[{"date_updated":"2025-04-15T08:39:16Z","quality_controlled":"1","external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"month":"06","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"volume":20,"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.","isi":1,"article_processing_charge":"Yes (via OA deal)","date_published":"2020-06-01T00:00:00Z","title":"Zero field splitting of heavy-hole states in quantum dots","related_material":{"record":[{"relation":"research_data","id":"7689","status":"public"}]},"status":"public","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"type":"journal_article","oa_version":"Published Version","citation":{"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>.","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>","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","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>.","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.","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>"},"abstract":[{"lang":"eng","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."}],"scopus_import":"1","publisher":"American Chemical Society","author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip"},{"orcid":"0000-0003-2424-8636","first_name":"Lada","last_name":"Vukušić","full_name":"Vukušić, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"full_name":"Wang, Ting","last_name":"Wang","first_name":"Ting","orcid":"0000-0002-4619-9575"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"},{"full_name":"Held, Karsten","first_name":"Karsten","last_name":"Held"}],"language":[{"iso":"eng"}],"ddc":["530"],"file_date_updated":"2020-08-06T09:35:37Z","intvolume":"        20","project":[{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"doi":"10.1021/acs.nanolett.0c01466","file":[{"file_size":3308906,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-08-06T09:35:37Z","date_created":"2020-08-06T09:35:37Z","success":1,"file_id":"8204","creator":"dernst","file_name":"2020_NanoLetters_Katsaros.pdf","access_level":"open_access"}],"oa":1,"publication_status":"published","year":"2020","article_type":"original","date_created":"2020-08-06T09:25:04Z","day":"01","publication":"Nano Letters","corr_author":"1","pmid":1,"issue":"7","ec_funded":1,"department":[{"_id":"GeKa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8203","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"5201-5206"},{"publication_identifier":{"eissn":["1091-6490"]},"type":"journal_article","status":"public","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"publisher":"National Academy of Sciences","oa_version":"Published Version","citation":{"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.","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.","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>","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>.","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."},"scopus_import":"1","abstract":[{"lang":"eng","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."}],"month":"07","external_id":{"isi":["000553292900014"],"pmid":["32611816"]},"date_updated":"2026-04-03T09:29:04Z","quality_controlled":"1","title":"Stem cell lineage survival as a noisy competition for niche access","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.","isi":1,"article_processing_charge":"No","date_published":"2020-07-21T00:00:00Z","volume":117,"corr_author":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"21","page":"16969-16975","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"EdHa"}],"issue":"29","ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"8220","pmid":1,"doi":"10.1073/pnas.1921205117","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"file":[{"file_size":1111604,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-08-10T06:50:28Z","date_created":"2020-08-10T06:50:28Z","file_id":"8223","success":1,"creator":"dernst","access_level":"open_access","file_name":"2020_PNAS_Corominas.pdf"}],"oa":1,"publication_status":"published","intvolume":"       117","file_date_updated":"2020-08-10T06:50:28Z","author":[{"orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","first_name":"Kasumi","last_name":"Kishi","orcid":"0000-0001-6060-4795"},{"full_name":"Ellenbroek, Saskia I.J.","last_name":"Ellenbroek","first_name":"Saskia I.J."},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"first_name":"Jacco","last_name":"Van Rheenen","full_name":"Van Rheenen, Jacco"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"language":[{"iso":"eng"}],"date_created":"2020-08-09T22:00:52Z","article_type":"original","year":"2020"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","pmid":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","_id":"8225","issue":"16","publication":"International Journal of Molecular Sciences","OA_place":"publisher","day":"08","article_type":"original","date_created":"2020-08-10T11:47:29Z","DOAJ_listed":"1","year":"2020","intvolume":"        21","oa":1,"publication_status":"published","extern":"1","doi":"10.3390/ijms21165693","file":[{"date_updated":"2020-09-10T07:06:22Z","content_type":"application/pdf","relation":"main_file","file_size":2680908,"success":1,"file_id":"8356","date_created":"2020-09-10T07:06:22Z","file_name":"2020_IntMolecSciences_Koehler.pdf","access_level":"open_access","checksum":"dac7ccef7cdcea9be292664d8c488425","creator":"dernst"}],"ddc":["570"],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-5581-398X","last_name":"Köhler","first_name":"Verena K.","full_name":"Köhler, Verena K."},{"first_name":"Silvia","last_name":"Crescioli","orcid":"0000-0002-1909-5957","full_name":"Crescioli, Silvia"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","first_name":"Judit","orcid":"0000-0002-8777-3502"},{"full_name":"Bax, Heather J.","orcid":"0000-0003-0432-4160","first_name":"Heather J.","last_name":"Bax"},{"last_name":"Hofer","first_name":"Gerhard","full_name":"Hofer, Gerhard"},{"full_name":"Pranger, Christina L.","first_name":"Christina L.","last_name":"Pranger"},{"full_name":"Hufnagl, Karin","first_name":"Karin","last_name":"Hufnagl"},{"full_name":"Bianchini, Rodolfo","orcid":"0000-0003-0351-6937","last_name":"Bianchini","first_name":"Rodolfo"},{"full_name":"Flicker, Sabine","last_name":"Flicker","first_name":"Sabine","orcid":"0000-0003-4768-8693"},{"orcid":"0000-0002-2261-958X","first_name":"Walter","last_name":"Keller","full_name":"Keller, Walter"},{"orcid":"0000-0002-4100-7810","first_name":"Sophia N.","last_name":"Karagiannis","full_name":"Karagiannis, Sophia N."},{"full_name":"Jensen-Jarolim, Erika","orcid":"0000-0003-4019-5765","first_name":"Erika","last_name":"Jensen-Jarolim"}],"file_date_updated":"2020-09-10T07:06:22Z","publisher":"MDPI","article_number":"5693","citation":{"ama":"Köhler VK, Crescioli S, Singer J, et al. Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. <i>International Journal of Molecular Sciences</i>. 2020;21(16). doi:<a href=\"https://doi.org/10.3390/ijms21165693\">10.3390/ijms21165693</a>","ieee":"V. K. Köhler <i>et al.</i>, “Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16. MDPI, 2020.","mla":"Köhler, Verena K., et al. “Filling the Antibody Pipeline in Allergy: PIPE Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen Allergen Bet v 1.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16, 5693, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21165693\">10.3390/ijms21165693</a>.","ista":"Köhler VK, Crescioli S, Singer J, Bax HJ, Hofer G, Pranger CL, Hufnagl K, Bianchini R, Flicker S, Keller W, Karagiannis SN, Jensen-Jarolim E. 2020. Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. International Journal of Molecular Sciences. 21(16), 5693.","short":"V.K. Köhler, S. Crescioli, J. Singer, H.J. Bax, G. Hofer, C.L. Pranger, K. Hufnagl, R. Bianchini, S. Flicker, W. Keller, S.N. Karagiannis, E. Jensen-Jarolim, International Journal of Molecular Sciences 21 (2020).","apa":"Köhler, V. K., Crescioli, S., Singer, J., Bax, H. J., Hofer, G., Pranger, C. L., … Jensen-Jarolim, E. (2020). Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21165693\">https://doi.org/10.3390/ijms21165693</a>","chicago":"Köhler, Verena K., Silvia Crescioli, Judit Singer, Heather J. Bax, Gerhard Hofer, Christina L. Pranger, Karin Hufnagl, et al. “Filling the Antibody Pipeline in Allergy: PIPE Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen Allergen Bet v 1.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21165693\">https://doi.org/10.3390/ijms21165693</a>."},"abstract":[{"text":"Birch pollen allergy is among the most prevalent pollen allergies in Northern and Central Europe. This IgE-mediated disease can be treated with allergen immunotherapy (AIT), which typically gives rise to IgG antibodies inducing tolerance. Although the main mechanisms of allergen immunotherapy (AIT) are known, questions regarding possible Fc-mediated effects of IgG antibodies remain unanswered. This can mainly be attributed to the unavailability of appropriate tools, i.e., well-characterised recombinant antibodies (rAbs). We hereby aimed at providing human rAbs of several classes for mechanistic studies and as possible candidates for passive immunotherapy. We engineered IgE, IgG1, and IgG4 sharing the same variable region against the major birch pollen allergen Bet v 1 using Polymerase Incomplete Primer Extension (PIPE) cloning. We tested IgE functionality and IgG blocking capabilities using appropriate model cell lines. In vitro studies showed IgE engagement with FcεRI and CD23 and Bet v 1-dependent degranulation. Overall, we hereby present fully functional, human IgE, IgG1, and IgG4 sharing the same variable region against Bet v 1 and showcase possible applications in first mechanistic studies. Furthermore, our IgG antibodies might be useful candidates for passive immunotherapy of birch pollen allergy.","lang":"eng"}],"oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"issn":["1422-0067"]},"OA_type":"gold","article_processing_charge":"No","date_published":"2020-08-08T00:00:00Z","title":"Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1","volume":21,"month":"08","date_updated":"2024-10-15T13:11:23Z","quality_controlled":"1","external_id":{"pmid":["32784509"]}},{"citation":{"ieee":"J. Gotovina <i>et al.</i>, “Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro,” <i>Allergy</i>. Wiley, 2020.","ama":"Gotovina J, Bianchini R, Singer J, et al. Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. <i>Allergy</i>. 2020. doi:<a href=\"https://doi.org/10.1111/all.14299\">10.1111/all.14299</a>","apa":"Gotovina, J., Bianchini, R., Singer, J., Herrmann, I., Pellizzari, G., Haidl, I. D., … Jensen‐Jarolim, E. (2020). Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. <i>Allergy</i>. Wiley. <a href=\"https://doi.org/10.1111/all.14299\">https://doi.org/10.1111/all.14299</a>","chicago":"Gotovina, Jelena, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Giulia Pellizzari, Ian D. Haidl, Karin Hufnagl, Sophia N. Karagiannis, Jean S. Marshall, and Erika Jensen‐Jarolim. “Epinephrine Drives Human M2a Allergic Macrophages to a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” <i>Allergy</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/all.14299\">https://doi.org/10.1111/all.14299</a>.","mla":"Gotovina, Jelena, et al. “Epinephrine Drives Human M2a Allergic Macrophages to a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” <i>Allergy</i>, Wiley, 2020, doi:<a href=\"https://doi.org/10.1111/all.14299\">10.1111/all.14299</a>.","ista":"Gotovina J, Bianchini R, Singer J, Herrmann I, Pellizzari G, Haidl ID, Hufnagl K, Karagiannis SN, Marshall JS, Jensen‐Jarolim E. 2020. Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. Allergy.","short":"J. Gotovina, R. Bianchini, J. Singer, I. Herrmann, G. Pellizzari, I.D. Haidl, K. Hufnagl, S.N. Karagiannis, J.S. Marshall, E. Jensen‐Jarolim, Allergy (2020)."},"oa_version":"Published Version","_id":"8226","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/all.14299"}],"publisher":"Wiley","day":"04","OA_type":"hybrid","publication":"Allergy","status":"public","type":"journal_article","publication_identifier":{"issn":["0105-4538","1398-9995"]},"OA_place":"publisher","year":"2020","article_processing_charge":"No","date_published":"2020-04-04T00:00:00Z","article_type":"letter_note","title":"Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro","date_created":"2020-08-10T11:50:30Z","language":[{"iso":"eng"}],"author":[{"full_name":"Gotovina, Jelena","last_name":"Gotovina","first_name":"Jelena","orcid":"0000-0003-1503-5276"},{"full_name":"Bianchini, Rodolfo","last_name":"Bianchini","first_name":"Rodolfo","orcid":"0000-0003-0351-6937"},{"orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer","first_name":"Judit","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Herrmann","first_name":"Ina","orcid":"0000-0003-2772-9144","full_name":"Herrmann, Ina"},{"full_name":"Pellizzari, Giulia","orcid":"0000-0003-0387-1912","first_name":"Giulia","last_name":"Pellizzari"},{"full_name":"Haidl, Ian D.","orcid":"0000-0002-5301-0822","last_name":"Haidl","first_name":"Ian D."},{"last_name":"Hufnagl","first_name":"Karin","orcid":"0000-0002-2288-2468","full_name":"Hufnagl, Karin"},{"first_name":"Sophia N.","last_name":"Karagiannis","orcid":"0000-0002-4100-7810","full_name":"Karagiannis, Sophia N."},{"first_name":"Jean S.","last_name":"Marshall","orcid":"0000-0002-5642-1379","full_name":"Marshall, Jean S."},{"full_name":"Jensen‐Jarolim, Erika","orcid":"0000-0003-4019-5765","first_name":"Erika","last_name":"Jensen‐Jarolim"}],"date_updated":"2024-10-15T13:13:56Z","quality_controlled":"1","oa":1,"publication_status":"epub_ahead","extern":"1","month":"04","doi":"10.1111/all.14299"},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"NiBa"}],"_id":"8254","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"citation":{"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>.","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>","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>.","short":"L.S. Arathoon, (2020).","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>.","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.","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>"},"corr_author":"1","type":"research_data","status":"public","related_material":{"record":[{"status":"public","relation":"later_version","id":"9192"},{"status":"public","id":"11321","relation":"later_version"}]},"contributor":[{"contributor_type":"data_collector","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S"},{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Carina","last_name":"Baskett"}],"day":"18","date_created":"2020-08-12T12:49:23Z","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","article_processing_charge":"No","date_published":"2020-08-18T00:00:00Z","year":"2020","month":"08","file":[{"checksum":"4f1382ed4384751b6013398c11557bf6","creator":"dernst","file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access","date_created":"2020-08-18T08:03:23Z","success":1,"file_id":"8280","file_size":5778420,"relation":"main_file","content_type":"application/x-zip-compressed","date_updated":"2020-08-18T08:03:23Z"}],"doi":"10.15479/AT:ISTA:8254","oa":1,"file_date_updated":"2020-08-18T08:03:23Z","author":[{"full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon"}],"date_updated":"2024-10-09T21:02:14Z","ddc":["576"]},{"date_created":"2020-08-14T09:36:05Z","article_type":"original","year":"2020","file":[{"date_created":"2020-12-04T09:29:21Z","success":1,"file_id":"8920","creator":"dernst","checksum":"44a5960fc083a4cb3488d22224859fdc","file_name":"2020_Neuron_Zhang.pdf","access_level":"open_access","file_size":3011120,"relation":"main_file","date_updated":"2020-12-04T09:29:21Z","content_type":"application/pdf"}],"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits"}],"doi":"10.1016/j.neuron.2020.07.006","publication_status":"published","oa":1,"intvolume":"       107","file_date_updated":"2020-12-04T09:29:21Z","author":[{"full_name":"Zhang, Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"language":[{"iso":"eng"}],"ddc":["570"],"page":"1212-1225","has_accepted_license":"1","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"ec_funded":1,"issue":"6","_id":"8261","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"corr_author":"1","publication":"Neuron","day":"23","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","isi":1,"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.","article_processing_charge":"No","date_published":"2020-09-23T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"volume":107,"month":"09","external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"quality_controlled":"1","date_updated":"2025-04-15T08:29:03Z","publisher":"Elsevier","oa_version":"Published Version","citation":{"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>","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>.","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>","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.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","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>."},"scopus_import":"1","abstract":[{"lang":"eng","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."}],"publication_identifier":{"issn":["0896-6273"]},"type":"journal_article","status":"public","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","description":"News on IST Website"}]}},{"publication":"IEEE Transactions on Signal Processing","day":"20","page":"4268-4282","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8268","department":[{"_id":"DaAl"}],"intvolume":"        68","publication_status":"published","oa":1,"doi":"10.1109/TSP.2020.3010355","language":[{"iso":"eng"}],"author":[{"full_name":"Gurel, Nezihe Merve","last_name":"Gurel","first_name":"Nezihe Merve"},{"full_name":"Kara, Kaan","last_name":"Kara","first_name":"Kaan"},{"full_name":"Stojanov, Alen","first_name":"Alen","last_name":"Stojanov"},{"last_name":"Smith","first_name":"Tyler","full_name":"Smith, Tyler"},{"last_name":"Lemmin","first_name":"Thomas","full_name":"Lemmin, Thomas"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Puschel, Markus","first_name":"Markus","last_name":"Puschel"},{"first_name":"Ce","last_name":"Zhang","full_name":"Zhang, Ce"}],"article_type":"original","date_created":"2020-08-16T22:00:56Z","year":"2020","status":"public","type":"journal_article","publication_identifier":{"eissn":["1941-0476"],"issn":["1053-587X"]},"main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"publisher":"IEEE","scopus_import":"1","citation":{"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>","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.","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.","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.","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>.","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>"},"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","month":"07","date_updated":"2025-07-10T11:55:10Z","quality_controlled":"1","external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"arxiv":1,"article_processing_charge":"No","date_published":"2020-07-20T00:00:00Z","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.","isi":1,"title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","volume":68},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molp.2020.07.006"}],"publisher":"Elsevier","citation":{"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>.","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>","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","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>.","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>"},"scopus_import":"1","oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"eissn":["1752-9867"],"issn":["1674-2052"]},"OA_type":"free access","article_processing_charge":"No","date_published":"2020-09-07T00:00:00Z","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.","isi":1,"title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","volume":13,"month":"09","quality_controlled":"1","date_updated":"2026-06-18T19:32:01Z","external_id":{"isi":["000566895400007"],"pmid":["32688032"]},"page":"1238-1240","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8271","issue":"9","department":[{"_id":"JiFr"}],"publication":"Molecular Plant","OA_place":"publisher","day":"07","article_type":"original","date_created":"2020-08-16T22:00:57Z","year":"2020","intvolume":"        13","publication_status":"published","oa":1,"doi":"10.1016/j.molp.2020.07.006","language":[{"iso":"eng"}],"ddc":["580"],"author":[{"first_name":"Peng","last_name":"He","full_name":"He, Peng"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956"},{"full_name":"Xiao, Guanghui","last_name":"Xiao","first_name":"Guanghui"}]},{"related_material":{"record":[{"status":"public","relation":"later_version","id":"12738"}]},"status":"public","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030532901"]},"type":"conference","oa_version":"Published Version","citation":{"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>","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.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, 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>.","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.","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>"},"scopus_import":"1","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."}],"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2026-04-16T09:31:14Z","external_id":{"isi":["000695272500021"],"arxiv":["2005.04018"]},"month":"07","volume":12225,"isi":1,"arxiv":1,"date_published":"2020-07-14T00:00:00Z","article_processing_charge":"No","title":"Stochastic games with lexicographic reachability-safety objectives","day":"14","publication":"International Conference on Computer Aided Verification","ec_funded":1,"conference":{"name":"CAV: Computer Aided Verification"},"department":[{"_id":"KrCh"}],"_id":"8272","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"398-420","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6143-1926","first_name":"Joost P","last_name":"Katoen"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"},{"full_name":"Winkler, Tobias","last_name":"Winkler","first_name":"Tobias"}],"ddc":["000"],"language":[{"iso":"eng"}],"file_date_updated":"2020-08-17T11:32:44Z","intvolume":"     12225","file":[{"date_updated":"2020-08-17T11:32:44Z","relation":"main_file","content_type":"application/pdf","file_size":625056,"success":1,"file_id":"8276","date_created":"2020-08-17T11:32:44Z","file_name":"2020_LNCS_CAV_Chatterjee.pdf","access_level":"open_access","checksum":"093d4788d7d5b2ce0ffe64fbe7820043","creator":"dernst"}],"doi":"10.1007/978-3-030-53291-8_21","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"oa":1,"publication_status":"published","year":"2020","alternative_title":["LNCS"],"date_created":"2020-08-16T22:00:58Z"},{"day":"31","publication":"eLife","pmid":1,"_id":"8284","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"LeSa"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","full_name":"Steiner, Julia","first_name":"Julia","last_name":"Steiner","orcid":"0000-0003-0493-3775"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A"}],"file_date_updated":"2020-08-24T13:31:53Z","intvolume":"         9","publication_status":"published","oa":1,"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"file":[{"access_level":"open_access","file_name":"2020_eLife_Steiner.pdf","creator":"cziletti","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","file_id":"8289","success":1,"date_created":"2020-08-24T13:31:53Z","date_updated":"2020-08-24T13:31:53Z","content_type":"application/pdf","relation":"main_file","file_size":7320493}],"doi":"10.7554/eLife.59407","year":"2020","article_type":"original","date_created":"2020-08-24T06:24:04Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8353"}]},"status":"public","type":"journal_article","publication_identifier":{"eissn":["2050-084X"]},"citation":{"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>.","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","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>","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>.","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>","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."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements."}],"article_number":"e59407","oa_version":"Published Version","publisher":"eLife Sciences Publications","quality_controlled":"1","date_updated":"2026-04-08T07:23:36Z","external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"month":"07","volume":9,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"article_processing_charge":"No","date_published":"2020-07-31T00:00:00Z","isi":1,"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.","title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter"},{"year":"2020","date_created":"2020-08-24T12:56:20Z","file_date_updated":"2020-08-24T12:53:15Z","author":[{"last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"first_name":"Kostiantyn","last_name":"Potomkin","full_name":"Potomkin, Kostiantyn"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065"}],"language":[{"iso":"eng"}],"ddc":["000"],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"file":[{"content_type":"application/pdf","date_updated":"2020-08-24T12:53:15Z","relation":"main_file","file_size":696384,"file_name":"2020EMSOFT.pdf","access_level":"open_access","checksum":"d19e97d0f8a3a441dc078ec812297d75","creator":"cschilli","success":1,"file_id":"8288","date_created":"2020-08-24T12:53:15Z"}],"oa":1,"publication_status":"published","conference":{"location":"Virtual ","start_date":"2020-09-20","name":"EMSOFT: Embedded Software","end_date":"2020-09-25"},"ec_funded":1,"department":[{"_id":"ToHe"}],"_id":"8287","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","publication":"Proceedings of the International Conference on Embedded Software","title":"Reachability analysis of linear hybrid systems via block decomposition","isi":1,"date_published":"2020-10-01T00:00:00Z","article_processing_charge":"No","arxiv":1,"external_id":{"arxiv":["1905.02458"],"isi":["000587712700072"]},"date_updated":"2026-04-03T09:32:00Z","quality_controlled":"1","month":"10","oa_version":"Preprint","citation":{"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.","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.","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.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 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: Embedded Software.","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 .","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."},"keyword":["reachability","hybrid systems","decomposition"],"abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"8790","status":"public"}]},"type":"conference","status":"public"},{"year":"2020","date_published":"2020-09-10T00:00:00Z","date_created":"2020-08-25T12:52:48Z","title":"RGtracker","author":[{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"}],"date_updated":"2024-10-09T21:05:14Z","license":"https://opensource.org/licenses/BSD-3-Clause","ddc":["570"],"file_date_updated":"2020-09-08T14:26:33Z","doi":"10.15479/AT:ISTA:8294","month":"09","file":[{"file_id":"8346","success":1,"date_created":"2020-09-08T14:26:31Z","access_level":"open_access","file_name":"readme.txt","checksum":"108352149987ac6f066e4925bd56e35e","creator":"rhauschild","date_updated":"2020-09-08T14:26:31Z","relation":"main_file","content_type":"text/plain","file_size":882},{"file_id":"8347","success":1,"date_created":"2020-09-08T14:26:33Z","access_level":"open_access","file_name":"RGtracker.mlappinstall","checksum":"ffd6c643b28e0cc7c6d0060a18a7e8ea","creator":"rhauschild","content_type":"application/octet-stream","relation":"main_file","date_updated":"2020-09-08T14:26:33Z","file_size":246121}],"oa":1,"citation":{"ista":"Hauschild R. 2020. RGtracker, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>.","short":"R. Hauschild, (2020).","mla":"Hauschild, Robert. <i>RGtracker</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>.","chicago":"Hauschild, Robert. “RGtracker.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">https://doi.org/10.15479/AT:ISTA:8294</a>.","apa":"Hauschild, R. (2020). RGtracker. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">https://doi.org/10.15479/AT:ISTA:8294</a>","ama":"Hauschild R. RGtracker. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>","ieee":"R. Hauschild, “RGtracker.” IST Austria, 2020."},"abstract":[{"text":"Automated root growth analysis and tracking of root tips. ","lang":"eng"}],"department":[{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8294","has_accepted_license":"1","tmp":{"short":"3-Clause BSD","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","name":"The 3-Clause BSD License"},"publisher":"IST Austria","day":"10","status":"public","corr_author":"1","type":"software"},{"day":"03","type":"preprint","status":"public","publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8307","citation":{"apa":"Stewart, A., &#38; Kokoris Kogias, E. (n.d.). GRANDPA: A Byzantine finality gadget. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2007.01560\">https://doi.org/10.48550/arXiv.2007.01560</a>","chicago":"Stewart, Alistair, and Eleftherios Kokoris Kogias. “GRANDPA: A Byzantine Finality Gadget.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2007.01560\">https://doi.org/10.48550/arXiv.2007.01560</a>.","mla":"Stewart, Alistair, and Eleftherios Kokoris Kogias. “GRANDPA: A Byzantine Finality Gadget.” <i>ArXiv</i>, 2007.01560, doi:<a href=\"https://doi.org/10.48550/arXiv.2007.01560\">10.48550/arXiv.2007.01560</a>.","short":"A. Stewart, E. Kokoris Kogias, ArXiv (n.d.).","ista":"Stewart A, Kokoris Kogias E. GRANDPA: A Byzantine finality gadget. arXiv, 2007.01560.","ieee":"A. Stewart and E. Kokoris Kogias, “GRANDPA: A Byzantine finality gadget,” <i>arXiv</i>. .","ama":"Stewart A, Kokoris Kogias E. GRANDPA: A Byzantine finality gadget. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2007.01560\">10.48550/arXiv.2007.01560</a>"},"article_number":"2007.01560","abstract":[{"text":"Classic Byzantine fault-tolerant consensus protocols forfeit liveness in the face of asynchrony in order to preserve safety, whereas most deployed blockchain protocols forfeit safety in order to remain live. In this work, we achieve the best of both worlds by proposing a novel abstractions called the finality gadget. A finality gadget allows for transactions to always optimistically commit but informs the clients that these transactions might be unsafe. As a result, a blockchain can execute transactions optimistically and only commit them after they have been sufficiently and provably audited. In\r\nthis work, we formally model the finality gadget abstraction, prove that it is impossible to solve it deterministically in full asynchrony (even though it is stronger than consensus) and provide a partially synchronous protocol which is currently securing a major blockchain. This way we show that the protocol designer can decouple safety and liveness in order to speed up recovery from failures. We believe that there can be other types of finality gadgets that provide weaker safety (e.g., probabilistic) in order to gain more efficiency and this can depend on the probability that the network is not in synchrony.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.01560"}],"external_id":{"arxiv":["2007.01560"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Stewart, Alistair","last_name":"Stewart","first_name":"Alistair"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"}],"date_updated":"2025-06-26T11:27:41Z","extern":"1","oa":1,"publication_status":"submitted","doi":"10.48550/arXiv.2007.01560","month":"07","year":"2020","title":"GRANDPA: A Byzantine finality gadget","date_created":"2020-08-26T12:32:10Z","article_processing_charge":"No","arxiv":1,"date_published":"2020-07-03T00:00:00Z"},{"volume":102,"title":"Stability of mobility edges in disordered interacting systems","date_published":"2020-08-26T00:00:00Z","arxiv":1,"article_processing_charge":"No","isi":1,"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).","external_id":{"arxiv":["2005.02999"],"isi":["000562628300001"]},"quality_controlled":"1","date_updated":"2026-04-07T13:26:31Z","month":"08","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"}],"scopus_import":"1","article_number":"060202(R)","citation":{"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>","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>","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>.","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).","short":"P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020)."},"oa_version":"Preprint","publisher":"American Physical Society","related_material":{"record":[{"relation":"dissertation_contains","id":"12732","status":"public"}]},"OA_type":"green","type":"journal_article","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"status":"public","year":"2020","date_created":"2020-08-26T19:27:42Z","article_type":"original","file_date_updated":"2020-08-26T19:29:00Z","ddc":["530"],"language":[{"iso":"eng"}],"author":[{"full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","last_name":"Brighi","first_name":"Pietro"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"publication_status":"published","oa":1,"file":[{"date_created":"2020-08-26T19:28:55Z","file_id":"8309","success":1,"creator":"mserbyn","checksum":"716442fa7861323fcc80b93718ca009c","access_level":"open_access","file_name":"PhysRevB.102.060202.pdf","file_size":488825,"date_updated":"2020-08-26T19:28:55Z","content_type":"application/pdf","relation":"main_file"},{"relation":"main_file","content_type":"application/pdf","date_updated":"2020-08-26T19:29:00Z","file_size":711405,"success":1,"file_id":"8310","date_created":"2020-08-26T19:29:00Z","file_name":"Supplementary-mbme.pdf","access_level":"open_access","creator":"mserbyn","checksum":"be0abdc8f60fe065ea6dc92e08487122"}],"doi":"10.1103/physrevb.102.060202","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"intvolume":"       102","_id":"8308","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaSe"}],"ec_funded":1,"issue":"6","has_accepted_license":"1","day":"26","corr_author":"1","OA_place":"repository","publication":"Physical Review B"},{"isi":1,"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.","article_processing_charge":"No","date_published":"2020-08-18T00:00:00Z","title":"Key role of quinone in the mechanism of respiratory complex I","volume":11,"month":"08","date_updated":"2026-04-02T14:36:31Z","quality_controlled":"1","external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"publisher":"Springer Nature","oa_version":"Published Version","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"}],"scopus_import":"1","article_number":"4135","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.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","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>.","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>","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."},"status":"public","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release"}]},"article_type":"original","date_created":"2020-08-30T22:01:10Z","year":"2020","intvolume":"        11","file":[{"creator":"cziletti","checksum":"52b96f41d7d0db9728064c08da00d030","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","access_level":"open_access","date_created":"2020-08-31T13:40:00Z","success":1,"file_id":"8326","file_size":7527373,"date_updated":"2020-08-31T13:40:00Z","relation":"main_file","content_type":"application/pdf"}],"doi":"10.1038/s41467-020-17957-0","publication_status":"published","oa":1,"author":[{"full_name":"Gutierrez-Fernandez, Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier","last_name":"Gutierrez-Fernandez"},{"last_name":"Kaszuba","first_name":"Karol","full_name":"Kaszuba, Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Minhas","first_name":"Gurdeep S.","full_name":"Minhas, Gurdeep S."},{"full_name":"Baradaran, Rozbeh","last_name":"Baradaran","first_name":"Rozbeh"},{"full_name":"Tambalo, Margherita","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","first_name":"Margherita"},{"first_name":"David T.","last_name":"Gallagher","full_name":"Gallagher, David T."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989"}],"language":[{"iso":"eng"}],"ddc":["570"],"file_date_updated":"2020-08-31T13:40:00Z","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"issue":"1","department":[{"_id":"LeSa"}],"_id":"8318","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"Nature Communications","day":"18"},{"month":"08","date_updated":"2025-07-10T11:57:02Z","quality_controlled":"1","external_id":{"isi":["000562110300001"]},"date_published":"2020-08-19T00:00:00Z","article_processing_charge":"No","isi":1,"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.","title":"Expanding the genetic code: Unnatural base pairs in biological systems","volume":54,"status":"public","type":"journal_article","publication_identifier":{"eissn":["1608-3245"],"issn":["0026-8933"]},"related_material":{"record":[{"id":"8321","relation":"original","status":"public"}]},"publisher":"Springer Nature","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."}],"citation":{"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>","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.","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>.","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.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","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>","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>."},"scopus_import":"1","oa_version":"None","intvolume":"        54","publication_status":"published","doi":"10.1134/S0026893320040111","language":[{"iso":"eng"}],"author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr"},{"first_name":"P. M.","last_name":"Kolosov","full_name":"Kolosov, P. M."},{"first_name":"E. Y.","last_name":"Shuvalova","full_name":"Shuvalova, E. Y."},{"last_name":"Egorova","first_name":"T. V.","full_name":"Egorova, T. V."},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"article_type":"original","date_created":"2020-08-30T22:01:11Z","year":"2020","publication":"Molecular Biology","day":"19","page":"475-484","_id":"8320","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","department":[{"_id":"FyKo"}]},{"doi":"10.31857/S0026898420040126","publication_status":"published","intvolume":"        54","author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr"},{"last_name":"Kolosov","first_name":"P. M.","full_name":"Kolosov, P. M."},{"full_name":"Shuvalova, E. Y.","first_name":"E. Y.","last_name":"Shuvalova"},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"language":[{"iso":"rus"}],"date_created":"2020-08-30T22:01:11Z","article_type":"original","year":"2020","publication":"Molekuliarnaia biologiia","day":"01","page":"531-541","issue":"4","department":[{"_id":"FyKo"}],"_id":"8321","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"month":"07","external_id":{"pmid":["32799218"]},"quality_controlled":"1","date_updated":"2025-07-10T11:57:03Z","title":"Expanding the genetic code: Unnatural base pairs in biological systems","date_published":"2020-07-01T00:00:00Z","article_processing_charge":"No","volume":54,"publication_identifier":{"issn":["0026-8984"]},"type":"journal_article","status":"public","related_material":{"record":[{"id":"8320","relation":"translation","status":"public"}]},"publisher":"Russian Academy of Sciences","oa_version":"None","citation":{"ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. 2020;54(4):531-541. doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>","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>Molekuliarnaia biologiia</i>, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</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>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</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>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>"},"abstract":[{"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.","lang":"eng"}],"scopus_import":"1"},{"intvolume":"        64","publication_status":"published","oa":1,"doi":"10.1007/s00454-020-00237-5","language":[{"iso":"eng"}],"author":[{"last_name":"Pach","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János"}],"article_type":"letter_note","date_created":"2020-08-30T22:01:12Z","year":"2020","publication":"Discrete and Computational Geometry","corr_author":"1","day":"01","page":"571-574","_id":"8323","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"}],"month":"10","date_updated":"2024-10-09T20:59:55Z","external_id":{"isi":["000561483500001"]},"article_processing_charge":"No","date_published":"2020-10-01T00:00:00Z","isi":1,"title":"A farewell to Ricky Pollack","volume":64,"status":"public","type":"journal_article","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00237-5"}],"publisher":"Springer Nature","citation":{"mla":"Pach, János. “A Farewell to Ricky Pollack.” <i>Discrete and Computational Geometry</i>, vol. 64, Springer Nature, 2020, pp. 571–74, doi:<a href=\"https://doi.org/10.1007/s00454-020-00237-5\">10.1007/s00454-020-00237-5</a>.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00237-5\">https://doi.org/10.1007/s00454-020-00237-5</a>","chicago":"Pach, János. “A Farewell to Ricky Pollack.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00454-020-00237-5\">https://doi.org/10.1007/s00454-020-00237-5</a>.","ama":"Pach J. A farewell to Ricky Pollack. <i>Discrete and Computational Geometry</i>. 2020;64:571-574. doi:<a href=\"https://doi.org/10.1007/s00454-020-00237-5\">10.1007/s00454-020-00237-5</a>","ieee":"J. Pach, “A farewell to Ricky Pollack,” <i>Discrete and Computational Geometry</i>, vol. 64. Springer Nature, pp. 571–574, 2020."},"scopus_import":"1","oa_version":"None"},{"file_date_updated":"2020-09-01T11:12:58Z","author":[{"first_name":"Peixin","last_name":"Wang","full_name":"Wang, Peixin"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Yuxin","last_name":"Deng","full_name":"Deng, Yuxin"},{"full_name":"Xu, Ming","last_name":"Xu","first_name":"Ming"}],"language":[{"iso":"eng"}],"ddc":["004"],"doi":"10.1145/3371093","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2020-09-01T11:12:58Z","file_size":564151,"access_level":"open_access","file_name":"2019_ACM_POPL_Wang.pdf","creator":"cziletti","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","file_id":"8328","success":1,"date_created":"2020-09-01T11:12:58Z"}],"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"publication_status":"published","oa":1,"intvolume":"         4","year":"2020","date_created":"2020-08-30T22:01:12Z","day":"01","publication":"Proceedings of the ACM on Programming Languages","issue":"POPL","department":[{"_id":"KrCh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8324","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["1902.04744"]},"date_updated":"2025-04-15T06:30:10Z","quality_controlled":"1","month":"01","volume":4,"title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","arxiv":1,"date_published":"2020-01-01T00:00:00Z","article_processing_charge":"No","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.3533633"}]},"publication_identifier":{"eissn":["2475-1421"]},"type":"conference","status":"public","oa_version":"Published Version","article_number":"25","citation":{"ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: <i>Proceedings of the ACM on Programming Languages</i>. Vol 4. ACM; 2020. doi:<a href=\"https://doi.org/10.1145/3371093\">10.1145/3371093</a>","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in <i>Proceedings of the ACM on Programming Languages</i>, 2020, vol. 4, no. POPL.","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 4, no. POPL, 25, ACM, 2020, doi:<a href=\"https://doi.org/10.1145/3371093\">10.1145/3371093</a>.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., &#38; Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In <i>Proceedings of the ACM on Programming Languages</i> (Vol. 4). ACM. <a href=\"https://doi.org/10.1145/3371093\">https://doi.org/10.1145/3371093</a>","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In <i>Proceedings of the ACM on Programming Languages</i>, Vol. 4. ACM, 2020. <a href=\"https://doi.org/10.1145/3371093\">https://doi.org/10.1145/3371093</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"publisher":"ACM"},{"type":"journal_article","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"status":"public","abstract":[{"text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. ","lang":"eng"}],"citation":{"apa":"Kalinin, N., &#38; Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-020-03828-8\">https://doi.org/10.1007/s00220-020-03828-8</a>","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-020-03828-8\">https://doi.org/10.1007/s00220-020-03828-8</a>.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” <i>Communications in Mathematical Physics</i>, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:<a href=\"https://doi.org/10.1007/s00220-020-03828-8\">10.1007/s00220-020-03828-8</a>.","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” <i>Communications in Mathematical Physics</i>, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. <i>Communications in Mathematical Physics</i>. 2020;378(9):1649-1675. doi:<a href=\"https://doi.org/10.1007/s00220-020-03828-8\">10.1007/s00220-020-03828-8</a>"},"scopus_import":"1","oa_version":"Preprint","publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/1711.04285","open_access":"1"}],"external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"date_updated":"2025-07-10T11:57:03Z","quality_controlled":"1","month":"09","volume":378,"title":"Sandpile solitons via smoothing of superharmonic functions","article_processing_charge":"No","date_published":"2020-09-01T00:00:00Z","arxiv":1,"isi":1,"acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","day":"01","publication":"Communications in Mathematical Physics","_id":"8325","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"department":[{"_id":"TaHa"}],"issue":"9","page":"1649-1675","language":[{"iso":"eng"}],"author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"orcid":"0000-0002-4310-178X","last_name":"Shkolnikov","first_name":"Mikhail","full_name":"Shkolnikov, Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.1007/s00220-020-03828-8","intvolume":"       378","year":"2020","date_created":"2020-08-30T22:01:13Z","article_type":"original"}]