[{"date_created":"2020-10-11T22:01:14Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 22","volume":22,"abstract":[{"text":"Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures.","lang":"eng"}],"publication_status":"published","article_number":"093026","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","grant_number":"25681","name":"Analytic and machine learning approaches to composite quantum impurities"},{"grant_number":"M02641","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ama":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44","ista":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026.","short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","chicago":"Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44.","mla":"Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44.","apa":"Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44","ieee":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020."},"department":[{"_id":"MiLe"}],"publication":"New Journal of Physics","ec_funded":1,"oa":1,"isi":1,"day":"01","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10759"}]},"issue":"9","file":[{"file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","access_level":"open_access","relation":"main_file","checksum":"c9238fff422e7a957c3a0d559f756b3a","content_type":"application/pdf","file_size":2725143,"date_updated":"2020-10-12T12:18:47Z","date_created":"2020-10-12T12:18:47Z","success":1,"creator":"dernst","file_id":"8650"}],"article_type":"original","external_id":{"isi":["000573298000001"]},"date_updated":"2024-08-07T07:16:53Z","quality_controlled":"1","date_published":"2020-09-01T00:00:00Z","language":[{"iso":"eng"}],"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","_id":"8644","publication_identifier":{"issn":["13672630"]},"doi":"10.1088/1367-2630/abae44","publisher":"IOP Publishing","ddc":["530"],"acknowledgement":"We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).","year":"2020","status":"public","title":"Detecting composite orders in layered models via machine learning","oa_version":"Published Version","has_accepted_license":"1","type":"journal_article","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","first_name":"Wojciech","orcid":"0000-0002-1106-4419"},{"full_name":"Defenu, N","last_name":"Defenu","first_name":"N"},{"full_name":"Chiacchiera, S","first_name":"S","last_name":"Chiacchiera"},{"full_name":"Trombettoni, A","first_name":"A","last_name":"Trombettoni"},{"orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo"}],"file_date_updated":"2020-10-12T12:18:47Z"},{"project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","call_identifier":"FP7"}],"publication_status":"published","abstract":[{"text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.","lang":"eng"}],"date_created":"2020-10-11T22:01:14Z","volume":36,"intvolume":" 36","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"isi":1,"day":"15","scopus_import":"1","ec_funded":1,"oa":1,"department":[{"_id":"FyKo"}],"citation":{"apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841"},"publication":"Bioinformatics","publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_processing_charge":"No","month":"03","_id":"8645","quality_controlled":"1","date_published":"2020-03-15T00:00:00Z","language":[{"iso":"eng"}],"file":[{"relation":"main_file","checksum":"21d6f71839deb3b83e4a356193f72767","access_level":"open_access","file_name":"2020_Bioinformatics_Esteban.pdf","content_type":"application/pdf","date_updated":"2020-10-12T12:02:09Z","file_size":308341,"success":1,"creator":"dernst","file_id":"8649","date_created":"2020-10-12T12:02:09Z"}],"page":"1960-1962","issue":"6","external_id":{"pmid":["31742320"],"isi":["000538696800054"]},"date_updated":"2023-08-22T09:57:29Z","article_type":"original","author":[{"full_name":"Esteban, Laura A","last_name":"Esteban","first_name":"Laura A"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"full_name":"Bobrovskiy, Daniil M","first_name":"Daniil M","last_name":"Bobrovskiy"},{"full_name":"Leleytner, Gregory","first_name":"Gregory","last_name":"Leleytner"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Ivankov, Dmitry N ","first_name":"Dmitry N ","last_name":"Ivankov"}],"file_date_updated":"2020-10-12T12:02:09Z","type":"journal_article","oa_version":"Published Version","has_accepted_license":"1","publisher":"Oxford Academic","ddc":["000","570"],"doi":"10.1093/bioinformatics/btz841","title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","status":"public","year":"2020","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). "},{"day":"09","scopus_import":"1","isi":1,"publication":"Communications Physics","citation":{"short":"A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).","ama":"Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178.","mla":"Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.","chicago":"Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8.","ieee":"A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020.","apa":"Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8"},"department":[{"_id":"MiLe"}],"oa":1,"ec_funded":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules."}],"project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"178","intvolume":" 3","volume":3,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-10-13T09:48:59Z","type":"journal_article","file_date_updated":"2020-10-14T15:16:28Z","author":[{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"status":"public","year":"2020","title":"Filtering spins by scattering from a lattice of point magnets","acknowledgement":"This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON).","publisher":"Springer Nature","ddc":["530"],"doi":"10.1038/s42005-020-00445-8","has_accepted_license":"1","oa_version":"Published Version","_id":"8652","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","month":"10","publication_identifier":{"issn":["2399-3650"]},"external_id":{"isi":["000581681000001"]},"date_updated":"2023-08-22T09:58:46Z","article_type":"original","file":[{"date_created":"2020-10-14T15:16:28Z","success":1,"file_id":"8662","creator":"dernst","file_size":1462934,"date_updated":"2020-10-14T15:16:28Z","content_type":"application/pdf","file_name":"2020_CommPhysics_Ghazaryan.pdf","access_level":"open_access","relation":"main_file","checksum":"60cd35b99f0780acffc7b6060e49ec8b"}],"language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-10-09T00:00:00Z"},{"day":"13","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"research_data","status":"public","id":"7652"}]},"citation":{"ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653."},"department":[{"_id":"CaGu"}],"keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"oa":1,"abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. ","lang":"eng"}],"publication_status":"published","supervisor":[{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","date_created":"2020-10-13T13:02:33Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","author":[{"first_name":"Isabella","last_name":"Tomanek","full_name":"Tomanek, Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X"}],"file_date_updated":"2021-10-20T22:30:03Z","doi":"10.15479/AT:ISTA:8653","publisher":"Institute of Science and Technology Austria","ddc":["576"],"year":"2020","status":"public","title":"The evolution of gene expression by copy number and point mutations","oa_version":"Published Version","has_accepted_license":"1","month":"10","article_processing_charge":"No","_id":"8653","publication_identifier":{"issn":["2663-337X"]},"page":"117","file":[{"checksum":"c01d9f59794b4b70528f37637c17ad02","relation":"source_file","access_level":"closed","file_name":"Thesis_ITomanek_final_201016.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2021-10-20T22:30:03Z","file_size":25131884,"file_id":"8666","creator":"itomanek","date_created":"2020-10-16T12:14:21Z"},{"file_name":"Thesis_ITomanek_final_201016.pdf","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":15405675,"embargo":"2021-10-19","date_updated":"2021-10-20T22:30:03Z","date_created":"2020-10-16T12:14:21Z","file_id":"8667","creator":"itomanek"}],"date_updated":"2023-09-07T13:22:42Z","date_published":"2020-10-13T00:00:00Z","language":[{"iso":"eng"}]},{"department":[{"_id":"GaTk"}],"citation":{"ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.","apa":"Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657","mla":"Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.","chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria."},"oa":1,"day":"14","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7673"},{"status":"public","relation":"part_of_dissertation","id":"8250"}]},"degree_awarded":"PhD","date_created":"2020-10-13T16:46:14Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation.","lang":"eng"}],"publication_status":"published","supervisor":[{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:8657","ddc":["571","530","570"],"publisher":"Institute of Science and Technology Austria","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop.","status":"public","title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","year":"2020","oa_version":"Published Version","has_accepted_license":"1","type":"dissertation","author":[{"orcid":"0000-0001-6041-254X","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-10-07T22:30:03Z","page":"271","file":[{"date_updated":"2021-10-07T22:30:03Z","file_size":52636162,"embargo":"2021-10-06","creator":"bkavcic","file_id":"8663","date_created":"2020-10-15T06:41:20Z","access_level":"open_access","relation":"main_file","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","file_name":"kavcicB_thesis202009.pdf","content_type":"application/pdf"},{"date_created":"2020-10-15T06:41:53Z","creator":"bkavcic","file_id":"8664","file_size":321681247,"date_updated":"2021-10-07T22:30:03Z","embargo_to":"open_access","content_type":"application/zip","file_name":"2020b.zip","relation":"source_file","checksum":"bb35f2352a04db19164da609f00501f3","access_level":"closed"}],"date_updated":"2023-09-07T13:20:48Z","date_published":"2020-10-14T00:00:00Z","language":[{"iso":"eng"}],"month":"10","article_processing_charge":"No","_id":"8657","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-011-4"]}},{"author":[{"full_name":"Sznurkowska, Magdalena K.","first_name":"Magdalena K.","last_name":"Sznurkowska"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Azzarelli, Roberta","last_name":"Azzarelli","first_name":"Roberta"},{"full_name":"Chatzeli, Lemonia","last_name":"Chatzeli","first_name":"Lemonia"},{"first_name":"Tatsuro","last_name":"Ikeda","full_name":"Ikeda, Tatsuro"},{"last_name":"Yoshida","first_name":"Shosei","full_name":"Yoshida, Shosei"},{"full_name":"Philpott, Anna","first_name":"Anna","last_name":"Philpott"},{"last_name":"Simons","first_name":"Benjamin D","full_name":"Simons, Benjamin D"}],"file_date_updated":"2020-10-19T11:27:46Z","type":"journal_article","has_accepted_license":"1","oa_version":"Published Version","ddc":["570"],"publisher":"Springer Nature","doi":"10.1038/s41467-020-18837-3","status":"public","title":"Tracing the cellular basis of islet specification in mouse pancreas","year":"2020","publication_identifier":{"eissn":["20411723"]},"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","_id":"8669","date_published":"2020-10-07T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"0ecc0eab72d2d50694852579611a6624","file_name":"2020_NatureComm_Sznurkowska.pdf","success":1,"file_id":"8677","creator":"dernst","date_created":"2020-10-19T11:27:46Z","date_updated":"2020-10-19T11:27:46Z","file_size":5540540}],"external_id":{"pmid":["33028844"],"isi":["000577244600003"]},"date_updated":"2023-08-22T10:18:17Z","article_type":"original","isi":1,"day":"07","scopus_import":"1","oa":1,"citation":{"ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3."},"department":[{"_id":"EdHa"}],"publication":"Nature Communications","article_number":"5037","publication_status":"published","abstract":[{"text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.","lang":"eng"}],"date_created":"2020-10-18T22:01:35Z","intvolume":" 11","volume":11,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1},{"type":"journal_article","author":[{"first_name":"Haonan","last_name":"Zhang","full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/2007.06644","open_access":"1"}],"publisher":"AIP Publishing","doi":"10.1063/5.0022787","year":"2020","status":"public","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","oa_version":"Preprint","article_processing_charge":"No","month":"10","_id":"8670","publication_identifier":{"issn":["00222488"]},"issue":"10","date_updated":"2023-08-22T10:32:29Z","external_id":{"isi":["000578529200001"],"arxiv":["2007.06644"]},"article_type":"original","quality_controlled":"1","date_published":"2020-10-01T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","day":"01","citation":{"mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787.","chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787.","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020.","apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201."},"department":[{"_id":"JaMa"}],"publication":"Journal of Mathematical Physics","ec_funded":1,"oa":1,"publication_status":"published","abstract":[{"text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].","lang":"eng"}],"arxiv":1,"article_number":"102201","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2020-10-18T22:01:36Z","intvolume":" 61","volume":61,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_created":"2020-10-18T22:01:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","volume":15,"abstract":[{"lang":"eng","text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. "}],"publication_status":"published","arxiv":1,"project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"citation":{"chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.","mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117.","apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128.","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128."},"department":[{"_id":"KrCh"}],"publication":"Iranian Journal of Mathematical Sciences and Informatics","oa":1,"scopus_import":"1","day":"01","page":"117-128","issue":"2","file":[{"date_created":"2020-10-19T11:14:20Z","creator":"dernst","file_id":"8676","success":1,"file_size":261688,"date_updated":"2020-10-19T11:14:20Z","content_type":"application/pdf","file_name":"2020_ijmsi_Shakiba_accepted.pdf","relation":"main_file","access_level":"open_access","checksum":"f299661a6d51cda6d255a76be696f48d"}],"article_type":"original","date_updated":"2023-10-16T09:25:00Z","external_id":{"arxiv":["1805.10672"]},"quality_controlled":"1","date_published":"2020-10-01T00:00:00Z","language":[{"iso":"eng"}],"month":"10","article_processing_charge":"No","_id":"8671","publication_identifier":{"eissn":["2008-9473"],"issn":["1735-4463"]},"doi":"10.29252/ijmsi.15.2.117","ddc":["000"],"publisher":"Iranian Academic Center for Education, Culture and Research","acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","status":"public","year":"2020","title":"A note on belief structures and s-approximation spaces","oa_version":"Submitted Version","has_accepted_license":"1","type":"journal_article","author":[{"first_name":"A.","last_name":"Shakiba","full_name":"Shakiba, A."},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hooshmandasl, M.R.","first_name":"M.R.","last_name":"Hooshmandasl"},{"full_name":"Alambardar Meybodi, M.","last_name":"Alambardar Meybodi","first_name":"M."}],"file_date_updated":"2020-10-19T11:14:20Z"},{"type":"journal_article","author":[{"last_name":"Chaigne","first_name":"Agathe","full_name":"Chaigne, Agathe"},{"full_name":"Labouesse, Céline","last_name":"Labouesse","first_name":"Céline"},{"full_name":"White, Ian J.","first_name":"Ian J.","last_name":"White"},{"full_name":"Agnew, Meghan","first_name":"Meghan","last_name":"Agnew"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"first_name":"Kevin J.","last_name":"Chalut","full_name":"Chalut, Kevin J."},{"full_name":"Paluch, Ewa K.","first_name":"Ewa K.","last_name":"Paluch"}],"file_date_updated":"2021-02-04T10:20:02Z","doi":"10.1016/j.devcel.2020.09.001","publisher":"Elsevier","ddc":["570"],"acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","title":"Abscission couples cell division to embryonic stem cell fate","year":"2020","status":"public","has_accepted_license":"1","oa_version":"Published Version","month":"10","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"8672","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"page":"195-208","issue":"2","file":[{"date_updated":"2021-02-04T10:20:02Z","file_size":6929686,"success":1,"creator":"dernst","file_id":"9086","date_created":"2021-02-04T10:20:02Z","relation":"main_file","checksum":"88e1a031a61689165d19a19c2f16d795","access_level":"open_access","file_name":"2020_DevelopmCell_Chaigne.pdf","content_type":"application/pdf"}],"article_type":"original","external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"date_updated":"2023-08-22T10:16:58Z","quality_controlled":"1","date_published":"2020-10-26T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","day":"26","department":[{"_id":"EdHa"}],"citation":{"apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001","ieee":"A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.","mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001.","ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001","ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208.","short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208."},"publication":"Developmental Cell","oa":1,"abstract":[{"lang":"eng","text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions."}],"publication_status":"published","pmid":1,"date_created":"2020-10-18T22:01:37Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 55","volume":55},{"date_published":"2020-12-09T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"page":"P919-936.E11","issue":"5","file":[{"file_size":7518960,"date_updated":"2020-12-10T14:42:09Z","date_created":"2020-12-10T14:42:09Z","file_id":"8939","success":1,"creator":"dernst","file_name":"2020_Neuron_Henneberger.pdf","access_level":"open_access","relation":"main_file","checksum":"054562bb50165ef9a1f46631c1c5e36b","content_type":"application/pdf"}],"article_type":"original","date_updated":"2023-08-22T09:59:29Z","external_id":{"pmid":["32976770"],"isi":["000603428000010"]},"publication_identifier":{"issn":["08966273"],"eissn":["10974199"]},"month":"12","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"8674","oa_version":"Published Version","has_accepted_license":"1","doi":"10.1016/j.neuron.2020.08.030","ddc":["570"],"publisher":"Elsevier","acknowledgement":"We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.).","year":"2020","status":"public","title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","author":[{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Bard, Lucie","last_name":"Bard","first_name":"Lucie"},{"first_name":"Aude","last_name":"Panatier","full_name":"Panatier, Aude"},{"first_name":"James P.","last_name":"Reynolds","full_name":"Reynolds, James P."},{"full_name":"Kopach, Olga","last_name":"Kopach","first_name":"Olga"},{"first_name":"Nikolay I.","last_name":"Medvedev","full_name":"Medvedev, Nikolay I."},{"full_name":"Minge, Daniel","first_name":"Daniel","last_name":"Minge"},{"full_name":"Herde, Michel K.","last_name":"Herde","first_name":"Michel K."},{"full_name":"Anders, Stefanie","last_name":"Anders","first_name":"Stefanie"},{"first_name":"Igor","last_name":"Kraev","full_name":"Kraev, Igor"},{"last_name":"Heller","first_name":"Janosch P.","full_name":"Heller, Janosch P."},{"full_name":"Rama, Sylvain","last_name":"Rama","first_name":"Sylvain"},{"last_name":"Zheng","first_name":"Kaiyu","full_name":"Zheng, Kaiyu"},{"full_name":"Jensen, Thomas P.","last_name":"Jensen","first_name":"Thomas P."},{"last_name":"Sanchez-Romero","first_name":"Inmaculada","full_name":"Sanchez-Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jackson, Colin J.","first_name":"Colin J.","last_name":"Jackson"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315"},{"first_name":"Ole Petter","last_name":"Ottersen","full_name":"Ottersen, Ole Petter"},{"last_name":"Nagelhus","first_name":"Erlend Arnulf","full_name":"Nagelhus, Erlend Arnulf"},{"first_name":"Stephane H.R.","last_name":"Oliet","full_name":"Oliet, Stephane H.R."},{"full_name":"Stewart, Michael G.","first_name":"Michael G.","last_name":"Stewart"},{"full_name":"Nägerl, U. VAlentin","first_name":"U. VAlentin","last_name":"Nägerl"},{"last_name":"Rusakov","first_name":"Dmitri A. ","full_name":"Rusakov, Dmitri A. "}],"file_date_updated":"2020-12-10T14:42:09Z","type":"journal_article","date_created":"2020-10-18T22:01:38Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 108","volume":108,"pmid":1,"abstract":[{"lang":"eng","text":"Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections."}],"publication_status":"published","oa":1,"citation":{"ama":"Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030","ista":"Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.","short":"C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.","apa":"Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030","ieee":"C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020.","chicago":"Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030.","mla":"Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030."},"department":[{"_id":"HaJa"}],"publication":"Neuron","isi":1,"day":"09","scopus_import":"1"},{"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"first_name":"Ramin","last_name":"Hasani","full_name":"Hasani, Ramin"},{"full_name":"Amini, Alexander","first_name":"Alexander","last_name":"Amini"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"type":"journal_article","oa_version":"None","status":"public","title":"Neural circuit policies enabling auditable autonomy","year":"2020","doi":"10.1038/s42256-020-00237-3","publisher":"Springer Nature","publication_identifier":{"eissn":["2522-5839"]},"_id":"8679","month":"10","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2020-10-01T00:00:00Z","quality_controlled":"1","article_type":"original","date_updated":"2023-08-22T10:36:06Z","external_id":{"isi":["000583337200011"]},"page":"642-652","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-deep-learning-models/","description":"News on IST Homepage"}]},"scopus_import":"1","day":"01","isi":1,"publication":"Nature Machine Intelligence","department":[{"_id":"ToHe"}],"citation":{"ieee":"M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” Nature Machine Intelligence, vol. 2. Springer Nature, pp. 642–652, 2020.","apa":"Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3","chicago":"Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.","mla":"Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52, doi:10.1038/s42256-020-00237-3.","ama":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652. doi:10.1038/s42256-020-00237-3","ista":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652."},"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system."}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":2,"intvolume":" 2","date_created":"2020-10-19T13:46:06Z"},{"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/803635v1","open_access":"1"}],"author":[{"first_name":"Tony Y.-C.","last_name":"Tsai","full_name":"Tsai, Tony Y.-C."},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng","last_name":"Xia","full_name":"Xia, Peng","orcid":"0000-0002-5419-7756"},{"first_name":"Tugba","last_name":"Colak-Champollion","full_name":"Colak-Champollion, Tugba"},{"full_name":"Knaut, Holger","first_name":"Holger","last_name":"Knaut"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"last_name":"Megason","first_name":"Sean G.","full_name":"Megason, Sean G."}],"type":"journal_article","oa_version":"Preprint","acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","year":"2020","status":"public","title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","doi":"10.1126/science.aba6637","publisher":"American Association for the Advancement of Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"_id":"8680","month":"10","article_processing_charge":"No","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-10-02T00:00:00Z","article_type":"original","external_id":{"isi":["000579169000053"]},"date_updated":"2023-08-22T10:36:35Z","issue":"6512","page":"113-116","related_material":{"link":[{"url":"https://ist.ac.at/en/news/sticking-together/","relation":"press_release","description":"News on IST Homepage"}]},"scopus_import":"1","day":"02","isi":1,"ec_funded":1,"oa":1,"publication":"Science","citation":{"short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116.","ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637."},"department":[{"_id":"CaHe"}],"keyword":["Multidisciplinary"],"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"abstract":[{"text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.","lang":"eng"}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":370,"intvolume":" 370","date_created":"2020-10-19T14:09:38Z"},{"day":"05","citation":{"ista":"Koudjinan E. 2020. A KAM theorem for finitely differentiable Hamiltonian systems. Journal of Differential Equations. 269(6), 4720–4750.","ama":"Koudjinan E. A KAM theorem for finitely differentiable Hamiltonian systems. Journal of Differential Equations. 2020;269(6):4720-4750. doi:10.1016/j.jde.2020.03.044","short":"E. Koudjinan, Journal of Differential Equations 269 (2020) 4720–4750.","chicago":"Koudjinan, Edmond. “A KAM Theorem for Finitely Differentiable Hamiltonian Systems.” Journal of Differential Equations. Elsevier, 2020. https://doi.org/10.1016/j.jde.2020.03.044.","mla":"Koudjinan, Edmond. “A KAM Theorem for Finitely Differentiable Hamiltonian Systems.” Journal of Differential Equations, vol. 269, no. 6, Elsevier, 2020, pp. 4720–50, doi:10.1016/j.jde.2020.03.044.","apa":"Koudjinan, E. (2020). A KAM theorem for finitely differentiable Hamiltonian systems. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2020.03.044","ieee":"E. Koudjinan, “A KAM theorem for finitely differentiable Hamiltonian systems,” Journal of Differential Equations, vol. 269, no. 6. Elsevier, pp. 4720–4750, 2020."},"keyword":["Analysis"],"publication":"Journal of Differential Equations","oa":1,"abstract":[{"text":"Given l>2ν>2d≥4, we prove the persistence of a Cantor--family of KAM tori of measure O(ε1/2−ν/l) for any non--degenerate nearly integrable Hamiltonian system of class Cl(D×Td), where D⊂Rd is a bounded domain, provided that the size ε of the perturbation is sufficiently small. This extends a result by D. Salamon in \\cite{salamon2004kolmogorov} according to which we do have the persistence of a single KAM torus in the same framework. Moreover, it is well--known that, for the persistence of a single torus, the regularity assumption can not be improved.","lang":"eng"}],"publication_status":"published","arxiv":1,"extern":"1","date_created":"2020-10-21T15:03:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":269,"intvolume":" 269","type":"journal_article","author":[{"orcid":"0000-0003-2640-4049","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","first_name":"Edmond","last_name":"Koudjinan","full_name":"Koudjinan, Edmond"}],"main_file_link":[{"url":"https://arxiv.org/abs/1909.04099","open_access":"1"}],"doi":"10.1016/j.jde.2020.03.044","publisher":"Elsevier","year":"2020","title":"A KAM theorem for finitely differentiable Hamiltonian systems","status":"public","oa_version":"Preprint","month":"09","article_processing_charge":"No","_id":"8691","publication_identifier":{"issn":["0022-0396"]},"issue":"6","page":"4720-4750","article_type":"original","date_updated":"2021-01-12T08:20:33Z","external_id":{"arxiv":["1909.04099"]},"date_published":"2020-09-05T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}]},{"author":[{"first_name":"Ali","last_name":"Golmakani","full_name":"Golmakani, Ali"},{"full_name":"Koudjinan, Edmond","first_name":"Edmond","last_name":"Koudjinan","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","orcid":"0000-0003-2640-4049"},{"first_name":"Stefano","last_name":"Luzzatto","full_name":"Luzzatto, Stefano"},{"full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.13444"}],"type":"journal_article","oa_version":"Preprint","publisher":"AIP","doi":"10.1063/5.0012822","year":"2020","status":"public","title":"Rigorous numerics for critical orbits in the quadratic family","article_processing_charge":"No","month":"07","_id":"8694","date_published":"2020-07-31T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"7","date_updated":"2021-01-12T08:20:34Z","external_id":{"arxiv":["2004.13444"]},"article_type":"original","day":"31","oa":1,"citation":{"ieee":"A. Golmakani, E. Koudjinan, S. Luzzatto, and P. Pilarczyk, “Rigorous numerics for critical orbits in the quadratic family,” Chaos, vol. 30, no. 7. AIP, 2020.","apa":"Golmakani, A., Koudjinan, E., Luzzatto, S., & Pilarczyk, P. (2020). Rigorous numerics for critical orbits in the quadratic family. Chaos. AIP. https://doi.org/10.1063/5.0012822","mla":"Golmakani, Ali, et al. “Rigorous Numerics for Critical Orbits in the Quadratic Family.” Chaos, vol. 30, no. 7, 073143, AIP, 2020, doi:10.1063/5.0012822.","chicago":"Golmakani, Ali, Edmond Koudjinan, Stefano Luzzatto, and Pawel Pilarczyk. “Rigorous Numerics for Critical Orbits in the Quadratic Family.” Chaos. AIP, 2020. https://doi.org/10.1063/5.0012822.","short":"A. Golmakani, E. Koudjinan, S. Luzzatto, P. Pilarczyk, Chaos 30 (2020).","ama":"Golmakani A, Koudjinan E, Luzzatto S, Pilarczyk P. Rigorous numerics for critical orbits in the quadratic family. Chaos. 2020;30(7). doi:10.1063/5.0012822","ista":"Golmakani A, Koudjinan E, Luzzatto S, Pilarczyk P. 2020. Rigorous numerics for critical orbits in the quadratic family. Chaos. 30(7), 073143."},"publication":"Chaos","article_number":"073143","arxiv":1,"abstract":[{"text":"We develop algorithms and techniques to compute rigorous bounds for finite pieces of orbits of the critical points, for intervals of parameter values, in the quadratic family of one-dimensional maps fa(x)=a−x2. We illustrate the effectiveness of our approach by constructing a dynamically defined partition 𝒫 of the parameter interval Ω=[1.4,2] into almost 4×106 subintervals, for each of which we compute to high precision the orbits of the critical points up to some time N and other dynamically relevant quantities, several of which can vary greatly, possibly spanning several orders of magnitude. We also subdivide 𝒫 into a family 𝒫+ of intervals, which we call stochastic intervals, and a family 𝒫− of intervals, which we call regular intervals. We numerically prove that each interval ω∈𝒫+ has an escape time, which roughly means that some iterate of the critical point taken over all the parameters in ω has considerable width in the phase space. This suggests, in turn, that most parameters belonging to the intervals in 𝒫+ are stochastic and most parameters belonging to the intervals in 𝒫− are regular, thus the names. We prove that the intervals in 𝒫+ occupy almost 90% of the total measure of Ω. The software and the data are freely available at http://www.pawelpilarczyk.com/quadr/, and a web page is provided for carrying out the calculations. The ideas and procedures can be easily generalized to apply to other parameterized families of dynamical systems.","lang":"eng"}],"publication_status":"published","date_created":"2020-10-21T15:43:05Z","intvolume":" 30","volume":30,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"oa":1,"oa_version":"Published Version","has_accepted_license":"1","year":"2020","status":"public","title":"Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria","publisher":"OANA","ddc":["020"],"citation":{"ista":"Mayer K, Rieck K, Reichmann S, Danowski P, Graschopf A, König T, Kraker P, Lehner P, Reckling F, Ross-Hellauer T, Spichtinger D, Tzatzanis M, Schürz S. 2020. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 36p.","ama":"Mayer K, Rieck K, Reichmann S, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA; 2020. doi:10.5281/ZENODO.4109242","short":"K. Mayer, K. Rieck, S. Reichmann, P. Danowski, A. Graschopf, T. König, P. Kraker, P. Lehner, F. Reckling, T. Ross-Hellauer, D. Spichtinger, M. Tzatzanis, S. Schürz, Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 2020.","chicago":"Mayer, Katja, Katharina Rieck, Stefan Reichmann, Patrick Danowski, Anton Graschopf, Thomas König, Peter Kraker, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020. https://doi.org/10.5281/ZENODO.4109242.","mla":"Mayer, Katja, et al. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020, doi:10.5281/ZENODO.4109242.","ieee":"K. Mayer et al., Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA, 2020.","apa":"Mayer, K., Rieck, K., Reichmann, S., Danowski, P., Graschopf, A., König, T., … Schürz, S. (2020). Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria. OANA. https://doi.org/10.5281/ZENODO.4109242"},"doi":"10.5281/ZENODO.4109242","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-10-23T09:29:45Z","author":[{"last_name":"Mayer","first_name":"Katja","full_name":"Mayer, Katja"},{"first_name":"Katharina","last_name":"Rieck","full_name":"Rieck, Katharina"},{"full_name":"Reichmann, Stefan","first_name":"Stefan","last_name":"Reichmann"},{"full_name":"Danowski, Patrick","last_name":"Danowski","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409"},{"first_name":"Anton","last_name":"Graschopf","full_name":"Graschopf, Anton"},{"full_name":"König, Thomas","first_name":"Thomas","last_name":"König"},{"last_name":"Kraker","first_name":"Peter","full_name":"Kraker, Peter"},{"first_name":"Patrick","last_name":"Lehner","full_name":"Lehner, Patrick"},{"full_name":"Reckling, Falk","last_name":"Reckling","first_name":"Falk"},{"last_name":"Ross-Hellauer","first_name":"Tony","full_name":"Ross-Hellauer, Tony"},{"first_name":"Daniel","last_name":"Spichtinger","full_name":"Spichtinger, Daniel"},{"full_name":"Tzatzanis, Michalis","first_name":"Michalis","last_name":"Tzatzanis"},{"full_name":"Schürz, Stefanie","last_name":"Schürz","first_name":"Stefanie"}],"day":"21","type":"working_paper","language":[{"iso":"ger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-10-23T09:08:28Z","date_published":"2020-10-21T00:00:00Z","date_updated":"2020-10-23T09:34:40Z","file":[{"content_type":"application/pdf","access_level":"open_access","checksum":"8eba912bb4b20b4f82f8010f2110461a","relation":"main_file","file_name":"2020_OANA_Mayer.pdf","creator":"dernst","file_id":"8696","success":1,"date_created":"2020-10-23T09:29:45Z","date_updated":"2020-10-23T09:29:45Z","file_size":2298363}],"page":"36","_id":"8695","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","month":"10","publication_status":"published","abstract":[{"lang":"eng","text":"A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group \"Open Science Strategy\" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions."},{"lang":"ger","text":"Der Blick auf internationale Aktivitäten zu Open Science zeigt ein breites Spektrum von einzelnen institutionellen Policies bis hin zu nationalen Aktionsplänen. Die vorliegenden Empfehlungen für eine nationale Open Science Strategie in Österreich orientieren sich an diesen internationalen Initiativen und stellen praktische Überlegungen für ihre koordinierte Implementierung im Hinblick auf strategische Entwicklungen in Forschung, Technologie und Innovation (FTI) bis 2030 in Österreich dar. Dabei richten sie sich an alle relevanten Akteur*innen im FTI System, im Besonderen an Forschungsstätten, Forschungsförderer, Forschungspolitik, Gedächtnisinstitutionen wie Bibliotheken und Wissenschafter*innen. Das Empfehlungspapier wurde von 2018 bis 2020 von der OANA-Arbeitsgruppe \"Open Science Strategie\" entwickelt und im Frühling 2020 das erste Mal für eine öffentliche Konsultation veröffentlicht. Die nun vorliegende finale Version des Empfehlungsdokuments, die Feedback und Kommentare aus der Konsultation enthält, soll ein Anstoß für die weitere Diskussion und Umsetzung von Open Science in Österreich sein und als Beitrag und Grundlage einer potentiellen nationalen Open Science Strategie in Österreich dienen. Das Dokument baut auf der vielfältigen Expertise der Autor*innen auf (Wissenschaft, Administration, Bibliothek und Archiv, Informationstechnologie, Wissenschaftspolitik, Förderwesen etc.) und spiegelt deren persönliche Erfahrungen und Meinung wider."}]},{"has_accepted_license":"1","oa_version":"Published Version","year":"2020","status":"public","title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","doi":"10.1088/1361-6544/ab9728","publisher":"IOP Publishing","ddc":["510"],"file_date_updated":"2020-10-27T12:09:57Z","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","full_name":"Kniely, Michael","last_name":"Kniely","first_name":"Michael"}],"type":"journal_article","language":[{"iso":"eng"}],"date_published":"2020-11-01T00:00:00Z","quality_controlled":"1","article_type":"original","date_updated":"2023-08-22T10:38:38Z","external_id":{"arxiv":["1906.12245"],"isi":["000576492700001"]},"issue":"11","page":"5733-5772","file":[{"date_created":"2020-10-27T12:09:57Z","file_id":"8710","creator":"cziletti","success":1,"file_size":1223899,"date_updated":"2020-10-27T12:09:57Z","content_type":"application/pdf","file_name":"2020_Nonlinearity_Fischer.pdf","checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","access_level":"open_access","relation":"main_file"}],"publication_identifier":{"issn":["09517715"],"eissn":["13616544"]},"_id":"8697","month":"11","article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"oa":1,"publication":"Nonlinearity","citation":{"apa":"Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728","ieee":"J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.","mla":"Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.","chicago":"Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.","ama":"Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728","ista":"Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772."},"department":[{"_id":"JuFi"}],"day":"01","scopus_import":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":33,"intvolume":" 33","date_created":"2020-10-25T23:01:16Z","arxiv":1,"publication_status":"published","abstract":[{"text":"In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.","lang":"eng"}]},{"_id":"8698","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_processing_charge":"No","month":"10","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"date_updated":"2023-08-22T12:11:23Z","external_id":{"isi":["000579045200012"],"pmid":["32948691"]},"article_type":"original","file":[{"creator":"cziletti","file_id":"8713","success":1,"date_created":"2020-10-27T14:57:50Z","date_updated":"2020-10-27T14:57:50Z","file_size":1755359,"content_type":"application/pdf","checksum":"c6a24fdecf3f28faf447078e7a274a88","access_level":"open_access","relation":"main_file","file_name":"2020_PNAS_Maoz.pdf"}],"issue":"40","page":"25066-25073","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-10-06T00:00:00Z","type":"journal_article","file_date_updated":"2020-10-27T14:57:50Z","author":[{"last_name":"Maoz","first_name":"Ori","full_name":"Maoz, Ori"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"full_name":"Esteki, Mohamad Saleh","first_name":"Mohamad Saleh","last_name":"Esteki"},{"first_name":"Roozbeh","last_name":"Kiani","full_name":"Kiani, Roozbeh"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"}],"year":"2020","status":"public","title":"Learning probabilistic neural representations with randomly connected circuits","acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","ddc":["570"],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1912804117","has_accepted_license":"1","oa_version":"Published Version","abstract":[{"text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.","lang":"eng"}],"publication_status":"published","pmid":1,"volume":117,"intvolume":" 117","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-10-25T23:01:16Z","day":"06","scopus_import":"1","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","department":[{"_id":"GaTk"}],"citation":{"ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073.","ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117","short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.","mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117.","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117"},"oa":1},{"abstract":[{"lang":"eng","text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling."}],"publication_status":"published","arxiv":1,"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"pmid":1,"date_created":"2020-10-25T23:01:17Z","intvolume":" 117","volume":117,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"scopus_import":"1","day":"06","department":[{"_id":"MiLe"}],"citation":{"apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117","ieee":"E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020.","chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117.","mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117.","ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117","ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770.","short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","ec_funded":1,"oa":1,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"month":"10","_id":"8699","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"file":[{"content_type":"application/pdf","file_name":"2020_PNAS_Paris.pdf","checksum":"1638fa36b442e2868576c6dd7d6dc505","relation":"main_file","access_level":"open_access","date_created":"2020-10-28T11:53:12Z","creator":"cziletti","file_id":"8715","success":1,"file_size":1176522,"date_updated":"2020-10-28T11:53:12Z"}],"page":"24764-24770","issue":"40","date_updated":"2023-08-22T12:11:52Z","external_id":{"arxiv":["2009.12262"],"pmid":["32958669"],"isi":["000579059100029"]},"article_type":"original","quality_controlled":"1","date_published":"2020-10-06T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","author":[{"full_name":"Paris, Eugenio","first_name":"Eugenio","last_name":"Paris"},{"full_name":"Tseng, Yi","last_name":"Tseng","first_name":"Yi"},{"orcid":"0000-0003-0853-8182","id":"8275014E-6063-11E9-9B7F-6338E6697425","full_name":"Paerschke, Ekaterina","last_name":"Paerschke","first_name":"Ekaterina"},{"full_name":"Zhang, Wenliang","last_name":"Zhang","first_name":"Wenliang"},{"full_name":"Upton, Mary H","last_name":"Upton","first_name":"Mary H"},{"full_name":"Efimenko, Anna","last_name":"Efimenko","first_name":"Anna"},{"first_name":"Katharina","last_name":"Rolfs","full_name":"Rolfs, Katharina"},{"full_name":"McNally, Daniel E","last_name":"McNally","first_name":"Daniel E"},{"full_name":"Maurel, Laura","first_name":"Laura","last_name":"Maurel"},{"first_name":"Muntaser","last_name":"Naamneh","full_name":"Naamneh, Muntaser"},{"last_name":"Caputo","first_name":"Marco","full_name":"Caputo, Marco"},{"first_name":"Vladimir N","last_name":"Strocov","full_name":"Strocov, Vladimir N"},{"full_name":"Wang, Zhiming","first_name":"Zhiming","last_name":"Wang"},{"first_name":"Diego","last_name":"Casa","full_name":"Casa, Diego"},{"last_name":"Schneider","first_name":"Christof W","full_name":"Schneider, Christof W"},{"full_name":"Pomjakushina, Ekaterina","first_name":"Ekaterina","last_name":"Pomjakushina"},{"full_name":"Wohlfeld, Krzysztof","last_name":"Wohlfeld","first_name":"Krzysztof"},{"full_name":"Radovic, Milan","first_name":"Milan","last_name":"Radovic"},{"first_name":"Thorsten","last_name":"Schmitt","full_name":"Schmitt, Thorsten"}],"file_date_updated":"2020-10-28T11:53:12Z","ddc":["530"],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.2012043117","status":"public","year":"2020","title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","oa_version":"Published Version","has_accepted_license":"1"},{"publication_identifier":{"eissn":["16083245"],"issn":["00268933"]},"_id":"8700","month":"09","article_processing_charge":"No","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-09-01T00:00:00Z","article_type":"original","external_id":{"isi":["000579441200009"]},"date_updated":"2023-08-22T10:39:38Z","issue":"5","page":"739-748","author":[{"full_name":"Sokolova, E. E.","first_name":"E. E.","last_name":"Sokolova"},{"first_name":"Petr","last_name":"Vlasov","full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"last_name":"Shuvalov","first_name":"A. V.","full_name":"Shuvalov, A. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"type":"journal_article","oa_version":"None","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","status":"public","year":"2020","doi":"10.1134/S0026893320050088","publisher":"Springer Nature","abstract":[{"text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.","lang":"eng"}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 54","volume":54,"date_created":"2020-10-25T23:01:17Z","related_material":{"record":[{"id":"8701","status":"public","relation":"original"}]},"scopus_import":"1","day":"01","isi":1,"publication":"Molecular Biology","citation":{"ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320050088","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320050088.","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748.","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748."},"department":[{"_id":"FyKo"}]},{"publication_status":"published","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"pmid":1,"date_created":"2020-10-25T23:01:17Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 54","volume":54,"day":"01","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"translation","id":"8700"}]},"department":[{"_id":"FyKo"}],"citation":{"ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080.","mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:10.31857/S0026898420050080.","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420050080"},"publication":"Molekuliarnaia biologiia","month":"09","article_processing_charge":"No","_id":"8701","publication_identifier":{"issn":["00268984"]},"page":"837-848","issue":"5","article_type":"original","external_id":{"pmid":["33009793"]},"date_updated":"2023-08-22T10:39:37Z","quality_controlled":"1","date_published":"2020-09-01T00:00:00Z","language":[{"iso":"rus"}],"type":"journal_article","author":[{"full_name":"Sokolova, E. E.","first_name":"E. E.","last_name":"Sokolova"},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr","full_name":"Vlasov, Petr"},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"full_name":"Shuvalov, A. V.","first_name":"A. V.","last_name":"Shuvalov"},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"doi":"10.31857/S0026898420050080","publisher":"Russian Academy of Sciences","year":"2020","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","status":"public","oa_version":"None"}]