[{"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.","volume":84,"external_id":{"isi":["000812509800001"]},"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","day":"17","year":"2022","issue":"8","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"citation":{"short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","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.","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022."},"date_updated":"2023-08-03T07:20:53Z","_id":"11447","file_date_updated":"2022-06-20T07:51:32Z","project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"},{"grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","name":"Evolutionary analysis of gene regulation"}],"date_created":"2022-06-17T16:16:15Z","publication_status":"published","file":[{"success":1,"date_updated":"2022-06-20T07:51:32Z","file_name":"2022_BulletinMathBiology_Saona.pdf","access_level":"open_access","file_size":463025,"file_id":"11455","content_type":"application/pdf","creator":"dernst","checksum":"05a1fe7d10914a00c2bca9b447993a65","date_created":"2022-06-20T07:51:32Z","relation":"main_file"}],"ddc":["510","570"],"abstract":[{"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.","lang":"eng"}],"date_published":"2022-06-17T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","article_number":"74","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","month":"06","author":[{"last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11538-022-01118-z"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication":"Bulletin of Mathematical Biology","oa_version":"Published Version","doi":"10.1007/s11538-022-01029-z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"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"],"oa":1,"publisher":"Springer Nature","intvolume":"        84","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"publication_status":"published","date_created":"2022-06-18T09:06:59Z","date_updated":"2023-08-03T07:20:15Z","_id":"11448","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file_date_updated":"2022-06-20T07:44:19Z","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"citation":{"ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","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.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>.","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. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>","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.","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 <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"year":"2022","external_id":{"isi":["000799197200001"]},"title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","day":"05","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.","volume":11,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"eLife Sciences Publications","oa":1,"intvolume":"        11","isi":1,"doi":"10.7554/elife.75842","type":"journal_article","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"issn":["2050-084X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"ec_funded":1,"language":[{"iso":"eng"}],"publication":"eLife","oa_version":"Published Version","article_processing_charge":"No","scopus_import":"1","month":"05","author":[{"last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","first_name":"Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aubin","last_name":"Fleiss","full_name":"Fleiss, 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"},{"full_name":"Igolkina, Anna A","last_name":"Igolkina","first_name":"Anna A"},{"last_name":"Meiler","full_name":"Meiler, Jens","first_name":"Jens"},{"last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda","first_name":"Maria-Elisenda"},{"first_name":"Ekaterina V","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V"},{"first_name":"Karen S","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"has_accepted_license":"1","article_number":"75842","status":"public","article_type":"original","quality_controlled":"1","file":[{"creator":"dernst","checksum":"7573c28f44028ab0cc81faef30039e44","relation":"main_file","date_created":"2022-06-20T07:44:19Z","success":1,"file_name":"2022_eLife_Somermeyer.pdf","date_updated":"2022-06-20T07:44:19Z","file_size":5297213,"access_level":"open_access","content_type":"application/pdf","file_id":"11454"}],"ddc":["570"],"abstract":[{"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.","lang":"eng"}],"date_published":"2022-05-05T00:00:00Z"},{"date_published":"2022-06-09T00:00:00Z","ddc":["000"],"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."}],"file":[{"date_created":"2022-06-27T07:38:21Z","relation":"main_file","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","creator":"dernst","file_id":"11466","content_type":"application/pdf","access_level":"open_access","file_size":318697,"date_updated":"2022-06-27T07:38:21Z","file_name":"2022_PLDI_Zikelic.pdf","success":1}],"quality_controlled":"1","status":"public","has_accepted_license":"1","author":[{"first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","full_name":"Zikelic, Dorde"},{"full_name":"Chang, Bor-Yuh Evan","last_name":"Chang","first_name":"Bor-Yuh Evan"},{"last_name":"Bolignano","full_name":"Bolignano, Pauline","first_name":"Pauline"},{"first_name":"Franco","last_name":"Raimondi","full_name":"Raimondi, Franco"}],"month":"06","scopus_import":"1","article_processing_charge":"No","arxiv":1,"oa_version":"Published Version","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450392655"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","page":"442-457","doi":"10.1145/3519939.3523435","isi":1,"publisher":"Association for Computing Machinery","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"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).","day":"09","title":"Differential cost analysis with simultaneous potentials and anti-potentials","external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]},"year":"2022","citation":{"ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>.","ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>","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.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>"},"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2022-06-17","start_date":"2022-06-13","location":"San Diego, CA, United States"},"file_date_updated":"2022-06-27T07:38:21Z","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"_id":"11459","date_updated":"2025-07-14T09:09:54Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2022-06-21T09:26:15Z","publication_status":"published"},{"volume":106,"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","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","external_id":{"pmid":["35723693"],"isi":["000813677500001"]},"year":"2022","citation":{"ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","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.","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","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.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>"},"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"_id":"11462","date_updated":"2023-10-10T07:15:02Z","pmid":1,"date_created":"2022-06-26T22:01:34Z","publication_status":"published","date_published":"2022-08-01T00:00:00Z","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","article_type":"original","status":"public","author":[{"first_name":"Dmitri","full_name":"Dormeshkin, Dmitri","last_name":"Dormeshkin"},{"last_name":"Shapira","full_name":"Shapira, Michail","first_name":"Michail"},{"full_name":"Karputs, Alena","last_name":"Karputs","first_name":"Alena"},{"full_name":"Kavaleuski, Anton","last_name":"Kavaleuski","id":"62304f89-eb97-11eb-a6c2-8903dd183976","orcid":"0000-0003-2091-526X","first_name":"Anton"},{"full_name":"Kuzminski, Ivan","last_name":"Kuzminski","first_name":"Ivan"},{"first_name":"Elena","full_name":"Stepanova, Elena","last_name":"Stepanova"},{"full_name":"Gilep, Andrei","last_name":"Gilep","first_name":"Andrei"}],"month":"08","article_processing_charge":"No","scopus_import":"1","publication":"Applied Microbiology and Biotechnology","oa_version":"None","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"type":"journal_article","doi":"10.1007/s00253-022-12022-w","page":"5093-5103","isi":1,"intvolume":"       106","publisher":"Springer Nature"},{"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2022-06-30T12:15:03Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"file_date_updated":"2022-07-05T08:17:12Z","_id":"11473","date_updated":"2023-09-07T13:43:52Z","citation":{"ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","apa":"Mysliwy, K. (2022). <i>Polarons in Bose gases and polar crystals: Some rigorous energy estimates</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>","mla":"Mysliwy, Krzysztof. <i>Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>.","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>."},"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"year":"2022","day":"01","title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"SSU"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","page":"138","degree_awarded":"PhD","doi":"10.15479/at:ista:11473","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"id":"10564","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8705"}]},"author":[{"first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof"}],"month":"07","article_processing_charge":"No","has_accepted_license":"1","status":"public","date_published":"2022-07-01T00:00:00Z","ddc":["515","539"],"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"}],"file":[{"relation":"main_file","date_created":"2022-07-05T08:12:56Z","checksum":"7970714a20a6052f75fb27a6c3e9976e","creator":"kmysliwy","content_type":"application/pdf","file_id":"11486","file_size":1830973,"access_level":"open_access","file_name":"thes1_no_isbn_2_1b.pdf","date_updated":"2022-07-05T08:12:56Z","success":1},{"file_name":"thes_source.zip","date_updated":"2022-07-05T08:17:12Z","file_id":"11487","content_type":"application/zip","access_level":"closed","file_size":5831060,"checksum":"647a2011fdf56277096c9350fefe1097","creator":"kmysliwy","date_created":"2022-07-05T08:15:52Z","relation":"source_file"}]},{"scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Alwen","full_name":"Alwen, Joël","first_name":"Joël"},{"first_name":"Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","full_name":"Auerbach, Benedikt"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","full_name":"Cueto Noval, Miguel","last_name":"Cueto Noval"},{"first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","full_name":"Klein, Karen"},{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","first_name":"Guillermo","full_name":"Pascual Perez, Guillermo","last_name":"Pascual Perez"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"last_name":"Walter","full_name":"Walter, Michael","first_name":"Michael"}],"month":"05","date_published":"2022-05-25T00:00:00Z","place":"Cham","abstract":[{"text":"Messaging platforms like Signal are widely deployed and provide strong security in an asynchronous setting. It is a challenging problem to construct a protocol with similar security guarantees that can efficiently scale to large groups. A major bottleneck are the frequent key rotations users need to perform to achieve post compromise forward security.\r\n\r\nIn current proposals – most notably in TreeKEM (which is part of the IETF’s Messaging Layer Security (MLS) protocol draft) – for users in a group of size n to rotate their keys, they must each craft a message of size log(n) to be broadcast to the group using an (untrusted) delivery server.\r\n\r\nIn larger groups, having users sequentially rotate their keys requires too much bandwidth (or takes too long), so variants allowing any T≤n users to simultaneously rotate their keys in just 2 communication rounds have been suggested (e.g. “Propose and Commit” by MLS). Unfortunately, 2-round concurrent updates are either damaging or expensive (or both); i.e. they either result in future operations being more costly (e.g. via “blanking” or “tainting”) or are costly themselves requiring Ω(T) communication for each user [Bienstock et al., TCC’20].\r\n\r\nIn this paper we propose CoCoA; a new scheme that allows for T concurrent updates that are neither damaging nor costly. That is, they add no cost to future operations yet they only require Ω(log2(n)) communication per user. To circumvent the [Bienstock et al.] lower bound, CoCoA increases the number of rounds needed to complete all updates from 2 up to (at most) log(n); though typically fewer rounds are needed.\r\n\r\nThe key insight of our protocol is the following: in the (non-concurrent version of) TreeKEM, a delivery server which gets T concurrent update requests will approve one and reject the remaining T−1. In contrast, our server attempts to apply all of them. If more than one user requests to rotate the same key during a round, the server arbitrarily picks a winner. Surprisingly, we prove that regardless of how the server chooses the winners, all previously compromised users will recover after at most log(n) such update rounds.\r\n\r\nTo keep the communication complexity low, CoCoA is a server-aided CGKA. That is, the delivery server no longer blindly forwards packets, but instead actively computes individualized packets tailored to each user. As the server is untrusted, this change requires us to develop new mechanisms ensuring robustness of the protocol.","lang":"eng"}],"status":"public","quality_controlled":"1","oa":1,"publisher":"Springer Nature","isi":1,"intvolume":"     13276","oa_version":"Preprint","publication":"Advances in Cryptology – EUROCRYPT 2022","ec_funded":1,"language":[{"iso":"eng"}],"page":"815–844","doi":"10.1007/978-3-031-07085-3_28","publication_identifier":{"eisbn":["9783031070853"],"issn":["0302-9743"],"isbn":["9783031070846"],"eissn":["1611-3349"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","year":"2022","volume":13276,"acknowledgement":"We thank Marta Mularczyk and Yiannis Tselekounis for their very helpful feedback on an earlier draft of this paper.","external_id":{"isi":["000832305300028"]},"day":"25","title":"CoCoA: Concurrent continuous group key agreement","date_created":"2022-06-30T16:48:00Z","alternative_title":["LNCS"],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/251"}],"citation":{"ieee":"J. Alwen <i>et al.</i>, “CoCoA: Concurrent continuous group key agreement,” in <i>Advances in Cryptology – EUROCRYPT 2022</i>, Trondheim, Norway, 2022, vol. 13276, pp. 815–844.","short":"J. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2022, Springer Nature, Cham, 2022, pp. 815–844.","apa":"Alwen, J., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., Pietrzak, K. Z., &#38; Walter, M. (2022). CoCoA: Concurrent continuous group key agreement. In <i>Advances in Cryptology – EUROCRYPT 2022</i> (Vol. 13276, pp. 815–844). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>","ista":"Alwen J, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2022. CoCoA: Concurrent continuous group key agreement. Advances in Cryptology – EUROCRYPT 2022. EUROCRYPT: Annual International Conference on the Theory and Applications of Cryptology and Information Security, LNCS, vol. 13276, 815–844.","chicago":"Alwen, Joël, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “CoCoA: Concurrent Continuous Group Key Agreement.” In <i>Advances in Cryptology – EUROCRYPT 2022</i>, 13276:815–844. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>.","mla":"Alwen, Joël, et al. “CoCoA: Concurrent Continuous Group Key Agreement.” <i>Advances in Cryptology – EUROCRYPT 2022</i>, vol. 13276, Springer Nature, 2022, pp. 815–844, doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>.","ama":"Alwen J, Auerbach B, Cueto Noval M, et al. CoCoA: Concurrent continuous group key agreement. In: <i>Advances in Cryptology – EUROCRYPT 2022</i>. Vol 13276. Cham: Springer Nature; 2022:815–844. doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>"},"department":[{"_id":"GradSch"},{"_id":"KrPi"}],"_id":"11476","date_updated":"2023-08-03T07:25:02Z","conference":{"end_date":"2022-06-03","name":"EUROCRYPT: Annual International Conference on the Theory and Applications of Cryptology and Information Security","location":"Trondheim, Norway","start_date":"2022-05-30"},"project":[{"grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}]},{"status":"public","title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","file":[{"relation":"main_file","date_created":"2022-07-08T10:56:52Z","creator":"rschulz","checksum":"71e8186583f3adbb6c69a88ac9e6e49b","file_size":135784571,"access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"11543","success":1,"date_updated":"2022-07-08T10:56:52Z","file_name":"Source Data.xlsx"}],"date_published":"2022-01-01T00:00:00Z","article_processing_charge":"No","author":[{"last_name":"Schulz","full_name":"Schulz, Rouven","first_name":"Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","has_accepted_license":"1","date_updated":"2024-02-21T12:34:51Z","_id":"11542","doi":"10.15479/AT:ISTA:11542","type":"research_data","file_date_updated":"2022-07-08T10:56:52Z","contributor":[{"contributor_type":"contact_person","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"11995","status":"public"}],"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1","relation":"contains"}]},"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"oa_version":"None","citation":{"ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","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, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"Institute of Science and Technology Austria","oa":1,"date_created":"2022-07-08T11:03:02Z"},{"article_processing_charge":"No","month":"10","author":[{"full_name":"Kalinov, Aleksei","last_name":"Kalinov","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","orcid":"0000-0003-2189-3904","first_name":"Aleksei"},{"last_name":"Osinskiy","full_name":"Osinskiy, A.I.","first_name":"A.I."},{"full_name":"Matveev, S.A.","last_name":"Matveev","first_name":"S.A."},{"full_name":"Otieno, W.","last_name":"Otieno","first_name":"W."},{"first_name":"N.V.","full_name":"Brilliantov, N.V.","last_name":"Brilliantov"}],"article_number":"111439","status":"public","article_type":"original","quality_controlled":"1","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"}],"date_published":"2022-10-15T00:00:00Z","publisher":"Elsevier","oa":1,"intvolume":"       467","isi":1,"doi":"10.1016/j.jcp.2022.111439","type":"journal_article","keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"publication_identifier":{"issn":["0021-9991"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"oa_version":"Preprint","arxiv":1,"publication":"Journal of Computational Physics","year":"2022","external_id":{"isi":["000917225500013"],"arxiv":["2103.09481"]},"title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","day":"15","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).","volume":467,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.09481","open_access":"1"}],"publication_status":"published","date_created":"2022-07-11T12:19:59Z","date_updated":"2023-08-03T11:55:06Z","_id":"11556","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"citation":{"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.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","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,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022."}},{"year":"2022","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"}],"day":"20","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","date_created":"2022-07-20T11:21:53Z","alternative_title":["ISTA Thesis"],"publication_status":"published","citation":{"chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022."},"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"_id":"11626","date_updated":"2024-10-29T10:22:45Z","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"file_date_updated":"2022-07-25T11:48:45Z","has_accepted_license":"1","article_processing_charge":"No","author":[{"first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei","full_name":"Gallei, Michelle C"}],"month":"07","file":[{"creator":"mgallei","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","relation":"main_file","date_created":"2022-07-25T09:08:47Z","date_updated":"2022-07-25T09:08:47Z","file_name":"Thesis_Gallei.pdf","file_size":9730864,"access_level":"open_access","content_type":"application/pdf","file_id":"11645"},{"file_name":"Thesis_Gallei_source.docx","date_updated":"2022-07-25T09:39:58Z","file_id":"11646","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":19560720,"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","creator":"mgallei","date_created":"2022-07-25T09:09:09Z","relation":"source_file"},{"checksum":"3994f7f20058941b5bb8a16886b21e71","creator":"mgallei","date_created":"2022-07-25T09:09:32Z","relation":"source_file","date_updated":"2022-07-25T09:39:58Z","file_name":"Thesis_Gallei_to_print.pdf","file_id":"11647","description":"This is the print version of the thesis including the full appendix","content_type":"application/pdf","access_level":"closed","file_size":24542837},{"date_updated":"2022-07-25T11:48:45Z","file_name":"Thesis_Gallei_Appendix.pdf","file_id":"11650","content_type":"application/pdf","access_level":"open_access","file_size":15435966,"checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","creator":"mgallei","date_created":"2022-07-25T11:48:45Z","relation":"main_file"}],"date_published":"2022-07-20T00:00:00Z","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"],"status":"public","publisher":"Institute of Science and Technology Austria","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"9287","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7142"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"status":"public","id":"8138","relation":"part_of_dissertation"},{"status":"public","id":"6260","relation":"part_of_dissertation"},{"id":"8931","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"10411","status":"public"}]},"oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"page":"248","degree_awarded":"PhD","doi":"10.15479/at:ista:11626","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation"},{"date_updated":"2024-02-21T12:35:53Z","doi":"10.15479/AT:ISTA:11653","_id":"11653","contributor":[{"last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"},{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Sax","first_name":"Luca"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"first_name":"Francisco","last_name":"Hontoria "},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"file_date_updated":"2022-08-08T22:30:04Z","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"12248","relation":"used_in_publication"}]},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"citation":{"ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","short":"M.N. Elkrewi, (2022).","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2022-07-26T11:01:47Z","publisher":"Institute of Science and Technology Austria","oa":1,"status":"public","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","day":"05","file":[{"creator":"melkrewi","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","embargo":"2022-08-07","date_created":"2022-07-26T12:37:52Z","relation":"main_file","title":"Supplementary Datasets","file_name":"Data.zip","date_updated":"2022-08-08T22:30:04Z","access_level":"open_access","file_size":2209382998,"file_id":"11655","content_type":"application/x-zip-compressed","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n"}],"ddc":["570"],"abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"date_published":"2022-08-05T00:00:00Z","article_processing_charge":"No","month":"08","author":[{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"year":"2022","has_accepted_license":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Leibniz International Proceedings on Mathematics","oa_version":"Submitted Version","ec_funded":1,"language":[{"iso":"eng"}],"author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","full_name":"Biswas, Ranita","last_name":"Biswas"},{"last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","full_name":"Saghafian, Morteza","last_name":"Saghafian"}],"month":"07","article_processing_charge":"No","has_accepted_license":"1","quality_controlled":"1","status":"public","date_published":"2022-07-27T00:00:00Z","ddc":["510"],"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":[{"checksum":"b2f511e8b1cae5f1892b0cdec341acac","creator":"scultrer","date_created":"2022-07-27T09:25:53Z","relation":"main_file","file_name":"D-S-E.pdf","date_updated":"2022-07-27T09:25:53Z","file_id":"11659","content_type":"application/pdf","access_level":"open_access","file_size":639266}],"publication_status":"submitted","date_created":"2022-07-27T09:27:34Z","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00342"},{"grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"file_date_updated":"2022-07-27T09:25:53Z","_id":"11658","date_updated":"2022-07-28T07:57:48Z","citation":{"ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","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.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik, n.d.","mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>, 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. <i>Leibniz International Proceedings on Mathematics</i>."},"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"year":"2022","day":"27","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","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."},{"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","publication":"LIPIcs","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["510"],"abstract":[{"lang":"eng","text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. "}],"date_published":"2022-07-25T00:00:00Z","file":[{"date_updated":"2022-07-27T09:30:30Z","file_name":"window 1.pdf","content_type":"application/pdf","file_id":"11661","file_size":564836,"access_level":"open_access","checksum":"95903f9d1649e8e437a967b6f2f64730","creator":"scultrer","relation":"main_file","date_created":"2022-07-27T09:30:30Z"}],"quality_controlled":"1","status":"public","has_accepted_license":"1","month":"07","author":[{"orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","full_name":"Biswas, Ranita","last_name":"Biswas"},{"last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","first_name":"Morteza"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"citation":{"ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>.","mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik."},"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"file_date_updated":"2022-07-27T09:30:30Z","date_updated":"2022-07-28T08:05:34Z","_id":"11660","date_created":"2022-07-27T09:31:15Z","publication_status":"submitted","alternative_title":["LIPIcs"],"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. ","title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","day":"25","year":"2022"},{"doi":"10.1073/pnas.2121058119","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Multidisciplinary"],"type":"journal_article","publication":"Proceedings of the National Academy of Sciences","oa_version":"Published Version","language":[{"iso":"eng"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa":1,"publisher":"Proceedings of the National Academy of Sciences","isi":1,"intvolume":"       119","article_type":"original","status":"public","quality_controlled":"1","file":[{"date_created":"2022-08-08T07:42:09Z","relation":"main_file","creator":"dernst","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","access_level":"open_access","file_size":2506262,"file_id":"11747","content_type":"application/pdf","success":1,"file_name":"2022_PNAS_Li.pdf","date_updated":"2022-08-08T07:42:09Z"}],"date_published":"2022-07-25T00:00:00Z","abstract":[{"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.","lang":"eng"}],"ddc":["580"],"article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"last_name":"Chen","full_name":"Chen, Huihuang","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"last_name":"Alotaibi","full_name":"Alotaibi, Saqer S.","first_name":"Saqer S."},{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"month":"07","article_number":"e2121058119","has_accepted_license":"1","_id":"11723","date_updated":"2024-10-29T10:12:30Z","file_date_updated":"2022-08-08T07:42:09Z","project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"citation":{"ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","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.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>","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. 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 119 (2022)."},"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","date_created":"2022-08-04T20:06:49Z","pmid":1,"external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"day":"25","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","volume":119,"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).”","issue":"31","year":"2022"},{"year":"2022","acknowledgement":"We are grateful to Robert Seiringer for helpful discussions and many valuable comments\r\non an earlier version of the manuscript. J.H. acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond’ No. 101020331. Open access funding provided by Institute of Science and Technology (IST Austria)","volume":189,"title":"The BCS energy gap at high density","day":"29","external_id":{"isi":["000833007200002"]},"date_created":"2022-08-05T11:36:56Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"citation":{"short":"S.J. Henheik, A.B. Lauritsen, Journal of Statistical Physics 189 (2022).","apa":"Henheik, S. J., &#38; Lauritsen, A. B. (2022). The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>","ista":"Henheik SJ, Lauritsen AB. 2022. The BCS energy gap at high density. Journal of Statistical Physics. 189, 5.","chicago":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>.","mla":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>, vol. 189, 5, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>.","ama":"Henheik SJ, Lauritsen AB. The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. 2022;189. doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>","ieee":"S. J. Henheik and A. B. Lauritsen, “The BCS energy gap at high density,” <i>Journal of Statistical Physics</i>, vol. 189. Springer Nature, 2022."},"file_date_updated":"2022-08-08T07:36:34Z","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"date_updated":"2023-09-05T14:57:49Z","_id":"11732","article_number":"5","has_accepted_license":"1","month":"07","author":[{"last_name":"Henheik","full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha","orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","abstract":[{"text":"We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic formula, which strongly depends on the strength of the interaction potential V on the Fermi surface. In combination with the recent result by one of us (Math. Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities, we prove the universality of the ratio of the energy gap and the critical temperature.","lang":"eng"}],"ddc":["530"],"date_published":"2022-07-29T00:00:00Z","file":[{"date_created":"2022-08-08T07:36:34Z","relation":"main_file","checksum":"b398c4dbf65f71d417981d6e366427e9","creator":"dernst","file_id":"11746","content_type":"application/pdf","access_level":"open_access","file_size":419563,"file_name":"2022_JourStatisticalPhysics_Henheik.pdf","date_updated":"2022-08-08T07:36:34Z","success":1}],"quality_controlled":"1","status":"public","article_type":"original","intvolume":"       189","isi":1,"publisher":"Springer Nature","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"ec_funded":1,"publication":"Journal of Statistical Physics","oa_version":"Published Version","type":"journal_article","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1007/s10955-022-02965-9"},{"file":[{"date_created":"2023-01-20T07:34:50Z","relation":"main_file","checksum":"05c7dcfbb9053a98f46441fb2eccb213","creator":"dernst","file_id":"12317","content_type":"application/pdf","access_level":"open_access","file_size":477110,"date_updated":"2023-01-20T07:34:50Z","file_name":"2022_LNCS_RV_Henzinger.pdf","success":1}],"date_published":"2022-09-23T00:00:00Z","abstract":[{"lang":"eng","text":"Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time. "}],"ddc":["000"],"status":"public","quality_controlled":"1","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"Yes","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"month":"09","publication":"22nd International Conference on Runtime Verification","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-17196-3_11","page":"200-220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0302-9743"]},"type":"conference","publisher":"Springer Nature","oa":1,"isi":1,"intvolume":"     13498","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":13498,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","external_id":{"isi":["000866539700011"]},"day":"23","title":"Abstract monitors for quantitative specifications","year":"2022","citation":{"ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for quantitative specifications,” in <i>22nd International Conference on Runtime Verification</i>, Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference on Runtime Verification, Springer Nature, 2022, pp. 200–220.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2022). Abstract monitors for quantitative specifications. In <i>22nd International Conference on Runtime Verification</i> (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative specifications. 22nd International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 13498, 200–220.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract Monitors for Quantitative Specifications.” In <i>22nd International Conference on Runtime Verification</i>, 13498:200–220. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>.","mla":"Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.” <i>22nd International Conference on Runtime Verification</i>, vol. 13498, Springer Nature, 2022, pp. 200–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications. In: <i>22nd International Conference on Runtime Verification</i>. Vol 13498. Springer Nature; 2022:200-220. doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>"},"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"_id":"11775","date_updated":"2023-08-03T13:38:46Z","conference":{"end_date":"2022-09-30","name":"RV: Runtime Verification","location":"Tbilisi, Georgia","start_date":"2022-09-28"},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"file_date_updated":"2023-01-20T07:34:50Z","date_created":"2022-08-08T17:09:09Z","alternative_title":["LNCS"],"publication_status":"published"},{"year":"2022","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"}],"title":"High-dimensional expansion and crossing numbers of simplicial complexes","day":"11","alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2022-08-10T15:51:19Z","date_updated":"2023-06-22T09:56:36Z","_id":"11777","file_date_updated":"2022-08-11T16:09:19Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"department":[{"_id":"GradSch"},{"_id":"UlWa"}],"citation":{"mla":"Wild, Pascal. <i>High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes</i>. Institute of Science and Technology, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","apa":"Wild, P. (2022). <i>High-dimensional expansion and crossing numbers of simplicial complexes</i>. Institute of Science and Technology. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022."},"article_processing_charge":"No","month":"08","author":[{"last_name":"Wild","full_name":"Wild, Pascal","first_name":"Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","status":"public","file":[{"description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","content_type":"text/x-python","file_id":"11780","file_size":16828,"access_level":"open_access","file_name":"flags.py","date_updated":"2022-08-10T15:34:04Z","relation":"supplementary_material","date_created":"2022-08-10T15:34:04Z","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","creator":"pwild"},{"date_created":"2022-08-10T15:34:10Z","relation":"supplementary_material","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","creator":"pwild","file_id":"11781","description":"Code for proof of Lemma 8.20 in Thesis","content_type":"text/x-c++src","access_level":"open_access","file_size":12226,"file_name":"lowerbound.cpp","date_updated":"2022-08-10T15:34:10Z"},{"date_updated":"2022-08-10T15:34:17Z","file_name":"upperbound.py","file_size":3240,"access_level":"open_access","content_type":"text/x-python","description":"Code for proof of Proposition 7.9 in Thesis","file_id":"11782","creator":"pwild","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","relation":"supplementary_material","date_created":"2022-08-10T15:34:17Z"},{"relation":"main_file","date_created":"2022-08-11T16:08:33Z","checksum":"4e96575b10cbe4e0d0db2045b2847774","creator":"pwild","content_type":"application/pdf","file_id":"11809","file_size":5086282,"access_level":"open_access","file_name":"finalthesisPascalWildPDFA.pdf","date_updated":"2022-08-11T16:08:33Z","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes"},{"file_size":18150068,"access_level":"closed","content_type":"application/zip","file_id":"11810","date_updated":"2022-08-11T16:09:19Z","file_name":"ThesisSubmission.zip","relation":"source_file","date_created":"2022-08-11T16:09:19Z","creator":"pwild","checksum":"92d94842a1fb6dca5808448137573b2e"}],"ddc":["500","516","514"],"abstract":[{"text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.","lang":"eng"}],"date_published":"2022-08-11T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology","degree_awarded":"PhD","doi":"10.15479/at:ista:11777","page":"170","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-021-3"],"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version"},{"intvolume":"     13681","publisher":"Springer Nature","oa":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","publication":"Computer Vision – ECCV 2022","arxiv":1,"type":"conference","publication_identifier":{"eisbn":["9783031198038"],"isbn":["9783031198021"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"350-365","doi":"10.1007/978-3-031-19803-8_21","month":"10","author":[{"id":"2D561D42-C427-11E9-89B4-9C1AE6697425","first_name":"Bernd","full_name":"Prach, Bernd","last_name":"Prach"},{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"scopus_import":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"It is a highly desirable property for deep networks to be robust against\r\nsmall input changes. One popular way to achieve this property is by designing\r\nnetworks with a small Lipschitz constant. In this work, we propose a new\r\ntechnique for constructing such Lipschitz networks that has a number of\r\ndesirable properties: it can be applied to any linear network layer\r\n(fully-connected or convolutional), it provides formal guarantees on the\r\nLipschitz constant, it is easy to implement and efficient to run, and it can be\r\ncombined with any training objective and optimization method. In fact, our\r\ntechnique is the first one in the literature that achieves all of these\r\nproperties simultaneously. Our main contribution is a rescaling-based weight\r\nmatrix parametrization that guarantees each network layer to have a Lipschitz\r\nconstant of at most 1 and results in the learned weight matrices to be close to\r\northogonal. Hence we call such layers almost-orthogonal Lipschitz (AOL).\r\nExperiments and ablation studies in the context of image classification with\r\ncertified robust accuracy confirm that AOL layers achieve results that are on\r\npar with most existing methods. Yet, they are simpler to implement and more\r\nbroadly applicable, because they do not require computationally expensive\r\nmatrix orthogonalization or inversion steps as part of the network\r\narchitecture. We provide code at https://github.com/berndprach/AOL."}],"date_published":"2022-10-23T00:00:00Z","quality_controlled":"1","status":"public","date_created":"2022-08-12T15:09:47Z","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2208.03160"}],"publication_status":"published","alternative_title":["LNCS"],"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"citation":{"chicago":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” In <i>Computer Vision – ECCV 2022</i>, 13681:350–65. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>.","ama":"Prach B, Lampert C. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In: <i>Computer Vision – ECCV 2022</i>. Vol 13681. Springer Nature; 2022:350-365. doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>","mla":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” <i>Computer Vision – ECCV 2022</i>, vol. 13681, Springer Nature, 2022, pp. 350–65, doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>.","short":"B. Prach, C. Lampert, in:, Computer Vision – ECCV 2022, Springer Nature, 2022, pp. 350–365.","apa":"Prach, B., &#38; Lampert, C. (2022). Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In <i>Computer Vision – ECCV 2022</i> (Vol. 13681, pp. 350–365). Tel Aviv, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>","ista":"Prach B, Lampert C. 2022. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. Computer Vision – ECCV 2022. ECCV: European Conference on Computer Vision, LNCS, vol. 13681, 350–365.","ieee":"B. Prach and C. Lampert, “Almost-orthogonal layers for efficient general-purpose Lipschitz networks,” in <i>Computer Vision – ECCV 2022</i>, Tel Aviv, Israel, 2022, vol. 13681, pp. 350–365."},"conference":{"start_date":"2022-10-23","location":"Tel Aviv, Israel","name":"ECCV: European Conference on Computer Vision","end_date":"2022-10-27"},"date_updated":"2023-05-03T08:00:46Z","_id":"11839","year":"2022","volume":13681,"title":"Almost-orthogonal layers for efficient general-purpose Lipschitz networks","day":"23","external_id":{"arxiv":["2208.03160"]}},{"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"citation":{"chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>.","mla":"Artner, Christina. <i>Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>.","ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","apa":"Artner, C. (2022). <i>Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022."},"project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"file_date_updated":"2023-09-09T22:30:03Z","date_updated":"2023-09-09T22:30:04Z","_id":"11879","date_created":"2022-08-17T07:58:53Z","publication_status":"published","alternative_title":["ISTA Thesis"],"acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","day":"17","supervisor":[{"full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva"}],"year":"2022","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"dissertation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"degree_awarded":"PhD","page":"128","doi":"10.15479/at:ista:11879","publisher":"Institute of Science and Technology Austria","oa":1,"abstract":[{"lang":"eng","text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT."}],"ddc":["580"],"date_published":"2022-08-17T00:00:00Z","file":[{"file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","date_updated":"2023-09-09T22:30:03Z","content_type":"application/pdf","file_id":"11907","file_size":11113608,"access_level":"open_access","checksum":"a2c2fdc28002538840490bfa6a08b2cb","creator":"cartner","relation":"main_file","date_created":"2022-08-17T12:08:49Z","embargo":"2023-09-08"},{"relation":"source_file","date_created":"2022-08-17T12:08:59Z","creator":"cartner","checksum":"66b461c074b815fbe63481b3f46a9f43","file_size":19097730,"access_level":"closed","content_type":"application/octet-stream","file_id":"11908","date_updated":"2023-09-09T22:30:03Z","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","embargo_to":"open_access"}],"status":"public","has_accepted_license":"1","month":"08","author":[{"last_name":"Artner","full_name":"Artner, Christina","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"publisher":"Institute of Science and Technology Austria","oa":1,"related_material":{"record":[{"status":"public","id":"10077","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6194"}]},"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"136","doi":"10.15479/at:ista:11932","degree_awarded":"PhD","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","article_processing_charge":"No","month":"08","author":[{"first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","full_name":"Nardin, Michele"}],"file":[{"date_updated":"2023-06-20T22:30:04Z","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","embargo_to":"open_access","content_type":"application/zip","file_id":"11935","file_size":13515457,"access_level":"closed","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","creator":"mnardin","relation":"source_file","date_created":"2022-08-19T16:31:34Z"},{"content_type":"application/pdf","file_id":"11941","file_size":9906458,"access_level":"open_access","date_updated":"2023-06-20T22:30:04Z","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","relation":"main_file","date_created":"2022-08-22T09:43:50Z","embargo":"2023-06-19","checksum":"0ec94035ea35a47a9f589ed168e60b48","creator":"mnardin"}],"abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"ddc":["573"],"date_published":"2022-08-19T00:00:00Z","status":"public","date_created":"2022-08-19T08:52:30Z","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"citation":{"ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>.","mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>.","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>"},"date_updated":"2023-09-05T12:02:14Z","_id":"11932","file_date_updated":"2023-06-20T22:30:04Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"year":"2022","supervisor":[{"last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"}],"acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","title":"On the encoding, transfer, and consolidation of spatial memories","day":"19"},{"oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"11995","relation":"dissertation_contains"}]},"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663-337X"]},"page":"133","doi":"10.15479/at:ista:11945","degree_awarded":"PhD","has_accepted_license":"1","month":"08","author":[{"last_name":"Schulz","full_name":"Schulz, Rouven","first_name":"Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","abstract":[{"text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level.","lang":"eng"}],"ddc":["570"],"date_published":"2022-08-23T00:00:00Z","file":[{"checksum":"61b1b666a210ff7cdd0e95ea75207a13","creator":"rschulz","date_created":"2022-08-25T08:59:57Z","relation":"main_file","date_updated":"2022-08-25T08:59:57Z","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","success":1,"file_id":"11970","content_type":"application/pdf","access_level":"open_access","file_size":28079331},{"creator":"rschulz","checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","date_created":"2022-08-25T09:00:11Z","relation":"source_file","file_name":"Thesis_Rouven_Schulz_2022_final.docx","date_updated":"2022-08-25T09:33:31Z","access_level":"closed","file_size":27226963,"file_id":"11971","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"status":"public","date_created":"2022-08-23T11:33:11Z","publication_status":"published","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"citation":{"ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","apa":"Schulz, R. (2022). <i>Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11945\">https://doi.org/10.15479/at:ista:11945</a>","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria.","short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11945\">10.15479/at:ista:11945</a>","mla":"Schulz, Rouven. <i>Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11945\">10.15479/at:ista:11945</a>.","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11945\">https://doi.org/10.15479/at:ista:11945</a>."},"file_date_updated":"2022-08-25T09:33:31Z","project":[{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"date_updated":"2023-08-03T13:02:26Z","_id":"11945","supervisor":[{"last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","day":"23"}]