[{"related_material":{"record":[{"relation":"used_in_publication","id":"8755","status":"public"}]},"date_created":"2023-05-23T16:42:30Z","citation":{"short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>.","mla":"Peruzzo, Matilda, et al. <i>Surpassing the Resistance Quantum with a Geometric Superinductor</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.4052882\">10.5281/ZENODO.4052882</a>.","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. <a href=\"https://doi.org/10.5281/ZENODO.4052882\">https://doi.org/10.5281/ZENODO.4052882</a>.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., &#38; Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.4052882\">https://doi.org/10.5281/ZENODO.4052882</a>"},"title":"Surpassing the resistance quantum with a geometric superinductor","date_updated":"2024-09-10T12:23:56Z","oa":1,"year":"2020","article_processing_charge":"No","doi":"10.5281/ZENODO.4052882","_id":"13070","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4052883"}],"day":"27","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Matilda","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","full_name":"Trioni, Andrea","first_name":"Andrea"},{"first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"},{"last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Zemlicka, Martin"},{"first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JoFi"}],"publisher":"Zenodo","status":"public","type":"research_data_reference","date_published":"2020-09-27T00:00:00Z"},{"related_material":{"record":[{"id":"9114","relation":"used_in_publication","status":"public"}]},"oa":1,"date_updated":"2024-09-10T12:23:54Z","article_processing_charge":"No","year":"2020","citation":{"mla":"Hease, William J., et al. <i>Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State</i>. Zenodo, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. <a href=\"https://doi.org/10.5281/ZENODO.4266025\">https://doi.org/10.5281/ZENODO.4266025</a>.","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.4266025\">10.5281/ZENODO.4266025</a>","ieee":"W. J. Hease <i>et al.</i>, “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., &#38; Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.4266025\">https://doi.org/10.5281/ZENODO.4266025</a>"},"date_created":"2023-05-23T16:44:11Z","title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","doi":"10.5281/ZENODO.4266025","_id":"13071","ddc":["530"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","day":"10","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4266026"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the plots of the main part of the submitted article \"Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State\". Additional raw data are available from the corresponding author on reasonable request."}],"author":[{"last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","full_name":"Hease, William J"},{"last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R"},{"orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh","full_name":"Sahu, Rishabh"},{"full_name":"Wulf, Matthias","first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378"},{"first_name":"Georg M","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","orcid":"0000-0003-1397-7876"},{"last_name":"Schwefel","first_name":"Harald","full_name":"Schwefel, Harald"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M"}],"publisher":"Zenodo","type":"research_data_reference","status":"public","date_published":"2020-11-10T00:00:00Z","department":[{"_id":"JoFi"}]},{"author":[{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075"},{"first_name":"Tahani","full_name":"El Ayari, Tahani","last_name":"El Ayari"},{"last_name":"Liautard-Haag","full_name":"Liautard-Haag, Cathy","first_name":"Cathy"},{"first_name":"Petr","full_name":"Strelkov, Petr","last_name":"Strelkov"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"day":"22","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"month":"09","department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","date_published":"2020-09-22T00:00:00Z","type":"research_data_reference","citation":{"ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","mla":"Simon, Alexis, et al. <i>How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., &#38; Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>"},"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","date_created":"2023-05-23T16:48:27Z","oa":1,"date_updated":"2023-08-04T11:04:11Z","article_processing_charge":"No","year":"2020","related_material":{"record":[{"relation":"used_in_publication","id":"8708","status":"public"}]},"_id":"13073","doi":"10.5061/DRYAD.R4XGXD29N"},{"publication_identifier":{"issn":["2542-4653"]},"month":"07","oa_version":"Published Version","day":"29","file":[{"access_level":"open_access","file_size":531137,"relation":"main_file","content_type":"application/pdf","creator":"dernst","date_updated":"2020-08-06T08:56:06Z","date_created":"2020-08-06T08:56:06Z","file_name":"2020_SciPostPhys_Gulden.pdf","file_id":"8202","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Tobias","full_name":"Gulden, Tobias","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden","orcid":"0000-0001-6814-7541"},{"full_name":"Berg, Erez","first_name":"Erez","last_name":"Berg"},{"last_name":"Rudner","first_name":"Mark Spencer","full_name":"Rudner, Mark Spencer"},{"last_name":"Lindner","full_name":"Lindner, Netanel","first_name":"Netanel"}],"status":"public","type":"journal_article","isi":1,"has_accepted_license":"1","scopus_import":"1","intvolume":"         9","oa":1,"date_updated":"2023-08-22T08:28:24Z","article_processing_charge":"No","title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","publication":"SciPost Physics","language":[{"iso":"eng"}],"ddc":["530"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000557362300008"]},"abstract":[{"lang":"eng","text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist."}],"publication_status":"published","publisher":"SciPost Foundation","date_published":"2020-07-29T00:00:00Z","department":[{"_id":"MaSe"}],"volume":9,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"article_number":"015","acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","year":"2020","citation":{"short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. 2020;9. doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” <i>SciPost Physics</i>, vol. 9. SciPost Foundation, 2020.","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>. SciPost Foundation, 2020. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>.","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>, vol. 9, 015, SciPost Foundation, 2020, doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>.","apa":"Gulden, T., Berg, E., Rudner, M. S., &#38; Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>"},"date_created":"2020-08-04T13:04:15Z","doi":"10.21468/scipostphys.9.1.015","file_date_updated":"2020-08-06T08:56:06Z","_id":"8199","article_type":"original"},{"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"month":"06","file":[{"date_updated":"2020-08-06T09:35:37Z","date_created":"2020-08-06T09:35:37Z","file_id":"8204","file_name":"2020_NanoLetters_Katsaros.pdf","success":1,"file_size":3308906,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","day":"01","author":[{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","full_name":"Katsaros, Georgios","first_name":"Georgios"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip"},{"orcid":"0000-0003-2424-8636","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","full_name":"Vukušić, Lada"},{"last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","full_name":"Watzinger, Hannes"},{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"first_name":"Ting","full_name":"Wang, Ting","last_name":"Wang","orcid":"0000-0002-4619-9575"},{"last_name":"Zhang","full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun"},{"last_name":"Held","first_name":"Karsten","full_name":"Held, Karsten"}],"type":"journal_article","status":"public","pmid":1,"isi":1,"intvolume":"        20","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","issue":"7","oa":1,"date_updated":"2024-02-21T12:44:01Z","title":"Zero field splitting of heavy-hole states in quantum dots","publication":"Nano Letters","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530"],"abstract":[{"text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits.","lang":"eng"}],"external_id":{"isi":["000548893200066"],"pmid":["32479090"]},"publication_status":"published","date_published":"2020-06-01T00:00:00Z","publisher":"American Chemical Society","volume":20,"quality_controlled":"1","department":[{"_id":"GeKa"}],"page":"5201-5206","project":[{"_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"7689"}]},"ec_funded":1,"year":"2020","acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","citation":{"ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>.","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. 2020;20(7):5201-5206. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>","ieee":"G. Katsaros <i>et al.</i>, “Zero field splitting of heavy-hole states in quantum dots,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>"},"date_created":"2020-08-06T09:25:04Z","doi":"10.1021/acs.nanolett.0c01466","article_type":"original","_id":"8203","file_date_updated":"2020-08-06T09:35:37Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}]},{"title":"Stem cell lineage survival as a noisy competition for niche access","article_processing_charge":"No","issue":"29","date_updated":"2023-08-22T08:29:30Z","oa":1,"intvolume":"       117","has_accepted_license":"1","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","author":[{"first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra"},{"last_name":"Scheele","full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J."},{"last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","full_name":"Kishi, Kasumi"},{"first_name":"Saskia I.J.","full_name":"Ellenbroek, Saskia I.J.","last_name":"Ellenbroek"},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"},{"last_name":"Van Rheenen","first_name":"Jacco","full_name":"Van Rheenen, Jacco"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":1111604,"relation":"main_file","creator":"dernst","date_updated":"2020-08-10T06:50:28Z","date_created":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf","file_id":"8223","success":1}],"day":"21","oa_version":"Published Version","publication_identifier":{"eissn":["10916490"]},"month":"07","status":"public","type":"journal_article","pmid":1,"date_created":"2020-08-09T22:00:52Z","citation":{"apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., &#38; Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(29):16969-16975. doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>","ieee":"B. Corominas-Murtra <i>et al.</i>, “Stem cell lineage survival as a noisy competition for niche access,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020."},"year":"2020","acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","related_material":{"link":[{"url":"https://ist.ac.at/en/news/order-from-noise/","relation":"press_release"}]},"ec_funded":1,"article_type":"original","_id":"8220","file_date_updated":"2020-08-10T06:50:28Z","doi":"10.1073/pnas.1921205117","publication_status":"published","abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}],"external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"volume":117,"quality_controlled":"1","page":"16969-16975","department":[{"_id":"EdHa"}],"date_published":"2020-07-21T00:00:00Z","publisher":"National Academy of Sciences"},{"doi":"10.1038/s41467-020-17734-z","file_date_updated":"2020-08-17T07:36:57Z","_id":"8250","article_type":"original","article_number":"4013","related_material":{"record":[{"id":"8657","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-08-12T09:13:50Z","citation":{"ama":"Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17734-z\">10.1038/s41467-020-17734-z</a>","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).","mla":"Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” <i>Nature Communications</i>, vol. 11, 4013, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17734-z\">10.1038/s41467-020-17734-z</a>.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17734-z\">https://doi.org/10.1038/s41467-020-17734-z</a>.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17734-z\">https://doi.org/10.1038/s41467-020-17734-z</a>"},"acknowledgement":"We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL.","year":"2020","department":[{"_id":"GaTk"}],"quality_controlled":"1","volume":11,"publisher":"Springer Nature","date_published":"2020-08-11T00:00:00Z","project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"external_id":{"isi":["000562769300008"]},"abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible 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 causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.","lang":"eng"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","publication":"Nature Communications","language":[{"iso":"eng"}],"intvolume":"        11","has_accepted_license":"1","isi":1,"title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","oa":1,"date_updated":"2024-03-25T23:30:05Z","article_processing_charge":"No","status":"public","type":"journal_article","day":"11","oa_version":"Published Version","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":1965672,"creator":"dernst","date_created":"2020-08-17T07:36:57Z","date_updated":"2020-08-17T07:36:57Z","success":1,"checksum":"986bebb308850a55850028d3d2b5b664","file_id":"8275","file_name":"2020_NatureComm_Kavcic.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"08","publication_identifier":{"issn":["2041-1723"]},"author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"full_name":"Bollenbach, Tobias","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"}]},{"doi":"10.15479/AT:ISTA:8254","_id":"8254","file_date_updated":"2020-08-18T08:03:23Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"11321"},{"status":"public","id":"9192","relation":"later_version"}]},"year":"2020","article_processing_charge":"No","date_updated":"2024-02-21T12:41:09Z","oa":1,"citation":{"apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>","short":"L.S. Arathoon, (2020).","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>.","mla":"Arathoon, Louise S. <i>Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus)</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>."},"date_created":"2020-08-12T12:49:23Z","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","date_published":"2020-08-18T00:00:00Z","type":"research_data","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"08","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"contributor_type":"data_collector","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","orcid":"0000-0002-4014-8478"},{"contributor_type":"project_member","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","contributor_type":"project_member"}],"abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"file":[{"creator":"dernst","access_level":"open_access","content_type":"application/x-zip-compressed","relation":"main_file","file_size":5778420,"checksum":"4f1382ed4384751b6013398c11557bf6","file_name":"Data_Rcode_MathematicaNB.zip","file_id":"8280","success":1,"date_updated":"2020-08-18T08:03:23Z","date_created":"2020-08-18T08:03:23Z"}],"oa_version":"Published Version","day":"18","author":[{"full_name":"Arathoon, Louise S","first_name":"Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}]},{"isi":1,"has_accepted_license":"1","intvolume":"       107","oa":1,"date_updated":"2023-08-22T08:30:55Z","article_processing_charge":"No","issue":"6","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","publication":"Neuron","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"month":"09","oa_version":"Published Version","day":"23","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2020-12-04T09:29:21Z","date_created":"2020-12-04T09:29:21Z","file_id":"8920","checksum":"44a5960fc083a4cb3488d22224859fdc","file_name":"2020_Neuron_Zhang.pdf","success":1,"content_type":"application/pdf","relation":"main_file","file_size":3011120,"access_level":"open_access","creator":"dernst"}],"author":[{"full_name":"Zhang, Xiaomin","first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois"},{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"status":"public","type":"journal_article","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","description":"News on IST Website","relation":"press_release"}]},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","year":"2020","date_created":"2020-08-14T09:36:05Z","citation":{"short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” <i>Neuron</i>, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. 2020;107(6):1212-1225. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>.","chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>.","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","apa":"Zhang, X., Schlögl, A., &#38; Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>"},"doi":"10.1016/j.neuron.2020.07.006","file_date_updated":"2020-12-04T09:29:21Z","article_type":"original","_id":"8261","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"external_id":{"isi":["000579698700009"],"pmid":["32763145"]},"abstract":[{"text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.","lang":"eng"}],"publication_status":"published","publisher":"Elsevier","date_published":"2020-09-23T00:00:00Z","page":"1212-1225","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"volume":107,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}]},{"citation":{"apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. IEEE. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>, vol. 68, IEEE, 2020, pp. 4268–82, doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>.","chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>.","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.","ieee":"N. M. Gurel <i>et al.</i>, “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” <i>IEEE Transactions on Signal Processing</i>, vol. 68. IEEE, pp. 4268–4282, 2020.","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. 2020;68:4268-4282. doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282."},"date_created":"2020-08-16T22:00:56Z","year":"2020","acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","_id":"8268","article_type":"original","doi":"10.1109/TSP.2020.3010355","publication_status":"published","abstract":[{"lang":"eng","text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality."}],"external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"quality_controlled":"1","volume":68,"page":"4268-4282","department":[{"_id":"DaAl"}],"date_published":"2020-07-20T00:00:00Z","publisher":"IEEE","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","article_processing_charge":"No","date_updated":"2023-08-22T08:40:08Z","oa":1,"scopus_import":"1","intvolume":"        68","isi":1,"language":[{"iso":"eng"}],"publication":"IEEE Transactions on Signal Processing","arxiv":1,"author":[{"first_name":"Nezihe Merve","full_name":"Gurel, Nezihe Merve","last_name":"Gurel"},{"last_name":"Kara","full_name":"Kara, Kaan","first_name":"Kaan"},{"last_name":"Stojanov","full_name":"Stojanov, Alen","first_name":"Alen"},{"first_name":"Tyler","full_name":"Smith, Tyler","last_name":"Smith"},{"last_name":"Lemmin","first_name":"Thomas","full_name":"Lemmin, Thomas"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Puschel","full_name":"Puschel, Markus","first_name":"Markus"},{"full_name":"Zhang, Ce","first_name":"Ce","last_name":"Zhang"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","day":"20","main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"month":"07","publication_identifier":{"issn":["1053587X"],"eissn":["19410476"]},"type":"journal_article","status":"public"},{"quality_controlled":"1","volume":13,"department":[{"_id":"JiFr"}],"page":"1238-1240","date_published":"2020-09-07T00:00:00Z","publisher":"Elsevier","external_id":{"pmid":["32688032"],"isi":["000566895400007"]},"publication_status":"published","doi":"10.1016/j.molp.2020.07.006","article_type":"original","_id":"8271","date_created":"2020-08-16T22:00:57Z","citation":{"apa":"He, P., Zhang, Y., &#38; Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>","ieee":"P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” <i>Molecular Plant</i>, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020.","ama":"He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. 2020;13(9):1238-1240. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","chicago":"He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>.","ista":"He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.","mla":"He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>."},"year":"2020","acknowledgement":"We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared.","status":"public","type":"journal_article","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"07","oa_version":"None","publication_identifier":{"issn":["16742052"],"eissn":["17529867"]},"month":"09","author":[{"first_name":"Peng","full_name":"He, Peng","last_name":"He"},{"orcid":"0000-0003-2627-6956","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","first_name":"Yuzhou"},{"last_name":"Xiao","full_name":"Xiao, Guanghui","first_name":"Guanghui"}],"publication":"Molecular Plant","language":[{"iso":"eng"}],"intvolume":"        13","scopus_import":"1","isi":1,"title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","article_processing_charge":"No","issue":"9","date_updated":"2023-08-22T08:40:35Z"},{"status":"public","type":"conference","alternative_title":["LNCS"],"month":"07","publication_identifier":{"isbn":["9783030532901"],"eissn":["16113349"],"issn":["03029743"]},"conference":{"name":"CAV: Computer Aided Verification"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":625056,"checksum":"093d4788d7d5b2ce0ffe64fbe7820043","file_name":"2020_LNCS_CAV_Chatterjee.pdf","file_id":"8276","success":1,"date_updated":"2020-08-17T11:32:44Z","date_created":"2020-08-17T11:32:44Z"}],"oa_version":"Published Version","day":"14","arxiv":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Katoen, Joost P","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"},{"last_name":"Winkler","first_name":"Tobias","full_name":"Winkler, Tobias"}],"publication":"International Conference on Computer Aided Verification","language":[{"iso":"eng"}],"isi":1,"has_accepted_license":"1","intvolume":"     12225","scopus_import":"1","article_processing_charge":"No","date_updated":"2025-07-14T09:10:14Z","oa":1,"title":"Stochastic games with lexicographic reachability-safety objectives","date_published":"2020-07-14T00:00:00Z","publisher":"Springer Nature","volume":12225,"quality_controlled":"1","page":"398-420","department":[{"_id":"KrCh"}],"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["000"],"abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in   NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is   PSPACE -hard and can be solved in   NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies."}],"external_id":{"arxiv":["2005.04018"],"isi":["000695272500021"]},"publication_status":"published","doi":"10.1007/978-3-030-53291-8_21","_id":"8272","file_date_updated":"2020-08-17T11:32:44Z","related_material":{"record":[{"status":"public","id":"12738","relation":"later_version"}]},"ec_funded":1,"year":"2020","date_created":"2020-08-16T22:00:58Z","citation":{"short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 12225. Springer Nature; 2020:398-420. doi:<a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">10.1007/978-3-030-53291-8_21</a>","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in <i>International Conference on Computer Aided Verification</i>, 2020, vol. 12225, pp. 398–420.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:<a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">10.1007/978-3-030-53291-8_21</a>.","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 12225:398–420. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">https://doi.org/10.1007/978-3-030-53291-8_21</a>.","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., &#38; Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 12225, pp. 398–420). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">https://doi.org/10.1007/978-3-030-53291-8_21</a>"}},{"external_id":{"pmid":["32785037"],"isi":["000565090300001"]},"abstract":[{"lang":"eng","text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. "}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","department":[{"_id":"JiFr"}],"volume":21,"quality_controlled":"1","publisher":"MDPI","date_published":"2020-08-10T00:00:00Z","related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"article_number":"5272","date_created":"2020-08-24T06:24:03Z","citation":{"apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21165727\">https://doi.org/10.3390/ijms21165727</a>","short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).","ieee":"H. Chen <i>et al.</i>, “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16. MDPI, 2020.","ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. <i>International Journal of Molecular Sciences</i>. 2020;21(16). doi:<a href=\"https://doi.org/10.3390/ijms21165727\">10.3390/ijms21165727</a>","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21165727\">https://doi.org/10.3390/ijms21165727</a>.","ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272.","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16, 5272, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21165727\">10.3390/ijms21165727</a>."},"acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","year":"2020","doi":"10.3390/ijms21165727","file_date_updated":"2020-08-25T09:53:50Z","article_type":"original","_id":"8283","oa_version":"Published Version","day":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"cziletti","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":5718755,"checksum":"03b039244e6ae80580385fd9f577e2b2","file_id":"8292","file_name":"2020_IntMolecSciences_Chen.pdf","success":1,"date_updated":"2020-08-25T09:53:50Z","date_created":"2020-08-25T09:53:50Z"}],"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"month":"08","author":[{"first_name":"Huihuang","full_name":"Chen, Huihuang","last_name":"Chen"},{"last_name":"Lai","full_name":"Lai, Linyi","first_name":"Linyi"},{"last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin"},{"full_name":"Liu, Liping","first_name":"Liping","last_name":"Liu"},{"last_name":"Jakada","first_name":"Bello Hassan","full_name":"Jakada, Bello Hassan"},{"last_name":"Huang","first_name":"Youmei","full_name":"Huang, Youmei"},{"last_name":"He","full_name":"He, Qing","first_name":"Qing"},{"first_name":"Mengnan","full_name":"Chai, Mengnan","last_name":"Chai"},{"first_name":"Xiaoping","full_name":"Niu, Xiaoping","last_name":"Niu"},{"first_name":"Yuan","full_name":"Qin, Yuan","last_name":"Qin"}],"pmid":1,"type":"journal_article","status":"public","intvolume":"        21","has_accepted_license":"1","scopus_import":"1","isi":1,"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","oa":1,"date_updated":"2024-10-29T10:22:43Z","article_processing_charge":"No","issue":"16","publication":"International Journal of Molecular Sciences","language":[{"iso":"eng"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"external_id":{"pmid":["32735215"],"isi":["000562123600001"]},"publication_status":"published","date_published":"2020-07-31T00:00:00Z","publisher":"eLife Sciences Publications","quality_controlled":"1","volume":9,"department":[{"_id":"LeSa"}],"project":[{"grant_number":"24741","_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8353","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release"}]},"article_number":"e59407","year":"2020","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","date_created":"2020-08-24T06:24:04Z","citation":{"apa":"Steiner, J., &#38; Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>, vol. 9, e59407, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>.","chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>.","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020)."},"doi":"10.7554/eLife.59407","article_type":"original","_id":"8284","file_date_updated":"2020-08-24T13:31:53Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"month":"07","publication_identifier":{"eissn":["2050084X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","file_id":"8289","file_name":"2020_eLife_Steiner.pdf","date_created":"2020-08-24T13:31:53Z","date_updated":"2020-08-24T13:31:53Z","creator":"cziletti","access_level":"open_access","relation":"main_file","file_size":7320493,"content_type":"application/pdf"}],"oa_version":"Published Version","day":"31","author":[{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","last_name":"Steiner","orcid":"0000-0003-0493-3775","first_name":"Julia","full_name":"Steiner, Julia"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989"}],"status":"public","type":"journal_article","pmid":1,"isi":1,"has_accepted_license":"1","intvolume":"         9","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-09-07T13:14:08Z","oa":1,"title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","publication":"eLife","language":[{"iso":"eng"}]},{"intvolume":"       125","scopus_import":"1","isi":1,"title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","oa":1,"date_updated":"2023-10-18T08:38:35Z","issue":"4","article_processing_charge":"No","publication":"Physical Review Letters","language":[{"iso":"eng"}],"day":"24","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"author":[{"full_name":"Malia, Benjamin K.","first_name":"Benjamin K.","last_name":"Malia"},{"last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián","first_name":"Julián"},{"last_name":"Wu","first_name":"Yunfan","full_name":"Wu, Yunfan"},{"orcid":"0000-0002-2031-204X","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","full_name":"Hosten, Onur"},{"last_name":"Kasevich","first_name":"Mark A.","full_name":"Kasevich, Mark A."}],"arxiv":1,"pmid":1,"status":"public","type":"journal_article","article_number":"043202","date_created":"2020-08-24T06:24:04Z","citation":{"ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. <i>Physical Review Letters</i>. 2020;125(4). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">10.1103/PhysRevLett.125.043202</a>","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” <i>Physical Review Letters</i>, vol. 125, no. 4. American Physical Society, 2020.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” <i>Physical Review Letters</i>, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">10.1103/PhysRevLett.125.043202</a>.","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">https://doi.org/10.1103/PhysRevLett.125.043202</a>.","ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., &#38; Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">https://doi.org/10.1103/PhysRevLett.125.043202</a>"},"acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","year":"2020","doi":"10.1103/PhysRevLett.125.043202","article_type":"original","_id":"8285","external_id":{"arxiv":["1912.10218"],"pmid":["32794788"],"isi":["000552227400008"]},"abstract":[{"text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200  μm radius and falls roughly 300  μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively.","lang":"eng"}],"publication_status":"published","department":[{"_id":"OnHo"}],"quality_controlled":"1","volume":125,"publisher":"American Physical Society","date_published":"2020-07-24T00:00:00Z"},{"publication_status":"published","abstract":[{"lang":"eng","text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks."}],"external_id":{"arxiv":["1905.02458"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["000"],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","department":[{"_id":"ToHe"}],"date_published":"2020-01-01T00:00:00Z","keyword":["reachability","hybrid systems","decomposition"],"date_created":"2020-08-24T12:56:20Z","citation":{"apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In <i>Proceedings of the International Conference on Embedded Software</i>. Virtual .","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>Proceedings of the International Conference on Embedded Software</i>, 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In <i>Proceedings of the International Conference on Embedded Software</i>, 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in <i>Proceedings of the International Conference on Embedded Software</i>, Virtual , 2020.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: <i>Proceedings of the International Conference on Embedded Software</i>. ; 2020."},"year":"2020","related_material":{"record":[{"relation":"later_version","id":"8790","status":"public"}]},"ec_funded":1,"_id":"8287","file_date_updated":"2020-08-24T12:53:15Z","arxiv":1,"author":[{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","last_name":"Bogomolov"},{"last_name":"Forets","full_name":"Forets, Marcelo","first_name":"Marcelo"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn","last_name":"Potomkin"},{"last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","full_name":"Schilling, Christian"}],"file":[{"content_type":"application/pdf","file_size":696384,"access_level":"open_access","relation":"main_file","creator":"cschilli","date_updated":"2020-08-24T12:53:15Z","date_created":"2020-08-24T12:53:15Z","checksum":"d19e97d0f8a3a441dc078ec812297d75","file_name":"2020EMSOFT.pdf","file_id":"8288","success":1}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","conference":{"start_date":"2020-09-20","name":"EMSOFT: International Conference on Embedded Software","end_date":"2020-09-25","location":"Virtual "},"type":"conference","status":"public","title":"Reachability analysis of linear hybrid systems via block decomposition","article_processing_charge":"No","date_updated":"2023-08-22T13:27:32Z","oa":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the International Conference on Embedded Software"},{"author":[{"first_name":"Pietro","full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"file":[{"date_created":"2020-08-26T19:28:55Z","date_updated":"2020-08-26T19:28:55Z","success":1,"file_name":"PhysRevB.102.060202.pdf","checksum":"716442fa7861323fcc80b93718ca009c","file_id":"8309","access_level":"open_access","file_size":488825,"content_type":"application/pdf","relation":"main_file","creator":"mserbyn"},{"content_type":"application/pdf","file_size":711405,"relation":"main_file","access_level":"open_access","creator":"mserbyn","date_updated":"2020-08-26T19:29:00Z","date_created":"2020-08-26T19:29:00Z","file_id":"8310","checksum":"be0abdc8f60fe065ea6dc92e08487122","file_name":"Supplementary-mbme.pdf","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"26","oa_version":"None","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"08","status":"public","type":"journal_article","title":"Stability of mobility edges in disordered interacting systems","issue":"6","article_processing_charge":"No","oa":1,"date_updated":"2023-08-24T14:20:21Z","scopus_import":"1","has_accepted_license":"1","intvolume":"       102","isi":1,"language":[{"iso":"eng"}],"publication":"Physical Review B","publication_status":"published","abstract":[{"text":"Many-body localization provides a mechanism to avoid thermalization in isolated interacting quantum systems. The breakdown of thermalization may be complete, when all eigenstates in the many-body spectrum become localized, or partial, when the so-called many-body mobility edge separates localized and delocalized parts of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)] suggested a possible instability of the many-body mobility edge in energy density. The local ergodic regions—so-called “bubbles”—resonantly spread throughout the system, leading to delocalization. In order to study such instability mechanism, in this work we design a model featuring many-body mobility edge in particle density: the states at small particle density are localized, while increasing the density of particles leads to delocalization. Using numerical simulations with matrix product states, we demonstrate the stability of many-body localization with respect to small bubbles in large dilute systems for experimentally relevant timescales. In addition, we demonstrate that processes where the bubble spreads are favored over processes that lead to resonant tunneling, suggesting a possible mechanism behind the observed stability of many-body mobility edge. We conclude by proposing experiments to probe particle density mobility edge in the Bose-Hubbard model.","lang":"eng"}],"external_id":{"isi":["000562628300001"]},"ddc":["530"],"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"volume":102,"quality_controlled":"1","department":[{"_id":"MaSe"}],"date_published":"2020-08-26T00:00:00Z","publisher":"American Physical Society","citation":{"mla":"Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>, vol. 102, no. 6, 060202(R), American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>.","ista":"Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R).","chicago":"Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>.","ieee":"P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered interacting systems,” <i>Physical Review B</i>, vol. 102, no. 6. American Physical Society, 2020.","ama":"Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. 2020;102(6). doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>","short":"P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).","apa":"Brighi, P., Abanin, D. A., &#38; Serbyn, M. (2020). Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>"},"date_created":"2020-08-26T19:27:42Z","year":"2020","acknowledgement":"Acknowledgments. We acknowledge useful discussions with W. De Roeck and A. Michailidis. P.B. was supported by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385. D.A. was supported by the Swiss National Science Foundation. M.S. was supported by European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). This work benefited from visits to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958 and from the program “Thermalization, Many Body Localization and Hydrodynamics” at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).","related_material":{"record":[{"id":"12732","relation":"dissertation_contains","status":"public"}]},"article_number":"060202(R)","ec_funded":1,"_id":"8308","article_type":"original","file_date_updated":"2020-08-26T19:29:00Z","doi":"10.1103/physrevb.102.060202"},{"title":"Key role of quinone in the mechanism of respiratory complex I","article_processing_charge":"No","issue":"1","oa":1,"date_updated":"2023-08-22T09:03:00Z","scopus_import":"1","intvolume":"        11","has_accepted_license":"1","isi":1,"language":[{"iso":"eng"}],"publication":"Nature Communications","author":[{"last_name":"Gutierrez-Fernandez","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier","full_name":"Gutierrez-Fernandez, Javier"},{"first_name":"Karol","full_name":"Kaszuba, Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","last_name":"Kaszuba"},{"last_name":"Minhas","first_name":"Gurdeep S.","full_name":"Minhas, Gurdeep S."},{"last_name":"Baradaran","first_name":"Rozbeh","full_name":"Baradaran, Rozbeh"},{"id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","first_name":"Margherita","full_name":"Tambalo, Margherita"},{"last_name":"Gallagher","first_name":"David T.","full_name":"Gallagher, David T."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"52b96f41d7d0db9728064c08da00d030","file_id":"8326","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","date_created":"2020-08-31T13:40:00Z","date_updated":"2020-08-31T13:40:00Z","creator":"cziletti","file_size":7527373,"relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"day":"18","oa_version":"Published Version","month":"08","publication_identifier":{"eissn":["20411723"]},"status":"public","type":"journal_article","pmid":1,"citation":{"ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” <i>Nature Communications</i>, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>.","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>.","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. 2020;11(1). doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>","ieee":"J. Gutierrez-Fernandez <i>et al.</i>, “Key role of quinone in the mechanism of respiratory complex I,” <i>Nature Communications</i>, vol. 11, no. 1. Springer Nature, 2020.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., &#38; Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>"},"date_created":"2020-08-30T22:01:10Z","year":"2020","acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage"}]},"article_number":"4135","article_type":"original","_id":"8318","file_date_updated":"2020-08-31T13:40:00Z","doi":"10.1038/s41467-020-17957-0","publication_status":"published","abstract":[{"text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.","lang":"eng"}],"external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"quality_controlled":"1","volume":11,"department":[{"_id":"LeSa"}],"date_published":"2020-08-18T00:00:00Z","publisher":"Springer Nature"},{"month":"07","publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"day":"30","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08334"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yunfan","full_name":"Wu, Yunfan","last_name":"Wu"},{"last_name":"Krishnakumar","full_name":"Krishnakumar, Rajiv","first_name":"Rajiv"},{"last_name":"Martínez-Rincón","first_name":"Julián","full_name":"Martínez-Rincón, Julián"},{"first_name":"Benjamin K.","full_name":"Malia, Benjamin K.","last_name":"Malia"},{"first_name":"Onur","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","orcid":"0000-0002-2031-204X"},{"full_name":"Kasevich, Mark A.","first_name":"Mark A.","last_name":"Kasevich"}],"arxiv":1,"type":"journal_article","status":"public","isi":1,"intvolume":"       102","scopus_import":"1","date_updated":"2024-02-28T13:11:28Z","oa":1,"issue":"1","article_processing_charge":"No","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","publication":"Physical Review A","language":[{"iso":"eng"}],"external_id":{"isi":["000555104200011"],"arxiv":["1912.08334"]},"abstract":[{"text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.","lang":"eng"}],"publication_status":"published","publisher":"American Physical Society","date_published":"2020-07-30T00:00:00Z","department":[{"_id":"OnHo"}],"volume":102,"quality_controlled":"1","article_number":"012224","acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","year":"2020","citation":{"ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” <i>Physical Review A</i>, vol. 102, no. 1. American Physical Society, 2020.","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. <i>Physical Review A</i>. 2020;102(1). doi:<a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">10.1103/PhysRevA.102.012224</a>","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” <i>Physical Review A</i>, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">10.1103/PhysRevA.102.012224</a>.","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” <i>Physical Review A</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">https://doi.org/10.1103/PhysRevA.102.012224</a>.","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., &#38; Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">https://doi.org/10.1103/PhysRevA.102.012224</a>"},"date_created":"2020-08-30T22:01:10Z","doi":"10.1103/PhysRevA.102.012224","article_type":"original","_id":"8319"},{"author":[{"last_name":"Mukba","first_name":"S. A.","full_name":"Mukba, S. A."},{"full_name":"Vlasov, Petr","first_name":"Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolosov, P. M.","first_name":"P. M.","last_name":"Kolosov"},{"last_name":"Shuvalova","full_name":"Shuvalova, E. Y.","first_name":"E. Y."},{"last_name":"Egorova","first_name":"T. V.","full_name":"Egorova, T. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"month":"08","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","day":"19","status":"public","type":"journal_article","article_processing_charge":"No","issue":"4","date_updated":"2023-08-22T09:01:03Z","title":"Expanding the genetic code: Unnatural base pairs in biological systems","isi":1,"intvolume":"        54","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Molecular Biology","publication_status":"published","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"external_id":{"isi":["000562110300001"]},"date_published":"2020-08-19T00:00:00Z","publisher":"Springer Nature","volume":54,"quality_controlled":"1","page":"475-484","department":[{"_id":"FyKo"}],"year":"2020","acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","citation":{"ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” <i>Molecular Biology</i>, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. 2020;54(4):475-484. doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>"},"date_created":"2020-08-30T22:01:11Z","related_material":{"record":[{"id":"8321","relation":"original","status":"public"}]},"article_type":"original","_id":"8320","doi":"10.1134/S0026893320040111"}]