[{"date_updated":"2023-09-06T15:23:04Z","department":[{"_id":"JiFr"}],"_id":"7417","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1559-2324"]},"publication_status":"published","volume":15,"issue":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development."}],"month":"01","intvolume":" 15","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:10.1080/15592324.2019.1687185.","apa":"Sinclair, S. A., Gille, S., Pauly, M., & Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. Informa UK Limited. https://doi.org/10.1080/15592324.2019.1687185","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687185","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” Plant Signaling & Behavior, vol. 15, no. 1. Informa UK Limited, 2020.","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling & Behavior 15 (2020).","chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior. Informa UK Limited, 2020. https://doi.org/10.1080/15592324.2019.1687185.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 15(1), e1687185."},"title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","author":[{"last_name":"Sinclair","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"first_name":"S.","last_name":"Gille","full_name":"Gille, S."},{"full_name":"Pauly, M.","last_name":"Pauly","first_name":"M."},{"first_name":"U.","last_name":"Krämer","full_name":"Krämer, U."}],"external_id":{"isi":["000494907500001"],"pmid":["31696770"]},"article_processing_charge":"No","article_number":"e1687185","day":"01","publication":"Plant Signaling & Behavior","isi":1,"year":"2020","doi":"10.1080/15592324.2019.1687185","date_published":"2020-01-01T00:00:00Z","date_created":"2020-01-30T10:14:14Z","publisher":"Informa UK Limited","quality_controlled":"1","oa":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"6185","file_date_updated":"2020-11-18T11:14:37Z","department":[{"_id":"LaEr"}],"date_updated":"2023-09-07T12:54:12Z","ddc":["530","510"],"scopus_import":"1","intvolume":" 378","month":"09","abstract":[{"text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":378,"related_material":{"record":[{"status":"public","id":"6179","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":2904574,"date_updated":"2020-11-18T11:14:37Z","file_name":"2020_CommMathPhysics_Erdoes.pdf","date_created":"2020-11-18T11:14:37Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c3a683e2afdcea27afa6880b01e53dc2","file_id":"8771"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"external_id":{"arxiv":["1809.03971"],"isi":["000529483000001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","citation":{"chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03657-4.","ista":"Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278.","mla":"Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:10.1007/s00220-019-03657-4.","ama":"Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 2020;378:1203-1278. doi:10.1007/s00220-019-03657-4","apa":"Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03657-4","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278.","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” Communications in Mathematical Physics, vol. 378. Springer Nature, pp. 1203–1278, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work.","page":"1203-1278","date_created":"2019-03-28T10:21:15Z","doi":"10.1007/s00220-019-03657-4","date_published":"2020-09-01T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Communications in Mathematical Physics","day":"01"},{"file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"JaMa"}],"ddc":["510"],"date_updated":"2023-09-07T13:03:12Z","supervisor":[{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"dissertation","_id":"7629","ec_funded":1,"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_Forkert_PDFA.pdf","date_created":"2020-04-14T10:47:59Z","creator":"dernst","file_size":3297129,"date_updated":"2020-07-14T12:48:01Z","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","file_id":"7657","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","file_id":"7658","creator":"dernst","file_size":1063908,"date_updated":"2020-07-14T12:48:01Z","file_name":"Thesis_Forkert_source.zip","date_created":"2020-04-14T10:47:59Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","article_processing_charge":"No","author":[{"full_name":"Forkert, Dominik L","last_name":"Forkert","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629."},"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-04-02T06:40:23Z","date_published":"2020-03-31T00:00:00Z","doi":"10.15479/AT:ISTA:7629","page":"154","day":"31","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"citation":{"ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","full_name":"Szep, Eniko"}],"title":"Local adaptation in metapopulations","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"20","page":"158","date_created":"2020-09-28T07:33:38Z","doi":"10.15479/AT:ISTA:8574","date_published":"2020-09-20T00:00:00Z","_id":"8574","type":"dissertation","status":"public","date_updated":"2023-09-07T13:11:39Z","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"ddc":["570"],"file_date_updated":"2020-09-28T07:25:37Z","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8575","checksum":"20e71f015fbbd78fea708893ad634ed0","success":1,"date_updated":"2020-09-28T07:25:35Z","file_size":6354833,"creator":"dernst","date_created":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf"},{"date_updated":"2020-09-28T07:25:37Z","file_size":23020401,"creator":"dernst","date_created":"2020-09-28T07:25:37Z","file_name":"thesisFiles_EnikoSzep.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","checksum":"a8de2c14a1bb4e53c857787efbb289e1","file_id":"8576"}]},{"related_material":{"record":[{"id":"7524","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","file_id":"7515","creator":"dernst","file_size":1563429,"date_updated":"2020-07-14T12:47:59Z","file_name":"thesis.pdf","date_created":"2020-02-24T09:15:06Z"},{"file_id":"7516","checksum":"ad7425867b52d7d9e72296e87bc9cb67","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"thesis_source.zip","date_created":"2020-02-24T09:15:16Z","file_size":2028038,"date_updated":"2020-07-14T12:47:59Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks."}],"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"ddc":["510"],"supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"date_updated":"2023-09-07T13:12:42Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7514","date_published":"2020-02-24T00:00:00Z","doi":"10.15479/AT:ISTA:7514","date_created":"2020-02-24T09:17:27Z","page":"148","day":"24","has_accepted_license":"1","year":"2020","publisher":"Institute of Science and Technology Austria","oa":1,"title":"The free energy of a dilute two-dimensional Bose gas","author":[{"last_name":"Mayer","full_name":"Mayer, Simon","first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514."},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}]},{"_id":"8353","type":"dissertation","status":"public","supervisor":[{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:14:09Z","ddc":["572"],"file_date_updated":"2021-09-16T12:40:56Z","department":[{"_id":"LeSa"}],"abstract":[{"text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"oa_version":"None","alternative_title":["ISTA Thesis"],"month":"09","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"date_created":"2020-09-09T14:22:35Z","file_name":"Thesis_Julia_Steiner_pdfA.pdf","creator":"jsteiner","date_updated":"2021-09-16T12:40:56Z","file_size":117547589,"checksum":"2388d7e6e7a4d364c096fa89f305c3de","file_id":"8354","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_name":"Thesis_Julia_Steiner.docx","date_created":"2020-09-09T14:23:25Z","file_size":223328668,"date_updated":"2020-09-15T08:48:37Z","creator":"jsteiner","file_id":"8355","checksum":"ba112f957b7145462d0ab79044873ee9","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8284","status":"public"}]},"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"citation":{"chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","last_name":"Steiner"}],"article_processing_charge":"No","title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2020","day":"09","page":"191","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8353","date_created":"2020-09-09T14:27:01Z"},{"file":[{"date_created":"2020-09-30T14:50:20Z","file_name":"2020_Han_Thesis.docx","date_updated":"2020-09-30T14:50:20Z","file_size":49198118,"creator":"dernst","checksum":"c4bda1947d4c09c428ac9ce667b02327","file_id":"8590","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"date_updated":"2021-10-01T13:33:02Z","file_size":15513963,"creator":"dernst","date_created":"2020-09-30T14:49:59Z","file_name":"2020_Han_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8591","checksum":"3f4f5d1718c2230adf30639ecaf8a00b"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"7643","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["580"],"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:13:05Z","file_date_updated":"2021-10-01T13:33:02Z","department":[{"_id":"JiFr"}],"_id":"8589","status":"public","type":"dissertation","day":"30","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:8589","date_published":"2020-09-30T00:00:00Z","date_created":"2020-09-30T14:50:51Z","page":"164","acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589."},"title":"Novel insights into PIN polarity regulation during Arabidopsis development","author":[{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 9","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8289","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","creator":"cziletti","file_size":7320493,"date_updated":"2020-08-24T13:31:53Z","file_name":"2020_eLife_Steiner.pdf","date_created":"2020-08-24T13:31:53Z"}],"language":[{"iso":"eng"}],"volume":9,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8353"}]},"_id":"8284","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-07T13:14:08Z","ddc":["570"],"file_date_updated":"2020-08-24T13:31:53Z","department":[{"_id":"LeSa"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"31","publication":"eLife","doi":"10.7554/eLife.59407","date_published":"2020-07-31T00:00:00Z","date_created":"2020-08-24T06:24:04Z","article_number":"e59407","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741"}],"citation":{"chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407.","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407.","apa":"Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Steiner","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"article_processing_charge":"No","external_id":{"pmid":["32735215"],"isi":["000562123600001"]},"title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter"},{"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","date_created":"2020-07-23T09:51:28Z","date_published":"2020-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:8155","page":"310","day":"24","year":"2020","has_accepted_license":"1","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"title":"Gene regulation across scales – how biophysical constraints shape evolution","article_processing_charge":"No","author":[{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020."},"month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. "}],"related_material":{"record":[{"status":"public","id":"7675","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7569","status":"public"},{"status":"public","id":"7652","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"8176","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-07-27T12:00:07Z","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","creator":"rgrah","date_updated":"2020-07-27T12:00:07Z","file_size":16638998},{"creator":"rgrah","file_size":347459978,"date_updated":"2020-07-30T13:04:55Z","file_name":"Thesis_new.zip","date_created":"2020-07-27T12:02:23Z","relation":"main_file","access_level":"closed","content_type":"application/zip","file_id":"8177"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"status":"public","type":"dissertation","_id":"8155","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-30T13:04:55Z","ddc":["530","570"],"date_updated":"2023-09-07T13:13:27Z","supervisor":[{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}]},{"citation":{"chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212.","ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40.","mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212.","ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” Plant Physiology, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212","ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40. doi:10.1104/pp.20.00212"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000536641800018"],"pmid":["32107280"]},"author":[{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","last_name":"Rakusova","full_name":"Rakusova, Hana"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"year":"2020","isi":1,"publication":"Plant Physiology","day":"08","page":"37-40","date_created":"2020-04-06T10:06:40Z","date_published":"2020-05-08T00:00:00Z","doi":"10.1104/pp.20.00212","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). ","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","date_updated":"2023-09-07T13:13:04Z","department":[{"_id":"JiFr"}],"_id":"7643","article_type":"letter_note","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"5","related_material":{"record":[{"status":"public","id":"8589","relation":"dissertation_contains"}]},"volume":183,"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.20.00212"}],"scopus_import":"1","intvolume":" 183","month":"05"},{"type":"preprint","project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"status":"public","_id":"7675","author":[{"last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"article_processing_charge":"No","title":"Normative models of enhancer function","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_updated":"2023-09-07T13:13:26Z","citation":{"ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"month":"04","abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.","lang":"eng"}],"oa_version":"Preprint","doi":"10.1101/2020.04.08.029405","date_published":"2020-04-09T00:00:00Z","related_material":{"record":[{"status":"public","id":"8155","relation":"dissertation_contains"}]},"date_created":"2020-04-23T10:12:51Z","publication_status":"published","year":"2020","day":"09","publication":"bioRxiv","language":[{"iso":"eng"}]},{"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7461","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","date_updated":"2020-07-14T12:47:58Z","file_size":76195184,"creator":"koelsboe","date_created":"2020-02-06T14:43:54Z","file_name":"thesis_ist-final_noack.pdf"},{"content_type":"application/x-zip-compressed","description":"latex source files, figures","access_level":"closed","relation":"source_file","file_id":"7462","checksum":"7a52383c812b0be64d3826546509e5a4","date_updated":"2020-07-14T12:47:58Z","file_size":122103715,"creator":"koelsboe","date_created":"2020-02-06T14:52:45Z","file_name":"latex-files.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"6608","status":"public","relation":"part_of_dissertation"}]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}],"month":"02","alternative_title":["ISTA Thesis"],"ddc":["514"],"supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"date_updated":"2023-09-07T13:15:30Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:58Z","_id":"7460","status":"public","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"day":"10","has_accepted_license":"1","year":"2020","date_published":"2020-02-10T00:00:00Z","doi":"10.15479/AT:ISTA:7460","date_created":"2020-02-06T14:56:53Z","page":"155","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria."},"title":"The hole system of triangulated shapes","author":[{"first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina","orcid":"0000-0002-4672-8297","last_name":"Ölsböck"}],"article_processing_charge":"No"},{"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:48:04Z","ddc":["000"],"supervisor":[{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:15:55Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7896","related_material":{"record":[{"status":"public","id":"6677","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7897","checksum":"b39e2e1c376f5819b823fb7077491c64","file_size":1622742,"date_updated":"2020-07-14T12:48:04Z","creator":"dernst","file_name":"2020_Thesis_Kamath.pdf","date_created":"2020-05-26T14:08:13Z"},{"file_id":"7898","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"Thesis_Kamath.zip","date_created":"2020-05-26T14:08:23Z","file_size":15301529,"date_updated":"2020-07-14T12:48:04Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. "}],"title":"On the average-case hardness of total search problems","author":[{"last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896."},"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"},{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"date_published":"2020-05-25T00:00:00Z","doi":"10.15479/AT:ISTA:7896","date_created":"2020-05-26T14:08:55Z","page":"126","day":"25","has_accepted_license":"1","year":"2020","publisher":"Institute of Science and Technology Austria","oa":1},{"month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.12623"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures.","lang":"eng"}],"related_material":{"record":[{"status":"deleted","id":"8331","relation":"dissertation_contains"},{"id":"8390","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781728165530"]},"status":"public","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","start_date":"2020-03-01","end_date":"2020-03-05","location":" Snowmass Village, CO, United States"},"type":"conference","_id":"7936","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:17Z","oa":1,"publisher":"IEEE","quality_controlled":"1","date_created":"2020-06-07T22:00:53Z","doi":"10.1109/WACV45572.2020.9093288","date_published":"2020-03-01T00:00:00Z","publication":"IEEE Winter Conference on Applications of Computer Vision","day":"01","year":"2020","article_number":"1716-1725","title":"Localizing grouped instances for efficient detection in low-resource scenarios","article_processing_charge":"No","external_id":{"arxiv":["2004.12623"]},"author":[{"orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093288.","ista":"Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.","mla":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” IEEE Winter Conference on Applications of Computer Vision, 1716–1725, IEEE, 2020, doi:10.1109/WACV45572.2020.9093288.","ama":"Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093288","apa":"Royer, A., & Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093288","short":"A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","ieee":"A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020."}},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning."}],"month":"03","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/2008.11995","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781728165530"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"deleted","id":"8331"},{"status":"public","id":"8390","relation":"dissertation_contains"}]},"_id":"7937","status":"public","type":"conference","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","location":"Snowmass Village, CO, United States","end_date":"2020-03-05","start_date":"2020-03-01"},"date_updated":"2023-09-07T13:16:17Z","department":[{"_id":"ChLa"}],"publisher":"IEEE","quality_controlled":"1","oa":1,"day":"01","publication":"2020 IEEE Winter Conference on Applications of Computer Vision","year":"2020","doi":"10.1109/WACV45572.2020.9093635","date_published":"2020-03-01T00:00:00Z","date_created":"2020-06-07T22:00:53Z","article_number":"2180-2189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189.","chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093635.","ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093635","apa":"Royer, A., & Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In 2020 IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093635","ieee":"A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in 2020 IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” 2020 IEEE Winter Conference on Applications of Computer Vision, 2180–2189, IEEE, 2020, doi:10.1109/WACV45572.2020.9093635."},"title":"A flexible selection scheme for minimum-effort transfer learning","author":[{"last_name":"Royer","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"external_id":{"arxiv":["2008.11995"]},"article_processing_charge":"No"},{"page":"33-49","date_created":"2020-07-05T22:00:46Z","doi":"10.1007/978-3-030-30671-7_3","date_published":"2020-01-08T00:00:00Z","year":"2020","publication":"Domain Adaptation for Visual Understanding","day":"08","oa":1,"publisher":"Springer Nature","quality_controlled":"1","article_processing_charge":"No","external_id":{"arxiv":["1711.05139"]},"author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","last_name":"Royer"},{"full_name":"Bousmalis, Konstantinos","last_name":"Bousmalis","first_name":"Konstantinos"},{"first_name":"Stephan","full_name":"Gouws, Stephan","last_name":"Gouws"},{"last_name":"Bertsch","full_name":"Bertsch, Fred","first_name":"Fred"},{"first_name":"Inbar","full_name":"Mosseri, Inbar","last_name":"Mosseri"},{"first_name":"Forrester","full_name":"Cole, Forrester","last_name":"Cole"},{"last_name":"Murphy","full_name":"Murphy, Kevin","first_name":"Kevin"}],"editor":[{"last_name":"Singh","full_name":"Singh, Richa","first_name":"Richa"},{"first_name":"Mayank","last_name":"Vatsa","full_name":"Vatsa, Mayank"},{"last_name":"Patel","full_name":"Patel, Vishal M.","first_name":"Vishal M."},{"full_name":"Ratha, Nalini","last_name":"Ratha","first_name":"Nalini"}],"title":"XGAN: Unsupervised image-to-image translation for many-to-many mappings","citation":{"ista":"Royer A, Bousmalis K, Gouws S, Bertsch F, Mosseri I, Cole F, Murphy K. 2020.XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Domain Adaptation for Visual Understanding. , 33–49.","chicago":"Royer, Amélie, Konstantinos Bousmalis, Stephan Gouws, Fred Bertsch, Inbar Mosseri, Forrester Cole, and Kevin Murphy. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” In Domain Adaptation for Visual Understanding, edited by Richa Singh, Mayank Vatsa, Vishal M. Patel, and Nalini Ratha, 33–49. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-30671-7_3.","short":"A. Royer, K. Bousmalis, S. Gouws, F. Bertsch, I. Mosseri, F. Cole, K. Murphy, in:, R. Singh, M. Vatsa, V.M. Patel, N. Ratha (Eds.), Domain Adaptation for Visual Understanding, Springer Nature, 2020, pp. 33–49.","ieee":"A. Royer et al., “XGAN: Unsupervised image-to-image translation for many-to-many mappings,” in Domain Adaptation for Visual Understanding, R. Singh, M. Vatsa, V. M. Patel, and N. Ratha, Eds. Springer Nature, 2020, pp. 33–49.","apa":"Royer, A., Bousmalis, K., Gouws, S., Bertsch, F., Mosseri, I., Cole, F., & Murphy, K. (2020). XGAN: Unsupervised image-to-image translation for many-to-many mappings. In R. Singh, M. Vatsa, V. M. Patel, & N. Ratha (Eds.), Domain Adaptation for Visual Understanding (pp. 33–49). Springer Nature. https://doi.org/10.1007/978-3-030-30671-7_3","ama":"Royer A, Bousmalis K, Gouws S, et al. XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Singh R, Vatsa M, Patel VM, Ratha N, eds. Domain Adaptation for Visual Understanding. Springer Nature; 2020:33-49. doi:10.1007/978-3-030-30671-7_3","mla":"Royer, Amélie, et al. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” Domain Adaptation for Visual Understanding, edited by Richa Singh et al., Springer Nature, 2020, pp. 33–49, doi:10.1007/978-3-030-30671-7_3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"deleted","id":"8331","relation":"dissertation_contains"},{"id":"8390","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"isbn":["9783030306717"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.05139"}],"scopus_import":"1","month":"01","abstract":[{"text":"Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:18Z","type":"book_chapter","status":"public","_id":"8092"},{"month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","related_material":{"record":[{"status":"public","id":"7950","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5986"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7945","checksum":"df688bc5a82b50baee0b99d25fc7b7f0","file_size":13661779,"date_updated":"2020-07-14T12:48:05Z","creator":"zmasarov","file_name":"THESIS_Zuzka_Masarova.pdf","date_created":"2020-06-08T00:34:00Z"},{"checksum":"45341a35b8f5529c74010b7af43ac188","file_id":"7946","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2020-06-08T00:35:30Z","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","creator":"zmasarov","date_updated":"2020-07-14T12:48:05Z","file_size":32184006}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-005-3"],"issn":["2663-337X"]},"keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"status":"public","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"dissertation","_id":"7944","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:05Z","ddc":["516","514"],"date_updated":"2023-09-07T13:17:37Z","supervisor":[{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2020-06-08T00:49:46Z","date_published":"2020-06-09T00:00:00Z","doi":"10.15479/AT:ISTA:7944","page":"160","day":"09","year":"2020","has_accepted_license":"1","title":"Reconfiguration problems","article_processing_charge":"No","author":[{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Masárová","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944."}},{"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"},{"name":"A path-integral approach to composite impurities","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_number":"164302","author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang","last_name":"Li","full_name":"Li, Xiang"},{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746"}],"article_processing_charge":"No","external_id":{"arxiv":["1912.02658"],"isi":["000530448300001"]},"title":"Intermolecular forces and correlations mediated by a phonon bath","citation":{"mla":"Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:10.1063/1.5144759.","ieee":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” The Journal of Chemical Physics, vol. 152, no. 16. AIP Publishing, 2020.","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020).","apa":"Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., & Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5144759","ama":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 2020;152(16). doi:10.1063/1.5144759","chicago":"Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/1.5144759.","ista":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"acknowledgement":"We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868.","date_published":"2020-04-27T00:00:00Z","doi":"10.1063/1.5144759","date_created":"2020-09-30T10:33:17Z","isi":1,"year":"2020","day":"27","publication":"The Journal of Chemical Physics","article_type":"original","type":"journal_article","status":"public","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"_id":"8587","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"date_updated":"2023-09-07T13:16:42Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"month":"04","intvolume":" 152","abstract":[{"lang":"eng","text":"Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"oa_version":"Preprint","related_material":{"record":[{"status":"public","id":"8958","relation":"dissertation_contains"}]},"issue":"16","volume":152,"ec_funded":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","language":[{"iso":"eng"}]},{"supervisor":[{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"date_updated":"2023-09-07T13:17:06Z","ddc":["570"],"file_date_updated":"2021-09-16T12:49:12Z","department":[{"_id":"MaLo"}],"_id":"8341","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","date_created":"2020-09-08T09:00:29Z","creator":"dernst","file_size":65246782,"date_updated":"2021-09-16T12:49:12Z","checksum":"70871b335a595252a66c6bbf0824fb02","file_id":"8342","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"59a62275088b00b7241e6ff4136434c7","file_id":"8343","creator":"dernst","file_size":31259058,"date_updated":"2021-09-16T12:49:12Z","file_name":"2020_Urban_Bezeljak_Thesis.pdf","date_created":"2020-09-08T09:00:27Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"7580","status":"public","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","citation":{"mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","last_name":"Bezeljak","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631"}],"article_processing_charge":"No","title":"In vitro reconstitution of a Rab activation switch","has_accepted_license":"1","year":"2020","day":"08","page":"215","doi":"10.15479/AT:ISTA:8341","date_published":"2020-09-08T00:00:00Z","date_created":"2020-09-08T08:53:53Z","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","publisher":"Institute of Science and Technology Austria","oa":1},{"oa_version":"Preprint","abstract":[{"text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":" 117","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"volume":117,"issue":"12","related_material":{"record":[{"relation":"dissertation_contains","id":"8341","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","description":"News on IST Homepage"}]},"_id":"7580","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-07T13:17:06Z","department":[{"_id":"MaLo"},{"_id":"CaBe"}],"oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","day":"24","year":"2020","isi":1,"date_created":"2020-03-12T05:32:26Z","date_published":"2020-03-24T00:00:00Z","doi":"10.1073/pnas.1921027117","page":"6504-6549","project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” Proceedings of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020.","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:10.1073/pnas.1921027117.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117."},"title":"Stochastic activation and bistability in a Rab GTPase regulatory network","article_processing_charge":"No","external_id":{"isi":["000521821800040"]},"author":[{"id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban","orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","last_name":"Bezeljak"},{"full_name":"Loya, Hrushikesh","last_name":"Loya","first_name":"Hrushikesh"},{"id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M","full_name":"Kaczmarek, Beata M","last_name":"Kaczmarek"},{"full_name":"Saunders, Timothy E.","last_name":"Saunders","first_name":"Timothy E."},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}]}]