing effort over the sessions is known in advance. In contrast, for more general attackers without such a restriction, a strong, composable notion of security cannot be achieved.' article_processing_charge: No article_type: original author: - first_name: Gregory full_name: Demay, Gregory last_name: Demay - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Ueli full_name: Maurer, Ueli last_name: Maurer - first_name: Bjorn full_name: Tackmann, Bjorn last_name: Tackmann citation: ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 2019;27(1):75-111. doi:10.3233/JCS-181131' apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2019). Per-session security: Password-based cryptography revisited. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-181131' chicago: 'Demay, Gregory, Peter Gazi, Ueli Maurer, and Bjorn Tackmann. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security. IOS Press, 2019. https://doi.org/10.3233/JCS-181131.' ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Per-session security: Password-based cryptography revisited,” Journal of Computer Security, vol. 27, no. 1. IOS Press, pp. 75–111, 2019.' ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2019. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 27(1), 75–111.' mla: 'Demay, Gregory, et al. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security, vol. 27, no. 1, IOS Press, 2019, pp. 75–111, doi:10.3233/JCS-181131.' short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, Journal of Computer Security 27 (2019) 75–111. date_created: 2019-01-27T22:59:10Z date_published: 2019-01-01T00:00:00Z date_updated: 2021-01-12T08:05:08Z day: '1' department: - _id: KrPi doi: 10.3233/JCS-181131 ec_funded: 1 intvolume: ' 27' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/166 month: '01' oa: 1 oa_version: Preprint page: 75-111 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Journal of Computer Security publication_identifier: issn: - 0926227X publication_status: published publisher: IOS Press quality_controlled: '1' scopus_import: '1' status: public title: 'Per-session security: Password-based cryptography revisited' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2019' ... --- _id: '6515' abstract: - lang: eng text: We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature. author: - first_name: Ramsay full_name: Dyer, Ramsay last_name: Dyer - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Dyer R, Vegter G, Wintraecken M. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 2019;10(1):223–256. doi:10.20382/jocg.v10i1a9 apa: Dyer, R., Vegter, G., & Wintraecken, M. (2019). Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . Carleton University. https://doi.org/10.20382/jocg.v10i1a9 chicago: Dyer, Ramsay, Gert Vegter, and Mathijs Wintraecken. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry . Carleton University, 2019. https://doi.org/10.20382/jocg.v10i1a9. ieee: R. Dyer, G. Vegter, and M. Wintraecken, “Simplices modelled on spaces of constant curvature,” Journal of Computational Geometry , vol. 10, no. 1. Carleton University, pp. 223–256, 2019. ista: Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 10(1), 223–256. mla: Dyer, Ramsay, et al. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry , vol. 10, no. 1, Carleton University, 2019, pp. 223–256, doi:10.20382/jocg.v10i1a9. short: R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry 10 (2019) 223–256. date_created: 2019-06-03T09:35:33Z date_published: 2019-07-01T00:00:00Z date_updated: 2021-01-12T08:07:50Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.20382/jocg.v10i1a9 ec_funded: 1 file: - access_level: open_access checksum: 57b4df2f16a74eb499734ec8ee240178 content_type: application/pdf creator: mwintrae date_created: 2019-06-03T09:30:01Z date_updated: 2020-07-14T12:47:32Z file_id: '6516' file_name: mainJournalFinal.pdf file_size: 2170882 relation: main_file file_date_updated: 2020-07-14T12:47:32Z has_accepted_license: '1' intvolume: ' 10' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 223–256 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 'Journal of Computational Geometry ' publication_identifier: issn: - 1920-180X publication_status: published publisher: Carleton University quality_controlled: '1' scopus_import: 1 status: public title: Simplices modelled on spaces of constant curvature tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _id: '6528' abstract: - lang: eng text: We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism. alternative_title: - LIPIcs article_number: '60' article_processing_charge: No author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Simple verifiable delay functions. In: 10th Innovations in Theoretical Computer Science Conference. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.ITCS.2019.60' apa: 'Pietrzak, K. Z. (2019). Simple verifiable delay functions. In 10th Innovations in Theoretical Computer Science Conference (Vol. 124). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.60' chicago: Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” In 10th Innovations in Theoretical Computer Science Conference, Vol. 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ITCS.2019.60. ieee: K. Z. Pietrzak, “Simple verifiable delay functions,” in 10th Innovations in Theoretical Computer Science Conference, San Diego, CA, United States, 2019, vol. 124. ista: 'Pietrzak KZ. 2019. Simple verifiable delay functions. 10th Innovations in Theoretical Computer Science Conference. ITCS 2019: Innovations in Theoretical Computer Science, LIPIcs, vol. 124, 60.' mla: Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” 10th Innovations in Theoretical Computer Science Conference, vol. 124, 60, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.ITCS.2019.60. short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-01-12 location: San Diego, CA, United States name: 'ITCS 2019: Innovations in Theoretical Computer Science' start_date: 2019-01-10 date_created: 2019-06-06T14:12:36Z date_published: 2019-01-10T00:00:00Z date_updated: 2021-01-12T08:07:53Z day: '10' ddc: - '000' department: - _id: KrPi doi: 10.4230/LIPICS.ITCS.2019.60 ec_funded: 1 file: - access_level: open_access checksum: f0ae1bb161431d9db3dea5ace082bfb5 content_type: application/pdf creator: dernst date_created: 2019-06-06T14:22:04Z date_updated: 2020-07-14T12:47:33Z file_id: '6529' file_name: 2019_LIPIcs_Pietrzak.pdf file_size: 558770 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 124' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/627 month: '01' oa: 1 oa_version: Published Version project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 10th Innovations in Theoretical Computer Science Conference publication_identifier: isbn: - 978-3-95977-095-8 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Simple verifiable delay functions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2019' ... --- _id: '6565' abstract: - lang: eng text: In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example. article_number: '8715598' article_processing_charge: No author: - first_name: Atreyee full_name: Kundu, Atreyee last_name: Kundu - 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: Pavithra full_name: Prabhakar, Pavithra last_name: Prabhakar citation: ama: 'Kundu A, Garcia Soto M, Prabhakar P. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In: 5th Indian Control Conference Proceedings. IEEE; 2019. doi:10.1109/INDIANCC.2019.8715598' apa: 'Kundu, A., Garcia Soto, M., & Prabhakar, P. (2019). Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In 5th Indian Control Conference Proceedings. Delhi, India: IEEE. https://doi.org/10.1109/INDIANCC.2019.8715598' chicago: Kundu, Atreyee, Miriam Garcia Soto, and Pavithra Prabhakar. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” In 5th Indian Control Conference Proceedings. IEEE, 2019. https://doi.org/10.1109/INDIANCC.2019.8715598. ieee: A. Kundu, M. Garcia Soto, and P. Prabhakar, “Formal synthesis of stabilizing controllers for periodically controlled linear switched systems,” in 5th Indian Control Conference Proceedings, Delhi, India, 2019. ista: Kundu A, Garcia Soto M, Prabhakar P. 2019. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. 5th Indian Control Conference Proceedings. ICC 2019 - Indian Control Conference, 8715598. mla: Kundu, Atreyee, et al. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” 5th Indian Control Conference Proceedings, 8715598, IEEE, 2019, doi:10.1109/INDIANCC.2019.8715598. short: A. Kundu, M. Garcia Soto, P. Prabhakar, in:, 5th Indian Control Conference Proceedings, IEEE, 2019. conference: end_date: 2019-01-11 location: Delhi, India name: ICC 2019 - Indian Control Conference start_date: 2019-01-09 date_created: 2019-06-17T06:57:33Z date_published: 2019-05-16T00:00:00Z date_updated: 2021-01-12T08:08:01Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1109/INDIANCC.2019.8715598 file: - access_level: open_access checksum: d622a91af1e427f6b1e0ba8e18a2b767 content_type: application/pdf creator: dernst date_created: 2020-10-21T13:13:49Z date_updated: 2020-10-21T13:13:49Z file_id: '8687' file_name: 2019_ICC_Kundu.pdf file_size: 396031 relation: main_file success: 1 file_date_updated: 2020-10-21T13:13:49Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version 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: 5th Indian Control Conference Proceedings publication_identifier: isbn: - 978-153866246-5 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Formal synthesis of stabilizing controllers for periodically controlled linear switched systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6628' abstract: - lang: eng text: Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space. author: - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: 'Vegter G, Wintraecken M. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In: The 31st Canadian Conference in Computational Geometry. ; 2019:275-279.' apa: Vegter, G., & Wintraecken, M. (2019). The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In The 31st Canadian Conference in Computational Geometry (pp. 275–279). Edmonton, Canada. chicago: Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” In The 31st Canadian Conference in Computational Geometry, 275–79, 2019. ieee: G. Vegter and M. Wintraecken, “The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds,” in The 31st Canadian Conference in Computational Geometry, Edmonton, Canada, 2019, pp. 275–279. ista: 'Vegter G, Wintraecken M. 2019. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. The 31st Canadian Conference in Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 275–279.' mla: Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–79. short: G. Vegter, M. Wintraecken, in:, The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–279. conference: end_date: 2019-08-10 location: Edmonton, Canada name: 'CCCG: Canadian Conference in Computational Geometry' start_date: 2019-08-08 date_created: 2019-07-12T08:34:57Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:08:16Z day: '01' ddc: - '004' department: - _id: HeEd ec_funded: 1 file: - access_level: open_access checksum: ceabd152cfa55170d57763f9c6c60a53 content_type: application/pdf creator: mwintrae date_created: 2019-07-12T08:32:46Z date_updated: 2020-07-14T12:47:34Z file_id: '6629' file_name: IntrinsicExtrinsicCCCG2019.pdf file_size: 321176 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 275-279 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: The 31st Canadian Conference in Computational Geometry publication_status: published quality_controlled: '1' scopus_import: 1 status: public title: The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6648' abstract: - lang: eng text: "Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory\r\nneeded for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context." alternative_title: - LIPIcs author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ziga full_name: Virk, Ziga last_name: Virk - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: 'Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information space. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:31:1-31:14. doi:10.4230/LIPICS.SOCG.2019.31' apa: 'Edelsbrunner, H., Virk, Z., & Wagner, H. (2019). Topological data analysis in information space. In 35th International Symposium on Computational Geometry (Vol. 129, p. 31:1-31:14). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.31' chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data Analysis in Information Space.” In 35th International Symposium on Computational Geometry, 129:31:1-31:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.31. ieee: H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information space,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 31:1-31:14. ista: 'Edelsbrunner H, Virk Z, Wagner H. 2019. Topological data analysis in information space. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 31:1-31:14.' mla: Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14, doi:10.4230/LIPICS.SOCG.2019.31. short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14. conference: end_date: 2019-06-21 location: Portland, OR, United States name: 'SoCG 2019: Symposium on Computational Geometry' start_date: 2019-06-18 date_created: 2019-07-17T10:36:09Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:08:23Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.4230/LIPICS.SOCG.2019.31 external_id: arxiv: - '1903.08510' file: - access_level: open_access checksum: 8ec8720730d4c789bf7b06540f1c29f4 content_type: application/pdf creator: dernst date_created: 2019-07-24T06:40:01Z date_updated: 2020-07-14T12:47:35Z file_id: '6666' file_name: 2019_LIPICS_Edelsbrunner.pdf file_size: 1355179 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 129' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 31:1-31:14 project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: 35th International Symposium on Computational Geometry publication_identifier: isbn: - '9783959771047' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Topological data analysis in information space tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2019' ... --- _id: '6659' abstract: - lang: eng text: Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research. acknowledgement: his work was supported by the Grant-in-Aid for Scientific Research B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no. JP17H06349 to A. O.); and the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges the financial support of the Takeda Science Foundation. article_processing_charge: No article_type: original author: - first_name: Naoki full_name: Zenmyo, Naoki last_name: Zenmyo - first_name: Hiroki full_name: Tokumaru, Hiroki last_name: Tokumaru - first_name: Shohei full_name: Uchinomiya, Shohei last_name: Uchinomiya - first_name: Hirokazu full_name: Fuchida, Hirokazu last_name: Fuchida - first_name: Shigekazu full_name: Tabata, Shigekazu id: 4427179E-F248-11E8-B48F-1D18A9856A87 last_name: Tabata - first_name: Itaru full_name: Hamachi, Itaru last_name: Hamachi - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Akio full_name: Ojida, Akio last_name: Ojida citation: ama: Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 2019;92(5):995-1000. doi:10.1246/bcsj.20190034 apa: Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi, I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan. https://doi.org/10.1246/bcsj.20190034 chicago: Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan, 2019. https://doi.org/10.1246/bcsj.20190034. ieee: N. Zenmyo et al., “Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins,” Bulletin of the Chemical Society of Japan, vol. 92, no. 5. Bulletin of the Chemical Society of Japan, pp. 995–1000, 2019. ista: Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 92(5), 995–1000. mla: Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan, vol. 92, no. 5, Bulletin of the Chemical Society of Japan, 2019, pp. 995–1000, doi:10.1246/bcsj.20190034. short: N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi, R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000. date_created: 2019-07-21T21:59:16Z date_published: 2019-05-15T00:00:00Z date_updated: 2021-01-12T08:08:26Z day: '15' ddc: - '570' department: - _id: RySh doi: 10.1246/bcsj.20190034 ec_funded: 1 file: - access_level: open_access checksum: 186de511d6e0ca93f5d981e2443eb8cd content_type: application/pdf creator: dernst date_created: 2020-10-02T08:49:58Z date_updated: 2020-10-02T08:49:58Z file_id: '8594' file_name: 2019_BCSJ_Zenmyo.pdf file_size: 2464903 relation: main_file success: 1 file_date_updated: 2020-10-02T08:49:58Z has_accepted_license: '1' intvolume: ' 92' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 995-1000 project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' publication: Bulletin of the Chemical Society of Japan publication_identifier: issn: - '00092673' publication_status: published publisher: Bulletin of the Chemical Society of Japan quality_controlled: '1' scopus_import: '1' status: public title: Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2019' ... --- _id: '6725' abstract: - lang: eng text: "A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds." alternative_title: - LIPIcs author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th International Colloquium on Automata, Languages and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77' apa: 'Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In 46th International Colloquium on Automata, Languages and Programming (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.77' chicago: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In 46th International Colloquium on Automata, Languages and Programming, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77. ieee: V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, 2019, vol. 132, p. 77:1-77:12. ista: 'Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP 2019: International Colloquim on Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.' mla: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th International Colloquium on Automata, Languages and Programming, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77. short: V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12. conference: end_date: 2019-07-12 location: Patras, Greece name: 'ICALP 2019: International Colloquim on Automata, Languages and Programming' start_date: 2019-07-08 date_created: 2019-07-29T12:23:29Z date_published: 2019-07-01T00:00:00Z date_updated: 2021-01-12T08:08:40Z day: '01' ddc: - '000' department: - _id: VlKo doi: 10.4230/LIPICS.ICALP.2019.77 ec_funded: 1 external_id: arxiv: - '1803.02289' file: - access_level: open_access checksum: f5ebee8eec6ae09e30365578ee63a492 content_type: application/pdf creator: dernst date_created: 2019-07-31T07:01:45Z date_updated: 2020-07-14T12:47:38Z file_id: '6738' file_name: 2019_LIPICS_Kolmogorov.pdf file_size: 575475 relation: main_file file_date_updated: 2020-07-14T12:47:38Z has_accepted_license: '1' intvolume: ' 132' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 77:1-77:12 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: 46th International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - 978-3-95977-109-2 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Testing the complexity of a valued CSP language tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 132 year: '2019' ... --- _id: '6726' abstract: - lang: eng text: Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so. article_processing_charge: No author: - first_name: Michael full_name: Walter, Michael id: 488F98B0-F248-11E8-B48F-1D18A9856A87 last_name: Walter orcid: 0000-0003-3186-2482 citation: ama: 'Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj A, Rachidi T, eds. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627. LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9' apa: 'Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann, A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019 (Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9' chicago: 'Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi, 11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.' ieee: 'M. Walter, “Sampling the integers with low relative error,” in Progress in Cryptology – AFRICACRYPT 2019, vol. 11627, J. Buchmann, A. Nitaj, and T. Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.' ista: 'Walter M. 2019.Sampling the integers with low relative error. In: Progress in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.' mla: Walter, Michael. “Sampling the Integers with Low Relative Error.” Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627, Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9. short: M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180. conference: end_date: 2019-07-11 location: Rabat, Morocco name: 'AFRICACRYPT: International Conference on Cryptology in Africa' start_date: 2019-07-09 date_created: 2019-07-29T12:25:31Z date_published: 2019-06-29T00:00:00Z date_updated: 2023-02-23T12:50:15Z day: '29' department: - _id: KrPi doi: 10.1007/978-3-030-23696-0_9 ec_funded: 1 editor: - first_name: J full_name: Buchmann, J last_name: Buchmann - first_name: A full_name: Nitaj, A last_name: Nitaj - first_name: T full_name: Rachidi, T last_name: Rachidi intvolume: ' 11627' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/068 month: '06' oa: 1 oa_version: Preprint page: 157-180 place: Cham project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Progress in Cryptology – AFRICACRYPT 2019 publication_identifier: eisbn: - 978-3-0302-3696-0 isbn: - 978-3-0302-3695-3 issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Sampling the integers with low relative error type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11627 year: '2019' ... --- _id: '6750' abstract: - lang: eng text: 'Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. ' article_number: '8854897' article_processing_charge: No article_type: original author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Carlo full_name: Condo, Carlo last_name: Condo - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Warren J full_name: Gross, Warren J last_name: Gross citation: ama: Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738 apa: Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738 chicago: Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019. https://doi.org/10.1109/TSP.2019.2944738. ieee: S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast polar decoders,” IEEE Transactions on Signal Processing, vol. 67, no. 22. IEEE, 2019. ista: Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 67(22), 8854897. mla: Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738. short: S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal Processing 67 (2019). date_created: 2019-07-31T09:51:14Z date_published: 2019-11-15T00:00:00Z date_updated: 2021-01-12T08:08:51Z day: '15' department: - _id: MaMo doi: 10.1109/TSP.2019.2944738 external_id: arxiv: - '1903.09203' intvolume: ' 67' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.09203 month: '11' oa: 1 oa_version: Preprint publication: IEEE Transactions on Signal Processing publication_identifier: issn: - 1053587X publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: 1 status: public title: Rate-flexible fast polar decoders type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 67 year: '2019' ... --- _id: '6759' abstract: - lang: eng text: "We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions." article_number: P3.17 article_processing_charge: No article_type: original author: - first_name: Vít full_name: Jelínek, Vít last_name: Jelínek - first_name: Martin full_name: Töpfer, Martin id: 4B865388-F248-11E8-B48F-1D18A9856A87 last_name: Töpfer citation: ama: Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 2019;26(3). doi:10.37236/8096 apa: Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/8096 chicago: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2019. https://doi.org/10.37236/8096. ieee: V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019. ista: Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17. mla: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:10.37236/8096. short: V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019). date_created: 2019-08-04T21:59:20Z date_published: 2019-07-19T00:00:00Z date_updated: 2022-03-18T12:32:02Z day: '19' ddc: - '510' department: - _id: DaAl doi: 10.37236/8096 ec_funded: 1 external_id: arxiv: - '1808.04148' file: - access_level: open_access checksum: 20fc366fc6683ef0b074a019b73a663a content_type: application/pdf creator: dernst date_created: 2019-08-05T06:46:55Z date_updated: 2020-07-14T12:47:39Z file_id: '6764' file_name: 2019_eJourCombinatorics_Jelinek.pdf file_size: 533697 relation: main_file file_date_updated: 2020-07-14T12:47:39Z has_accepted_license: '1' intvolume: ' 26' issue: '3' language: - iso: eng month: '07' 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: Electronic Journal of Combinatorics publication_identifier: eissn: - '10778926' publication_status: published publisher: Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: On grounded L-graphs and their relatives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2019' ... --- _id: '6822' abstract: - lang: eng text: "In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher\r\nbidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called \r\n randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one." alternative_title: - LNCS author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Petr full_name: Novotny, Petr last_name: Novotny citation: ama: 'Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. Bidding games on Markov decision processes. In: Proceedings of the 13th International Conference of Reachability Problems. Vol 11674. Springer; 2019:1-12. doi:10.1007/978-3-030-30806-3_1' apa: 'Avni, G., Henzinger, T. A., Ibsen-Jensen, R., & Novotny, P. (2019). Bidding games on Markov decision processes. In Proceedings of the 13th International Conference of Reachability Problems (Vol. 11674, pp. 1–12). Brussels, Belgium: Springer. https://doi.org/10.1007/978-3-030-30806-3_1' chicago: Avni, Guy, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Petr Novotny. “Bidding Games on Markov Decision Processes.” In Proceedings of the 13th International Conference of Reachability Problems, 11674:1–12. Springer, 2019. https://doi.org/10.1007/978-3-030-30806-3_1. ieee: G. Avni, T. A. Henzinger, R. Ibsen-Jensen, and P. Novotny, “Bidding games on Markov decision processes,” in Proceedings of the 13th International Conference of Reachability Problems, Brussels, Belgium, 2019, vol. 11674, pp. 1–12. ista: 'Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. 2019. Bidding games on Markov decision processes. Proceedings of the 13th International Conference of Reachability Problems. RP: Reachability Problems, LNCS, vol. 11674, 1–12.' mla: Avni, Guy, et al. “Bidding Games on Markov Decision Processes.” Proceedings of the 13th International Conference of Reachability Problems, vol. 11674, Springer, 2019, pp. 1–12, doi:10.1007/978-3-030-30806-3_1. short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, P. Novotny, in:, Proceedings of the 13th International Conference of Reachability Problems, Springer, 2019, pp. 1–12. conference: end_date: 2019-09-13 location: Brussels, Belgium name: 'RP: Reachability Problems' start_date: 2019-09-11 date_created: 2019-08-19T07:58:10Z date_published: 2019-09-06T00:00:00Z date_updated: 2021-01-12T08:09:12Z day: '06' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-30806-3_1 file: - access_level: open_access checksum: 45ebbc709af2b247d28c7c293c01504b content_type: application/pdf creator: gavni date_created: 2019-08-19T07:56:40Z date_updated: 2020-07-14T12:47:41Z file_id: '6823' file_name: prob.pdf file_size: 436635 relation: main_file file_date_updated: 2020-07-14T12:47:41Z has_accepted_license: '1' intvolume: ' 11674' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1-12 project: - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-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 13th International Conference of Reachability Problems' publication_identifier: isbn: - 978-303030805-6 issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: 1 status: public title: Bidding games on Markov decision processes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11674 year: '2019' ... --- _id: '6887' abstract: - lang: eng text: 'The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors. ' alternative_title: - LIPIcs article_number: '7' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvorák, Wolfgang last_name: Dvorák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Svozil, Alexander last_name: Svozil citation: ama: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Near-linear time algorithms for Streett objectives in graphs and MDPs. In: Leibniz International Proceedings in Informatics. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.7' apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2019). Near-linear time algorithms for Streett objectives in graphs and MDPs. In Leibniz International Proceedings in Informatics (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.7' chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” In Leibniz International Proceedings in Informatics, Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.7. ieee: K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Near-linear time algorithms for Streett objectives in graphs and MDPs,” in Leibniz International Proceedings in Informatics, Amsterdam, Netherlands, 2019, vol. 140. ista: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2019. Near-linear time algorithms for Streett objectives in graphs and MDPs. Leibniz International Proceedings in Informatics. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 7.' mla: Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” Leibniz International Proceedings in Informatics, vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.7. short: K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:07:58Z date_published: 2019-08-01T00:00:00Z date_updated: 2022-08-12T10:54:34Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPICS.CONCUR.2019.7 ec_funded: 1 file: - access_level: open_access checksum: e1f0e4061212454574f34a1368d018ec content_type: application/pdf creator: kschuh date_created: 2019-10-01T08:20:30Z date_updated: 2020-07-14T12:47:43Z file_id: '6922' file_name: 2019_LIPIcs_Chatterjee.pdf file_size: 730112 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Leibniz International Proceedings in Informatics publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Near-linear time algorithms for Streett objectives in graphs and MDPs 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: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 140 year: '2019' ... --- _id: '6888' abstract: - lang: eng text: In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods. alternative_title: - ICRA article_number: '8793840' article_processing_charge: No author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Manuel full_name: Zimmer, Manuel last_name: Zimmer - 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: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired neural networks for interpretable robotic control. In: Proceedings - IEEE International Conference on Robotics and Automation. Vol 2019-May. IEEE; 2019. doi:10.1109/icra.2019.8793840' apa: 'Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., & Grosu, R. (2019). Designing worm-inspired neural networks for interpretable robotic control. In Proceedings - IEEE International Conference on Robotics and Automation (Vol. 2019–May). Montreal, QC, Canada: IEEE. https://doi.org/10.1109/icra.2019.8793840' chicago: Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” In Proceedings - IEEE International Conference on Robotics and Automation, Vol. 2019–May. IEEE, 2019. https://doi.org/10.1109/icra.2019.8793840. ieee: M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing worm-inspired neural networks for interpretable robotic control,” in Proceedings - IEEE International Conference on Robotics and Automation, Montreal, QC, Canada, 2019, vol. 2019–May. ista: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired neural networks for interpretable robotic control. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, vol. 2019–May, 8793840.' mla: Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” Proceedings - IEEE International Conference on Robotics and Automation, vol. 2019–May, 8793840, IEEE, 2019, doi:10.1109/icra.2019.8793840. short: M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2019. conference: end_date: 2019-05-24 location: Montreal, QC, Canada name: 'ICRA: International Conference on Robotics and Automation' start_date: 2019-05-20 date_created: 2019-09-18T08:09:51Z date_published: 2019-05-01T00:00:00Z date_updated: 2021-01-12T08:09:28Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/icra.2019.8793840 file: - access_level: open_access checksum: f5545a6b60c3ffd01feb3613f81d03b6 content_type: application/pdf creator: dernst date_created: 2020-10-08T17:30:38Z date_updated: 2020-10-08T17:30:38Z file_id: '8636' file_name: 2019_ICRA_Lechner.pdf file_size: 3265107 relation: main_file success: 1 file_date_updated: 2020-10-08T17:30:38Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings - IEEE International Conference on Robotics and Automation publication_identifier: isbn: - '9781538660270' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Designing worm-inspired neural networks for interpretable robotic control type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 2019-May year: '2019' ... --- _id: '6886' abstract: - lang: eng text: 'In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets. ' alternative_title: - LIPIcs article_number: '20' article_processing_charge: No author: - first_name: Milad full_name: Aghajohari, Milad last_name: Aghajohari - 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 citation: ama: 'Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.20' apa: 'Aghajohari, M., Avni, G., & Henzinger, T. A. (2019). Determinacy in discrete-bidding infinite-duration games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.20' chicago: Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.20. ieee: 'M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.' ista: 'Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding infinite-duration games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 20.' mla: Aghajohari, Milad, et al. Determinacy in Discrete-Bidding Infinite-Duration Games. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.20. short: M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:06:58Z date_published: 2019-08-01T00:00:00Z date_updated: 2022-01-26T08:27:10Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.4230/LIPICS.CONCUR.2019.20 external_id: arxiv: - '1905.03588' file: - access_level: open_access checksum: 4df6d3575c506edb17215adada03cc8e content_type: application/pdf creator: kschuh date_created: 2019-09-27T12:21:38Z date_updated: 2020-07-14T12:47:43Z file_id: '6915' file_name: 2019_LIPIcs_Aghajohari.pdf file_size: 741425 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '08' oa: 1 oa_version: Published Version project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Determinacy in discrete-bidding infinite-duration games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 140 year: '2019' ... --- _id: '6885' abstract: - lang: eng text: 'A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. ' alternative_title: - LIPIcs article_number: '27' author: - 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: Jan full_name: Otop, Jan last_name: Otop citation: ama: 'Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.27' apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2019). Long-run average behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.27' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.27. ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of vector addition systems with states,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.' ista: 'Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector addition systems with states. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 27.' mla: Chatterjee, Krishnendu, et al. Long-Run Average Behavior of Vector Addition Systems with States. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.27. short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:06:14Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:09:27Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPICS.CONCUR.2019.27 file: - access_level: open_access checksum: 4985e26e1572d1575d64d38acabd71d6 content_type: application/pdf creator: kschuh date_created: 2019-09-27T12:09:35Z date_updated: 2020-07-14T12:47:43Z file_id: '6914' file_name: 2019_LIPIcs_Chatterjee.pdf file_size: 538120 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Long-run average behavior of vector addition systems with states 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 140 year: '2019' ... --- _id: '6889' abstract: - lang: eng text: 'We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. ' alternative_title: - LIPIcs article_number: '6' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.6' apa: 'Chatterjee, K., & Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.6' chicago: Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.6. ieee: 'K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.' ista: 'Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 6.' mla: Chatterjee, Krishnendu, and Nir Piterman. Combinations of Qualitative Winning for Stochastic Parity Games. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.6. short: K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:11:43Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:09:28Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPICS.CONCUR.2019.6 file: - access_level: open_access checksum: 7b2ecfd4d9d02360308c0ca986fc10a7 content_type: application/pdf creator: kschuh date_created: 2019-10-01T08:49:45Z date_updated: 2020-07-14T12:47:43Z file_id: '6923' file_name: 2019_LIPIcs_Chatterjee.pdf file_size: 509163 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Combinations of Qualitative Winning for Stochastic Parity 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 140 year: '2019' ... --- _id: '6931' abstract: - lang: eng text: "Consider a distributed system with n processors out of which f can be Byzantine faulty. In the\r\napproximate agreement task, each processor i receives an input value xi and has to decide on an\r\noutput value yi such that\r\n1. the output values are in the convex hull of the non-faulty processors’ input values,\r\n2. the output values are within distance d of each other.\r\n\r\n\r\nClassically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.\r\nIn this work, we study the task in a discrete setting, where input values with some structure\r\nexpressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to\r\noutput vertices that are within distance d of each other in G, but still remain in the graph-induced\r\nconvex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with\r\na deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact\r\nvariants of these and related tasks over a large class of combinatorial structures." alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Thomas full_name: Nowak, Thomas last_name: Nowak - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 citation: ama: 'Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: 33rd International Symposium on Distributed Computing. Vol 146. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:10.4230/LIPICS.DISC.2019.29' apa: 'Nowak, T., & Rybicki, J. (2019). Byzantine approximate agreement on graphs. In 33rd International Symposium on Distributed Computing (Vol. 146, p. 29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.DISC.2019.29' chicago: Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” In 33rd International Symposium on Distributed Computing, 146:29:1--29:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.DISC.2019.29. ieee: T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in 33rd International Symposium on Distributed Computing, Budapest, Hungary, 2019, vol. 146, p. 29:1--29:17. ista: 'Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd International Symposium on Distributed Computing. DISC: International Symposium on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.' mla: Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” 33rd International Symposium on Distributed Computing, vol. 146, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:10.4230/LIPICS.DISC.2019.29. short: T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17. conference: end_date: 2019-10-18 location: Budapest, Hungary name: 'DISC: International Symposium on Distributed Computing' start_date: 2019-10-14 date_created: 2019-10-08T12:41:38Z date_published: 2019-01-01T00:00:00Z date_updated: 2021-01-12T08:09:38Z ddc: - '004' department: - _id: DaAl doi: 10.4230/LIPICS.DISC.2019.29 ec_funded: 1 external_id: arxiv: - '1908.02743' file: - access_level: open_access checksum: 2d2202f90c6ac991e50876451627c4b5 content_type: application/pdf creator: jrybicki date_created: 2019-10-08T12:47:19Z date_updated: 2020-07-14T12:47:44Z file_id: '6934' file_name: LIPIcs-DISC-2019-29.pdf file_size: 639378 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 146' keyword: - consensus - approximate agreement - Byzantine faults - chordal graphs - lattice agreement language: - iso: eng oa: 1 oa_version: Published Version page: 29:1--29:17 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 33rd International Symposium on Distributed Computing publication_identifier: eisbn: - 978-3-95977-126-9 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Byzantine approximate agreement on graphs 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2019' ... --- _id: '6985' abstract: - lang: eng text: In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets. article_number: '8851954' author: - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Felix full_name: Naser, Felix last_name: Naser - first_name: Radu full_name: Grosu, Radu last_name: Grosu - first_name: Daniela full_name: Rus, Daniela last_name: Rus citation: ama: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization for auditing cell dynamics in long short-term memory networks. In: Proceedings of the International Joint Conference on Neural Networks. IEEE; 2019. doi:10.1109/ijcnn.2019.8851954' apa: 'Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., & Rus, D. (2019). Response characterization for auditing cell dynamics in long short-term memory networks. In Proceedings of the International Joint Conference on Neural Networks. Budapest, Hungary: IEEE. https://doi.org/10.1109/ijcnn.2019.8851954' chicago: Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu, and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” In Proceedings of the International Joint Conference on Neural Networks. IEEE, 2019. https://doi.org/10.1109/ijcnn.2019.8851954. ieee: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response characterization for auditing cell dynamics in long short-term memory networks,” in Proceedings of the International Joint Conference on Neural Networks, Budapest, Hungary, 2019. ista: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization for auditing cell dynamics in long short-term memory networks. Proceedings of the International Joint Conference on Neural Networks. IJCNN: International Joint Conference on Neural Networks, 8851954.' mla: Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” Proceedings of the International Joint Conference on Neural Networks, 8851954, IEEE, 2019, doi:10.1109/ijcnn.2019.8851954. short: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings of the International Joint Conference on Neural Networks, IEEE, 2019. conference: end_date: 2019-07-19 location: Budapest, Hungary name: 'IJCNN: International Joint Conference on Neural Networks' start_date: 2019-07-14 date_created: 2019-11-04T15:59:58Z date_published: 2019-09-30T00:00:00Z date_updated: 2021-01-12T08:11:19Z day: '30' department: - _id: ToHe doi: 10.1109/ijcnn.2019.8851954 external_id: arxiv: - '1809.03864' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.03864 month: '09' oa: 1 oa_version: Preprint publication: Proceedings of the International Joint Conference on Neural Networks publication_identifier: isbn: - '9781728119854' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: 1 status: public title: Response characterization for auditing cell dynamics in long short-term memory networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7007' abstract: - lang: eng text: 'We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds.' article_number: '218' article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: S. Hamed full_name: Hassani, S. Hamed last_name: Hassani - first_name: Rüdiger full_name: Urbanke, Rüdiger last_name: Urbanke citation: ama: Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218 apa: Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218 chicago: Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218. ieee: M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019. ista: Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218. mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218. short: M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019). date_created: 2019-11-12T14:46:19Z date_published: 2019-10-18T00:00:00Z date_updated: 2023-02-23T12:49:28Z day: '18' ddc: - '510' department: - _id: MaMo doi: 10.3390/a12100218 external_id: arxiv: - '1801.03153' file: - access_level: open_access checksum: 267756d8f9db572f496cd1663c89d59a content_type: application/pdf creator: dernst date_created: 2019-11-12T14:48:45Z date_updated: 2020-07-14T12:47:47Z file_id: '7008' file_name: 2019_Algorithms_Mondelli.pdf file_size: 696791 relation: main_file file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' intvolume: ' 12' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Algorithms publication_identifier: issn: - 1999-4893 publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '6675' relation: earlier_version status: public scopus_import: 1 status: public title: A new coding paradigm for the primitive relay channel tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '7035' abstract: - lang: eng text: 'The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.' article_processing_charge: No author: - first_name: Gyorgy Pal full_name: Geher, Gyorgy Pal last_name: Geher - first_name: Tamas full_name: Titkos, Tamas last_name: Titkos - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 citation: ama: 'Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41.' apa: 'Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.' chicago: Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019. ieee: G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41. ista: Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity. Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related topics vol. 2125, 34–41. mla: Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41. short: G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41. conference: end_date: 2019-01-30 location: Kyoto, Japan name: Research on isometries as preserver problems and related topics start_date: 2019-01-28 date_created: 2019-11-18T15:39:53Z date_published: 2019-01-30T00:00:00Z date_updated: 2021-01-12T08:11:33Z day: '30' department: - _id: LaEr intvolume: ' 2125' language: - iso: eng main_file_link: - open_access: '1' url: http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html month: '01' oa: 1 oa_version: Submitted Version page: 34-41 publication: Kyoto RIMS Kôkyûroku publication_status: published publisher: Research Institute for Mathematical Sciences, Kyoto University quality_controlled: '1' status: public title: Dirac masses and isometric rigidity type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2125 year: '2019' ... --- _id: '7171' abstract: - lang: ger text: "Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!" article_processing_charge: No citation: ama: 'Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019. doi:10.1007/978-3-658-26763-6' apa: 'Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden: Springer Nature. https://doi.org/10.1007/978-3-658-26763-6' chicago: 'Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.' ieee: 'K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature, 2019.' ista: 'Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.' mla: 'Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.' short: 'K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.' date_created: 2019-12-11T14:15:56Z date_published: 2019-10-30T00:00:00Z date_updated: 2021-12-22T14:40:58Z day: '30' department: - _id: ChLa doi: 10.1007/978-3-658-26763-6 edition: '1' editor: - first_name: Kristian full_name: Kersting, Kristian last_name: Kersting - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Constantin full_name: Rothkopf, Constantin last_name: Rothkopf language: - iso: ger month: '10' oa_version: None page: XIV, 245 place: Wiesbaden publication_identifier: eisbn: - 978-3-658-26763-6 isbn: - 978-3-658-26762-9 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/book-release-how-machines-learn/ status: public title: 'Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt' type: book_editor user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '7401' abstract: - lang: eng text: 'The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. ' alternative_title: - LIPIcs article_number: '39' article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kyncl, Jan last_name: Kyncl citation: ama: 'Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In: 35th International Symposium on Computational Geometry (SoCG 2019). Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.SOCG.2019.39' apa: 'Fulek, R., & Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In 35th International Symposium on Computational Geometry (SoCG 2019) (Vol. 129). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.39' chicago: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” In 35th International Symposium on Computational Geometry (SoCG 2019), Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.39. ieee: R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric matrices,” in 35th International Symposium on Computational Geometry (SoCG 2019), Portland, OR, United States, 2019, vol. 129. ista: 'Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. 35th International Symposium on Computational Geometry (SoCG 2019). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.' mla: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” 35th International Symposium on Computational Geometry (SoCG 2019), vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.SOCG.2019.39. short: R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry (SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-06-21 location: Portland, OR, United States name: 'SoCG: Symposium on Computational Geometry' start_date: 2019-06-18 date_created: 2020-01-29T16:17:05Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:13:24Z day: '01' ddc: - '000' department: - _id: UlWa doi: 10.4230/LIPICS.SOCG.2019.39 external_id: arxiv: - '1903.08637' file: - access_level: open_access checksum: aac37b09118cc0ab58cf77129e691f8c content_type: application/pdf creator: dernst date_created: 2020-02-04T09:14:31Z date_updated: 2020-07-14T12:47:57Z file_id: '7445' file_name: 2019_LIPIcs_Fulek.pdf file_size: 628347 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 129' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: 35th International Symposium on Computational Geometry (SoCG 2019) publication_identifier: isbn: - 978-3-95977-104-7 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Z_2-Genus of graphs and minimum rank of partial symmetric matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2019' ... --- _id: '7453' abstract: - lang: eng text: We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS, funded by the Danish National Research Foundation and the National Science Foundation, China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant LASSO. alternative_title: - Lecture Notes in Computer Science article_processing_charge: No author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - 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: Kim G. full_name: Larsen, Kim G. last_name: Larsen - first_name: Marius full_name: Mikučionis, Marius last_name: Mikučionis citation: ama: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22' apa: Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis, M. (2019). Continuous-time models for system design and analysis. In B. Steffen & G. Woeginger (Eds.), Computing and Software Science (Vol. 10000, pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22 chicago: Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77. LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22. ieee: R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time models for system design and analysis,” in Computing and Software Science, vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477. ista: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time models for system design and analysis. In: Computing and Software Science. Lecture Notes in Computer Science, vol. 10000, 452–477.' mla: Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.” Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22. short: R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B. Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature, 2019, pp. 452–477. date_created: 2020-02-05T10:51:44Z date_published: 2019-10-05T00:00:00Z date_updated: 2022-09-06T08:25:52Z day: '05' department: - _id: ToHe doi: 10.1007/978-3-319-91908-9_22 editor: - first_name: Bernhard full_name: Steffen, Bernhard last_name: Steffen - first_name: Gerhard full_name: Woeginger, Gerhard last_name: Woeginger intvolume: ' 10000' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-319-91908-9_22 month: '10' oa: 1 oa_version: Published Version page: 452-477 project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Computing and Software Science publication_identifier: eisbn: - '9783319919089' eissn: - 0302-9743 isbn: - '9783319919072' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Continuous-time models for system design and analysis type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10000 year: '2019' ... --- _id: '7550' abstract: - lang: eng text: 'We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. ' acknowledgement: This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375. article_processing_charge: No article_type: original author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale - first_name: Ulisse full_name: Stefanelli, Ulisse last_name: Stefanelli citation: ama: Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 2019;28(2):425-447. apa: Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. Gakko Tosho. chicago: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications. Gakko Tosho, 2019. ieee: L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” Advances in Mathematical Sciences and Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019. ista: Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447. mla: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47. short: L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447. date_created: 2020-02-28T10:54:41Z date_published: 2019-10-22T00:00:00Z date_updated: 2022-06-17T07:52:41Z day: '22' department: - _id: JaMa external_id: arxiv: - '1910.10050' intvolume: ' 28' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1910.10050' month: '10' oa: 1 oa_version: Preprint page: 425-447 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Advances in Mathematical Sciences and Applications publication_identifier: issn: - 1343-4373 publication_status: published publisher: Gakko Tosho quality_controlled: '1' status: public title: Penalization via global functionals of optimal-control problems for dissipative evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2019' ... --- _id: '7552' abstract: - lang: eng text: 'There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. ' article_processing_charge: No author: - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579. apa: Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. arXiv:1912.08579. ArXiv. chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d. ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv. ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, . mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv. short: W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.). date_created: 2020-02-28T10:57:08Z date_published: 2019-12-18T00:00:00Z date_updated: 2021-01-12T08:14:09Z day: '18' department: - _id: GaTk external_id: arxiv: - '1912.08579' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.08579 month: '12' oa: 1 oa_version: Preprint page: '5' project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: arXiv:1912.08579 publication_status: submitted publisher: ArXiv status: public title: Action at a distance in transcriptional regulation type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7576' abstract: - lang: eng text: We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools. article_processing_charge: No author: - first_name: Fabian full_name: Immler, Fabian last_name: Immler - first_name: Matthias full_name: Althoff, Matthias last_name: Althoff - first_name: Luis full_name: Benet, Luis last_name: Benet - first_name: Alexandre full_name: Chapoutot, Alexandre last_name: Chapoutot - first_name: Xin full_name: Chen, Xin last_name: Chen - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Luca full_name: Geretti, Luca last_name: Geretti - first_name: Niklas full_name: Kochdumper, Niklas last_name: Kochdumper - first_name: David P. full_name: Sanders, David P. last_name: Sanders - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing. Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b' apa: 'Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b' chicago: 'Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications, 2019. https://doi.org/10.29007/m75b.' ieee: 'F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 41–61.' ista: 'Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.' mla: 'Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:10.29007/m75b.' short: F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61. conference: end_date: 2019-04-15 location: Montreal, Canada name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems' start_date: 2019-04-15 date_created: 2020-03-08T23:00:49Z date_published: 2019-05-25T00:00:00Z date_updated: 2021-01-12T08:14:17Z day: '25' ddc: - '000' department: - _id: ToHe doi: 10.29007/m75b file: - access_level: open_access checksum: 9138977a06fcd6a95976eb4bca875f0c content_type: application/pdf creator: dernst date_created: 2020-03-24T07:36:36Z date_updated: 2020-07-14T12:48:00Z file_id: '7617' file_name: 2019_ARCH19_Immler.pdf file_size: 1934830 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 61' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 41-61 publication: EPiC Series in Computing publication_identifier: eissn: - '23987340' publication_status: published publisher: EasyChair Publications quality_controlled: '1' scopus_import: 1 status: public title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2019' ... --- _id: '8175' abstract: - lang: eng text: We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices. acknowledgement: "D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n" article_number: '34' article_processing_charge: No author: - first_name: Dan full_name: Betea, Dan last_name: Betea - first_name: Jérémie full_name: Bouttier, Jérémie last_name: Bouttier - first_name: Peter full_name: Nejjar, Peter id: 4BF426E2-F248-11E8-B48F-1D18A9856A87 last_name: Nejjar - first_name: Mirjana full_name: Vuletíc, Mirjana last_name: Vuletíc citation: ama: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.' apa: 'Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.' chicago: Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019. ieee: D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019. ista: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.' mla: Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019. short: D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019. conference: end_date: 2019-07-05 location: Ljubljana, Slovenia name: 'FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics' start_date: 2019-07-01 date_created: 2020-07-26T22:01:04Z date_published: 2019-07-01T00:00:00Z date_updated: 2021-01-12T08:17:18Z day: '01' department: - _id: LaEr ec_funded: 1 external_id: arxiv: - '1902.08750' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.08750 month: '07' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics publication_status: published publisher: Formal Power Series and Algebraic Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: New edge asymptotics of skew Young diagrams via free boundaries type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8570' abstract: - lang: eng text: 'This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.' article_processing_charge: No author: - first_name: Matthias full_name: Althoff, Matthias last_name: Althoff - first_name: Stanley full_name: Bak, Stanley last_name: Bak - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Niklas full_name: Kochdumper, Niklas last_name: Kochdumper - first_name: Rajarshi full_name: Ray, Rajarshi last_name: Ray - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Stefan full_name: Schupp, Stefan last_name: Schupp citation: ama: 'Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w' apa: 'Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w' chicago: 'Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.' ieee: 'M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.' ista: 'Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.' mla: 'Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.' short: M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40. conference: end_date: 2019-04-15 location: Montreal, Canada name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems' start_date: 2019-04-15 date_created: 2020-09-26T14:23:54Z date_published: 2019-05-25T00:00:00Z date_updated: 2021-01-12T08:20:05Z day: '25' department: - _id: ToHe doi: 10.29007/bj1w intvolume: ' 61' language: - iso: eng main_file_link: - open_access: '1' url: https://easychair.org/publications/open/1gbP month: '05' oa: 1 oa_version: Published Version page: 14-40 publication: EPiC Series in Computing publication_identifier: eissn: - '23987340' publication_status: published publisher: EasyChair quality_controlled: '1' status: public title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2019' ... --- _id: '9460' abstract: - lang: eng text: Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion. article_processing_charge: No article_type: original author: - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Akemi full_name: Ono, Akemi last_name: Ono - first_name: Stefan full_name: Scholten, Stefan last_name: Scholten - first_name: Tetsu full_name: Kinoshita, Tetsu last_name: Kinoshita - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Takashi full_name: Okamoto, Takashi last_name: Okamoto - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116 apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116 chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116. ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019. ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657. mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116. short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657. date_created: 2021-06-04T12:38:20Z date_published: 2019-05-07T00:00:00Z date_updated: 2021-12-14T07:52:30Z day: '07' ddc: - '580' department: - _id: DaZi doi: 10.1073/pnas.1821435116 extern: '1' external_id: pmid: - '31000601' file: - access_level: open_access checksum: 5b0ae3779b8b21b5223bd2d3cceede3a content_type: application/pdf creator: asandaue date_created: 2021-06-04T12:50:47Z date_updated: 2021-06-04T12:50:47Z file_id: '9461' file_name: 2019_PNAS_Kim.pdf file_size: 1142540 relation: main_file success: 1 file_date_updated: 2021-06-04T12:50:47Z has_accepted_license: '1' intvolume: ' 116' issue: '19' keyword: - Multidisciplinary language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 9652-9657 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 116 year: '2019' ... --- _id: '6819' abstract: - lang: eng text: Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome. article_number: '494' article_processing_charge: No author: - first_name: Michael N. full_name: Antoniou, Michael N. last_name: Antoniou - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - first_name: Robin full_name: Mesnage, Robin last_name: Mesnage - first_name: Martina full_name: Biserni, Martina last_name: Biserni - first_name: Francesco V. full_name: Rao, Francesco V. last_name: Rao - first_name: Cristina Vazquez full_name: Martin, Cristina Vazquez last_name: Martin citation: ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3 apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3 chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3. ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019. ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494. mla: Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3. short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019). date_created: 2019-08-18T22:00:39Z date_published: 2019-08-08T00:00:00Z date_updated: 2023-02-23T14:08:14Z day: '08' ddc: - '570' department: - _id: LifeSc doi: 10.1186/s13104-019-4534-3 external_id: pmid: - '31395095' file: - access_level: open_access checksum: 4a2bb7994b7f2c432bf44f5127ea3102 content_type: application/pdf creator: dernst date_created: 2019-08-23T11:10:35Z date_updated: 2020-07-14T12:47:40Z file_id: '6829' file_name: 2019_BMC_Antoniou.pdf file_size: 1177482 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Research Notes publication_identifier: eissn: - 1756-0500 publication_status: published publisher: BioMed Central quality_controlled: '1' related_material: record: - id: '9784' relation: research_data status: public scopus_import: 1 status: public title: Glyphosate does not substitute for glycine in proteins of actively dividing 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '9784' abstract: - lang: eng text: 'Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.' article_processing_charge: No author: - first_name: Michael N. full_name: Antoniou, Michael N. last_name: Antoniou - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - first_name: Robin full_name: Mesnage, Robin last_name: Mesnage - first_name: Martina full_name: Biserni, Martina last_name: Biserni - first_name: Francesco V. full_name: Rao, Francesco V. last_name: Rao - first_name: Cristina Vazquez full_name: Martin, Cristina Vazquez last_name: Martin citation: ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1 apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1 chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1. ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019. ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1. mla: Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1. short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019). date_created: 2021-08-06T08:14:05Z date_published: 2019-08-09T00:00:00Z date_updated: 2023-02-23T12:52:29Z day: '09' department: - _id: LifeSc doi: 10.6084/m9.figshare.9411761.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9411761.v1 month: '08' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6819' relation: used_in_publication status: public status: public title: MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9839' abstract: - lang: eng text: 'More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.' article_processing_charge: No author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: 'Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37' apa: 'Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37' chicago: 'Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.' ieee: 'J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.' ista: 'Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.' mla: 'Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.' short: J. Polechova, (2019). date_created: 2021-08-09T13:07:28Z date_published: 2019-06-22T00:00:00Z date_updated: 2023-02-23T11:14:30Z day: '22' department: - _id: NiBa doi: 10.5061/dryad.5vv37 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.5vv37 month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '315' relation: used_in_publication status: public status: public title: 'Data from: Is the sky the limit? On the expansion threshold of a species'' range' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9530' abstract: - lang: eng text: "Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems." article_number: '62' article_processing_charge: No article_type: original author: - first_name: Keith D. full_name: Harris, Keith D. last_name: Harris - first_name: James P. B. full_name: Lloyd, James P. B. last_name: Lloyd - first_name: Katherine full_name: Domb, Katherine last_name: Domb - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach citation: ama: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4 apa: Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4 chicago: Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4. ieee: K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019. ista: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62. mla: Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4. short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019). date_created: 2021-06-08T09:21:51Z date_published: 2019-10-10T00:00:00Z date_updated: 2021-12-14T07:53:00Z day: '10' ddc: - '570' department: - _id: DaZi doi: 10.1186/s13072-019-0307-4 extern: '1' external_id: pmid: - '31601251' file: - access_level: open_access checksum: 86ff50a7517891511af2733c76c81b67 content_type: application/pdf creator: asandaue date_created: 2021-06-08T09:29:19Z date_updated: 2021-06-08T09:29:19Z file_id: '9531' file_name: 2019_EpigeneticsAndChromatin_Harris.pdf file_size: 3221067 relation: main_file success: 1 file_date_updated: 2021-06-08T09:29:19Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Epigenetics and Chromatin publication_identifier: eissn: - 1756-8935 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 year: '2019' ... --- _id: '12192' abstract: - lang: eng text: Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation. acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF). article_number: '42530' article_processing_charge: No article_type: original author: - first_name: Shengbo full_name: He, Shengbo last_name: He - first_name: Martin full_name: Vickers, Martin last_name: Vickers - first_name: Jingyi full_name: Zhang, Jingyi last_name: Zhang - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530 apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530 chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530. ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019. ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530. mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530. short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019). date_created: 2023-01-16T09:17:21Z date_published: 2019-05-28T00:00:00Z date_updated: 2023-05-08T10:54:12Z day: '28' ddc: - '580' department: - _id: XiFe doi: 10.7554/elife.42530 extern: '1' external_id: unknown: - '31135340' file: - access_level: open_access checksum: ea6b89c20d59e5eb3646916fe5d568ad content_type: application/pdf creator: alisjak date_created: 2023-02-07T09:42:46Z date_updated: 2023-02-07T09:42:46Z file_id: '12525' file_name: 2019_elife_He.pdf file_size: 2493837 relation: main_file success: 1 file_date_updated: 2023-02-07T09:42:46Z has_accepted_license: '1' intvolume: ' 8' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/ month: '05' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications, Ltd quality_controlled: '1' scopus_import: '1' status: public title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2019' ... --- _id: '12190' abstract: - lang: eng text: Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor. acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)." article_processing_charge: No article_type: original author: - first_name: Emma J. full_name: Lawrence, Emma J. last_name: Lawrence - first_name: Hongbo full_name: Gao, Hongbo last_name: Gao - first_name: Andrew J. full_name: Tock, Andrew J. last_name: Tock - first_name: Christophe full_name: Lambing, Christophe last_name: Lambing - first_name: Alexander R. full_name: Blackwell, Alexander R. last_name: Blackwell - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Ian R. full_name: Henderson, Ian R. last_name: Henderson citation: ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084 apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084 chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084. ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019. ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3. mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084. short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3. date_created: 2023-01-16T09:16:33Z date_published: 2019-08-19T00:00:00Z date_updated: 2023-05-08T10:54:54Z day: '19' department: - _id: XiFe doi: 10.1016/j.cub.2019.06.084 extern: '1' external_id: pmid: - '31378616' intvolume: ' 29' issue: '16' keyword: - General Agricultural and Biological Sciences - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '08' oa_version: None page: 2676-2686.e3 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier BV quality_controlled: '1' scopus_import: '1' status: public title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2019' ... --- _id: '12901' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Janos full_name: Kiss, Janos id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87 last_name: Kiss - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante citation: ama: 'Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.' apa: 'Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.' chicago: Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019. ieee: A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25. ista: 'Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.' mla: Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25. short: A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25. conference: end_date: 2019-02-27 location: Grundlsee, Austria name: 'AHPC: Austrian HPC Meeting' start_date: 2019-02-25 date_created: 2023-05-05T12:48:48Z date_published: 2019-02-27T00:00:00Z date_updated: 2023-05-16T07:29:32Z day: '27' ddc: - '000' department: - _id: ScienComp file: - access_level: open_access checksum: acc8272027faaf30709c51ac5c58ffa4 content_type: application/pdf creator: dernst date_created: 2023-05-16T07:27:09Z date_updated: 2023-05-16T07:27:09Z file_id: '12970' file_name: 2019_AHPC_Schloegl.pdf file_size: 1097603 relation: main_file success: 1 file_date_updated: 2023-05-16T07:27:09Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf month: '02' oa: 1 oa_version: Published Version page: '25' publication: 'AHPC19 - Austrian HPC Meeting 2019 ' publication_status: published publisher: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz status: public title: Is Debian suitable for running an HPC Cluster? type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6989' abstract: - lang: eng text: 'When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. ' acknowledgement: This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere. article_processing_charge: No author: - first_name: Oswin full_name: Aichholzer, Oswin last_name: Aichholzer - first_name: Hugo A full_name: Akitaya, Hugo A last_name: Akitaya - first_name: Kenneth C full_name: Cheung, Kenneth C last_name: Cheung - first_name: Erik D full_name: Demaine, Erik D last_name: Demaine - first_name: Martin L full_name: Demaine, Martin L last_name: Demaine - first_name: Sandor P full_name: Fekete, Sandor P last_name: Fekete - first_name: Linda full_name: Kleist, Linda last_name: Kleist - first_name: Irina full_name: Kostitsyna, Irina last_name: Kostitsyna - first_name: Maarten full_name: Löffler, Maarten last_name: Löffler - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Klara full_name: Mundilova, Klara last_name: Mundilova - first_name: Christiane full_name: Schmidt, Christiane last_name: Schmidt citation: ama: 'Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.' apa: 'Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.' chicago: Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019. ieee: O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170. ista: 'Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170.' mla: Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70. short: O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170. conference: end_date: 2019-08-10 location: Edmonton, Canada name: 'CCCG: Canadian Conference in Computational Geometry' start_date: 2019-08-08 date_created: 2019-11-04T16:46:11Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-04T10:57:42Z day: '01' department: - _id: HeEd external_id: arxiv: - '1910.09917' language: - iso: eng main_file_link: - open_access: '1' url: https://cccg.ca/proceedings/2019/proceedings.pdf month: '08' oa: 1 oa_version: Published Version page: 164-170 publication: Proceedings of the 31st Canadian Conference on Computational Geometry publication_status: published publisher: Canadian Conference on Computational Geometry quality_controlled: '1' related_material: record: - id: '8317' relation: extended_version status: public scopus_import: '1' status: public title: Folding polyominoes with holes into a cube type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 year: '2019' ... --- _id: '6884' abstract: - lang: eng text: 'In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the "bank" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players'' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. ' alternative_title: - LIPIcs article_number: '11' 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: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic citation: ama: 'Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11' apa: 'Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11' chicago: Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.MFCS.2019.11. ieee: 'G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138.' ista: 'Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: nternational Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.' mla: Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11. short: G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Aachen, Germany name: 'MFCS: nternational Symposium on Mathematical Foundations of Computer Science' start_date: 2019-08-26 date_created: 2019-09-18T08:04:26Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-07T14:08:34Z day: '01' ddc: - '004' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPICS.MFCS.2019.11 ec_funded: 1 external_id: arxiv: - '1905.03835' file: - access_level: open_access checksum: 6346e116a4f4ed1414174d96d2c4fbd7 content_type: application/pdf creator: kschuh date_created: 2019-09-27T11:45:15Z date_updated: 2020-07-14T12:47:42Z file_id: '6913' file_name: 2019_LIPIcs_Avni.pdf file_size: 554457 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 138' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _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: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '9239' relation: later_version status: public scopus_import: 1 status: public title: Bidding mechanisms in graph 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 138 year: '2019' ... --- _id: '9726' abstract: - lang: eng text: A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF) article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Reinhard full_name: Lipowsky, Reinhard last_name: Lipowsky citation: ama: Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001 apa: Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001 chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001. ieee: M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019. ista: Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001. mla: Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001. short: M.C. Ucar, R. Lipowsky, (2019). date_created: 2021-07-27T09:51:46Z date_published: 2019-12-19T00:00:00Z date_updated: 2023-08-17T14:07:52Z day: '19' department: - _id: EdHa doi: 10.1021/acs.nanolett.9b04445.s001 month: '12' oa_version: Published Version publisher: 'American Chemical Society ' related_material: record: - id: '7166' relation: used_in_publication status: public status: public title: Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6671' abstract: - lang: eng text: 'In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jean-Daniel full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: André full_name: Lieutier, André last_name: Lieutier - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8 apa: Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8 chicago: Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8. ieee: J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019. ista: Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58. mla: Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8. short: J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58. date_created: 2019-07-24T08:37:29Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-22T12:37:47Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s41468-019-00029-8 ec_funded: 1 file: - access_level: open_access checksum: a5b244db9f751221409cf09c97ee0935 content_type: application/pdf creator: dernst date_created: 2019-07-31T08:09:56Z date_updated: 2020-07-14T12:47:36Z file_id: '6741' file_name: 2019_JournAppliedComputTopol_Boissonnat.pdf file_size: 2215157 relation: main_file file_date_updated: 2020-07-14T12:47:36Z has_accepted_license: '1' intvolume: ' 3' issue: 1-2 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 29–58 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Journal of Applied and Computational Topology publication_identifier: eissn: - 2367-1734 issn: - 2367-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: The reach, metric distortion, geodesic convexity and the variation of tangent 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2019' ... --- _id: '301' abstract: - lang: eng text: A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense. article_processing_charge: No article_type: original author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: István full_name: Gyöngy, István last_name: Gyöngy citation: ama: Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003 apa: Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003 chicago: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003. ieee: M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019. ista: Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012. mla: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003. short: M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012. date_created: 2018-12-11T11:45:42Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:20:49Z day: '01' department: - _id: JaMa doi: 10.1016/j.spa.2018.04.003 external_id: arxiv: - '1611.04177' isi: - '000458945300012' intvolume: ' 129' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.04177 month: '03' oa: 1 oa_version: Preprint page: 995-1012 publication: Stochastic Processes and their Applications publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A Feynman–Kac formula for stochastic Dirichlet problems type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 129 year: '2019' ... --- _id: '80' abstract: - lang: eng text: 'We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0 apa: Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0 chicago: Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0. ieee: A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019. ista: Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776. mla: Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0. short: A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776. date_created: 2018-12-11T11:44:31Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-24T14:27:51Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00220-018-3239-0 ec_funded: 1 external_id: isi: - '000467796800007' file: - access_level: open_access checksum: c7e9880b43ac726712c1365e9f2f73a6 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:34:06Z date_updated: 2020-07-14T12:48:07Z file_id: '5688' file_name: 2018_CommunMathPhys_Deuchert.pdf file_size: 893902 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 368' isi: 1 issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 723-776 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '7974' quality_controlled: '1' scopus_import: '1' status: public title: Bose–Einstein condensation in a dilute, trapped gas at positive temperature 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: 368 year: '2019' ... --- _id: '5911' abstract: - lang: eng text: Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved. article_processing_charge: No article_type: original author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005 apa: Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005 chicago: Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005. ieee: R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019. ista: Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248. mla: Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005. short: R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248. date_created: 2019-02-03T22:59:15Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:29:48Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tree.2018.12.005 ec_funded: 1 external_id: isi: - '000459899000013' file: - access_level: open_access checksum: ef24572d6ebcc1452c067e05410cc4a2 content_type: application/pdf creator: cziletti date_created: 2020-01-09T10:55:58Z date_updated: 2020-07-14T12:47:13Z file_id: '7245' file_name: 2019_Trends_Evolution_Faria.pdf file_size: 1946795 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 239-248 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Trends in Ecology and Evolution publication_identifier: issn: - '01695347' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Evolving inversions 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: 34 year: '2019' ... --- _id: '439' abstract: - lang: eng text: "We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system." article_processing_charge: No article_type: original author: - first_name: Tamas full_name: Hausel, Tamas id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Martin full_name: Mereb, Martin id: 43D735EE-F248-11E8-B48F-1D18A9856A87 last_name: Mereb - first_name: Michael full_name: Wong, Michael last_name: Wong citation: ama: Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052. doi:10.4171/JEMS/896 apa: Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/896 chicago: Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society. European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896. ieee: T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” Journal of the European Mathematical Society, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019. ista: Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052. mla: Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896. short: T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052. date_created: 2018-12-11T11:46:29Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-24T14:24:49Z day: '01' department: - _id: TaHa doi: 10.4171/JEMS/896 ec_funded: 1 external_id: arxiv: - '1604.03382' isi: - '000480413600002' intvolume: ' 21' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.03382 month: '10' oa: 1 oa_version: Preprint page: 2995-3052 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Journal of the European Mathematical Society publication_identifier: eissn: - 1435-9855 publication_status: published publisher: European Mathematical Society publist_id: '7384' quality_controlled: '1' scopus_import: '1' status: public title: Arithmetic and representation theory of wild character varieties type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2019' ... --- _id: '105' abstract: - lang: eng text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.' acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.' article_processing_charge: No article_type: original author: - first_name: Ashley full_name: Marsh, Ashley last_name: Marsh - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Paul full_name: Lockhart, Paul last_name: Lockhart - first_name: Richard full_name: Leventer, Richard last_name: Leventer citation: ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2 apa: Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2 chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2. ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019. ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166. mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2. short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166. date_created: 2018-12-11T11:44:39Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:28:24Z day: '01' department: - _id: GaNo doi: 10.1038/s41431-018-0231-2 external_id: isi: - '000454111500019' pmid: - '30089829' intvolume: ' 27' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41431-018-0231-2 month: '01' oa: 1 oa_version: Published Version page: 161-166 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Springer Nature publist_id: '7949' quality_controlled: '1' scopus_import: '1' status: public title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2019' ... --- _id: '65' abstract: - lang: eng text: We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2. article_processing_charge: No article_type: original author: - first_name: Konstantinos full_name: Dareiotis, Konstantinos last_name: Dareiotis - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Benjamin full_name: Gess, Benjamin last_name: Gess citation: ama: Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012 apa: Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for stochastic porous media equations. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.09.012 chicago: Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012. ieee: K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” Journal of Differential Equations, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019. ista: Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763. mla: Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012. short: K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763. date_created: 2018-12-11T11:44:26Z date_published: 2019-03-05T00:00:00Z date_updated: 2023-08-24T14:30:16Z day: '5' department: - _id: JaMa doi: 10.1016/j.jde.2018.09.012 external_id: arxiv: - '1803.06953' isi: - '000456332500026' intvolume: ' 266' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1803.06953 month: '03' oa: 1 oa_version: Preprint page: 3732-3763 publication: Journal of Differential Equations publication_status: published publisher: Elsevier publist_id: '7989' quality_controlled: '1' scopus_import: '1' status: public title: Entropy solutions for stochastic porous media equations type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 266 year: '2019' ... --- _id: '5907' abstract: - lang: eng text: Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins. article_number: '331' article_processing_charge: No author: - first_name: Réka full_name: Mócsai, Réka last_name: Mócsai - first_name: Rudolf full_name: Figl, Rudolf last_name: Figl - first_name: Clemens full_name: Troschl, Clemens last_name: Troschl - first_name: Richard full_name: Strasser, Richard last_name: Strasser - first_name: Elisabeth full_name: Svehla, Elisabeth last_name: Svehla - first_name: Markus full_name: Windwarder, Markus last_name: Windwarder - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Friedrich full_name: Altmann, Friedrich last_name: Altmann citation: ama: Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-36884-1 apa: Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-36884-1 chicago: Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1. ieee: R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019. ista: Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331. mla: Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1. short: R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019). date_created: 2019-02-03T22:59:13Z date_published: 2019-01-23T00:00:00Z date_updated: 2023-08-24T14:33:16Z day: '23' ddc: - '580' department: - _id: FlSc doi: 10.1038/s41598-018-36884-1 external_id: isi: - '000456392400012' file: - access_level: open_access checksum: 4129c7d7663d1f8a1edf8c4232372f66 content_type: application/pdf creator: dernst date_created: 2019-02-05T13:10:02Z date_updated: 2020-07-14T12:47:13Z file_id: '5923' file_name: 2019_ScientificReports_Mocsai.pdf file_size: 2124292 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '01' 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: N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated 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: '5908' abstract: - lang: eng text: The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants. article_processing_charge: No article_type: original author: - first_name: Eunkyoung full_name: Lee, Eunkyoung last_name: Lee - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jessica full_name: Pérez-Sancho, Jessica last_name: Pérez-Sancho - first_name: Francisco full_name: Benitez-Fuente, Francisco last_name: Benitez-Fuente - first_name: Matthew full_name: Strelau, Matthew last_name: Strelau - first_name: Alberto P. full_name: Macho, Alberto P. last_name: Macho - first_name: Miguel A. full_name: Botella, Miguel A. last_name: Botella - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Abel full_name: Rosado, Abel last_name: Rosado citation: ama: Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429. doi:10.1073/pnas.1818099116 apa: Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1818099116 chicago: Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1818099116. ieee: E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019. ista: Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429. mla: Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116. short: E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429. date_created: 2019-02-03T22:59:14Z date_published: 2019-01-22T00:00:00Z date_updated: 2023-08-24T14:31:09Z day: '22' department: - _id: JiFr doi: 10.1073/pnas.1818099116 external_id: isi: - '000456336100050' pmid: - '30610176' intvolume: ' 116' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1818099116 month: '01' oa: 1 oa_version: Published Version page: 1420-1429 pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 116 year: '2019' ... --- _id: '5680' abstract: - lang: eng text: Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones. article_processing_charge: No author: - first_name: Christophe full_name: Andalo, Christophe last_name: Andalo - first_name: Monique full_name: Burrus, Monique last_name: Burrus - first_name: Sandrine full_name: Paute, Sandrine last_name: Paute - first_name: Christine full_name: Lauzeral, Christine last_name: Lauzeral - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 citation: ama: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142 apa: Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142 chicago: Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142. ieee: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019. ista: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92. mla: Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142. short: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92. date_created: 2018-12-16T22:59:20Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:34:12Z day: '01' department: - _id: NiBa doi: 10.1080/23818107.2018.1545142 external_id: isi: - '000463802800009' intvolume: ' 166' isi: 1 issue: '1' language: - iso: eng month: '01' oa_version: None page: 80-92 publication: Botany Letters publication_identifier: eissn: - '23818115' issn: - '23818107' publication_status: published publisher: Taylor and Francis quality_controlled: '1' scopus_import: '1' status: public title: Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 166 year: '2019' ... --- _id: '5790' abstract: - lang: eng text: The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest. article_processing_charge: No article_type: original author: - first_name: Steven full_name: Chaplick, Steven last_name: Chaplick - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Pavel full_name: Klavík, Pavel last_name: Klavík citation: ama: Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436 apa: Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436 chicago: Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436. ieee: S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019. ista: Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394. mla: Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436. short: S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394. date_created: 2018-12-30T22:59:15Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-24T14:30:43Z day: '01' department: - _id: UlWa doi: 10.1002/jgt.22436 ec_funded: 1 external_id: arxiv: - '1309.2399' isi: - '000485392800004' intvolume: ' 91' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1309.2399 month: '08' oa: 1 oa_version: Preprint page: 365-394 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Graph Theory publication_identifier: issn: - '03649024' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Extending partial representations of circle graphs type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 91 year: '2019' ... --- _id: '405' abstract: - lang: eng text: We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently. acknowledgement: The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152) article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 citation: ama: Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002 apa: Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002 chicago: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002. ieee: D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019. ista: Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78. mla: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002. short: D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78. date_created: 2018-12-11T11:46:17Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-08-24T14:31:47Z day: '01' department: - _id: LaEr doi: 10.1016/j.laa.2018.03.002 ec_funded: 1 external_id: arxiv: - '1712.05324' isi: - '000470955300005' intvolume: ' 576' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.05324 month: '09' oa: 1 oa_version: Preprint page: 67-78 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Linear Algebra and Its Applications publication_status: published publisher: Elsevier publist_id: '7424' quality_controlled: '1' scopus_import: '1' status: public title: Jointly convex quantum Jensen divergences type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 576 year: '2019' ... --- _id: '175' abstract: - lang: eng text: An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Daniel full_name: Loughran, Daniel last_name: Loughran citation: ama: Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514 apa: Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514 chicago: Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514. ieee: T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019. ista: Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785. mla: Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514. short: T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785. date_created: 2018-12-11T11:45:01Z date_published: 2019-04-15T00:00:00Z date_updated: 2023-08-24T14:34:56Z day: '15' department: - _id: TiBr doi: 10.1090/tran/7514 external_id: arxiv: - '1705.01999' isi: - '000464034200019' intvolume: ' 371' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.01999 month: '04' oa: 1 oa_version: Preprint page: 5757-5785 publication: Transactions of the American Mathematical Society publication_identifier: eissn: - '10886850' issn: - '00029947' publication_status: published publisher: American Mathematical Society publist_id: '7746' quality_controlled: '1' scopus_import: '1' status: public title: Sieving rational points on varieties type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 371 year: '2019' ... --- _id: '319' abstract: - lang: eng text: We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition. acknowledgement: "MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n" article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Martin full_name: Hairer, Martin last_name: Hairer citation: ama: Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1 apa: Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1 chicago: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1. ieee: M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019. ista: Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758. mla: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:10.1007/s00440-018-0841-1. short: M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758. date_created: 2018-12-11T11:45:48Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-24T14:38:32Z day: '01' ddc: - '510' department: - _id: JaMa doi: 10.1007/s00440-018-0841-1 external_id: isi: - '000463613800001' file: - access_level: open_access checksum: 288d16ef7291242f485a9660979486e3 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:25:24Z date_updated: 2020-07-14T12:46:03Z file_id: '5722' file_name: 2018_ProbTheory_Gerencser.pdf file_size: 893182 relation: main_file file_date_updated: 2020-07-14T12:46:03Z has_accepted_license: '1' intvolume: ' 173' isi: 1 issue: 3-4 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 697–758 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Probability Theory and Related Fields publication_identifier: eissn: - '14322064' issn: - '01788051' publication_status: published publisher: Springer publist_id: '7546' quality_controlled: '1' scopus_import: '1' status: public title: Singular SPDEs in domains with boundaries 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: 173 year: '2019' ... --- _id: '429' abstract: - lang: eng text: We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent. acknowledgement: "Open access funding provided by Institute of Science and Technology (IST Austria).\r\n" article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Oskari H full_name: Ajanki, Oskari H id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87 last_name: Ajanki - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373. doi:10.1007/s00440-018-0835-z apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z. ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” Probability Theory and Related Fields, vol. 173, no. 1–2. Springer, pp. 293–373, 2019. ista: Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373. mla: Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z. short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373. date_created: 2018-12-11T11:46:25Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-08-24T14:39:00Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00440-018-0835-z ec_funded: 1 external_id: isi: - '000459396500007' file: - access_level: open_access checksum: f9354fa5c71f9edd17132588f0dc7d01 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:12:08Z date_updated: 2020-07-14T12:46:26Z file_id: '5720' file_name: 2018_ProbTheory_Ajanki.pdf file_size: 1201840 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 173' isi: 1 issue: 1-2 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 293–373 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Probability Theory and Related Fields publication_identifier: eissn: - '14322064' issn: - '01788051' publication_status: published publisher: Springer publist_id: '7394' quality_controlled: '1' scopus_import: '1' status: public title: Stability of the matrix Dyson equation and random matrices with correlations 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: 173 year: '2019' ... --- _id: '5947' abstract: - lang: eng text: Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking. article_processing_charge: No author: - first_name: Bapi full_name: Chatterjee, Bapi id: 3C41A08A-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-2742-4028 - first_name: Sathya full_name: Peri, Sathya last_name: Peri - first_name: Muktikanta full_name: Sa, Muktikanta last_name: Sa - first_name: Nandini full_name: Singhal, Nandini last_name: Singhal citation: ama: 'Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: ACM International Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617' apa: 'Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In ACM International Conference Proceeding Series (pp. 168–177). Bangalore, India: ACM. https://doi.org/10.1145/3288599.3288617' chicago: Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In ACM International Conference Proceeding Series, 168–77. ACM, 2019. https://doi.org/10.1145/3288599.3288617. ieee: B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in ACM International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177. ista: 'Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.' mla: Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” ACM International Conference Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617. short: B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177. conference: end_date: 2019-01-07 location: Bangalore, India name: 'ICDCN: Conference on Distributed Computing and Networking' start_date: 2019-01-04 date_created: 2019-02-10T22:59:17Z date_published: 2019-01-04T00:00:00Z date_updated: 2023-08-24T14:41:53Z day: '04' department: - _id: DaAl doi: 10.1145/3288599.3288617 external_id: arxiv: - '1809.00896' isi: - '000484491600019' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.00896 month: '01' oa: 1 oa_version: Preprint page: 168-177 publication: ACM International Conference Proceeding Series publication_identifier: isbn: - '978-1-4503-6094-4 ' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '5857' abstract: - lang: eng text: 'A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n.' article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: János full_name: Pach, János last_name: Pach citation: ama: 'Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics. 2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025' apa: 'Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025' chicago: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.' ieee: 'R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.' ista: 'Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231.' mla: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.' short: R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231. date_created: 2019-01-20T22:59:17Z date_published: 2019-04-30T00:00:00Z date_updated: 2023-08-24T14:39:33Z day: '30' department: - _id: UlWa doi: 10.1016/j.dam.2018.12.025 external_id: arxiv: - '1708.08037' isi: - '000466061100020' intvolume: ' 259' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.08037 month: '04' oa: 1 oa_version: Preprint page: 266-231 project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: Discrete Applied Mathematics publication_identifier: issn: - 0166218X publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '433' relation: earlier_version status: public scopus_import: '1' status: public title: 'Thrackles: An improved upper bound' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 259 year: '2019' ... --- _id: '5944' abstract: - lang: eng text: Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it. article_number: '9' article_processing_charge: No author: - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 citation: ama: Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009 apa: Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009 chicago: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009. ieee: B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019. ista: Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9. mla: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009. short: B. Corominas-Murtra, Life 9 (2019). date_created: 2019-02-10T22:59:15Z date_published: 2019-01-15T00:00:00Z date_updated: 2023-08-24T14:43:41Z day: '15' ddc: - '570' department: - _id: EdHa doi: 10.3390/life9010009 external_id: isi: - '000464125500001' file: - access_level: open_access checksum: 7d2322cd96ace41959909b66702d5cf4 content_type: application/pdf creator: dernst date_created: 2019-02-11T10:45:27Z date_updated: 2020-07-14T12:47:13Z file_id: '5951' file_name: 2019_Life_Corominas.pdf file_size: 963454 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Life publication_identifier: eissn: - '20751729' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Thermodynamics of duplication thresholds in synthetic protocell systems 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: '6029' abstract: - lang: eng text: Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy. article_number: '655' article_processing_charge: No author: - first_name: Marco full_name: Lindner, Marco last_name: Lindner - first_name: Aliz full_name: Tresztenyak, Aliz last_name: Tresztenyak - first_name: Gergö full_name: Fülöp, Gergö last_name: Fülöp - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - first_name: Adrian full_name: Prinz, Adrian last_name: Prinz - first_name: Iris full_name: Prinz, Iris last_name: Prinz - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Gerhard J. full_name: Schütz, Gerhard J. last_name: Schütz - first_name: Eva full_name: Sevcsik, Eva last_name: Sevcsik citation: ama: Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6. doi:10.3389/fchem.2018.00655 apa: Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655 chicago: Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655. ieee: M. Lindner et al., “A fast and simple contact printing approach to generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers Media S.A., 2019. ista: Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655. mla: Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers Media S.A., 2019, doi:10.3389/fchem.2018.00655. short: M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019). date_created: 2019-02-17T22:59:24Z date_published: 2019-01-24T00:00:00Z date_updated: 2023-08-24T14:45:38Z day: '24' ddc: - '540' department: - _id: JoDa doi: 10.3389/fchem.2018.00655 external_id: isi: - '000456718000001' file: - access_level: open_access checksum: 7841301d7c53b56ef873791b4b6f7b24 content_type: application/pdf creator: dernst date_created: 2019-02-18T15:10:34Z date_updated: 2020-07-14T12:47:17Z file_id: '6039' file_name: 2019_frontiers_Lindner.pdf file_size: 1766820 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Frontiers in Chemistry publication_identifier: eissn: - '22962646' publication_status: published publisher: Frontiers Media S.A. quality_controlled: '1' scopus_import: '1' status: public title: A fast and simple contact printing approach to generate 2D protein nanopatterns 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: '6028' abstract: - lang: eng text: We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small. article_processing_charge: Yes (via OA deal) author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Martin full_name: Hairer, Martin last_name: Hairer citation: ama: Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816 apa: Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816 chicago: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816. ieee: M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019. ista: Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005. mla: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816. short: M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005. date_created: 2019-02-17T22:59:24Z date_published: 2019-02-08T00:00:00Z date_updated: 2023-08-24T14:44:31Z day: '08' ddc: - '500' department: - _id: JaMa doi: 10.1002/cpa.21816 external_id: isi: - '000475465000003' file: - access_level: open_access checksum: 09aec427eb48c0f96a1cce9ff53f013b content_type: application/pdf creator: kschuh date_created: 2020-01-07T13:25:55Z date_updated: 2020-07-14T12:47:17Z file_id: '7237' file_name: 2019_Wiley_Gerencser.pdf file_size: 381350 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 72' isi: 1 issue: '9' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1983-2005 publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: A solution theory for quasilinear singular SPDEs 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: 72 year: '2019' ... --- _id: '5948' abstract: - lang: eng text: We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Hongfei full_name: Fu, Hongfei last_name: Fu - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: International Conference on Verification, Model Checking, and Abstract Interpretation. Vol 11388. Springer Nature; 2019:468-490. doi:10.1007/978-3-030-11245-5_22' apa: 'Fu, H., & Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In International Conference on Verification, Model Checking, and Abstract Interpretation (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-11245-5_22' chicago: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In International Conference on Verification, Model Checking, and Abstract Interpretation, 11388:468–90. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-11245-5_22. ieee: H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in International Conference on Verification, Model Checking, and Abstract Interpretation, Cascais, Portugal, 2019, vol. 11388, pp. 468–490. ista: 'Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490.' mla: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” International Conference on Verification, Model Checking, and Abstract Interpretation, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:10.1007/978-3-030-11245-5_22. short: H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490. conference: end_date: 2019-01-15 location: Cascais, Portugal name: 'VMCAI: Verification, Model Checking, and Abstract Interpretation' start_date: 2019-01-13 date_created: 2019-02-10T22:59:17Z date_published: 2019-01-11T00:00:00Z date_updated: 2023-08-24T14:42:22Z day: '11' department: - _id: KrCh doi: 10.1007/978-3-030-11245-5_22 external_id: arxiv: - '1701.02944' isi: - '000931943000022' intvolume: ' 11388' isi: 1 language: - iso: eng main_file_link: - url: https://arxiv.org/abs/1701.02944 month: '01' oa_version: Preprint page: 468-490 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: International Conference on Verification, Model Checking, and Abstract Interpretation publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Termination of nondeterministic probabilistic programs type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11388 year: '2019' ... --- _id: '5945' abstract: - lang: eng text: In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy. article_processing_charge: No article_type: original author: - first_name: Mariela D. full_name: Petkova, Mariela D. last_name: Petkova - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Eric F. full_name: Wieschaus, Eric F. last_name: Wieschaus - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor citation: ama: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007 apa: Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.01.007 chicago: Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007. ieee: M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019. ista: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15. mla: Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007. short: M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15. date_created: 2019-02-10T22:59:16Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:42:47Z day: '07' department: - _id: GaTk doi: 10.1016/j.cell.2019.01.007 external_id: isi: - '000457969200015' pmid: - '30712870' intvolume: ' 176' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2019.01.007 month: '02' oa: 1 oa_version: Published Version page: 844-855.e15 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Cell publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/ scopus_import: '1' status: public title: Optimal decoding of cellular identities in a genetic network type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 176 year: '2019' ... --- _id: '5943' abstract: - lang: eng text: The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour. article_processing_charge: No article_type: original author: - first_name: Lukasz full_name: Klotz, Lukasz id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87 last_name: Klotz orcid: 0000-0003-1740-7635 - first_name: Konrad full_name: Gumowski, Konrad last_name: Gumowski - first_name: José Eduardo full_name: Wesfreid, José Eduardo last_name: Wesfreid citation: ama: Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406. doi:10.1017/jfm.2018.974 apa: Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2018.974 chicago: Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974. ieee: L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863. Cambridge University Press, pp. 386–406, 2019. ista: Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406. mla: Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:10.1017/jfm.2018.974. short: L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406. date_created: 2019-02-10T22:59:15Z date_published: 2019-03-25T00:00:00Z date_updated: 2023-08-24T14:43:13Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2018.974 ec_funded: 1 external_id: arxiv: - '1902.07931' isi: - '000526029100016' intvolume: ' 863' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07931 month: '03' oa: 1 oa_version: Preprint page: 386-406 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Experiments on a jet in a crossflow in the low-velocity-ratio regime type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 863 year: '2019' ... --- _id: '6042' abstract: - lang: eng text: Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques. alternative_title: - LNCS article_processing_charge: No author: - first_name: Maria full_name: Christakis, Maria last_name: Christakis - first_name: Matthias full_name: Heizmann, Matthias last_name: Heizmann - first_name: Muhammad Numair full_name: Mansur, Muhammad Numair last_name: Mansur - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Valentin full_name: Wüstholz, Valentin last_name: Wüstholz citation: ama: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13' apa: 'Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-17462-0_13' chicago: Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17462-0_13. ieee: M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Prague, Czech Republic, 2019, vol. 11427, pp. 226–243. ista: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.' mla: Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13. short: M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243. conference: end_date: 2019-04-11 location: Prague, Czech Republic name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2019-04-06 date_created: 2019-02-18T16:44:06Z date_published: 2019-04-04T00:00:00Z date_updated: 2023-08-24T14:47:45Z day: '04' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-17462-0_13 ec_funded: 1 external_id: isi: - '000681166500013' file: - access_level: open_access checksum: 9998496f6fe202c0a19124b4209154c6 content_type: application/pdf creator: dernst date_created: 2019-05-10T14:16:05Z date_updated: 2020-07-14T12:47:17Z file_id: '6408' file_name: 2019_LNCS_Christakis.pdf file_size: 773083 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 11427' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 226-243 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _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: '25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Semantic fault localization and suspiciousness ranking 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: 11427 year: '2019' ... --- _id: '6035' abstract: - lang: eng text: 'We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.' article_processing_charge: No author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Kostiantyn full_name: Potomkin, Kostiantyn last_name: Potomkin - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804' apa: 'Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804' chicago: 'Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.' ieee: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44.' ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control vol. 22, 39–44.' mla: 'Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.' short: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.' conference: end_date: 2019-04-18 location: Montreal, QC, Canada name: 'HSCC: Hybrid Systems Computation and Control' start_date: 2019-04-16 date_created: 2019-02-18T14:43:28Z date_published: 2019-04-16T00:00:00Z date_updated: 2023-08-24T14:47:21Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1145/3302504.3311804 ec_funded: 1 external_id: arxiv: - '1901.10736' isi: - '000516713900005' file: - access_level: open_access checksum: 28ed56439aea5991c3122d4730fd828f content_type: application/pdf creator: cschilli date_created: 2019-03-05T09:27:18Z date_updated: 2020-07-14T12:47:17Z file_id: '6067' file_name: hscc19.pdf file_size: 3784414 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 22' isi: 1 keyword: - reachability analysis - hybrid systems - lazy computation language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 39-44 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 'Proceedings of the 22nd 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: 'JuliaReach: A toolbox for set-based reachability' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2019' ... --- _id: '6052' abstract: - lang: eng text: 'Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.' article_processing_charge: No article_type: original author: - first_name: Sven M full_name: Truckenbrodt, Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Silvio O full_name: Rizzoli, Silvio O last_name: Rizzoli - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3 apa: Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3 chicago: Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3. ieee: S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019. ista: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863. mla: Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:10.1038/s41596-018-0117-3. short: S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863. date_created: 2019-02-24T22:59:20Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:48:33Z day: '01' ddc: - '570' department: - _id: JoDa - _id: Bio doi: 10.1038/s41596-018-0117-3 ec_funded: 1 external_id: isi: - '000459890700008' pmid: - '30778205' file: - access_level: open_access checksum: 7efb9951e7ddf3e3dcc2fb92b859c623 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: kschuh date_created: 2021-06-29T14:41:46Z date_updated: 2021-06-29T14:41:46Z file_id: '9619' file_name: 181031_Truckenbrodt_ExM_NatProtoc.docx file_size: 84478958 relation: main_file success: 1 file_date_updated: 2021-06-29T14:41:46Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 832–863 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules publication: Nature Protocols publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: A practical guide to optimization in X10 expansion microscopy type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2019' ... --- _id: '6025' abstract: - lang: eng text: Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation. acknowledged_ssus: - _id: Bio - _id: LifeSc article_number: e42093 article_processing_charge: No author: - first_name: Daniel full_name: Capek, Daniel id: 31C42484-F248-11E8-B48F-1D18A9856A87 last_name: Capek orcid: 0000-0001-5199-9940 - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Alexandra Madelaine full_name: Tichy, Alexandra Madelaine last_name: Tichy - first_name: Maurizio full_name: Morri, Maurizio id: 4863116E-F248-11E8-B48F-1D18A9856A87 last_name: Morri - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: 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: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 2019;8. doi:10.7554/eLife.42093 apa: Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42093 chicago: Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42093. ieee: D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093. mla: Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife, vol. 8, e42093, eLife Sciences Publications, 2019, doi:10.7554/eLife.42093. short: D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019). date_created: 2019-02-17T22:59:22Z date_published: 2019-02-06T00:00:00Z date_updated: 2023-08-24T14:46:01Z day: '06' ddc: - '570' department: - _id: CaHe - _id: HaJa doi: 10.7554/eLife.42093 ec_funded: 1 external_id: isi: - '000458025300001' file: - access_level: open_access checksum: 6cb4ca6d4aa96f6f187a5983aa3e660a content_type: application/pdf creator: dernst date_created: 2019-02-18T15:17:21Z date_updated: 2020-07-14T12:47:17Z file_id: '6041' file_name: 2019_elife_Capek.pdf file_size: 5500707 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version 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 publication: eLife publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration 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: '6022' abstract: - lang: eng text: The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation. article_number: e2005902 article_processing_charge: No author: - first_name: Richard M. full_name: Merrill, Richard M. last_name: Merrill - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Simon H. full_name: Martin, Simon H. last_name: Martin - first_name: Maria C full_name: Melo Hurtado, Maria C id: 386D7308-F248-11E8-B48F-1D18A9856A87 last_name: Melo Hurtado - first_name: Sarah full_name: Barker, Sarah last_name: Barker - first_name: John full_name: Davey, John last_name: Davey - first_name: W. Owen full_name: Mcmillan, W. Owen last_name: Mcmillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins citation: ama: Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902 apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902 chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902. ieee: R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019. ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902. mla: Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902. short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019). date_created: 2019-02-17T22:59:21Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:46:23Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1371/journal.pbio.2005902 external_id: isi: - '000460317100001' file: - access_level: open_access checksum: 5f34001617ee729314ca520c049b1112 content_type: application/pdf creator: dernst date_created: 2019-02-18T14:57:24Z date_updated: 2020-07-14T12:47:17Z file_id: '6036' file_name: 2019_PLOS_Merrill.pdf file_size: 2005949 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '2' language: - iso: eng license: https://creativecommons.org/publicdomain/zero/1.0/ month: '02' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9801' relation: research_data status: public scopus_import: '1' status: public title: Genetic dissection of assortative mating behavior tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2019' ... --- _id: '6023' abstract: - lang: eng text: Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain. article_processing_charge: No author: - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida - first_name: Alja full_name: Van Der Schuren, Alja last_name: Van Der Schuren - first_name: Maritza full_name: Van Dop, Maritza last_name: Van Dop - first_name: Luc full_name: Van Galen, Luc last_name: Van Galen - first_name: Shunsuke full_name: Saiga, Shunsuke last_name: Saiga - first_name: Milad full_name: Adibi, Milad last_name: Adibi - first_name: Barbara full_name: Möller, Barbara last_name: Möller - first_name: Colette A. full_name: Ten Hove, Colette A. last_name: Ten Hove - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Richard full_name: Smith, Richard last_name: Smith - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166. doi:10.1038/s41477-019-0363-6 apa: Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6 chicago: Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0363-6. ieee: S. Yoshida et al., “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019. ista: Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166. mla: Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:10.1038/s41477-019-0363-6. short: S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166. date_created: 2019-02-17T22:59:21Z date_published: 2019-02-08T00:00:00Z date_updated: 2023-08-24T14:46:47Z day: '08' department: - _id: JiFr - _id: EvBe doi: 10.1038/s41477-019-0363-6 ec_funded: 1 external_id: isi: - '000460479600014' intvolume: ' 5' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/479113v1.abstract month: '02' oa: 1 oa_version: Submitted Version page: 160-166 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Plants publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2019' ... --- _id: '6053' abstract: - lang: eng text: Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information. article_processing_charge: No article_type: original author: - first_name: Mahmoud full_name: Kalaee, Mahmoud last_name: Kalaee - first_name: Mohammad full_name: Mirhosseini, Mohammad last_name: Mirhosseini - first_name: Paul B. full_name: Dieterle, Paul B. last_name: Dieterle - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Oskar full_name: Painter, Oskar last_name: Painter citation: ama: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339. doi:10.1038/s41565-019-0377-2 apa: Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., & Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2 chicago: Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo, Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2. ieee: M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O. Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology, vol. 14, no. 4. Springer Nature, pp. 334–339, 2019. ista: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4), 334–339. mla: Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339, doi:10.1038/s41565-019-0377-2. short: M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339. date_created: 2019-02-24T22:59:21Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-24T14:48:08Z day: '01' department: - _id: JoFi doi: 10.1038/s41565-019-0377-2 external_id: isi: - '000463195700014' intvolume: ' 14' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://authors.library.caltech.edu/92123/ month: '04' oa: 1 oa_version: Submitted Version page: 334–339 publication: Nature Nanotechnology publication_identifier: eissn: - 1748-3395 issn: - 1748-3387 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quantum electromechanics of a hypersonic crystal type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2019' ... --- _id: '6050' abstract: - lang: eng text: 'We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. ' 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: Roman full_name: Fedorov, Roman last_name: Fedorov citation: ama: Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240 apa: Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240 chicago: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240. ieee: A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019. ista: Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102. mla: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society, vol. 147, AMS, 2019, pp. 91–102, doi:10.1090/proc/14240. short: A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102. date_created: 2019-02-24T22:59:19Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:48:59Z day: '01' department: - _id: HeEd doi: 10.1090/proc/14240 external_id: arxiv: - '1709.02562' isi: - '000450363900008' intvolume: ' 147' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.02562 month: '01' oa: 1 oa_version: Preprint page: 91-102 publication: Proceedings of the American Mathematical Society publication_status: published publisher: AMS quality_controlled: '1' scopus_import: '1' status: public title: Two circles and only a straightedge type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 147 year: '2019' ... --- _id: '9801' article_processing_charge: No author: - first_name: Richard M. full_name: Merrill, Richard M. last_name: Merrill - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Simon H. full_name: Martin, Simon H. last_name: Martin - first_name: Maria C full_name: Melo Hurtado, Maria C id: 386D7308-F248-11E8-B48F-1D18A9856A87 last_name: Melo Hurtado - first_name: Sarah full_name: Barker, Sarah last_name: Barker - first_name: John full_name: Davey, John last_name: Davey - first_name: W. Owen full_name: Mcmillan, W. Owen last_name: Mcmillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins citation: ama: Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006 apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902.s006 chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006. ieee: R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019. ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006. mla: Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.s006. short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019). date_created: 2021-08-06T11:34:56Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:46:23Z day: '07' department: - _id: NiBa doi: 10.1371/journal.pbio.2005902.s006 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6022' relation: used_in_publication status: public status: public title: Raw behavioral data type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6095' abstract: - lang: eng text: Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients. article_processing_charge: No author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Pragya full_name: Chaube, Pragya last_name: Chaube - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Tomas full_name: Larsson, Tomas last_name: Larsson - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: Emily M. full_name: Lemmon, Emily M. last_name: Lemmon - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Marina full_name: Panova, Marina last_name: Panova - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972 apa: Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972 chicago: Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972. ieee: R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019. ista: Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393. mla: Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972. short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393. date_created: 2019-03-10T22:59:21Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:50:27Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.14972 external_id: isi: - '000465219200013' file: - access_level: open_access checksum: f915885756057ec0ca5912a41f46a887 content_type: application/pdf creator: dernst date_created: 2019-03-11T16:12:54Z date_updated: 2020-07-14T12:47:19Z file_id: '6097' file_name: 2019_MolecularEcology_Faria.pdf file_size: 1510715 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 28' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1375-1393 publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9837' relation: research_data status: public scopus_import: '1' status: public title: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes 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: '6049' abstract: - lang: eng text: 'In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape.' article_number: '045002' article_processing_charge: Yes (in subscription journal) author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: 'De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 2019;52(4). doi:10.1088/1751-8121/aaf2dd' apa: 'De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd' chicago: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.' ieee: 'D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4. IOP Publishing, 2019.' ista: 'De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.' mla: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.' short: 'D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).' date_created: 2019-02-24T22:59:19Z date_published: 2019-01-07T00:00:00Z date_updated: 2023-08-24T14:49:23Z day: '07' ddc: - '570' department: - _id: GaTk doi: 10.1088/1751-8121/aaf2dd ec_funded: 1 external_id: isi: - '000455379500001' file: - access_level: open_access checksum: 1112304ad363a6d8afaeccece36473cf content_type: application/pdf creator: kschuh date_created: 2019-04-19T12:18:57Z date_updated: 2020-07-14T12:47:17Z file_id: '6344' file_name: 2019_IOP_DeMartino.pdf file_size: 1804557 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 52' isi: 1 issue: '4' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Journal of Physics A: Mathematical and Theoretical' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Feedback-induced self-oscillations in large interacting systems subjected to phase transitions 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: 52 year: '2019' ... --- _id: '6091' abstract: - lang: eng text: Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons. article_number: e41563 article_processing_charge: No author: - first_name: Nathan T. full_name: Henderson, Nathan T. last_name: Henderson - first_name: Sylvain J. full_name: Le Marchand, Sylvain J. last_name: Le Marchand - first_name: Martin full_name: Hruska, Martin last_name: Hruska - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Matthew B. full_name: Dalva, Matthew B. last_name: Dalva citation: ama: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 2019;8. doi:10.7554/eLife.41563 apa: Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L., & Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563 chicago: Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer, Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.41563. ieee: N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 8, e41563. mla: Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife Sciences Publications, 2019, doi:10.7554/eLife.41563. short: N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019). date_created: 2019-03-10T22:59:20Z date_published: 2019-02-21T00:00:00Z date_updated: 2023-08-24T14:50:50Z day: '21' ddc: - '570' department: - _id: SiHi doi: 10.7554/eLife.41563 external_id: isi: - '000459380600001' pmid: - '30789343' file: - access_level: open_access checksum: 7b0800d003f14cd06b1802dea0c52941 content_type: application/pdf creator: dernst date_created: 2019-03-11T16:15:37Z date_updated: 2020-07-14T12:47:19Z file_id: '6098' file_name: 2019_eLife_Henderson.pdf file_size: 7260753 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs 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: '6046' abstract: - lang: eng text: Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses. acknowledged_ssus: - _id: Bio article_number: e8470 article_processing_charge: No author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 2019;15(2). doi:10.15252/msb.20188470 apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.20188470 chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470. ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” Molecular systems biology, vol. 15, no. 2. Embo Press, 2019. ista: Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470. mla: Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470, Embo Press, 2019, doi:10.15252/msb.20188470. short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019). date_created: 2019-02-24T22:59:18Z date_published: 2019-02-14T00:00:00Z date_updated: 2023-08-24T14:49:53Z day: '14' department: - _id: GaTk doi: 10.15252/msb.20188470 external_id: isi: - '000459628300003' pmid: - '30765425' intvolume: ' 15' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30765425 month: '02' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Molecular systems biology publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Temporal order and precision of complex stress responses in individual bacteria type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6105' abstract: - lang: eng text: " Hosts can alter their strategy towards pathogens during their lifetime; that is, they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e., resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fecundity consequences that result from a high pathogen burden. Finally, previous exposure may also lead to life‐history adjustments, such as terminal investment into reproduction.\r\n Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested whether previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute‐phase infection (one day post‐challenge). We then asked whether previous pathogen exposure affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).\r\n \ We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long‐term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses.\r\n We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection.\r\n \ To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi‐faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host–pathogen system and that infection persistence may be bacterium‐specific.\r\n" article_processing_charge: No article_type: original author: - first_name: Megan full_name: Kutzer, Megan id: 29D0B332-F248-11E8-B48F-1D18A9856A87 last_name: Kutzer orcid: 0000-0002-8696-6978 - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz - first_name: Sophie A.O. full_name: Armitage, Sophie A.O. last_name: Armitage citation: ama: Kutzer M, Kurtz J, Armitage SAO. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 2019;88(4):566-578. doi:10.1111/1365-2656.12953 apa: Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12953 chicago: Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology. Wiley, 2019. https://doi.org/10.1111/1365-2656.12953. ieee: M. Kutzer, J. Kurtz, and S. A. O. Armitage, “A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance,” Journal of Animal Ecology, vol. 88, no. 4. Wiley, pp. 566–578, 2019. ista: Kutzer M, Kurtz J, Armitage SAO. 2019. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 88(4), 566–578. mla: Kutzer, Megan, et al. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology, vol. 88, no. 4, Wiley, 2019, pp. 566–78, doi:10.1111/1365-2656.12953. short: M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019) 566–578. date_created: 2019-03-17T22:59:15Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-25T08:04:53Z day: '01' ddc: - '570' department: - _id: SyCr doi: 10.1111/1365-2656.12953 ec_funded: 1 external_id: isi: - '000467994800007' file: - access_level: open_access checksum: 405cde15120de26018b3bd0dfa29986c content_type: application/pdf creator: dernst date_created: 2019-03-18T07:43:06Z date_updated: 2020-07-14T12:47:19Z file_id: '6107' file_name: 2019_JournalAnimalEcology_Kutzer.pdf file_size: 1460662 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 88' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 566-578 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Animal Ecology publication_identifier: eissn: - '13652656' issn: - '00218790' publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9806' relation: research_data status: public scopus_import: '1' status: public title: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance 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: 88 year: '2019' ... --- _id: '6088' abstract: - lang: eng text: P-Glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) are two efflux transporters at the blood–brain barrier (BBB), which effectively restrict brain distribution of diverse drugs, such as tyrosine kinase inhibitors. There is a crucial need for pharmacological ABCB1 and ABCG2 inhibition protocols for a more effective treatment of brain diseases. In the present study, seven marketed drugs (osimertinib, erlotinib, nilotinib, imatinib, lapatinib, pazopanib, and cyclosporine A) and one nonmarketed drug (tariquidar), with known in vitro ABCB1/ABCG2 inhibitory properties, were screened for their inhibitory potency at the BBB in vivo. Positron emission tomography (PET) using the model ABCB1/ABCG2 substrate [11C]erlotinib was performed in mice. Tested inhibitors were administered as i.v. bolus injections at 30 min before the start of the PET scan, followed by a continuous i.v. infusion for the duration of the PET scan. Five of the tested drugs increased total distribution volume of [11C]erlotinib in the brain (VT,brain) compared to vehicle-treated animals (tariquidar, + 69%; erlotinib, + 19% and +23% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 22%; lapatinib, + 25%; and cyclosporine A, + 49%). For all drugs, increases in [11C]erlotinib brain distribution were lower than in Abcb1a/b(−/−)Abcg2(−/−) mice (+149%), which suggested that only partial ABCB1/ABCG2 inhibition was reached at the mouse BBB. The plasma concentrations of the tested drugs at the time of the PET scan were higher than clinically achievable plasma concentrations. Some of the tested drugs led to significant increases in blood radioactivity concentrations measured at the end of the PET scan (erlotinib, + 103% and +113% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 125%; and cyclosporine A, + 101%), which was most likely caused by decreased hepatobiliary excretion of radioactivity. Taken together, our data suggest that some marketed tyrosine kinase inhibitors may be repurposed to inhibit ABCB1 and ABCG2 at the BBB. From a clinical perspective, moderate increases in brain delivery despite the administration of high i.v. doses as well as peripheral drug–drug interactions due to transporter inhibition in clearance organs question the translatability of this concept. article_processing_charge: No author: - first_name: Alexander full_name: Traxl, Alexander last_name: Traxl - first_name: Severin full_name: Mairinger, Severin last_name: Mairinger - first_name: Thomas full_name: Filip, Thomas last_name: Filip - first_name: Michael full_name: Sauberer, Michael last_name: Sauberer - first_name: Johann full_name: Stanek, Johann last_name: Stanek - first_name: Stefan full_name: Poschner, Stefan last_name: Poschner - first_name: Walter full_name: Jäger, Walter last_name: Jäger - first_name: Viktoria full_name: Zoufal, Viktoria last_name: Zoufal - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Nicolas full_name: Tournier, Nicolas last_name: Tournier - first_name: Martin full_name: Bauer, Martin last_name: Bauer - first_name: Thomas full_name: Wanek, Thomas last_name: Wanek - first_name: Oliver full_name: Langer, Oliver last_name: Langer citation: ama: Traxl A, Mairinger S, Filip T, et al. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 2019;16(3):1282-1293. doi:10.1021/acs.molpharmaceut.8b01217 apa: Traxl, A., Mairinger, S., Filip, T., Sauberer, M., Stanek, J., Poschner, S., … Langer, O. (2019). Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. American Chemical Society. https://doi.org/10.1021/acs.molpharmaceut.8b01217 chicago: Traxl, Alexander, Severin Mairinger, Thomas Filip, Michael Sauberer, Johann Stanek, Stefan Poschner, Walter Jäger, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics. American Chemical Society, 2019. https://doi.org/10.1021/acs.molpharmaceut.8b01217. ieee: A. Traxl et al., “Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Molecular Pharmaceutics, vol. 16, no. 3. American Chemical Society, pp. 1282–1293, 2019. ista: Traxl A, Mairinger S, Filip T, Sauberer M, Stanek J, Poschner S, Jäger W, Zoufal V, Novarino G, Tournier N, Bauer M, Wanek T, Langer O. 2019. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 16(3), 1282–1293. mla: Traxl, Alexander, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics, vol. 16, no. 3, American Chemical Society, 2019, pp. 1282–93, doi:10.1021/acs.molpharmaceut.8b01217. short: A. Traxl, S. Mairinger, T. Filip, M. Sauberer, J. Stanek, S. Poschner, W. Jäger, V. Zoufal, G. Novarino, N. Tournier, M. Bauer, T. Wanek, O. Langer, Molecular Pharmaceutics 16 (2019) 1282–1293. date_created: 2019-03-10T22:59:19Z date_published: 2019-03-04T00:00:00Z date_updated: 2023-08-25T08:02:51Z day: '04' department: - _id: GaNo doi: 10.1021/acs.molpharmaceut.8b01217 external_id: isi: - '000460600400031' pmid: - '30694684' intvolume: ' 16' isi: 1 issue: '3' language: - iso: eng month: '03' oa_version: None page: 1282-1293 pmid: 1 publication: Molecular Pharmaceutics publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2019' ... --- _id: '6087' abstract: - lang: eng text: Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: LifeSc acknowledgement: We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins, and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish facilities of IST Austria for continuous support. This work was supported by an ERC advanced grant ( MECSPEC to C.-P.H.). article_processing_charge: No article_type: original author: - first_name: Peng full_name: Xia, Peng id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87 last_name: Xia orcid: 0000-0002-5419-7756 - first_name: Daniel J full_name: Gütl, Daniel J id: 381929CE-F248-11E8-B48F-1D18A9856A87 last_name: Gütl - first_name: Vanessa full_name: Zheden, Vanessa id: 39C5A68A-F248-11E8-B48F-1D18A9856A87 last_name: Zheden orcid: 0000-0002-9438-4783 - 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: Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 2019;176(6):1379-1392.e14. doi:10.1016/j.cell.2019.01.019 apa: Xia, P., Gütl, D. J., Zheden, V., & Heisenberg, C.-P. J. (2019). Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.01.019 chicago: Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.01.019. ieee: P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity,” Cell, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019. ista: Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6), 1379–1392.e14. mla: Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell, vol. 176, no. 6, Elsevier, 2019, p. 1379–1392.e14, doi:10.1016/j.cell.2019.01.019. short: P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14. date_created: 2019-03-10T22:59:19Z date_published: 2019-03-07T00:00:00Z date_updated: 2023-08-25T08:02:23Z day: '07' department: - _id: CaHe - _id: EM-Fac doi: 10.1016/j.cell.2019.01.019 ec_funded: 1 external_id: isi: - '000460509600013' pmid: - '30773315' intvolume: ' 176' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2019.01.019 month: '03' oa: 1 oa_version: Published Version page: 1379-1392.e14 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 publication: Cell publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/ scopus_import: '1' status: public title: Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 176 year: '2019' ... --- _id: '9806' abstract: - lang: eng text: 1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific. article_processing_charge: No author: - first_name: Megan full_name: Kutzer, Megan id: 29D0B332-F248-11E8-B48F-1D18A9856A87 last_name: Kutzer orcid: 0000-0002-8696-6978 - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz - first_name: Sophie A.O. full_name: Armitage, Sophie A.O. last_name: Armitage citation: ama: 'Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:10.5061/dryad.9kj41f0' apa: 'Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. https://doi.org/10.5061/dryad.9kj41f0' chicago: 'Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. https://doi.org/10.5061/dryad.9kj41f0.' ieee: 'M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019.' ista: 'Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, 10.5061/dryad.9kj41f0.' mla: 'Kutzer, Megan, et al. Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance. Dryad, 2019, doi:10.5061/dryad.9kj41f0.' short: M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019). date_created: 2021-08-06T12:06:40Z date_published: 2019-02-05T00:00:00Z date_updated: 2023-08-25T08:04:52Z day: '05' department: - _id: SyCr doi: 10.5061/dryad.9kj41f0 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.9kj41f0 month: '02' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '6105' relation: used_in_publication status: public status: public title: 'Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6086' abstract: - lang: eng text: We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part. article_processing_charge: No author: - first_name: Christian full_name: Sadel, Christian id: 4760E9F8-F248-11E8-B48F-1D18A9856A87 last_name: Sadel orcid: 0000-0001-8255-3968 - first_name: Disheng full_name: Xu, Disheng last_name: Xu citation: ama: Sadel C, Xu D. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 2019;39(4):1082-1098. doi:10.1017/etds.2017.52 apa: Sadel, C., & Xu, D. (2019). Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2017.52 chicago: Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2019. https://doi.org/10.1017/etds.2017.52. ieee: C. Sadel and D. Xu, “Singular analytic linear cocycles with negative infinite Lyapunov exponents,” Ergodic Theory and Dynamical Systems, vol. 39, no. 4. Cambridge University Press, pp. 1082–1098, 2019. ista: Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098. mla: Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems, vol. 39, no. 4, Cambridge University Press, 2019, pp. 1082–98, doi:10.1017/etds.2017.52. short: C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 1082–1098. date_created: 2019-03-10T22:59:18Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-25T08:03:30Z day: '01' department: - _id: LaEr doi: 10.1017/etds.2017.52 ec_funded: 1 external_id: arxiv: - '1601.06118' isi: - '000459725600012' intvolume: ' 39' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1601.06118 month: '04' oa: 1 oa_version: Preprint page: 1082-1098 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Ergodic Theory and Dynamical Systems publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Singular analytic linear cocycles with negative infinite Lyapunov exponents type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 39 year: '2019' ... --- _id: '6102' abstract: - lang: eng text: 'Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior.' article_number: '28' article_processing_charge: No author: - first_name: B. full_name: Le Feber, B. last_name: Le Feber - first_name: J. E. full_name: Sipe, J. E. last_name: Sipe - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: L. full_name: Kuipers, L. last_name: Kuipers - first_name: N. full_name: Rotenberg, N. last_name: Rotenberg citation: ama: 'Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 2019;8(1). doi:10.1038/s41377-019-0124-3' apa: 'Le Feber, B., Sipe, J. E., Wulf, M., Kuipers, L., & Rotenberg, N. (2019). A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. Springer Nature. https://doi.org/10.1038/s41377-019-0124-3' chicago: 'Le Feber, B., J. E. Sipe, Matthias Wulf, L. Kuipers, and N. Rotenberg. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications. Springer Nature, 2019. https://doi.org/10.1038/s41377-019-0124-3.' ieee: 'B. Le Feber, J. E. Sipe, M. Wulf, L. Kuipers, and N. Rotenberg, “A full vectorial mapping of nanophotonic light fields,” Light: Science and Applications, vol. 8, no. 1. Springer Nature, 2019.' ista: 'Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. 2019. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 8(1), 28.' mla: 'Le Feber, B., et al. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications, vol. 8, no. 1, 28, Springer Nature, 2019, doi:10.1038/s41377-019-0124-3.' short: 'B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019).' date_created: 2019-03-17T22:59:13Z date_published: 2019-03-06T00:00:00Z date_updated: 2023-08-25T08:06:10Z day: '06' ddc: - '530' department: - _id: JoFi doi: 10.1038/s41377-019-0124-3 external_id: arxiv: - '1803.10145' isi: - '000460470700004' file: - access_level: open_access checksum: d71e528cff9c56f70ccc29dd7005257f content_type: application/pdf creator: dernst date_created: 2019-03-18T08:08:22Z date_updated: 2020-07-14T12:47:19Z file_id: '6108' file_name: 2019_Light_LeFeber.pdf file_size: 1119947 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: 'Light: Science and Applications' publication_identifier: eissn: - '20477538' issn: - '20955545' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A full vectorial mapping of nanophotonic light fields 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: '6104' abstract: - lang: eng text: Abiotic stress poses constant challenges for plant survival and is a serious problem for global agricultural productivity. On a molecular level, stress conditions result in elevation of reactive oxygen species (ROS) production causing oxidative stress associated with oxidation of proteins and nucleic acids as well as impairment of membrane functions. Adaptation of root growth to ROS accumulation is facilitated through modification of auxin and cytokinin hormone homeostasis. Here, we report that in Arabidopsis root meristem, ROS-induced changes of auxin levels correspond to decreased abundance of PIN auxin efflux carriers at the plasma membrane (PM). Specifically, increase in H2O2 levels affects PIN2 endocytic recycling. We show that the PIN2 intracellular trafficking during adaptation to oxidative stress requires the function of the ADP-ribosylation factor (ARF)-guanine-nucleotide exchange factor (GEF) BEN1, an actin-associated regulator of the trafficking from the PM to early endosomes and, presumably, indirectly, trafficking to the vacuoles. We propose that H2O2 levels affect the actin dynamics thus modulating ARF-GEF-dependent trafficking of PIN2. This mechanism provides a way how root growth acclimates to stress and adapts to a changing environment. article_processing_charge: No author: - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Prashanth full_name: Tamizhselvan, Prashanth last_name: Tamizhselvan - first_name: Sharmila full_name: Madhavan, Sharmila last_name: Madhavan - first_name: Eman Elrefaay full_name: Ryad, Eman Elrefaay last_name: Ryad - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Mónika full_name: Hrtyan, Mónika id: 45A71A74-F248-11E8-B48F-1D18A9856A87 last_name: Hrtyan - first_name: Petre full_name: Dobrev, Petre last_name: Dobrev - first_name: Radomira full_name: Vanková, Radomira last_name: Vanková - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Vanesa B. full_name: Tognetti, Vanesa B. last_name: Tognetti citation: ama: Zwiewka M, Bielach A, Tamizhselvan P, et al. Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell Physiology. 2019;60(2):255-273. doi:10.1093/pcp/pcz001 apa: Zwiewka, M., Bielach, A., Tamizhselvan, P., Madhavan, S., Ryad, E. E., Tan, S., … Tognetti, V. B. (2019). Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcz001 chicago: Zwiewka, Marta, Agnieszka Bielach, Prashanth Tamizhselvan, Sharmila Madhavan, Eman Elrefaay Ryad, Shutang Tan, Mónika Hrtyan, et al. “Root Adaptation to H2O2-Induced Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.” Plant and Cell Physiology. Oxford University Press, 2019. https://doi.org/10.1093/pcp/pcz001. ieee: M. Zwiewka et al., “Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking,” Plant and Cell Physiology, vol. 60, no. 2. Oxford University Press, pp. 255–273, 2019. ista: Zwiewka M, Bielach A, Tamizhselvan P, Madhavan S, Ryad EE, Tan S, Hrtyan M, Dobrev P, Vanková R, Friml J, Tognetti VB. 2019. Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell Physiology. 60(2), 255–273. mla: Zwiewka, Marta, et al. “Root Adaptation to H2O2-Induced Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.” Plant and Cell Physiology, vol. 60, no. 2, Oxford University Press, 2019, pp. 255–73, doi:10.1093/pcp/pcz001. short: M. Zwiewka, A. Bielach, P. Tamizhselvan, S. Madhavan, E.E. Ryad, S. Tan, M. Hrtyan, P. Dobrev, R. Vanková, J. Friml, V.B. Tognetti, Plant and Cell Physiology 60 (2019) 255–273. date_created: 2019-03-17T22:59:14Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-08-25T08:05:28Z day: '01' department: - _id: JiFr doi: 10.1093/pcp/pcz001 external_id: isi: - '000459634300002' pmid: - '30668780' intvolume: ' 60' isi: 1 issue: '2' language: - iso: eng month: '02' oa_version: None page: 255-273 pmid: 1 publication: Plant and Cell Physiology publication_identifier: eissn: - 1471-9053 issn: - 0032-0781 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 60 year: '2019' ... --- _id: '6191' abstract: - lang: eng text: The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis. article_processing_charge: No author: - first_name: Pierre full_name: Recho, Pierre last_name: Recho - first_name: Adrien full_name: Hallou, Adrien last_name: Hallou - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116 apa: Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1813255116 chicago: Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1813255116. ieee: P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019. ista: Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349. mla: Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:10.1073/pnas.1813255116. short: P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349. date_created: 2019-03-31T21:59:13Z date_published: 2019-03-19T00:00:00Z date_updated: 2023-08-25T08:57:30Z day: '19' ddc: - '570' department: - _id: EdHa doi: 10.1073/pnas.1813255116 external_id: isi: - '000461679000027' pmid: - '30819884' file: - access_level: open_access checksum: 8b67eee0ea8e5db61583e4d485215258 content_type: application/pdf creator: dernst date_created: 2019-04-03T14:10:30Z date_updated: 2020-07-14T12:47:23Z file_id: '6193' file_name: 2019_PNAS_Recho.pdf file_size: 3456045 relation: main_file file_date_updated: 2020-07-14T12:47:23Z has_accepted_license: '1' intvolume: ' 116' isi: 1 issue: '12' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 5344-5349 pmid: 1 project: - _id: 268294B6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31639 name: Active mechano-chemical description of the cell cytoskeleton publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: supplementary_material url: www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental scopus_import: '1' status: public title: Theory of mechanochemical patterning in biphasic biological tissues 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: 116 year: '2019' ... --- _id: '6190' abstract: - lang: eng text: "Increased levels of the chemokine CCL2 in cancer patients are associated with poor prognosis. Experimental evidence suggests that CCL2 correlates with inflammatory monocyte recruitment and induction of vascular activation, but the functionality remains open. Here, we show that endothelial Ccr2 facilitates pulmonary metastasis using an endothelial-specific Ccr2-deficient mouse model (Ccr2ecKO). Similar levels of circulating monocytes and equal leukocyte recruitment to metastatic lesions of Ccr2ecKO and Ccr2fl/fl littermates were observed. The absence of endothelial Ccr2 strongly reduced pulmonary metastasis, while the primary tumor growth was unaffected. Despite a comparable cytokine milieu in Ccr2ecKO and Ccr2fl/fl littermates the absence of vascular permeability induction was observed only in Ccr2ecKO mice. CCL2 stimulation of pulmonary endothelial cells resulted in increased phosphorylation of MLC2, endothelial cell retraction, and vascular leakiness that was blocked by an addition of a CCR2 inhibitor. These data demonstrate that endothelial CCR2 expression is required for tumor cell extravasation and pulmonary metastasis.\r\n\r\nImplications: The findings provide mechanistic insight into how CCL2–CCR2 signaling in endothelial cells promotes their activation through myosin light chain phosphorylation, resulting in endothelial retraction and enhanced tumor cell migration and metastasis." article_processing_charge: No article_type: original author: - first_name: Marko full_name: Roblek, Marko id: 3047D808-F248-11E8-B48F-1D18A9856A87 last_name: Roblek orcid: 0000-0001-9588-1389 - first_name: Darya full_name: Protsyuk, Darya last_name: Protsyuk - first_name: Paul F. full_name: Becker, Paul F. last_name: Becker - first_name: Cristina full_name: Stefanescu, Cristina last_name: Stefanescu - first_name: Christian full_name: Gorzelanny, Christian last_name: Gorzelanny - first_name: Jesus F. full_name: Glaus Garzon, Jesus F. last_name: Glaus Garzon - first_name: Lucia full_name: Knopfova, Lucia last_name: Knopfova - first_name: Mathias full_name: Heikenwalder, Mathias last_name: Heikenwalder - first_name: Bruno full_name: Luckow, Bruno last_name: Luckow - first_name: Stefan W. full_name: Schneider, Stefan W. last_name: Schneider - first_name: Lubor full_name: Borsig, Lubor last_name: Borsig citation: ama: Roblek M, Protsyuk D, Becker PF, et al. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 2019;17(3):783-793. doi:10.1158/1541-7786.MCR-18-0530 apa: Roblek, M., Protsyuk, D., Becker, P. F., Stefanescu, C., Gorzelanny, C., Glaus Garzon, J. F., … Borsig, L. (2019). CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. AACR. https://doi.org/10.1158/1541-7786.MCR-18-0530 chicago: Roblek, Marko, Darya Protsyuk, Paul F. Becker, Cristina Stefanescu, Christian Gorzelanny, Jesus F. Glaus Garzon, Lucia Knopfova, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research. AACR, 2019. https://doi.org/10.1158/1541-7786.MCR-18-0530. ieee: M. Roblek et al., “CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis,” Molecular Cancer Research, vol. 17, no. 3. AACR, pp. 783–793, 2019. ista: Roblek M, Protsyuk D, Becker PF, Stefanescu C, Gorzelanny C, Glaus Garzon JF, Knopfova L, Heikenwalder M, Luckow B, Schneider SW, Borsig L. 2019. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 17(3), 783–793. mla: Roblek, Marko, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research, vol. 17, no. 3, AACR, 2019, pp. 783–93, doi:10.1158/1541-7786.MCR-18-0530. short: M. Roblek, D. Protsyuk, P.F. Becker, C. Stefanescu, C. Gorzelanny, J.F. Glaus Garzon, L. Knopfova, M. Heikenwalder, B. Luckow, S.W. Schneider, L. Borsig, Molecular Cancer Research 17 (2019) 783–793. date_created: 2019-03-31T21:59:12Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-25T08:57:01Z day: '01' department: - _id: DaSi doi: 10.1158/1541-7786.MCR-18-0530 external_id: isi: - '000460099800012' pmid: - '30552233' intvolume: ' 17' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1158/1541-7786.MCR-18-0530 month: '03' oa: 1 oa_version: Published Version page: 783-793 pmid: 1 publication: Molecular Cancer Research publication_identifier: eissn: - '15573125' issn: - '15417786' publication_status: published publisher: AACR quality_controlled: '1' scopus_import: '1' status: public title: CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2019' ... --- _id: '6230' abstract: - lang: eng text: Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies. article_number: e45380 article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Joachim full_name: Hermisson, Joachim last_name: Hermisson - first_name: Magnus full_name: Nordborg, Magnus last_name: Nordborg citation: ama: Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380 apa: Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380 chicago: Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380. ieee: N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380. mla: Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380. short: N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019). date_created: 2019-04-07T21:59:15Z date_published: 2019-03-21T00:00:00Z date_updated: 2023-08-25T08:59:38Z day: '21' ddc: - '570' department: - _id: NiBa doi: 10.7554/eLife.45380 external_id: isi: - '000461988300001' file: - access_level: open_access checksum: 130d7544b57df4a6787e1263c2d7ea43 content_type: application/pdf creator: dernst date_created: 2019-04-11T11:43:38Z date_updated: 2020-07-14T12:47:24Z file_id: '6293' file_name: 2019_eLife_Barton.pdf file_size: 298466 relation: main_file file_date_updated: 2020-07-14T12:47:24Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/ scopus_import: '1' status: public title: Why structure matters 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: '6232' abstract: - lang: eng text: 'The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0.' article_processing_charge: No author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser citation: ama: Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability. 2019;47(2):804-834. doi:10.1214/18-AOP1272 apa: Gerencser, M. (2019). Boundary regularity of stochastic PDEs. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1272 chicago: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272. ieee: M. Gerencser, “Boundary regularity of stochastic PDEs,” Annals of Probability, vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019. ista: Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834. mla: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability, vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:10.1214/18-AOP1272. short: M. Gerencser, Annals of Probability 47 (2019) 804–834. date_created: 2019-04-07T21:59:15Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-25T08:59:11Z day: '01' department: - _id: JaMa doi: 10.1214/18-AOP1272 external_id: arxiv: - '1705.05364' isi: - '000459681900005' intvolume: ' 47' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.05364 month: '03' oa: 1 oa_version: Preprint page: 804-834 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: Boundary regularity of stochastic PDEs type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 47 year: '2019' ... --- _id: '6262' abstract: - lang: eng text: "Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Petr full_name: Valošek, Petr id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87 last_name: Valošek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 2019;98(6):1048-1059. doi:10.1111/tpj.14301 apa: Rakusová, H., Han, H., Valošek, P., & Friml, J. (2019). Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.14301 chicago: Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301. ieee: H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,” The Plant Journal, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019. ista: Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 98(6), 1048–1059. mla: Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301. short: H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059. date_created: 2019-04-09T08:46:44Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-25T10:11:03Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/tpj.14301 ec_funded: 1 external_id: isi: - '000473644100008' pmid: - '30821050' file: - access_level: open_access checksum: ad3b5e270b67ba2a45f894ce3be27920 content_type: application/pdf creator: dernst date_created: 2019-04-15T09:38:43Z date_updated: 2020-07-14T12:47:25Z file_id: '6304' file_name: 2019_PlantJournal_Rakusov.pdf file_size: 1383100 relation: main_file file_date_updated: 2020-07-14T12:47:25Z has_accepted_license: '1' intvolume: ' 98' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1048-1059 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: The Plant Journal publication_identifier: eissn: - 1365-313x issn: - 0960-7412 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls 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: 98 year: '2019' ... --- _id: '6297' abstract: - lang: eng text: Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow. article_processing_charge: No article_type: original 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. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002 apa: Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002 chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier, 2019. https://doi.org/10.1016/j.matbio.2018.12.002. ieee: H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019. ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59. mla: Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002. short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59. date_created: 2019-04-11T20:55:01Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-08-25T10:11:28Z day: '01' ddc: - '570' department: - _id: MaLo doi: 10.1016/j.matbio.2018.12.002 external_id: isi: - '000468707600005' file: - access_level: open_access checksum: 790878cd78bfc54a147ddcc7c8f286a0 content_type: application/pdf creator: dernst date_created: 2020-05-14T09:02:07Z date_updated: 2020-07-14T12:47:27Z file_id: '7825' file_name: 2018_MatrixBiology_Davies.pdf file_size: 4444339 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 47-59 publication: Matrix Biology publication_identifier: issn: - 0945-053X publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments 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: 78-79 year: '2019' ... --- _id: '6310' abstract: - lang: eng text: An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary smooth biquadratic hypersurface in sufficiently many variables. The proof uses the Hardy–Littlewood circle method. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: L.Q. full_name: Hu, L.Q. last_name: Hu citation: ama: Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031 apa: Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031 chicago: Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031. ieee: T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,” Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019. ista: Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 349, 920–940. mla: Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp. 920–40, doi:10.1016/j.aim.2019.04.031. short: T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940. date_created: 2019-04-16T09:13:25Z date_published: 2019-06-20T00:00:00Z date_updated: 2023-08-25T10:11:55Z day: '20' ddc: - '512' department: - _id: TiBr doi: 10.1016/j.aim.2019.04.031 external_id: arxiv: - '1810.08426' isi: - '000468857300025' file: - access_level: open_access checksum: a63594a3a91b4ba6e2a1b78b0720b3d0 content_type: application/pdf creator: tbrownin date_created: 2019-04-16T09:12:20Z date_updated: 2020-07-14T12:47:27Z file_id: '6311' file_name: wliqun.pdf file_size: 379158 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' intvolume: ' 349' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 920-940 publication: Advances in Mathematics publication_identifier: eissn: - '10902082' issn: - '00018708' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Counting rational points on biquadratic hypersurfaces type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 349 year: '2019' ... --- _id: '6261' abstract: - lang: eng text: Nitrate regulation of root stem cell activity is auxin-dependent. article_processing_charge: No article_type: letter_note author: - first_name: Y full_name: Wang, Y last_name: Wang - first_name: Z full_name: Gong, Z last_name: Gong - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: J full_name: Zhang, J last_name: Zhang citation: ama: Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305 apa: Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305 chicago: Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305. ieee: Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp. 22–25, 2019. ista: Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 180(1), 22–25. mla: Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305. short: Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25. date_created: 2019-04-09T08:46:17Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-08-25T10:10:23Z day: '01' department: - _id: JiFr doi: 10.1104/pp.18.01305 external_id: isi: - '000466860800010' pmid: - '30787134' intvolume: ' 180' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1104/pp.18.01305 month: '05' oa: 1 oa_version: Published Version page: 22-25 pmid: 1 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: ASPB quality_controlled: '1' scopus_import: '1' status: public title: Nitrate modulates the differentiation of root distal stem cells type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 180 year: '2019' ... --- _id: '6352' abstract: - lang: eng text: Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure. acknowledgement: The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275 article_processing_charge: Yes (via OA deal) author: - first_name: Andrey Alexandrovich full_name: Temnov, Andrey Alexandrovich last_name: Temnov - first_name: Konstantin Arkadevich full_name: Rogov, Konstantin Arkadevich last_name: Rogov - first_name: Alla Nikolaevna full_name: Sklifas, Alla Nikolaevna last_name: Sklifas - first_name: Elena Valerievna full_name: Klychnikova, Elena Valerievna last_name: Klychnikova - first_name: Markus full_name: Hartl, Markus last_name: Hartl - first_name: Kristina full_name: Djinovic-Carugo, Kristina last_name: Djinovic-Carugo - first_name: Alexej full_name: Charnagalov, Alexej id: 49F06DBA-F248-11E8-B48F-1D18A9856A87 last_name: Charnagalov citation: ama: Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z apa: Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z chicago: Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z. ieee: A. A. Temnov et al., “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” Molecular Biology Reports. Springer, 2019. ista: Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. mla: Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z. short: A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019). date_created: 2019-04-28T21:59:14Z date_published: 2019-04-12T00:00:00Z date_updated: 2023-08-25T10:14:26Z day: '12' ddc: - '570' department: - _id: LeSa doi: 10.1007/s11033-019-04765-z external_id: isi: - '000470332600049' file: - access_level: open_access checksum: 45bf040bbce1cea274f6013fa18ba21b content_type: application/pdf creator: dernst date_created: 2019-04-30T09:52:36Z date_updated: 2020-07-14T12:47:28Z file_id: '6362' file_name: 2019_MolecularBioReport_Temnov.pdf file_size: 1948014 relation: main_file file_date_updated: 2020-07-14T12:47:28Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Molecular Biology Reports publication_identifier: eissn: - '15734978' issn: - '03014851' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure 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 year: '2019' ... --- _id: '6348' abstract: - lang: eng text: 'High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.' article_processing_charge: No author: - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: Florian full_name: Sedlmeir, Florian last_name: Sedlmeir - first_name: Madhuri full_name: Kumari, Madhuri last_name: Kumari - first_name: Gerd full_name: Leuchs, Gerd last_name: Leuchs - first_name: Harald G.L. full_name: Schwefel, Harald G.L. last_name: Schwefel citation: ama: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x apa: Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1110-x chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x. ieee: A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019. ista: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381. mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x. short: A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381. date_created: 2019-04-28T21:59:13Z date_published: 2019-04-18T00:00:00Z date_updated: 2023-08-25T10:15:25Z day: '18' department: - _id: JoFi doi: 10.1038/s41586-019-1110-x external_id: arxiv: - '1808.10608' isi: - '000464950700053' intvolume: ' 568' isi: 1 issue: '7752' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.10608 month: '04' oa: 1 oa_version: Preprint page: 378-381 publication: Nature publication_identifier: eissn: - '14764687' issn: - '00280836' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41586-019-1220-5 scopus_import: '1' status: public title: Resonant electro-optic frequency comb type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 568 year: '2019' ... --- _id: '6338' abstract: - lang: eng text: Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning. article_processing_charge: No article_type: original author: - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Peter full_name: Baracskay, Peter id: 361CC00E-F248-11E8-B48F-1D18A9856A87 last_name: Baracskay - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461. doi:10.1016/j.neuron.2019.01.052 apa: Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052 chicago: Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052. ieee: F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” Neuron, vol. 102. Elsevier, pp. 450–461, 2019. ista: Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461. mla: Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052. short: F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461. date_created: 2019-04-17T08:28:59Z date_published: 2019-04-17T00:00:00Z date_updated: 2023-08-25T10:13:07Z day: '17' department: - _id: JoCs doi: 10.1016/j.neuron.2019.01.052 ec_funded: 1 external_id: isi: - '000465169700017' pmid: - '30819547' intvolume: ' 102' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2019.01.052 month: '04' oa: 1 oa_version: Published Version page: 450-461 pmid: 1 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex - _id: 2654F984-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03713 name: Interneuro Plasticity During Spatial Learning publication: Neuron publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/ scopus_import: '1' status: public title: Hippocampal reactivation of random trajectories resembling Brownian diffusion type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 102 year: '2019' ...