[{"date_created":"2023-04-23T16:11:03Z","citation":{"mla":"Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 2738–76.","apa":"Bombari, S., Kiyani, S., & Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.","chicago":"Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In Proceedings of the 40th International Conference on Machine Learning, 202:2738–76. ML Research Press, 2023.","ama":"Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:2738-2776.","ieee":"S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.","short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.","ista":"Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776."},"corr_author":"1","volume":202,"page":"2738-2776","type":"conference","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/simone-bombari/beyond-universal-robustness"}],"record":[{"id":"22857","relation":"dissertation_contains","status":"for_moderation"}]},"acknowledgement":"Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n","_id":"12859","day":"27","language":[{"iso":"eng"}],"quality_controlled":"1","conference":{"location":"Honolulu, HI, United States","end_date":"2023-07-29","name":"ICML: International Conference on Machine Learning","start_date":"2023-07-23"},"external_id":{"arxiv":["2302.01629"]},"main_file_link":[{"url":"https://arxiv.org/abs/2302.01629","open_access":"1"}],"publication_status":"published","intvolume":" 202","date_published":"2023-10-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ML Research Press","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"arxiv":1,"alternative_title":["PMLR"],"year":"2023","publication":"Proceedings of the 40th International Conference on Machine Learning","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this \"universal\" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an \"interaction matrix\", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10)."}],"oa":1,"status":"public","date_updated":"2026-09-17T11:31:16Z","author":[{"id":"ca726dda-de17-11ea-bc14-f9da834f63aa","first_name":"Simone","full_name":"Bombari, Simone","last_name":"Bombari"},{"id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","first_name":"Shayan","full_name":"Kiyani, Shayan","last_name":"Kiyani"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020"}],"title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","month":"10"},{"keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"external_id":{"isi":["000766422000002"]},"fulldoi":"https://doi.org/10.1007/s12095-022-00557-8","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1936-2455"],"issn":["1936-2447"]},"_id":"10842","day":"01","acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","department":[{"_id":"GradSch"}],"article_processing_charge":"No","type":"journal_article","volume":14,"page":"933-948","citation":{"mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” Cryptography and Communications, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:10.1007/s12095-022-00557-8.","ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 2022;14(4):933-948. doi:10.1007/s12095-022-00557-8","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” Cryptography and Communications. Springer Nature, 2022. https://doi.org/10.1007/s12095-022-00557-8.","apa":"Köse, S., & Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. Springer Nature. https://doi.org/10.1007/s12095-022-00557-8","ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” Cryptography and Communications, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022.","short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.","ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948."},"date_created":"2022-03-10T12:16:19Z","date_updated":"2023-09-05T15:35:55Z","status":"public","title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","scopus_import":"1","month":"07","issue":"4","author":[{"first_name":"Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","full_name":"Köse, Seyda","last_name":"Köse"},{"last_name":"Özbudak","full_name":"Özbudak, Ferruh","first_name":"Ferruh"}],"abstract":[{"lang":"eng","text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory."}],"oa_version":"None","article_type":"original","publication":"Cryptography and Communications","year":"2022","isi":1,"doi":"10.1007/s12095-022-00557-8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","intvolume":" 14","publication_status":"published","date_published":"2022-07-01T00:00:00Z"},{"file_date_updated":"2022-08-02T10:37:55Z","date_updated":"2026-04-07T13:27:39Z","oa":1,"status":"public","scopus_import":"1","month":"06","title":"Two-particle bound states at interfaces and corners","issue":"12","author":[{"full_name":"Roos, Barbara","last_name":"Roos","orcid":"0000-0002-9071-5880","first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"publication":"Journal of Functional Analysis","year":"2022","isi":1,"abstract":[{"text":"We study two interacting quantum particles forming a bound state in d-dimensional free\r\nspace, and constrain the particles in k directions to (0, ∞)k ×Rd−k, with Neumann boundary\r\nconditions. First, we prove that the ground state energy strictly decreases upon going from k\r\nto k+1. This shows that the particles stick to the corner where all boundary planes intersect.\r\nSecond, we show that for all k the resulting Hamiltonian, after removing the free part of the\r\nkinetic energy, has only finitely many eigenvalues below the essential spectrum. This paper\r\ngeneralizes the work of Egger, Kerner and Pankrashkin (J. Spectr. Theory 10(4):1413–1444,\r\n2020) to dimensions d > 1.","lang":"eng"}],"oa_version":"Published Version","ddc":["510"],"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"}],"publisher":"Elsevier","doi":"10.1016/j.jfa.2022.109455","article_number":"109455","arxiv":1,"publication_status":"published","intvolume":" 282","date_published":"2022-06-15T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.jfa.2022.109455","file":[{"file_name":"2022_JourFunctionalAnalysis_Roos.pdf","creator":"dernst","relation":"main_file","access_level":"open_access","date_updated":"2022-08-02T10:37:55Z","date_created":"2022-08-02T10:37:55Z","content_type":"application/pdf","file_id":"11720","file_size":631391,"checksum":"63efcefaa1f2717244ef5407bd564426","success":1}],"keyword":["Analysis"],"external_id":{"isi":["000795160200009"],"arxiv":["2105.04874"]},"publication_identifier":{"issn":["0022-1236"]},"_id":"10850","has_accepted_license":"1","day":"15","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"type":"journal_article","article_processing_charge":"Yes (via OA deal)","related_material":{"record":[{"status":"public","id":"14374","relation":"dissertation_contains"}]},"acknowledgement":"We thank Rupert Frank for contributing Appendix B. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 is gratefully acknowledged.","ec_funded":1,"citation":{"ieee":"B. Roos and R. Seiringer, “Two-particle bound states at interfaces and corners,” Journal of Functional Analysis, vol. 282, no. 12. Elsevier, 2022.","short":"B. Roos, R. Seiringer, Journal of Functional Analysis 282 (2022).","ista":"Roos B, Seiringer R. 2022. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 282(12), 109455.","mla":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” Journal of Functional Analysis, vol. 282, no. 12, 109455, Elsevier, 2022, doi:10.1016/j.jfa.2022.109455.","apa":"Roos, B., & Seiringer, R. (2022). Two-particle bound states at interfaces and corners. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2022.109455","chicago":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” Journal of Functional Analysis. Elsevier, 2022. https://doi.org/10.1016/j.jfa.2022.109455.","ama":"Roos B, Seiringer R. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 2022;282(12). doi:10.1016/j.jfa.2022.109455"},"date_created":"2022-03-16T08:41:53Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","volume":282},{"date_published":"2022-03-24T00:00:00Z","intvolume":" 128","publication_status":"published","article_number":"126803","arxiv":1,"doi":"10.1103/PhysRevLett.128.126803","project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","call_identifier":"H2020"},{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Long-range spin exchange for 2D qubits architectures","grant_number":"M03032","_id":"c08c05c4-5a5b-11eb-8a69-dc6ce49d7973"}],"publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"article_type":"original","abstract":[{"text":"The spin-orbit interaction permits to control the state of a spin qubit via electric fields. For holes it is particularly strong, allowing for fast all electrical qubit manipulation, and yet an in-depth understanding of this interaction in hole systems is missing. Here we investigate, experimentally and theoretically, the effect of the cubic Rashba spin-orbit interaction on the mixing of the spin states by studying singlet-triplet oscillations in a planar Ge hole double quantum dot. Landau-Zener sweeps at different magnetic field directions allow us to disentangle the effects of the spin-orbit induced spin-flip term from those caused by strongly site-dependent and anisotropic quantum dot g tensors. Our work, therefore, provides new insights into the hole spin-orbit interaction, necessary for optimizing future qubit experiments.","lang":"eng"}],"oa_version":"Published Version","isi":1,"publication":"Physical Review Letters","year":"2022","month":"03","title":"Dynamics of hole singlet-triplet qubits with large g-factor differences","scopus_import":"1","issue":"12","author":[{"full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"last_name":"Mutter","full_name":"Mutter, Philipp M.","first_name":"Philipp M."},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"full_name":"Crippa, Alessandro","last_name":"Crippa","first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","orcid":"0000-0002-2968-611X"},{"last_name":"Rychetsky","full_name":"Rychetsky, Marek","first_name":"Marek"},{"first_name":"David L.","full_name":"Craig, David L.","last_name":"Craig"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","first_name":"Frederico","orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico","last_name":"Martins"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"full_name":"Ares, Natalia","last_name":"Ares","first_name":"Natalia"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"first_name":"Guido ","last_name":"Burkard","full_name":"Burkard, Guido "},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"date_updated":"2025-04-14T07:44:07Z","status":"public","oa":1,"file_date_updated":"2022-03-28T06:53:39Z","volume":128,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","citation":{"mla":"Jirovec, Daniel, et al. “Dynamics of Hole Singlet-Triplet Qubits with Large g-Factor Differences.” Physical Review Letters, vol. 128, no. 12, 126803, American Physical Society, 2022, doi:10.1103/PhysRevLett.128.126803.","ama":"Jirovec D, Mutter PM, Hofmann AC, et al. Dynamics of hole singlet-triplet qubits with large g-factor differences. Physical Review Letters. 2022;128(12). doi:10.1103/PhysRevLett.128.126803","apa":"Jirovec, D., Mutter, P. M., Hofmann, A. C., Crippa, A., Rychetsky, M., Craig, D. L., … Katsaros, G. (2022). Dynamics of hole singlet-triplet qubits with large g-factor differences. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.128.126803","chicago":"Jirovec, Daniel, Philipp M. Mutter, Andrea C Hofmann, Alessandro Crippa, Marek Rychetsky, David L. Craig, Josip Kukucka, et al. “Dynamics of Hole Singlet-Triplet Qubits with Large g-Factor Differences.” Physical Review Letters. American Physical Society, 2022. https://doi.org/10.1103/PhysRevLett.128.126803.","ieee":"D. Jirovec et al., “Dynamics of hole singlet-triplet qubits with large g-factor differences,” Physical Review Letters, vol. 128, no. 12. American Physical Society, 2022.","short":"D. Jirovec, P.M. Mutter, A.C. Hofmann, A. Crippa, M. Rychetsky, D.L. Craig, J. Kukucka, F. Martins, A. Ballabio, N. Ares, D. Chrastina, G. Isella, G. Burkard, G. Katsaros, Physical Review Letters 128 (2022).","ista":"Jirovec D, Mutter PM, Hofmann AC, Crippa A, Rychetsky M, Craig DL, Kukucka J, Martins F, Ballabio A, Ares N, Chrastina D, Isella G, Burkard G, Katsaros G. 2022. Dynamics of hole singlet-triplet qubits with large g-factor differences. Physical Review Letters. 128(12), 126803."},"date_created":"2022-03-24T15:51:11Z","ec_funded":1,"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 844511, No. 75441, and by the FWF-P 30207, I05060, and M3032-N projects. A. B. acknowledges support from the EU Horizon-2020 FET project microSPIRE, ID: 766955. P.M. M. and G. B. acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG—German Research Foundation) under Project No. 450396347. This work was supported by the Royal Society (URF\\R1\\191150) and the European Research Council (Grant Agreement No. 948932), N. A. acknowledges the use of the University of Oxford Advanced Research Computing (ARC) facility.","related_material":{"record":[{"status":"public","relation":"popular_science","id":"18291"}]},"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"article_processing_charge":"No","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"day":"24","has_accepted_license":"1","publication_identifier":{"eissn":["1079-7114"]},"_id":"10920","external_id":{"isi":["000786542500004"],"pmid":["35394319"],"arxiv":["2111.05130"]},"file":[{"access_level":"open_access","file_name":"2022_PhysRevLetters_Jirovec.pdf","relation":"main_file","creator":"dernst","date_updated":"2022-03-28T06:53:39Z","file_id":"10928","file_size":1266515,"content_type":"application/pdf","date_created":"2022-03-28T06:53:39Z","success":1,"checksum":"6e66ad548d18db9c131f304acbd5a1f4"}],"pmid":1,"fulldoi":"https://doi.org/10.1103/PhysRevLett.128.126803"},{"arxiv":1,"article_number":"A39","doi":"10.1017/jfm.2022.137","publisher":"Cambridge University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-04-25T00:00:00Z","intvolume":" 937","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jfm.2022.137"}],"author":[{"last_name":"Yang","full_name":"Yang, Bowen","orcid":"0000-0002-4843-6853","id":"71b6ff4b-15b2-11ec-abd3-aef6b028cf7e","first_name":"Bowen"},{"first_name":"Zixuan","last_name":"Yang","full_name":"Yang, Zixuan"}],"scopus_import":"1","month":"04","title":"On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow","status":"public","oa":1,"date_updated":"2026-06-18T10:46:00Z","ddc":["530"],"article_type":"original","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Direct numerical simulations (DNS) of turbulent channel flows up to Reτ≈1000 are conducted to investigate the three-dimensional (consisting of streamwise wavenumber, spanwise wavenumber and frequency) spectrum of wall pressure fluctuations. To develop a predictive model of the wavenumber–frequency spectrum from the wavenumber spectrum, the time decorrelation mechanisms of wall pressure fluctuations are investigated. It is discovered that the energy-containing part of the wavenumber–frequency spectrum of wall pressure fluctuations can be well predicted using a similar random sweeping model for streamwise velocity fluctuations. To refine the investigation, we further decompose the spectrum of the total wall pressure fluctuations into the autospectra of rapid and slow pressure fluctuations, and the cross-spectrum between them. We focus on evaluating the assumption applied in many predictive models, that is, the magnitude of the cross-spectrum is negligibly small. The present DNS shows that neglecting the cross-spectrum causes a maximum error up to 4.7 dB in the subconvective region for all Reynolds numbers under test. Our analyses indicate that the approximation of neglecting the cross-spectrum needs to be applied carefully in the investigations of acoustics at low Mach numbers, in which the subconvective components of wall pressure fluctuations make important contributions to the radiated acoustic power."}],"isi":1,"year":"2022","publication":"Journal of Fluid Mechanics","acknowledgement":"This research is supported by the NSFC Basic Science Center Program for ‘Multiscale Problems in Nonlinear Mechanics’ (no. 11988102), National Key Project (GJXM92579) and the Strategic Priority Research Program (XDB22040104).","article_processing_charge":"No","type":"journal_article","department":[{"_id":"GradSch"}],"volume":937,"date_created":"2022-03-27T22:01:45Z","citation":{"chicago":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2022. https://doi.org/10.1017/jfm.2022.137.","ama":"Yang B, Yang Z. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics. 2022;937. doi:10.1017/jfm.2022.137","apa":"Yang, B., & Yang, Z. (2022). On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.137","mla":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” Journal of Fluid Mechanics, vol. 937, A39, Cambridge University Press, 2022, doi:10.1017/jfm.2022.137.","short":"B. Yang, Z. Yang, Journal of Fluid Mechanics 937 (2022).","ieee":"B. Yang and Z. Yang, “On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow,” Journal of Fluid Mechanics, vol. 937. Cambridge University Press, 2022.","ista":"Yang B, Yang Z. 2022. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics. 937, A39."},"external_id":{"arxiv":["2201.04702"],"isi":["000763547000001"]},"fulldoi":"https://doi.org/10.1017/jfm.2022.137","language":[{"iso":"eng"}],"quality_controlled":"1","day":"25","_id":"10925","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]}},{"date_published":"2022-04-06T00:00:00Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:11128","degree_awarded":"PhD","year":"2022","ddc":["576","582"],"abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2022-04-07T08:11:51Z","month":"04","title":"Genetic basis of flower colour as a model for adaptive evolution","author":[{"full_name":"Matejovicova, Lenka","last_name":"Matejovicova","first_name":"Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T14:12:19Z","oa":1,"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"corr_author":"1","citation":{"mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022."},"date_created":"2022-04-07T08:19:54Z","page":"112","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"type":"dissertation","article_processing_charge":"No","day":"06","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"_id":"11128","supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/at:ista:11128","file":[{"creator":"cchlebak","relation":"main_file","file_name":"LenkaPhD_Official_PDFA.pdf","access_level":"open_access","date_updated":"2022-04-07T08:11:34Z","content_type":"application/pdf","date_created":"2022-04-07T08:11:34Z","file_size":11906472,"file_id":"11129","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7"},{"access_level":"closed","file_name":"LenkaPhD Official_source.zip","relation":"source_file","creator":"cchlebak","date_updated":"2022-04-07T08:11:51Z","file_id":"11130","file_size":23036766,"content_type":"application/x-zip-compressed","date_created":"2022-04-07T08:11:51Z","checksum":"99d67040432fd07a225643a212ee8588"}]},{"oa":1,"status":"public","date_updated":"2026-04-07T13:02:12Z","author":[{"full_name":"Reker, Jana","last_name":"Reker","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9","first_name":"Jana"}],"issue":"4","month":"10","scopus_import":"1","title":"On the operator norm of a Hermitian random matrix with correlated entries","year":"2022","publication":"Random Matrices: Theory and Applications","isi":1,"oa_version":"Preprint","abstract":[{"text":"We consider a correlated NxN Hermitian random matrix with a polynomially decaying metric correlation structure. By calculating the trace of the moments of the matrix and using the summable decay of the cumulants, we show that its operator norm is stochastically dominated by one.","lang":"eng"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"World Scientific Publishing","doi":"10.1142/s2010326322500368","arxiv":1,"article_number":"2250036","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2103.03906","open_access":"1"}],"intvolume":" 11","publication_status":"published","date_published":"2022-10-01T00:00:00Z","fulldoi":"https://doi.org/10.1142/s2010326322500368","keyword":["Discrete Mathematics and Combinatorics","Statistics","Probability and Uncertainty","Statistics and Probability","Algebra and Number Theory"],"external_id":{"isi":["000848873800001"],"arxiv":["2103.03906"]},"_id":"11135","publication_identifier":{"eissn":["2010-3271"],"issn":["2010-3263"]},"day":"01","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","type":"journal_article","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"related_material":{"record":[{"id":"17164","relation":"dissertation_contains","status":"public"}]},"date_created":"2022-04-08T07:11:12Z","citation":{"ista":"Reker J. 2022. On the operator norm of a Hermitian random matrix with correlated entries. Random Matrices: Theory and Applications. 11(4), 2250036.","short":"J. Reker, Random Matrices: Theory and Applications 11 (2022).","ieee":"J. Reker, “On the operator norm of a Hermitian random matrix with correlated entries,” Random Matrices: Theory and Applications, vol. 11, no. 4. World Scientific Publishing, 2022.","apa":"Reker, J. (2022). On the operator norm of a Hermitian random matrix with correlated entries. Random Matrices: Theory and Applications. World Scientific Publishing. https://doi.org/10.1142/s2010326322500368","chicago":"Reker, Jana. “On the Operator Norm of a Hermitian Random Matrix with Correlated Entries.” Random Matrices: Theory and Applications. World Scientific Publishing, 2022. https://doi.org/10.1142/s2010326322500368.","ama":"Reker J. On the operator norm of a Hermitian random matrix with correlated entries. Random Matrices: Theory and Applications. 2022;11(4). doi:10.1142/s2010326322500368","mla":"Reker, Jana. “On the Operator Norm of a Hermitian Random Matrix with Correlated Entries.” Random Matrices: Theory and Applications, vol. 11, no. 4, 2250036, World Scientific Publishing, 2022, doi:10.1142/s2010326322500368."},"corr_author":"1","volume":11},{"doi":"10.15479/at:ista:11321","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"9192"},{"id":"8254","relation":"earlier_version","status":"public"},{"status":"public","relation":"used_in_publication","id":"11411"}]},"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","article_processing_charge":"No","date_published":"2022-04-28T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","citation":{"mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321.","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022)."},"date_created":"2022-04-22T09:42:24Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","month":"04","author":[{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","full_name":"Surendranadh, Parvathy"},{"first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","last_name":"Arathoon","full_name":"Arathoon, Louise S"},{"full_name":"Baskett, Carina","last_name":"Baskett","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574"},{"full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","last_name":"Pickup","full_name":"Pickup, Melinda"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"date_updated":"2025-04-15T08:20:40Z","file":[{"content_type":"application/x-zip-compressed","date_created":"2022-04-22T09:39:03Z","file_id":"11326","file_size":13260571,"checksum":"96c1b86cdf25481f2a52972fcc45ca7f","success":1,"file_name":"Data_Code.zip","creator":"larathoo","relation":"main_file","access_level":"open_access","date_updated":"2022-04-22T09:39:03Z"}],"contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon","contributor_type":"project_member"},{"last_name":"Baskett","contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","orcid":"0000-0002-7354-8574"},{"last_name":"Field","contributor_type":"project_member","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","contributor_type":"project_member","last_name":"Pickup"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","contributor_type":"project_member","last_name":"Barton"}],"oa":1,"status":"public","fulldoi":"https://doi.org/10.15479/at:ista:11321","file_date_updated":"2022-04-22T09:39:03Z","ddc":["570"],"abstract":[{"text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. ","lang":"eng"}],"oa_version":"Published Version","day":"28","has_accepted_license":"1","_id":"11321","year":"2022"},{"intvolume":" 3","publication_status":"published","date_published":"2022-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","doi":"10.1038/s43017-022-00302-y","year":"2022","publication":"Nature Reviews Earth and Environment","isi":1,"oa_version":"None","article_type":"original","status":"public","date_updated":"2024-10-09T21:02:28Z","issue":"6","author":[{"orcid":"0000-0002-0464-8440","first_name":"Andrea","id":"4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed","last_name":"Stöllner","full_name":"Stöllner, Andrea"}],"month":"06","title":"Measuring airborne nanoplastics using aerosol physics","scopus_import":"1","date_created":"2022-05-22T22:01:41Z","citation":{"mla":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” Nature Reviews Earth and Environment, vol. 3, no. 6, Springer Nature, 2022, p. 360, doi:10.1038/s43017-022-00302-y.","ama":"Stöllner A. Measuring airborne nanoplastics using aerosol physics. Nature Reviews Earth and Environment. 2022;3(6):360. doi:10.1038/s43017-022-00302-y","chicago":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” Nature Reviews Earth and Environment. Springer Nature, 2022. https://doi.org/10.1038/s43017-022-00302-y.","apa":"Stöllner, A. (2022). Measuring airborne nanoplastics using aerosol physics. Nature Reviews Earth and Environment. Springer Nature. https://doi.org/10.1038/s43017-022-00302-y","ieee":"A. Stöllner, “Measuring airborne nanoplastics using aerosol physics,” Nature Reviews Earth and Environment, vol. 3, no. 6. Springer Nature, p. 360, 2022.","short":"A. Stöllner, Nature Reviews Earth and Environment 3 (2022) 360.","ista":"Stöllner A. 2022. Measuring airborne nanoplastics using aerosol physics. Nature Reviews Earth and Environment. 3(6), 360."},"corr_author":"1","volume":3,"page":"360","article_processing_charge":"No","type":"journal_article","department":[{"_id":"GradSch"}],"_id":"11403","publication_identifier":{"eissn":["2662-138X"]},"day":"01","language":[{"iso":"eng"}],"quality_controlled":"1","fulldoi":"https://doi.org/10.1038/s43017-022-00302-y","external_id":{"isi":["000791125600002"]}},{"publisher":"Oxford University Press","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"iyac083","doi":"10.1093/genetics/iyac083","date_published":"2022-07-01T00:00:00Z","publication_status":"published","intvolume":" 221","file_date_updated":"2022-05-26T12:48:21Z","author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"full_name":"Arathoon, Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","orcid":"0000-0003-1771-714X"},{"last_name":"Baskett","full_name":"Baskett, Carina","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574"},{"last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"},{"full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"issue":"3","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","scopus_import":"1","month":"07","status":"public","oa":1,"date_updated":"2026-04-07T13:28:29Z","isi":1,"year":"2022","publication":"Genetics","article_type":"original","ddc":["576"],"oa_version":"Submitted Version","abstract":[{"text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"9192","relation":"research_data"},{"status":"public","id":"11321","relation":"research_data"},{"relation":"dissertation_contains","id":"14651","status":"public"}]},"article_processing_charge":"No","type":"journal_article","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2022-05-26T13:44:50Z","citation":{"mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac083","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3. Oxford University Press, 2022.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083."},"volume":221,"fulldoi":"https://doi.org/10.1093/genetics/iyac083","pmid":1,"external_id":{"pmid":["35639938"],"isi":["000803735800001"]},"file":[{"checksum":"cc2d56deb608bd53c5cc02f03a875107","success":1,"date_created":"2022-05-26T12:48:15Z","content_type":"application/pdf","file_size":885374,"file_id":"11412","date_updated":"2022-05-26T12:48:15Z","creator":"larathoo","relation":"main_file","file_name":"Manuscript.pdf","access_level":"open_access"},{"checksum":"693742595b6c7ed809423be01460d083","success":1,"content_type":"application/pdf","date_created":"2022-05-26T12:48:21Z","file_id":"11413","file_size":1401704,"date_updated":"2022-05-26T12:48:21Z","file_name":"SupplementalMaterial.pdf","creator":"larathoo","relation":"main_file","access_level":"open_access"}],"day":"01","has_accepted_license":"1","_id":"11411","publication_identifier":{"eissn":["1943-2631"]},"language":[{"iso":"eng"}],"quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"grant_number":"I05127","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation"}],"doi":"10.1007/s11538-022-01029-z","article_number":"74","intvolume":" 84","publication_status":"published","date_published":"2022-06-17T00:00:00Z","file_date_updated":"2022-06-20T07:51:32Z","oa":1,"status":"public","date_updated":"2026-06-12T12:43:34Z","issue":"8","author":[{"full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","orcid":"0000-0001-5103-038X","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova"}],"scopus_import":"1","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","month":"06","year":"2022","publication":"Bulletin of Mathematical Biology","isi":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks."}],"ddc":["510","570"],"article_type":"original","article_processing_charge":"Yes (via OA deal)","type":"journal_article","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}],"record":[{"status":"public","id":"21918","relation":"dissertation_contains"}]},"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","ec_funded":1,"date_created":"2022-06-17T16:16:15Z","citation":{"ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z.","apa":"Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z"},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","volume":84,"fulldoi":"https://doi.org/10.1007/s11538-022-01029-z","pmid":1,"keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"file":[{"date_created":"2022-06-20T07:51:32Z","content_type":"application/pdf","file_id":"11455","file_size":463025,"checksum":"05a1fe7d10914a00c2bca9b447993a65","success":1,"file_name":"2022_BulletinMathBiology_Saona.pdf","creator":"dernst","relation":"main_file","access_level":"open_access","date_updated":"2022-06-20T07:51:32Z"}],"external_id":{"isi":["000812509800001"],"pmid":["35713756"]},"_id":"11447","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"has_accepted_license":"1","day":"17","language":[{"iso":"eng"}],"quality_controlled":"1"},{"doi":"10.7554/elife.75842","article_number":"75842","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"eLife Sciences Publications","project":[{"name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"intvolume":" 11","publication_status":"published","date_published":"2022-05-05T00:00:00Z","oa":1,"status":"public","date_updated":"2026-04-07T13:25:01Z","author":[{"full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fleiss, Aubin","last_name":"Fleiss","first_name":"Aubin"},{"full_name":"Mishin, Alexander S","last_name":"Mishin","first_name":"Alexander S"},{"first_name":"Nina G","last_name":"Bozhanova","full_name":"Bozhanova, Nina G"},{"first_name":"Anna A","last_name":"Igolkina","full_name":"Igolkina, Anna A"},{"first_name":"Jens","last_name":"Meiler","full_name":"Meiler, Jens"},{"full_name":"Alaball Pujol, Maria-Elisenda","last_name":"Alaball Pujol","first_name":"Maria-Elisenda"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V"},{"full_name":"Sarkisyan, Karen S","last_name":"Sarkisyan","first_name":"Karen S"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"}],"scopus_import":"1","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","month":"05","file_date_updated":"2022-06-20T07:44:19Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering."}],"ddc":["570"],"article_type":"original","year":"2022","publication":"eLife","isi":1,"acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","ec_funded":1,"type":"journal_article","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"related_material":{"record":[{"id":"17850","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks","relation":"software"}]},"volume":11,"date_created":"2022-06-18T09:06:59Z","citation":{"short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","ieee":"L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications, 2022.","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.75842.","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842","ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences Publications, 2022, doi:10.7554/elife.75842."},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"corr_author":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"file":[{"creator":"dernst","relation":"main_file","file_name":"2022_eLife_Somermeyer.pdf","access_level":"open_access","date_updated":"2022-06-20T07:44:19Z","content_type":"application/pdf","date_created":"2022-06-20T07:44:19Z","file_size":5297213,"file_id":"11454","checksum":"7573c28f44028ab0cc81faef30039e44","success":1}],"external_id":{"pmid":["35510622"],"isi":["000799197200001"]},"fulldoi":"https://doi.org/10.7554/elife.75842","pmid":1,"language":[{"iso":"eng"}],"quality_controlled":"1","_id":"11448","publication_identifier":{"issn":["2050-084X"]},"has_accepted_license":"1","day":"05"},{"file_date_updated":"2022-06-27T07:38:21Z","oa":1,"status":"public","date_updated":"2025-04-14T07:52:47Z","author":[{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde"},{"last_name":"Chang","full_name":"Chang, Bor-Yuh Evan","first_name":"Bor-Yuh Evan"},{"full_name":"Bolignano, Pauline","last_name":"Bolignano","first_name":"Pauline"},{"last_name":"Raimondi","full_name":"Raimondi, Franco","first_name":"Franco"}],"month":"06","title":"Differential cost analysis with simultaneous potentials and anti-potentials","scopus_import":"1","year":"2022","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","isi":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples."}],"ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Association for Computing Machinery","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1145/3519939.3523435","arxiv":1,"publication_status":"published","date_published":"2022-06-09T00:00:00Z","fulldoi":"https://doi.org/10.1145/3519939.3523435","file":[{"success":1,"checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","file_size":318697,"file_id":"11466","date_created":"2022-06-27T07:38:21Z","content_type":"application/pdf","date_updated":"2022-06-27T07:38:21Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2022_PLDI_Zikelic.pdf"}],"conference":{"end_date":"2022-06-17","location":"San Diego, CA, United States","start_date":"2022-06-13","name":"PLDI: Programming Language Design and Implementation"},"external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]},"_id":"11459","publication_identifier":{"isbn":["9781450392655"]},"day":"09","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt).","ec_funded":1,"date_created":"2022-06-21T09:26:15Z","citation":{"ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, San Diego, CA, United States, 2022, pp. 442–457.","short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457.","ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–57, doi:10.1145/3519939.3523435.","ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2022:442-457. doi:10.1145/3519939.3523435","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 442–57. Association for Computing Machinery, 2022. https://doi.org/10.1145/3519939.3523435.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., & Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3519939.3523435"},"corr_author":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"page":"442-457"},{"date_published":"2022-08-01T00:00:00Z","publication_status":"published","intvolume":" 106","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00253-022-12022-w","isi":1,"publication":"Applied Microbiology and Biotechnology","year":"2022","article_type":"original","abstract":[{"text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens.","lang":"eng"}],"oa_version":"None","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","scopus_import":"1","month":"08","author":[{"last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri","first_name":"Dmitri"},{"first_name":"Michail","full_name":"Shapira, Michail","last_name":"Shapira"},{"last_name":"Karputs","full_name":"Karputs, Alena","first_name":"Alena"},{"full_name":"Kavaleuski, Anton","last_name":"Kavaleuski","first_name":"Anton","id":"62304f89-eb97-11eb-a6c2-8903dd183976","orcid":"0000-0003-2091-526X"},{"full_name":"Kuzminski, Ivan","last_name":"Kuzminski","first_name":"Ivan"},{"first_name":"Elena","full_name":"Stepanova, Elena","last_name":"Stepanova"},{"first_name":"Andrei","full_name":"Gilep, Andrei","last_name":"Gilep"}],"date_updated":"2023-10-10T07:15:02Z","status":"public","citation":{"ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","ieee":"D. Dormeshkin et al., “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” Applied Microbiology and Biotechnology, vol. 106. Springer Nature, pp. 5093–5103, 2022.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 2022;106:5093-5103. doi:10.1007/s00253-022-12022-w","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” Applied Microbiology and Biotechnology. Springer Nature, 2022. https://doi.org/10.1007/s00253-022-12022-w.","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., & Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. Springer Nature. https://doi.org/10.1007/s00253-022-12022-w","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” Applied Microbiology and Biotechnology, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:10.1007/s00253-022-12022-w."},"date_created":"2022-06-26T22:01:34Z","page":"5093-5103","volume":106,"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"article_processing_charge":"No","type":"journal_article","acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","day":"01","publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"_id":"11462","quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1007/s00253-022-12022-w","external_id":{"isi":["000813677500001"],"pmid":["35723693"]}},{"fulldoi":"https://doi.org/10.15479/at:ista:11473","file":[{"date_created":"2022-07-05T08:12:56Z","content_type":"application/pdf","file_id":"11486","file_size":1830973,"checksum":"7970714a20a6052f75fb27a6c3e9976e","success":1,"file_name":"thes1_no_isbn_2_1b.pdf","creator":"kmysliwy","relation":"main_file","access_level":"open_access","date_updated":"2022-07-05T08:12:56Z"},{"date_created":"2022-07-05T08:15:52Z","content_type":"application/zip","file_id":"11487","file_size":5831060,"checksum":"647a2011fdf56277096c9350fefe1097","file_name":"thes_source.zip","creator":"kmysliwy","relation":"source_file","access_level":"closed","date_updated":"2022-07-05T08:17:12Z"}],"_id":"11473","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","day":"01","supervisor":[{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"related_material":{"record":[{"status":"public","id":"10564","relation":"part_of_dissertation"},{"status":"public","id":"8705","relation":"part_of_dissertation"}]},"ec_funded":1,"date_created":"2022-06-30T12:15:03Z","citation":{"ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.","apa":"Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473","mla":"Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022."},"acknowledged_ssus":[{"_id":"SSU"}],"corr_author":"1","OA_place":"publisher","page":"138","file_date_updated":"2022-07-05T08:17:12Z","oa":1,"status":"public","date_updated":"2026-04-07T14:14:52Z","author":[{"first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof"}],"title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","month":"07","year":"2022","degree_awarded":"PhD","oa_version":"Published Version","abstract":[{"text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n","lang":"eng"}],"ddc":["515","539"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"doi":"10.15479/at:ista:11473","alternative_title":["ISTA Thesis"],"publication_status":"published","date_published":"2022-07-01T00:00:00Z"},{"oa_version":"None","has_accepted_license":"1","year":"2022","_id":"11542","title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","author":[{"full_name":"Schulz, Rouven","last_name":"Schulz","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven"}],"file":[{"success":1,"checksum":"71e8186583f3adbb6c69a88ac9e6e49b","file_id":"11543","file_size":135784571,"date_created":"2022-07-08T10:56:52Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","date_updated":"2022-07-08T10:56:52Z","access_level":"open_access","file_name":"Source Data.xlsx","creator":"rschulz","relation":"main_file"}],"date_updated":"2025-04-15T07:27:21Z","status":"public","contributor":[{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert","contributor_type":"contact_person"}],"oa":1,"fulldoi":"https://doi.org/10.15479/AT:ISTA:11542","file_date_updated":"2022-07-08T10:56:52Z","date_published":"2022-01-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","citation":{"mla":"Schulz, Rouven. Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses). Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11542.","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11542.","apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11542","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:10.15479/AT:ISTA:11542","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","short":"R. Schulz, (2022).","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, 10.15479/AT:ISTA:11542."},"date_created":"2022-07-08T11:03:02Z","doi":"10.15479/AT:ISTA:11542","related_material":{"record":[{"id":"11995","relation":"used_in_publication","status":"public"}],"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1","relation":"contains"}]},"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"research_data"},{"isi":1,"publication":"Journal of Computational Physics","year":"2022","article_type":"original","ddc":["518"],"abstract":[{"text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise.","lang":"eng"}],"oa_version":"Preprint","month":"10","scopus_import":"1","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","author":[{"full_name":"Kalinov, Aleksei","last_name":"Kalinov","first_name":"Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","orcid":"0000-0003-2189-3904"},{"last_name":"Osinskiy","full_name":"Osinskiy, A.I.","first_name":"A.I."},{"full_name":"Matveev, S.A.","last_name":"Matveev","first_name":"S.A."},{"first_name":"W.","full_name":"Otieno, W.","last_name":"Otieno"},{"last_name":"Brilliantov","full_name":"Brilliantov, N.V.","first_name":"N.V."}],"date_updated":"2024-10-21T06:01:47Z","status":"public","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.09481","open_access":"1"}],"date_published":"2022-10-15T00:00:00Z","intvolume":" 467","publication_status":"published","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"111439","arxiv":1,"doi":"10.1016/j.jcp.2022.111439","day":"15","publication_identifier":{"issn":["0021-9991"]},"_id":"11556","quality_controlled":"1","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.jcp.2022.111439","external_id":{"arxiv":["2103.09481"],"isi":["000917225500013"]},"keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"citation":{"mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” Journal of Computational Physics, vol. 467, 111439, Elsevier, 2022, doi:10.1016/j.jcp.2022.111439.","chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” Journal of Computational Physics. Elsevier, 2022. https://doi.org/10.1016/j.jcp.2022.111439.","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., & Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2022.111439","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 2022;467. doi:10.1016/j.jcp.2022.111439","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” Journal of Computational Physics, vol. 467. Elsevier, 2022.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022)."},"date_created":"2022-07-11T12:19:59Z","volume":467,"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"article_processing_charge":"No","type":"journal_article","acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021)."},{"OA_place":"publisher","page":"248","date_created":"2022-07-20T11:21:53Z","citation":{"ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626.","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626"},"corr_author":"1","ec_funded":1,"type":"dissertation","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8138","status":"public"},{"status":"public","id":"7142","relation":"part_of_dissertation"},{"status":"public","id":"10411","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8931"},{"status":"public","id":"7465","relation":"part_of_dissertation"},{"status":"public","id":"9287","relation":"part_of_dissertation"},{"id":"6260","relation":"part_of_dissertation","status":"public"}]},"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Eilon","full_name":"Shani, Eilon","last_name":"Shani"}],"language":[{"iso":"eng"}],"_id":"11626","publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"day":"20","has_accepted_license":"1","file":[{"access_level":"open_access","relation":"main_file","creator":"mgallei","file_name":"Thesis_Gallei.pdf","date_updated":"2022-07-25T09:08:47Z","file_size":9730864,"file_id":"11645","content_type":"application/pdf","date_created":"2022-07-25T09:08:47Z","checksum":"bd7ac35403cf5b4b2607287d2a104b3a"},{"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","date_created":"2022-07-25T09:09:09Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19560720,"file_id":"11646","date_updated":"2022-07-25T09:39:58Z","relation":"source_file","creator":"mgallei","file_name":"Thesis_Gallei_source.docx","access_level":"closed"},{"checksum":"3994f7f20058941b5bb8a16886b21e71","content_type":"application/pdf","date_created":"2022-07-25T09:09:32Z","file_id":"11647","description":"This is the print version of the thesis including the full appendix","file_size":24542837,"date_updated":"2022-07-25T09:39:58Z","file_name":"Thesis_Gallei_to_print.pdf","relation":"source_file","creator":"mgallei","access_level":"closed"},{"date_updated":"2022-07-25T11:48:45Z","access_level":"open_access","file_name":"Thesis_Gallei_Appendix.pdf","creator":"mgallei","relation":"main_file","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","file_id":"11650","file_size":15435966,"date_created":"2022-07-25T11:48:45Z","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.15479/at:ista:11626","publication_status":"published","date_published":"2022-07-20T00:00:00Z","doi":"10.15479/at:ista:11626","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"oa_version":"Published Version","abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"ddc":["575"],"year":"2022","degree_awarded":"PhD","status":"public","oa":1,"date_updated":"2026-06-18T19:02:05Z","author":[{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"}],"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","month":"07","file_date_updated":"2022-07-25T11:48:45Z"},{"year":"2022","publication":"Leibniz International Proceedings on Mathematics","ddc":["510"],"oa_version":"Submitted Version","abstract":[{"text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements.","lang":"eng"}],"file_date_updated":"2022-07-27T09:25:53Z","author":[{"orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita"},{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"month":"07","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","status":"public","oa":1,"date_updated":"2026-04-07T12:58:48Z","date_published":"2022-07-27T00:00:00Z","publication_status":"draft","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"name":"Mathematics, Computer Science","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"27","has_accepted_license":"1","_id":"11658","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"file_id":"11659","file_size":639266,"date_created":"2022-07-27T09:25:53Z","content_type":"application/pdf","checksum":"b2f511e8b1cae5f1892b0cdec341acac","access_level":"open_access","file_name":"D-S-E.pdf","creator":"scultrer","relation":"main_file","date_updated":"2022-07-27T09:25:53Z"}],"corr_author":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2022-07-27T09:27:34Z","citation":{"ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” Leibniz International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” Leibniz International Proceedings on Mathematics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” Leibniz International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics."},"related_material":{"record":[{"status":"public","id":"15380","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"15094"}]},"type":"journal_article","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35."},{"year":"2022","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"ddc":["580"],"article_type":"original","file_date_updated":"2022-08-08T07:42:09Z","oa":1,"status":"public","date_updated":"2025-05-14T11:01:00Z","issue":"31","author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li","full_name":"Li, Lanxin"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","full_name":"Chen, Huihuang","last_name":"Chen"},{"first_name":"Saqer S.","full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","scopus_import":"1","month":"07","intvolume":" 119","publication_status":"published","date_published":"2022-07-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","project":[{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1073/pnas.2121058119","article_number":"e2121058119","_id":"11723","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"has_accepted_license":"1","day":"25","language":[{"iso":"eng"}],"quality_controlled":"1","fulldoi":"https://doi.org/10.1073/pnas.2121058119","pmid":1,"keyword":["Multidisciplinary"],"file":[{"date_created":"2022-08-08T07:42:09Z","content_type":"application/pdf","file_size":2506262,"file_id":"11747","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","success":1,"creator":"dernst","relation":"main_file","file_name":"2022_PNAS_Li.pdf","access_level":"open_access","date_updated":"2022-08-08T07:42:09Z"}],"external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"date_created":"2022-08-04T20:06:49Z","citation":{"ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121058119.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31. National Academy of Sciences, 2022.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., & Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2121058119","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31, e2121058119, National Academy of Sciences, 2022, doi:10.1073/pnas.2121058119."},"corr_author":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"volume":119,"type":"journal_article","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”"}]