[{"article_type":"original","citation":{"ieee":"R. J. Beattie et al., “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” Journal of Visual Experiments, no. 159. MyJove Corporation, 2020.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. 2020;(159). doi:10.3791/61147","chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147."},"publication":"Journal of Visual Experiments","date_published":"2020-05-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"08","title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7815","file":[{"access_level":"open_access","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","file_size":1352186,"content_type":"application/pdf","creator":"rbeattie","relation":"main_file","file_id":"7816","checksum":"3154ea7f90b9fb45e084cd1c2770597d","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-11T08:28:38Z"}],"oa_version":"Published Version","type":"journal_article","issue":"159","abstract":[{"lang":"eng","text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present."}],"project":[{"call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000546406600043"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.3791/61147","publication_identifier":{"issn":["1940-087X"]},"month":"05","department":[{"_id":"SiHi"}],"publisher":"MyJove Corporation","publication_status":"published","year":"2020","date_updated":"2024-03-27T23:30:41Z","date_created":"2020-05-11T08:31:20Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"author":[{"full_name":"Beattie, Robert J","first_name":"Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"article_number":"e61147","ec_funded":1,"file_date_updated":"2020-07-14T12:48:03Z"},{"date_updated":"2023-10-18T08:45:16Z","date_created":"2020-05-29T08:27:32Z","related_material":{"record":[{"id":"6830","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"28"},{"status":"public","relation":"dissertation_contains","id":"7815"}]},"author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras","full_name":"Contreras, Ximena"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"SiHi"}],"publication_status":"published","year":"2020","ec_funded":1,"file_date_updated":"2021-06-07T22:30:03Z","language":[{"iso":"eng"}],"supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7902","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06","file":[{"checksum":"43c172bf006c95b65992d473c7240d13","date_updated":"2021-06-07T22:30:03Z","date_created":"2020-06-05T08:18:08Z","file_id":"7927","relation":"source_file","creator":"xcontreras","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":53134142,"access_level":"closed","file_name":"PhDThesis_Contreras.docx","embargo_to":"open_access"},{"file_name":"PhDThesis_Contreras.pdf","access_level":"open_access","content_type":"application/pdf","file_size":35117191,"creator":"xcontreras","relation":"main_file","file_id":"7928","embargo":"2021-06-06","date_created":"2020-06-05T08:18:07Z","date_updated":"2021-06-07T22:30:03Z","checksum":"addfed9128271be05cae3608e03a6ec0"}],"oa_version":"Published Version","status":"public","title":"Genetic dissection of neural development in health and disease at single cell resolution","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7902","abstract":[{"lang":"eng","text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-06-05T00:00:00Z","page":"214","citation":{"short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020.","mla":"Contreras, Ximena. Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7902.","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7902.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902","apa":"Contreras, X. (2020). Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7902","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria."},"article_processing_charge":"No","has_accepted_license":"1","day":"05"},{"volume":219,"date_updated":"2023-10-17T10:04:49Z","date_created":"2020-08-02T22:00:57Z","author":[{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Huttenlocher","first_name":"Anna","full_name":"Huttenlocher, Anna"}],"department":[{"_id":"MiSi"}],"publisher":"Rockefeller University Press","publication_status":"published","year":"2020","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2021-02-02T23:30:03Z","article_number":"e202007029","language":[{"iso":"eng"}],"doi":"10.1083/jcb.202007029","isi":1,"external_id":{"isi":["000573631000004"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"publication_identifier":{"eissn":["1540-8140"]},"month":"07","file":[{"access_level":"open_access","file_name":"2020_JCB_Sixt.pdf","content_type":"application/pdf","file_size":830725,"creator":"dernst","relation":"main_file","embargo":"2021-02-01","file_id":"8200","checksum":"30016d778d266b8e17d01094917873b8","date_updated":"2021-02-02T23:30:03Z","date_created":"2020-08-04T13:11:52Z"}],"oa_version":"Published Version","intvolume":" 219","status":"public","title":"Zena Werb (1945-2020): Cell biology in context","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8190","issue":"8","type":"journal_article","date_published":"2020-07-22T00:00:00Z","article_type":"letter_note","citation":{"apa":"Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202007029","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press, 2020.","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.202007029.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:10.1083/jcb.202007029."},"publication":"The Journal of Cell Biology","article_processing_charge":"No","has_accepted_license":"1","day":"22","scopus_import":"1"},{"publication_identifier":{"eissn":["2375-2548"]},"month":"12","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1126/sciadv.abc8895","language":[{"iso":"eng"}],"article_number":"eabc8895","ec_funded":1,"file_date_updated":"2021-01-07T12:44:33Z","pmid":1,"year":"2020","acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","publisher":"AAAS","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"author":[{"full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang"},{"full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","first_name":"Lesia","last_name":"Rodriguez Solovey"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"volume":6,"date_updated":"2024-03-27T23:30:43Z","date_created":"2021-01-03T23:01:23Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"11","citation":{"apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020.","ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895","chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abc8895.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895."},"publication":"Science Advances","article_type":"original","date_published":"2020-12-11T00:00:00Z","type":"journal_article","issue":"50","abstract":[{"text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8986","intvolume":" 6","status":"public","ddc":["580"],"title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","oa_version":"Published Version","file":[{"creator":"dernst","file_size":10578145,"content_type":"application/pdf","file_name":"2020_ScienceAdvances_Zhang.pdf","access_level":"open_access","date_updated":"2021-01-07T12:44:33Z","date_created":"2021-01-07T12:44:33Z","success":1,"checksum":"5ac2500b191c08ef6dab5327f40ff663","file_id":"8994","relation":"main_file"}]},{"day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-08-10T00:00:00Z","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272.","ieee":"H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.","apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727","ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727.","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727.","short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020)."},"abstract":[{"lang":"eng","text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. "}],"issue":"16","type":"journal_article","oa_version":"Published Version","file":[{"creator":"cziletti","content_type":"application/pdf","file_size":5718755,"file_name":"2020_IntMolecSciences_Chen.pdf","access_level":"open_access","date_created":"2020-08-25T09:53:50Z","date_updated":"2020-08-25T09:53:50Z","success":1,"checksum":"03b039244e6ae80580385fd9f577e2b2","file_id":"8292","relation":"main_file"}],"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","ddc":["570"],"status":"public","intvolume":" 21","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8283","month":"08","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms21165727","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["32785037"],"isi":["000565090300001"]},"file_date_updated":"2020-08-25T09:53:50Z","article_number":"5272","date_updated":"2024-03-27T23:30:43Z","date_created":"2020-08-24T06:24:03Z","volume":21,"author":[{"first_name":"Huihuang","last_name":"Chen","full_name":"Chen, Huihuang"},{"first_name":"Linyi","last_name":"Lai","full_name":"Lai, Linyi"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"first_name":"Liping","last_name":"Liu","full_name":"Liu, Liping"},{"full_name":"Jakada, Bello Hassan","last_name":"Jakada","first_name":"Bello Hassan"},{"last_name":"Huang","first_name":"Youmei","full_name":"Huang, Youmei"},{"full_name":"He, Qing","last_name":"He","first_name":"Qing"},{"last_name":"Chai","first_name":"Mengnan","full_name":"Chai, Mengnan"},{"last_name":"Niu","first_name":"Xiaoping","full_name":"Niu, Xiaoping"},{"full_name":"Qin, Yuan","last_name":"Qin","first_name":"Yuan"}],"related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","year":"2020","pmid":1},{"external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"oa":1,"project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"quality_controlled":"1","doi":"10.1242/jcs.248062","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"month":"08","pmid":1,"year":"2020","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publisher":"The Company of Biologists","publication_status":"published","related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","first_name":"Nataliia","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","first_name":"Madhumitha"},{"full_name":"Vert, G","last_name":"Vert","first_name":"G"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"volume":133,"date_created":"2020-07-21T08:58:19Z","date_updated":"2023-12-01T13:51:07Z","article_number":"jcs248062","ec_funded":1,"file_date_updated":"2021-08-08T22:30:03Z","citation":{"short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062.","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062."},"publication":"Journal of Cell Science","article_type":"original","date_published":"2020-08-06T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8139","intvolume":" 133","title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","ddc":["575"],"status":"public","file":[{"creator":"ajohnson","content_type":"application/pdf","file_size":15150403,"file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","access_level":"open_access","date_created":"2020-11-26T17:12:51Z","date_updated":"2021-08-08T22:30:03Z","checksum":"2d11f79a0b4e0a380fb002b933da331a","embargo":"2021-08-07","file_id":"8815","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"15","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples."}]},{"scopus_import":"1","day":"11","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Plant Communications","citation":{"chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048.","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.","apa":"Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048","ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.","ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048"},"date_published":"2020-05-11T00:00:00Z","type":"journal_article","abstract":[{"text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.","lang":"eng"}],"issue":"3","ddc":["580"],"title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","status":"public","intvolume":" 1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9160","file":[{"date_created":"2021-02-18T10:23:59Z","date_updated":"2021-02-18T10:23:59Z","success":1,"checksum":"785b266d82a94b007cf40dbbe7c4847e","file_id":"9161","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":840289,"file_name":"2020_PlantComm_Semeradova.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"05","publication_identifier":{"issn":["2590-3462"]},"quality_controlled":"1","isi":1,"project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["33367243"],"isi":["000654052800010"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.xplc.2020.100048","article_number":"100048","file_date_updated":"2021-02-18T10:23:59Z","publication_status":"published","publisher":"Elsevier","department":[{"_id":"EvBe"}],"acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","year":"2020","pmid":1,"date_updated":"2024-03-27T23:30:46Z","date_created":"2021-02-18T10:18:43Z","volume":1,"author":[{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana","last_name":"Semeradova","full_name":"Semeradova, Hana"},{"last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"related_material":{"record":[{"id":"10135","relation":"dissertation_contains","status":"public"}]}},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n","lang":"eng"}],"ddc":["570"],"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","status":"public","_id":"7525","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"content_type":"application/pdf","file_size":9646346,"creator":"pbhandari","access_level":"open_access","file_name":"Pradeep Bhandari Thesis.pdf","checksum":"4589234fdb12b4ad72273b311723a7b4","date_updated":"2021-03-01T23:30:04Z","date_created":"2020-02-28T08:37:53Z","relation":"main_file","embargo":"2021-02-28","file_id":"7538","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway"},{"relation":"source_file","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_id":"7539","date_created":"2020-02-28T08:47:14Z","date_updated":"2021-03-01T23:30:04Z","checksum":"aa79490553ca0a5c9b6fbcd152e93928","embargo_to":"open_access","file_name":"Pradeep Bhandari Thesis.docx","access_level":"closed","file_size":35252164,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"pbhandari"}],"oa_version":"Published Version","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"day":"28","article_processing_charge":"No","has_accepted_license":"1","page":"79","citation":{"short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","mla":"Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525.","chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.","ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","apa":"Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria."},"date_published":"2020-02-28T00:00:00Z","file_date_updated":"2021-03-01T23:30:04Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"RySh"}],"year":"2020","date_updated":"2023-09-07T13:20:03Z","date_created":"2020-02-26T10:56:37Z","author":[{"full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","first_name":"Pradeep","last_name":"Bhandari"}],"month":"02","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7525"},{"author":[{"last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"full_name":"Zens, Bettina","first_name":"Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"related_material":{"record":[{"id":"14592","relation":"used_in_publication","status":"public"},{"relation":"dissertation_contains","status":"public","id":"12491"}]},"date_updated":"2024-03-28T23:30:05Z","date_created":"2020-09-29T13:24:06Z","volume":212,"year":"2020","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Elsevier","file_date_updated":"2020-12-10T14:01:10Z","article_number":"107633","doi":"10.1016/j.jsb.2020.107633","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000600997800008"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"month":"12","publication_identifier":{"issn":["1047-8477"]},"file":[{"file_id":"8937","relation":"main_file","date_created":"2020-12-10T14:01:10Z","date_updated":"2020-12-10T14:01:10Z","success":1,"checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_name":"2020_JourStrucBiology_Faessler.pdf","access_level":"open_access","creator":"dernst","file_size":7076870,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"8586","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","intvolume":" 212","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2020-12-01T00:00:00Z","publication":"Journal of Structural Biology","citation":{"ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.","apa":"Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier, 2020. https://doi.org/10.1016/j.jsb.2020.107633."},"article_type":"original","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"]},{"day":"14","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-10-14T00:00:00Z","citation":{"ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.","ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.","apa":"Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657","mla":"Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657."},"page":"271","abstract":[{"lang":"eng","text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"kavcicB_thesis202009.pdf","creator":"bkavcic","content_type":"application/pdf","file_size":52636162,"file_id":"8663","embargo":"2021-10-06","relation":"main_file","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","date_created":"2020-10-15T06:41:20Z","date_updated":"2021-10-07T22:30:03Z"},{"checksum":"bb35f2352a04db19164da609f00501f3","date_updated":"2021-10-07T22:30:03Z","date_created":"2020-10-15T06:41:53Z","relation":"source_file","file_id":"8664","content_type":"application/zip","file_size":321681247,"creator":"bkavcic","access_level":"closed","embargo_to":"open_access","file_name":"2020b.zip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8657","ddc":["571","530","570"],"status":"public","title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","month":"10","publication_identifier":{"isbn":["978-3-99078-011-4"],"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8657","degree_awarded":"PhD","supervisor":[{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2021-10-07T22:30:03Z","author":[{"full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"}],"related_material":{"record":[{"id":"7673","relation":"part_of_dissertation","status":"public"},{"id":"8250","relation":"part_of_dissertation","status":"public"}]},"date_created":"2020-10-13T16:46:14Z","date_updated":"2023-09-07T13:20:48Z","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop.","year":"2020","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18","page":"992-1006","article_type":"original","citation":{"ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022","apa":"Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron, vol. 105. Elsevier, pp. 992–1006, 2020.","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron, vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022."},"publication":"Neuron","date_published":"2020-03-18T00:00:00Z","type":"journal_article","abstract":[{"text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses.","lang":"eng"}],"intvolume":" 105","ddc":["570"],"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7473","oa_version":"Published Version","file":[{"checksum":"3582664addf26859e86ac5bec3e01416","success":1,"date_updated":"2020-11-20T08:58:53Z","date_created":"2020-11-20T08:58:53Z","relation":"main_file","file_id":"8778","file_size":9712957,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_Neuron_BorgesMerjane.pdf"}],"publication_identifier":{"issn":["0896-6273"]},"month":"03","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["31928842"],"isi":["000520854700008"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.12.022","ec_funded":1,"file_date_updated":"2020-11-20T08:58:53Z","department":[{"_id":"PeJo"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","year":"2020","volume":105,"date_created":"2020-02-10T15:59:45Z","date_updated":"2024-03-28T23:30:07Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11196"}],"link":[{"url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"last_name":"Borges Merjane","first_name":"Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"full_name":"Kim, Olena","last_name":"Kim","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}]},{"volume":11,"date_updated":"2024-03-28T23:30:08Z","date_created":"2020-08-12T09:13:50Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8657"}]},"author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Tobias","last_name":"Bollenbach"}],"publisher":"Springer Nature","department":[{"_id":"GaTk"}],"publication_status":"published","acknowledgement":"We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL.","year":"2020","file_date_updated":"2020-08-17T07:36:57Z","article_number":"4013","language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-17734-z","project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000562769300008"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2041-1723"]},"month":"08","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8275","date_created":"2020-08-17T07:36:57Z","date_updated":"2020-08-17T07:36:57Z","checksum":"986bebb308850a55850028d3d2b5b664","success":1,"file_name":"2020_NatureComm_Kavcic.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1965672,"creator":"dernst"}],"intvolume":" 11","status":"public","ddc":["570"],"title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","_id":"8250","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.","lang":"eng"}],"type":"journal_article","date_published":"2020-08-11T00:00:00Z","article_type":"original","citation":{"short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).","mla":"Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17734-z","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013."},"publication":"Nature Communications","has_accepted_license":"1","article_processing_charge":"No","day":"11"},{"language":[{"iso":"eng"}],"doi":"10.1101/2020.04.18.047886","date_published":"2020-04-18T00:00:00Z","project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"publication":"bioRxiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.18.047886 "}],"citation":{"ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.18.047886","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.18.047886."},"day":"18","month":"04","article_processing_charge":"No","date_created":"2020-04-22T08:27:56Z","date_updated":"2024-03-28T23:30:08Z","oa_version":"Preprint","author":[{"full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"8997"},{"status":"public","relation":"dissertation_contains","id":"8657"}]},"publication_status":"published","status":"public","title":"A minimal biophysical model of combined antibiotic action","department":[{"_id":"GaTk"}],"publisher":"Cold Spring Harbor Laboratory","year":"2020","_id":"7673","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions."}],"type":"preprint"},{"article_processing_charge":"No","has_accepted_license":"1","day":"30","scopus_import":"1","date_published":"2020-06-30T00:00:00Z","article_type":"original","citation":{"chicago":"Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences 117 (2020).","mla":"Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346, Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.","ieee":"L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” Proceedings of the National Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy of Sciences, 2020.","apa":"Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., & Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2003346117","ista":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 117(26), 202003346.","ama":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117"},"publication":"Proceedings of the National Academy of Sciences","issue":"26","abstract":[{"text":"Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.","lang":"eng"}],"type":"journal_article","oa_version":"None","file":[{"date_created":"2020-06-23T11:30:53Z","date_updated":"2020-07-14T12:48:07Z","checksum":"908b09437680181de9990915f2113aca","file_id":"8009","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2407102,"file_name":"2020_PNAS_Hoermayer.pdf","access_level":"open_access"}],"intvolume":" 117","title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots","ddc":["580"],"status":"public","_id":"8002","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"06","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1073/pnas.2003346117","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["32541049"],"isi":["000565729700033"]},"oa":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:48:07Z","article_number":"202003346","volume":117,"date_created":"2020-06-22T13:33:52Z","date_updated":"2024-03-28T23:30:10Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9992"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/"}]},"author":[{"full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas","last_name":"Hörmayer"},{"full_name":"Montesinos López, Juan C","last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","last_name":"Marhavá","full_name":"Marhavá, Petra"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","pmid":1,"year":"2020"},{"issue":"1","abstract":[{"lang":"eng","text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2019_BMCBio_Harker_Kirschneck.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":1648926,"file_id":"10356","relation":"main_file","success":1,"checksum":"31d8bae55a376d30925f53f7e1a02396","date_created":"2021-11-26T11:37:54Z","date_updated":"2021-11-26T11:37:54Z"}],"oa_version":"Published Version","intvolume":" 17","status":"public","title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","ddc":["570"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10354","has_accepted_license":"1","article_processing_charge":"No","day":"22","keyword":["cell biology"],"scopus_import":"1","date_published":"2019-10-22T00:00:00Z","article_type":"original","citation":{"short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology, vol. 17, no. 1, 82, Springer Nature, 2019, doi:10.1186/s12915-019-0700-2.","chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology. Springer Nature, 2019. https://doi.org/10.1186/s12915-019-0700-2.","ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 2019;17(1). doi:10.1186/s12915-019-0700-2","apa":"Harker-Kirschneck, L., Baum, B., & Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0700-2","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” BMC Biology, vol. 17, no. 1. Springer Nature, 2019.","ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82."},"publication":"BMC Biology","extern":"1","file_date_updated":"2021-11-26T11:37:54Z","article_number":"82","volume":17,"date_updated":"2021-11-26T11:54:29Z","date_created":"2021-11-26T11:25:03Z","author":[{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","year":"2019","publication_identifier":{"issn":["1741-7007"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1186/s12915-019-0700-2","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/559898","open_access":"1"}],"oa":1,"external_id":{"pmid":["31640700"]}},{"abstract":[{"lang":"eng","text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments."}],"type":"journal_article","oa_version":"Preprint","title":"Minimal coarse-grained models for molecular self-organisation in biology","status":"public","intvolume":" 58","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10355","day":"18","article_processing_charge":"No","keyword":["molecular biology","structural biology"],"scopus_import":"1","date_published":"2019-06-18T00:00:00Z","article_type":"original","page":"43-52","publication":"Current Opinion in Structural Biology","citation":{"ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019.","apa":"Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018","ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018","chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018."},"extern":"1","date_updated":"2021-11-26T11:54:25Z","date_created":"2021-11-26T11:33:21Z","volume":58,"author":[{"first_name":"Anne E","last_name":"Hafner","full_name":"Hafner, Anne E"},{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"}],"publication_status":"published","publisher":"Elsevier","acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","year":"2019","pmid":1,"month":"06","publication_identifier":{"issn":["0959-440X"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.sbi.2019.05.018","quality_controlled":"1","external_id":{"pmid":["31226513"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.09349"}]},{"author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy"},{"last_name":"Yankowitz","first_name":"Matthew","full_name":"Yankowitz, Matthew"},{"full_name":"Chen, Shaowen","last_name":"Chen","first_name":"Shaowen"},{"first_name":"Yuxuan","last_name":"Zhang","full_name":"Zhang, Yuxuan"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."}],"volume":15,"date_created":"2022-01-13T15:00:58Z","date_updated":"2022-01-20T09:33:38Z","year":"2019","acknowledgement":"The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958.","publisher":"Springer Nature","publication_status":"published","extern":"1","doi":"10.1038/s41567-019-0596-3","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1902.00763","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1902.00763"]},"quality_controlled":"1","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"08","oa_version":"Preprint","_id":"10621","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","intvolume":" 15","status":"public","title":"Large linear-in-temperature resistivity in twisted bilayer graphene","issue":"10","abstract":[{"lang":"eng","text":"Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity."}],"type":"journal_article","date_published":"2019-08-05T00:00:00Z","citation":{"mla":"Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:10.1038/s41567-019-0596-3.","short":"H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016.","chicago":"Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics. Springer Nature, 2019. https://doi.org/10.1038/s41567-019-0596-3.","ama":"Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 2019;15(10):1011-1016. doi:10.1038/s41567-019-0596-3","ista":"Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016.","ieee":"H. Polshyn et al., “Large linear-in-temperature resistivity in twisted bilayer graphene,” Nature Physics, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019.","apa":"Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0596-3"},"publication":"Nature Physics","page":"1011-1016","article_type":"original","article_processing_charge":"No","day":"05","scopus_import":"1","keyword":["general physics and astronomy"]},{"oa_version":"Preprint","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","_id":"10622","status":"public","title":"Manipulating multivortex states in superconducting structures","intvolume":" 19","abstract":[{"lang":"eng","text":"We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing."}],"issue":"8","type":"journal_article","date_published":"2019-06-27T00:00:00Z","publication":"Nano Letters","citation":{"chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b01983.","mla":"Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:10.1021/acs.nanolett.9b01983.","short":"H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482.","ista":"Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482.","apa":"Polshyn, H., Naibert, T., & Budakian, R. (2019). Manipulating multivortex states in superconducting structures. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b01983","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” Nano Letters, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019.","ama":"Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. Nano Letters. 2019;19(8):5476-5482. doi:10.1021/acs.nanolett.9b01983"},"article_type":"original","page":"5476-5482","day":"27","article_processing_charge":"No","scopus_import":"1","keyword":["mechanical engineering","condensed matter physics","general materials science","general chemistry","bioengineering"],"author":[{"first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"last_name":"Naibert","first_name":"Tyler","full_name":"Naibert, Tyler"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"date_updated":"2022-01-13T15:41:24Z","date_created":"2022-01-13T15:11:14Z","volume":19,"acknowledgement":"We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.","year":"2019","pmid":1,"publication_status":"published","publisher":"American Chemical Society","extern":"1","doi":"10.1021/acs.nanolett.9b01983","language":[{"iso":"eng"}],"external_id":{"pmid":["31246034"],"arxiv":["1905.06303"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1905.06303","open_access":"1"}],"quality_controlled":"1","month":"06","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]}},{"month":"01","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.aav1910","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.07865","open_access":"1"}],"external_id":{"pmid":["30679385 "],"arxiv":["1808.07865"]},"oa":1,"extern":"1","date_created":"2022-01-14T12:14:58Z","date_updated":"2022-01-14T13:48:32Z","volume":363,"author":[{"first_name":"Matthew","last_name":"Yankowitz","full_name":"Yankowitz, Matthew"},{"first_name":"Shaowen","last_name":"Chen","full_name":"Chen, Shaowen"},{"full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"last_name":"Zhang","first_name":"Yuxuan","full_name":"Zhang, Yuxuan"},{"full_name":"Watanabe, K.","first_name":"K.","last_name":"Watanabe"},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"last_name":"Graf","first_name":"David","full_name":"Graf, David"},{"full_name":"Young, Andrea F.","last_name":"Young","first_name":"Andrea F."},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"}],"publication_status":"published","publisher":"American Association for the Advancement of Science (AAAS)","acknowledgement":"We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar, A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino, and P. Moon for helpful discussions.","year":"2019","pmid":1,"day":"24","article_processing_charge":"No","keyword":["multidisciplinary"],"scopus_import":"1","date_published":"2019-01-24T00:00:00Z","article_type":"original","page":"1059-1064","publication":"Science","citation":{"ista":"Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene. Science. 363(6431), 1059–1064.","ieee":"M. Yankowitz et al., “Tuning superconductivity in twisted bilayer graphene,” Science, vol. 363, no. 6431. American Association for the Advancement of Science (AAAS), pp. 1059–1064, 2019.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T., … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. Science. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aav1910","ama":"Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted bilayer graphene. Science. 2019;363(6431):1059-1064. doi:10.1126/science.aav1910","chicago":"Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science. American Association for the Advancement of Science (AAAS), 2019. https://doi.org/10.1126/science.aav1910.","mla":"Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science, vol. 363, no. 6431, American Association for the Advancement of Science (AAAS), 2019, pp. 1059–64, doi:10.1126/science.aav1910.","short":"M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064."},"abstract":[{"lang":"eng","text":"The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures."}],"issue":"6431","type":"journal_article","oa_version":"Preprint","status":"public","title":"Tuning superconductivity in twisted bilayer graphene","intvolume":" 363","_id":"10625","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"abstract":[{"text":"Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream\r\nof experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points.","lang":"eng"}],"type":"journal_article","author":[{"full_name":"Yankowitz, Mathew","last_name":"Yankowitz","first_name":"Mathew"},{"first_name":"Shaowen","last_name":"Chen","full_name":"Chen, Shaowen"},{"full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn"},{"full_name":"Watanabe, K.","first_name":"K.","last_name":"Watanabe"},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"full_name":"Graf, David","last_name":"Graf","first_name":"David"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."},{"first_name":"Cory R.","last_name":"Dean","full_name":"Dean, Cory R."},{"full_name":"Sharpe, Aaron L.","first_name":"Aaron L.","last_name":"Sharpe"},{"full_name":"Fox, E.J.","first_name":"E.J.","last_name":"Fox"},{"full_name":"Barnard, A.W.","last_name":"Barnard","first_name":"A.W."},{"first_name":"Joe","last_name":"Finney","full_name":"Finney, Joe"}],"volume":"03","oa_version":"Published Version","date_updated":"2022-01-25T15:56:39Z","date_created":"2022-01-25T15:09:58Z","year":"2019","_id":"10664","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Simons Foundation ; University of California, Riverside","intvolume":" 3","publication_status":"published","title":"New correlated phenomena in magic-angle twisted bilayer graphene/s","status":"public","article_processing_charge":"No","day":"28","month":"02","doi":"10.36471/jccm_february_2019_03","date_published":"2019-02-28T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"short":"M. Yankowitz, S. Chen, H. Polshyn, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, A.L. Sharpe, E.J. Fox, A.W. Barnard, J. Finney, Journal Club for Condensed Matter Physics 03 (2019).","mla":"Yankowitz, Mathew, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics, vol. 03, Simons Foundation ; University of California, Riverside, 2019, doi:10.36471/jccm_february_2019_03.","chicago":"Yankowitz, Mathew, Shaowen Chen, Hryhoriy Polshyn, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside, 2019. https://doi.org/10.36471/jccm_february_2019_03.","ama":"Yankowitz M, Chen S, Polshyn H, et al. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 2019;03. doi:10.36471/jccm_february_2019_03","ieee":"M. Yankowitz et al., “New correlated phenomena in magic-angle twisted bilayer graphene/s,” Journal Club for Condensed Matter Physics, vol. 03. Simons Foundation ; University of California, Riverside, 2019.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D., … Finney, J. (2019). New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside. https://doi.org/10.36471/jccm_february_2019_03","ista":"Yankowitz M, Chen S, Polshyn H, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR, Sharpe AL, Fox EJ, Barnard AW, Finney J. 2019. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 03."},"main_file_link":[{"url":"https://www.condmatjclub.org/?p=3541","open_access":"1"}],"publication":"Journal Club for Condensed Matter Physics","quality_controlled":"1","article_type":"original"},{"type":"journal_article","issue":"6480","abstract":[{"text":"The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize the electrons into a single spin- and valley-resolved moiré miniband with Chern number C = 1. In contrast to magnetically doped systems, the measured transport energy gap is larger than the Curie temperature for magnetic ordering, and quantization to within 0.1% of the von Klitzing constant persists to temperatures of several kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably switch the magnetic order between states of opposite polarization, forming an electrically rewritable magnetic memory.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10619","intvolume":" 367","status":"public","title":"Intrinsic quantized anomalous Hall effect in a moiré heterostructure","oa_version":"Preprint","scopus_import":"1","keyword":["multidisciplinary"],"article_processing_charge":"No","day":"19","citation":{"ama":"Serlin M, Tschirhart CL, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 2019;367(6480):900-903. doi:10.1126/science.aay5533","apa":"Serlin, M., Tschirhart, C. L., Polshyn, H., Zhang, Y., Zhu, J., Watanabe, K., … Young, A. F. (2019). Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aay5533","ieee":"M. Serlin et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure,” Science, vol. 367, no. 6480. American Association for the Advancement of Science, pp. 900–903, 2019.","ista":"Serlin M, Tschirhart CL, Polshyn H, Zhang Y, Zhu J, Watanabe K, Taniguchi T, Balents L, Young AF. 2019. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 367(6480), 900–903.","short":"M. Serlin, C.L. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, A.F. Young, Science 367 (2019) 900–903.","mla":"Serlin, M., et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” Science, vol. 367, no. 6480, American Association for the Advancement of Science, 2019, pp. 900–03, doi:10.1126/science.aay5533.","chicago":"Serlin, M., C. L. Tschirhart, Hryhoriy Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, and A. F. Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aay5533."},"publication":"Science","page":"900-903","article_type":"original","date_published":"2019-12-19T00:00:00Z","extern":"1","pmid":1,"year":"2019","acknowledgement":"The authors acknowledge discussions with A. Macdonald, Y. Saito, and M. Zaletel.","publisher":"American Association for the Advancement of Science","publication_status":"published","related_material":{"record":[{"status":"public","relation":"other","id":"10697"},{"id":"10698","relation":"other","status":"public"},{"id":"10699","relation":"other","status":"public"}]},"author":[{"full_name":"Serlin, M.","first_name":"M.","last_name":"Serlin"},{"full_name":"Tschirhart, C. L.","last_name":"Tschirhart","first_name":"C. L."},{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"full_name":"Zhang, Y.","last_name":"Zhang","first_name":"Y."},{"last_name":"Zhu","first_name":"J.","full_name":"Zhu, J."},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"full_name":"Balents, L.","first_name":"L.","last_name":"Balents"},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"volume":367,"date_updated":"2023-02-21T16:00:09Z","date_created":"2022-01-13T14:21:32Z","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.00261"}],"external_id":{"pmid":["31857492"],"arxiv":["1907.00261"]},"oa":1,"quality_controlled":"1","doi":"10.1126/science.aay5533","language":[{"iso":"eng"}]},{"day":"01","article_processing_charge":"No","publication":"APS March Meeting 2019","citation":{"chicago":"Polshyn, Hryhoriy, Yuxuan Zhang, Matthew Yankowitz, Shaowen Chen, Takashi Taniguchi, Kenji Watanabe, David E. Graf, Cory R. Dean, and Andrea Young. “Normal State Transport in Superconducting Twisted Bilayer Graphene.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019.","short":"H. Polshyn, Y. Zhang, M. Yankowitz, S. Chen, T. Taniguchi, K. Watanabe, D.E. Graf, C.R. Dean, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019.","mla":"Polshyn, Hryhoriy, et al. “Normal State Transport in Superconducting Twisted Bilayer Graphene.” APS March Meeting 2019, vol. 64, no. 2, V14.00008, American Physical Society, 2019.","apa":"Polshyn, H., Zhang, Y., Yankowitz, M., Chen, S., Taniguchi, T., Watanabe, K., … Young, A. (2019). Normal state transport in superconducting twisted bilayer graphene. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","ieee":"H. Polshyn et al., “Normal state transport in superconducting twisted bilayer graphene,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","ista":"Polshyn H, Zhang Y, Yankowitz M, Chen S, Taniguchi T, Watanabe K, Graf DE, Dean CR, Young A. 2019. Normal state transport in superconducting twisted bilayer graphene. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, V14.00008.","ama":"Polshyn H, Zhang Y, Yankowitz M, et al. Normal state transport in superconducting twisted bilayer graphene. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019."},"date_published":"2019-03-01T00:00:00Z","alternative_title":["Bulletin of the American Physical Society"],"type":"conference","abstract":[{"text":"Twisted bilayer graphene (tBLG) near the flat band condition is a versatile new platform for the study of correlated physics in 2D. Resistive states have been observed at several commensurate fillings of the flat miniband, along with superconducting states near half filling. To better understand the electronic structure of this system, we study electronic transport of graphite gated superconducting tBLG devices in the normal regime. At high magnetic fields, we observe full lifting of the spin and valley degeneracy. The transitions in the splitting of this four-fold degeneracy as a function of carrier density indicate Landau level (LL) crossings, which tilted field measurements show occur between LLs with different valley polarization. Similar LL structure measured in two devices, one with twist angle θ=1.08° at ambient pressure and one at θ=1.27° and 1.33GPa, suggests that the dimensionless combination of twist angle and interlayer coupling controls the relevant details of the band structure. In addition, we find that the temperature dependence of the resistance at B=0 shows linear growth at several hundred Ohm/K in a broad range of temperatures. We discuss the implications for modeling the scattering processes in this system.","lang":"eng"}],"issue":"2","status":"public","title":"Normal state transport in superconducting twisted bilayer graphene","intvolume":" 64","_id":"10724","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","month":"03","publication_identifier":{"issn":["0003-0503"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/V14.8"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Boston, MA, United States","start_date":"2019-03-04","end_date":"2019-03-08","name":"APS: American Physical Society"},"article_number":"V14.00008","extern":"1","publication_status":"published","publisher":"American Physical Society","year":"2019","date_created":"2022-02-04T12:25:04Z","date_updated":"2022-02-08T10:23:13Z","volume":64,"author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy"},{"first_name":"Yuxuan","last_name":"Zhang","full_name":"Zhang, Yuxuan"},{"full_name":"Yankowitz, Matthew","last_name":"Yankowitz","first_name":"Matthew"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"first_name":"Kenji","last_name":"Watanabe","full_name":"Watanabe, Kenji"},{"full_name":"Graf, David E.","first_name":"David E.","last_name":"Graf"},{"first_name":"Cory R.","last_name":"Dean","full_name":"Dean, Cory R."},{"last_name":"Young","first_name":"Andrea","full_name":"Young, Andrea"}]},{"abstract":[{"lang":"eng","text":"Bilayer graphene, rotationally faulted to ~1.1 degree misalignment, has recently been shown to host superconducting and resistive states associated with the formation of a flat electronic band. While numerous theories exist for the origins of both states, direct validation of these theories remains an outstanding experimental problem. Here, we focus on the resistive states occurring at commensurate filling (1/2, 1/4, and 3/4) of the two lowest superlattice bands. We test theoretical proposals that these states arise due to broken spin—and/or valley—symmetry by performing direct magnetic imaging with nanoscale SQUID-on-tip microscopy. This technique provides single-spin resolved magnetometry on sub-100nm length scales. I will present imaging data from our 4.2K nSOT microscope on graphite-gated twisted bilayers near the flat band condition and discuss the implications for the physics of the commensurate resistive states."}],"issue":"2","alternative_title":["Bulletin of the American Physical Society"],"type":"conference","oa_version":"Published Version","status":"public","title":"Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy","intvolume":" 64","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10722","day":"01","article_processing_charge":"No","date_published":"2019-03-01T00:00:00Z","publication":"APS March Meeting 2019","citation":{"ama":"Serlin M, Tschirhart C, Polshyn H, Zhu J, Huber ME, Young A. Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019.","ista":"Serlin M, Tschirhart C, Polshyn H, Zhu J, Huber ME, Young A. 2019. Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, L14.00006.","ieee":"M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, M. E. Huber, and A. Young, “Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","apa":"Serlin, M., Tschirhart, C., Polshyn, H., Zhu, J., Huber, M. E., & Young, A. (2019). Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","mla":"Serlin, Marec, et al. “Direct Imaging of Magnetic Structure in Twisted Bilayer Graphene with Scanning NanoSQUID-On-Tip Microscopy.” APS March Meeting 2019, vol. 64, no. 2, L14.00006, American Physical Society, 2019.","short":"M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, M.E. Huber, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019.","chicago":"Serlin, Marec, Charles Tschirhart, Hryhoriy Polshyn, Jiacheng Zhu, Martin E. Huber, and Andrea Young. “Direct Imaging of Magnetic Structure in Twisted Bilayer Graphene with Scanning NanoSQUID-On-Tip Microscopy.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019."},"extern":"1","article_number":"L14.00006","date_updated":"2022-02-08T10:25:30Z","date_created":"2022-02-04T11:54:21Z","volume":64,"author":[{"full_name":"Serlin, Marec","first_name":"Marec","last_name":"Serlin"},{"last_name":"Tschirhart","first_name":"Charles","full_name":"Tschirhart, Charles"},{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"first_name":"Jiacheng","last_name":"Zhu","full_name":"Zhu, Jiacheng"},{"full_name":"Huber, Martin E.","last_name":"Huber","first_name":"Martin E."},{"last_name":"Young","first_name":"Andrea","full_name":"Young, Andrea"}],"publication_status":"published","publisher":"American Physical Society","year":"2019","month":"03","publication_identifier":{"issn":["0003-0503"]},"language":[{"iso":"eng"}],"conference":{"name":"APS: American Physical Society","end_date":"2019-03-08","start_date":"2019-03-04","location":"Boston, MA, United States"},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR19/Session/L14.6","open_access":"1"}]},{"citation":{"chicago":"Chen, Shaowen, Matthew Yankowitz, Hryhoriy Polshyn, Kenji Watanabe, Takashi Taniguchi, David E. Graf, Andrea Young, and Cory R. Dean. “Correlated Insulating and Superconducting Phases in Twisted Bilayer Graphene.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019.","mla":"Chen, Shaowen, et al. “Correlated Insulating and Superconducting Phases in Twisted Bilayer Graphene.” APS March Meeting 2019, vol. 64, no. 2, R14.00004, American Physical Society, 2019.","short":"S. Chen, M. Yankowitz, H. Polshyn, K. Watanabe, T. Taniguchi, D.E. Graf, A. Young, C.R. Dean, in:, APS March Meeting 2019, American Physical Society, 2019.","ista":"Chen S, Yankowitz M, Polshyn H, Watanabe K, Taniguchi T, Graf DE, Young A, Dean CR. 2019. Correlated insulating and superconducting phases in twisted bilayer graphene. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, R14.00004.","ieee":"S. Chen et al., “Correlated insulating and superconducting phases in twisted bilayer graphene,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","apa":"Chen, S., Yankowitz, M., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D. E., … Dean, C. R. (2019). Correlated insulating and superconducting phases in twisted bilayer graphene. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","ama":"Chen S, Yankowitz M, Polshyn H, et al. Correlated insulating and superconducting phases in twisted bilayer graphene. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019."},"publication":"APS March Meeting 2019","date_published":"2019-03-01T00:00:00Z","article_processing_charge":"No","day":"01","intvolume":" 64","title":"Correlated insulating and superconducting phases in twisted bilayer graphene","status":"public","_id":"10725","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","alternative_title":["Bulletin of the American Physical Society"],"type":"conference","issue":"2","abstract":[{"lang":"eng","text":"Bilayer graphene with ~ 1.1 degrees twist mismatch between the layers hosts a low energy flat band in which the Coulomb interaction is large relative to the bandwidth, promoting correlated insulating states at half band filling, and superconducting (SC) phases with dome-like structure neighboring correlated insulating states. Here we show measurements of a dual-graphite-gated twisted bilayer graphene device, which minimizes charge inhomogeneity. We observe new correlated phases, including for the first time a SC pocket near half-filling of the electron-doped band and resistive states at quarter-filling of both bands that emerge in a magnetic field. Changing the layer polarization with vertical electric field reveals an unexpected competition between SC and correlated insulator phases, which we interpret to result from differences in disorder of each graphene layer and underscores the spatial inhomogeneity like twist angle as a significant source of disorder in these devices [1]."}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/R14.4"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2019-03-08","start_date":"2019-03-04","location":"Boston, MA, United States","name":"APS: American Physical Society"},"publication_identifier":{"issn":["0003-0503"]},"month":"03","publisher":"American Physical Society","publication_status":"published","year":"2019","volume":64,"date_created":"2022-02-04T13:48:04Z","date_updated":"2022-02-08T10:24:13Z","related_material":{"link":[{"relation":"used_in_publication","url":"https://arxiv.org/abs/1808.07865"}]},"author":[{"full_name":"Chen, Shaowen","first_name":"Shaowen","last_name":"Chen"},{"full_name":"Yankowitz, Matthew","first_name":"Matthew","last_name":"Yankowitz"},{"last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy"},{"last_name":"Watanabe","first_name":"Kenji","full_name":"Watanabe, Kenji"},{"full_name":"Taniguchi, Takashi","last_name":"Taniguchi","first_name":"Takashi"},{"last_name":"Graf","first_name":"David E.","full_name":"Graf, David E."},{"first_name":"Andrea","last_name":"Young","full_name":"Young, Andrea"},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"}],"article_number":"R14.00004","extern":"1"},{"language":[{"iso":"eng"}],"date_published":"2019-03-01T00:00:00Z","conference":{"name":"APS: American Physical Society","end_date":"2019-03-08","location":"Boston, MA, United States","start_date":"2019-03-04"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/P01.4"}],"oa":1,"citation":{"ama":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019.","apa":"Zhou, H., Polshyn, H., Tanaguchi, T., Watanabe, K., & Young, A. (2019). Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","ieee":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, and A. Young, “Spin wave transport through electron solids and fractional quantum Hall liquids in graphene,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","ista":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. 2019. Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. APS March Meeting 2019. APS: American Physical Society vol. 64, P01.00004.","short":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019.","mla":"Zhou, Haoxin, et al. “Spin Wave Transport through Electron Solids and Fractional Quantum Hall Liquids in Graphene.” APS March Meeting 2019, vol. 64, no. 2, P01.00004, American Physical Society, 2019.","chicago":"Zhou, Haoxin, Hryhoriy Polshyn, Takashi Tanaguchi, Kenji Watanabe, and Andrea Young. “Spin Wave Transport through Electron Solids and Fractional Quantum Hall Liquids in Graphene.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019."},"publication":"APS March Meeting 2019","article_processing_charge":"No","publication_identifier":{"issn":["0003-0503"]},"month":"03","day":"01","oa_version":"Published Version","volume":64,"date_created":"2022-02-04T12:14:02Z","date_updated":"2022-02-04T13:59:47Z","author":[{"full_name":"Zhou, Haoxin","first_name":"Haoxin","last_name":"Zhou"},{"full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn"},{"last_name":"Tanaguchi","first_name":"Takashi","full_name":"Tanaguchi, Takashi"},{"full_name":"Watanabe, Kenji","first_name":"Kenji","last_name":"Watanabe"},{"last_name":"Young","first_name":"Andrea","full_name":"Young, Andrea"}],"publisher":"American Physical Society","intvolume":" 64","title":"Spin wave transport through electron solids and fractional quantum Hall liquids in graphene","status":"public","publication_status":"published","_id":"10723","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2019","extern":"1","issue":"2","abstract":[{"text":"In monolayer graphene, the interplay of electronic correlations with the internal spin- and valley- degrees of freedom leads to a complex phase diagram of isospin symmetry breaking at high magnetic fields. Recently, Wei et al. (Science (2018)) demonstrated that spin waves can be electrically generated and detected in graphene heterojunctions, allowing direct experiment access to the spin degree of freedom. Here, we apply this technique to high quality graphite-gated graphene devices showing robust fractional quantum Hall phases and isospin phase transitions. We use an edgeless Corbino geometry to eliminate the contributions of edge states to the spin-wave mediated nonlocal voltage, allowing unambiguous identification of spin wave transport signatures. Our data reveal two phases within the ν = 1 plateau. For exactly ν=1, charge is localized but spin waves propagate freely while small carrier doping completely quenches the low-energy spin-wave transport, even as those charges remain localized. We identify this new phase as a spin textured electron solid. We also find that spin-wave transport is modulated by phase transitions in the valley order that preserve spin polarization, suggesting that this technique is sensitive to both spin and valley order.","lang":"eng"}],"type":"conference","article_number":"P01.00004"},{"has_accepted_license":"1","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2019-05-25T00:00:00Z","page":"1-13","citation":{"chicago":"Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” In ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, 61:1–13. EasyChair, 2019. https://doi.org/10.29007/rjwn.","mla":"Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, vol. 61, EasyChair, 2019, pp. 1–13, doi:10.29007/rjwn.","short":"G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe, A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G. Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13.","ista":"Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series in Computing, vol. 61, 1–13.","apa":"Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella, E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In G. Frehse & M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems (Vol. 61, pp. 1–13). Montreal, Canada: EasyChair. https://doi.org/10.29007/rjwn","ieee":"G. Frehse et al., “ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics,” in ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, Montreal, Canada, 2019, vol. 61, pp. 1–13.","ama":"Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In: Frehse G, Althoff M, eds. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. Vol 61. EasyChair; 2019:1-13. doi:10.29007/rjwn"},"publication":"ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems","abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with piecewise constant dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been applied to solve five different benchmark problems in the category for piecewise constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL. Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results probably provide the most complete assessment of tools for the safety verification of continuous and hybrid systems with piecewise constant dynamics up to this date.","lang":"eng"}],"alternative_title":["EPiC Series in Computing"],"type":"conference","file":[{"access_level":"open_access","file_name":"2019_EPiCs_Frehse.pdf","creator":"dernst","file_size":346415,"content_type":"application/pdf","file_id":"11391","relation":"main_file","success":1,"checksum":"4b92e333db7b4e2349501a804dfede69","date_updated":"2022-05-17T06:55:49Z","date_created":"2022-05-17T06:55:49Z"}],"oa_version":"Published Version","intvolume":" 61","ddc":["000"],"title":"ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics","status":"public","_id":"10877","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2398-7340"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.29007/rjwn","conference":{"end_date":"2019-04-15","location":"Montreal, Canada","start_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"quality_controlled":"1","oa":1,"file_date_updated":"2022-05-17T06:55:49Z","volume":61,"date_created":"2022-03-18T12:29:23Z","date_updated":"2022-05-17T07:09:47Z","author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"full_name":"Abate, Alessandro","first_name":"Alessandro","last_name":"Abate"},{"first_name":"Dieky","last_name":"Adzkiya","full_name":"Adzkiya, Dieky"},{"full_name":"Becchi, Anna","last_name":"Becchi","first_name":"Anna"},{"first_name":"Lei","last_name":"Bu","full_name":"Bu, Lei"},{"full_name":"Cimatti, Alessandro","last_name":"Cimatti","first_name":"Alessandro"},{"last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"},{"full_name":"Griggio, Alberto","last_name":"Griggio","first_name":"Alberto"},{"full_name":"Mover, Sergio","last_name":"Mover","first_name":"Sergio"},{"last_name":"Mufid","first_name":"Muhammad Syifa'ul","full_name":"Mufid, Muhammad Syifa'ul"},{"first_name":"Idriss","last_name":"Riouak","full_name":"Riouak, Idriss"},{"full_name":"Tonetta, Stefano","last_name":"Tonetta","first_name":"Stefano"},{"last_name":"Zaffanella","first_name":"Enea","full_name":"Zaffanella, Enea"}],"editor":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"last_name":"Althoff","first_name":"Matthias","full_name":"Althoff, Matthias"}],"department":[{"_id":"ToHe"}],"publisher":"EasyChair","publication_status":"published","year":"2019","acknowledgement":"The authors gratefully acknowledge \fnancial support by the European Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported by the National Natural Science\r\nFoundation of China (No.61572249)."},{"date_created":"2022-04-07T07:45:11Z","date_updated":"2022-07-18T08:31:52Z","volume":218,"author":[{"full_name":"Toyama, Brandon H.","first_name":"Brandon H.","last_name":"Toyama"},{"last_name":"Arrojo e Drigo","first_name":"Rafael","full_name":"Arrojo e Drigo, Rafael"},{"first_name":"Varda","last_name":"Lev-Ram","full_name":"Lev-Ram, Varda"},{"first_name":"Ranjan","last_name":"Ramachandra","full_name":"Ramachandra, Ranjan"},{"full_name":"Deerinck, Thomas J.","first_name":"Thomas J.","last_name":"Deerinck"},{"full_name":"Lechene, Claude","first_name":"Claude","last_name":"Lechene"},{"last_name":"Ellisman","first_name":"Mark H.","full_name":"Ellisman, Mark H."},{"full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"publication_status":"published","publisher":"Rockefeller University Press","year":"2019","pmid":1,"extern":"1","file_date_updated":"2022-04-08T08:26:32Z","language":[{"iso":"eng"}],"doi":"10.1083/jcb.201809123","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"external_id":{"pmid":["30552100"]},"month":"02","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"oa_version":"Published Version","file":[{"date_created":"2022-04-08T08:26:32Z","date_updated":"2022-04-08T08:26:32Z","success":1,"checksum":"7964ebbf833b0b35f9fba840eea9531d","file_id":"11139","relation":"main_file","creator":"dernst","file_size":2503838,"content_type":"application/pdf","file_name":"2019_JCB_Toyama.pdf","access_level":"open_access"}],"status":"public","title":"Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells","ddc":["570"],"intvolume":" 218","_id":"11061","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","abstract":[{"lang":"eng","text":"Many adult tissues contain postmitotic cells as old as the host organism. The only organelle that does not turn over in these cells is the nucleus, and its maintenance represents a formidable challenge, as it harbors regulatory proteins that persist throughout adulthood. Here we developed strategies to visualize two classes of such long-lived proteins, histones and nucleoporins, to understand the function of protein longevity in nuclear maintenance. Genome-wide mapping of histones revealed specific enrichment of long-lived variants at silent gene loci. Interestingly, nuclear pores are maintained by piecemeal replacement of subunits, resulting in mosaic complexes composed of polypeptides with vastly different ages. In contrast, nondividing quiescent cells remove old nuclear pores in an ESCRT-dependent manner. Our findings reveal distinct molecular strategies of nuclear maintenance, linking lifelong protein persistence to gene regulation and nuclear integrity."}],"issue":"2","type":"journal_article","date_published":"2019-02-04T00:00:00Z","article_type":"original","page":"433-444","publication":"Journal of Cell Biology","citation":{"ieee":"B. H. Toyama et al., “Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells,” Journal of Cell Biology, vol. 218, no. 2. Rockefeller University Press, pp. 433–444, 2019.","apa":"Toyama, B. H., Arrojo e Drigo, R., Lev-Ram, V., Ramachandra, R., Deerinck, T. J., Lechene, C., … Hetzer, M. (2019). Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201809123","ista":"Toyama BH, Arrojo e Drigo R, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene C, Ellisman MH, Hetzer M. 2019. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. 218(2), 433–444.","ama":"Toyama BH, Arrojo e Drigo R, Lev-Ram V, et al. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. 2019;218(2):433-444. doi:10.1083/jcb.201809123","chicago":"Toyama, Brandon H., Rafael Arrojo e Drigo, Varda Lev-Ram, Ranjan Ramachandra, Thomas J. Deerinck, Claude Lechene, Mark H. Ellisman, and Martin Hetzer. “Visualization of Long-Lived Proteins Reveals Age Mosaicism within Nuclei of Postmitotic Cells.” Journal of Cell Biology. Rockefeller University Press, 2019. https://doi.org/10.1083/jcb.201809123.","short":"B.H. Toyama, R. Arrojo e Drigo, V. Lev-Ram, R. Ramachandra, T.J. Deerinck, C. Lechene, M.H. Ellisman, M. Hetzer, Journal of Cell Biology 218 (2019) 433–444.","mla":"Toyama, Brandon H., et al. “Visualization of Long-Lived Proteins Reveals Age Mosaicism within Nuclei of Postmitotic Cells.” Journal of Cell Biology, vol. 218, no. 2, Rockefeller University Press, 2019, pp. 433–44, doi:10.1083/jcb.201809123."},"day":"04","has_accepted_license":"1","article_processing_charge":"No","keyword":["Cell Biology"],"scopus_import":"1"},{"oa_version":"Published Version","title":"Age mosaicism across multiple scales in adult tissues","status":"public","intvolume":" 30","_id":"11062","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","abstract":[{"text":"Most neurons are not replaced during an animal’s lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2019-08-06T00:00:00Z","article_type":"original","page":"343-351.e3","publication":"Cell Metabolism","citation":{"chicago":"Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra, Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism. Elsevier, 2019. https://doi.org/10.1016/j.cmet.2019.05.010.","mla":"Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3, doi:10.1016/j.cmet.2019.05.010.","short":"R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E. Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism 30 (2019) 343–351.e3.","ista":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3.","ieee":"R. Arrojo e Drigo et al., “Age mosaicism across multiple scales in adult tissues,” Cell Metabolism, vol. 30, no. 2. Elsevier, p. 343–351.e3, 2019.","apa":"Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T., Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult tissues. Cell Metabolism. Elsevier. https://doi.org/10.1016/j.cmet.2019.05.010","ama":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 2019;30(2):343-351.e3. doi:10.1016/j.cmet.2019.05.010"},"day":"06","article_processing_charge":"No","keyword":["Cell Biology","Molecular Biology","Physiology"],"scopus_import":"1","date_created":"2022-04-07T07:45:21Z","date_updated":"2022-07-18T08:32:30Z","volume":30,"author":[{"last_name":"Arrojo e Drigo","first_name":"Rafael","full_name":"Arrojo e Drigo, Rafael"},{"full_name":"Lev-Ram, Varda","first_name":"Varda","last_name":"Lev-Ram"},{"last_name":"Tyagi","first_name":"Swati","full_name":"Tyagi, Swati"},{"full_name":"Ramachandra, Ranjan","last_name":"Ramachandra","first_name":"Ranjan"},{"full_name":"Deerinck, Thomas","last_name":"Deerinck","first_name":"Thomas"},{"full_name":"Bushong, Eric","first_name":"Eric","last_name":"Bushong"},{"last_name":"Phan","first_name":"Sebastien","full_name":"Phan, Sebastien"},{"first_name":"Victoria","last_name":"Orphan","full_name":"Orphan, Victoria"},{"full_name":"Lechene, Claude","first_name":"Claude","last_name":"Lechene"},{"full_name":"Ellisman, Mark H.","last_name":"Ellisman","first_name":"Mark H."},{"first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"publication_status":"published","publisher":"Elsevier","year":"2019","pmid":1,"extern":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.cmet.2019.05.010","quality_controlled":"1","oa":1,"external_id":{"pmid":["31178361"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cmet.2019.05.010"}],"month":"08","publication_identifier":{"issn":["1550-4131"]}},{"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201834565","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.05960","open_access":"1"}],"external_id":{"arxiv":["1902.05960"]},"month":"04","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"date_created":"2022-07-06T09:07:06Z","date_updated":"2022-07-19T09:36:08Z","volume":648,"author":[{"full_name":"Nanayakkara, Themiya","first_name":"Themiya","last_name":"Nanayakkara"},{"first_name":"Jarle","last_name":"Brinchmann","full_name":"Brinchmann, Jarle"},{"first_name":"Leindert","last_name":"Boogaard","full_name":"Boogaard, Leindert"},{"full_name":"Bouwens, Rychard","last_name":"Bouwens","first_name":"Rychard"},{"full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo","first_name":"Sebastiano"},{"full_name":"Feltre, Anna","last_name":"Feltre","first_name":"Anna"},{"last_name":"Kollatschny","first_name":"Wolfram","full_name":"Kollatschny, Wolfram"},{"full_name":"Marino, Raffaella Anna","first_name":"Raffaella Anna","last_name":"Marino"},{"last_name":"Maseda","first_name":"Michael","full_name":"Maseda, Michael"},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"},{"last_name":"Paalvast","first_name":"Mieke","full_name":"Paalvast, Mieke"},{"last_name":"Richard","first_name":"Johan","full_name":"Richard, Johan"},{"full_name":"Verhamme, Anne","last_name":"Verhamme","first_name":"Anne"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1051/0004-6361/201834565e"}]},"publication_status":"published","publisher":"EDP Sciences","year":"2019","acknowledgement":"The authors wish to thank the referee for constructive comments that improved the paper substantially. We thank the BPASS team for making the stellar population models available. We thank Elizabeth Stanway, Claus Leitherer, Daniel Schaerer, Jorick Vink, and Nell Byler for insightful discussions. We thank the Lorentz Centre and the scientific organizers of the Characterizing galaxies with spectroscopy with a view for JWST workshop held at the Lorentz Centre in 2017 October, which promoted useful discussions in the wider community. TN, JB, and RB acknowledges the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) top grant TOP1.16.057. AF acknowledges support from the ERC via an Advanced Grant under grant agreement no. 339659-MUSICOS. JB acknowledges support by Fundação para a Ciência e a Tecnologia (FCT) through national funds (UID/FIS/04434/2013) and Investigador FCT contract IF/01654/2014/CP1215/CT0003, and by FEDER through COMPETE2020 (POCI-01-0145-FEDER-007672). JR acknowledges support from the ERC Starting grant 336736 (CALENDS). This research made use of astropy (http://www.astropy.org) a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018) and pandas (McKinney 2010). Figures were generated using matplotlib (Hunter 2007) and seaborn (https://seaborn.pydata.org). Facilities: VLT (MUSE).","extern":"1","article_number":"A89","date_published":"2019-04-16T00:00:00Z","article_type":"original","publication":"Astronomy & Astrophysics","citation":{"chicago":"Nanayakkara, Themiya, Jarle Brinchmann, Leindert Boogaard, Rychard Bouwens, Sebastiano Cantalupo, Anna Feltre, Wolfram Kollatschny, et al. “Exploring He II Λ1640 Emission Line Properties at z ∼2−4.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834565.","mla":"Nanayakkara, Themiya, et al. “Exploring He II Λ1640 Emission Line Properties at z ∼2−4.” Astronomy & Astrophysics, vol. 648, A89, EDP Sciences, 2019, doi:10.1051/0004-6361/201834565.","short":"T. Nanayakkara, J. Brinchmann, L. Boogaard, R. Bouwens, S. Cantalupo, A. Feltre, W. Kollatschny, R.A. Marino, M. Maseda, J.J. Matthee, M. Paalvast, J. Richard, A. Verhamme, Astronomy & Astrophysics 648 (2019).","ista":"Nanayakkara T, Brinchmann J, Boogaard L, Bouwens R, Cantalupo S, Feltre A, Kollatschny W, Marino RA, Maseda M, Matthee JJ, Paalvast M, Richard J, Verhamme A. 2019. Exploring He II λ1640 emission line properties at z ∼2−4. Astronomy & Astrophysics. 648, A89.","apa":"Nanayakkara, T., Brinchmann, J., Boogaard, L., Bouwens, R., Cantalupo, S., Feltre, A., … Verhamme, A. (2019). Exploring He II λ1640 emission line properties at z ∼2−4. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834565","ieee":"T. Nanayakkara et al., “Exploring He II λ1640 emission line properties at z ∼2−4,” Astronomy & Astrophysics, vol. 648. EDP Sciences, 2019.","ama":"Nanayakkara T, Brinchmann J, Boogaard L, et al. Exploring He II λ1640 emission line properties at z ∼2−4. Astronomy & Astrophysics. 2019;648. doi:10.1051/0004-6361/201834565"},"day":"16","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: ISM / galaxies: star formation / galaxies: evolution / galaxies: high-redshift"],"scopus_import":"1","oa_version":"Published Version","title":"Exploring He II λ1640 emission line properties at z ∼2−4","status":"public","intvolume":" 648","_id":"11499","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Deep optical spectroscopic surveys of galaxies provide a unique opportunity to investigate rest-frame ultra-violet (UV) emission line properties of galaxies at z ∼ 2 − 4.5. Here we combine VLT/MUSE Guaranteed Time Observations of the Hubble Deep Field South, Ultra Deep Field, COSMOS, and several quasar fields with other publicly available data from VLT/VIMOS and VLT/FORS2 to construct a catalogue of He II λ1640 emitters at z ≳ 2. The deepest areas of our MUSE pointings reach a 3σ line flux limit of 3.1 × 10−19 erg s−1 cm−2. After discarding broad-line active galactic nuclei, we find 13 He II λ1640 detections from MUSE with a median MUV = −20.1 and 21 tentative He II λ1640 detections from other public surveys. Excluding Lyα, all except two galaxies in our sample show at least one other rest-UV emission line, with C III] λ1907, λ1909 being the most prominent. We use multi-wavelength data available in the Hubble legacy fields to derive basic galaxy properties of our sample through spectral energy distribution fitting techniques. Taking advantage of the high-quality spectra obtained by MUSE (∼10 − 30 h of exposure time per pointing), we use photo-ionisation models to study the rest-UV emission line diagnostics of the He II λ1640 emitters. Line ratios of our sample can be reproduced by moderately sub-solar photo-ionisation models, however, we find that including effects of binary stars lead to degeneracies in most free parameters. Even after considering extra ionising photons produced by extreme sub-solar metallicity binary stellar models, photo-ionisation models are unable to reproduce rest-frame He II λ1640 equivalent widths (∼0.2 − 10 Å), thus additional mechanisms are necessary in models to match the observed He II λ1640 properties."}],"type":"journal_article"},{"doi":"10.1051/0004-6361/201834471","language":[{"iso":"eng"}],"external_id":{"arxiv":["1905.13696"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.13696"}],"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"month":"07","author":[{"last_name":"de La Vieuville","first_name":"G.","full_name":"de La Vieuville, G."},{"last_name":"Bina","first_name":"D.","full_name":"Bina, D."},{"first_name":"R.","last_name":"Pello","full_name":"Pello, R."},{"full_name":"Mahler, G.","first_name":"G.","last_name":"Mahler"},{"full_name":"Richard, J.","first_name":"J.","last_name":"Richard"},{"last_name":"Drake","first_name":"A. B.","full_name":"Drake, A. B."},{"first_name":"E. C.","last_name":"Herenz","full_name":"Herenz, E. C."},{"full_name":"Bauer, F. E.","first_name":"F. E.","last_name":"Bauer"},{"first_name":"B.","last_name":"Clément","full_name":"Clément, B."},{"full_name":"Lagattuta, D.","first_name":"D.","last_name":"Lagattuta"},{"full_name":"Laporte, N.","last_name":"Laporte","first_name":"N."},{"full_name":"Martinez, J.","first_name":"J.","last_name":"Martinez"},{"first_name":"V.","last_name":"Patrício","full_name":"Patrício, V."},{"last_name":"Wisotzki","first_name":"L.","full_name":"Wisotzki, L."},{"last_name":"Zabl","first_name":"J.","full_name":"Zabl, J."},{"last_name":"Bouwens","first_name":"R. J.","full_name":"Bouwens, R. J."},{"full_name":"Contini, T.","first_name":"T.","last_name":"Contini"},{"first_name":"T.","last_name":"Garel","full_name":"Garel, T."},{"full_name":"Guiderdoni, B.","last_name":"Guiderdoni","first_name":"B."},{"first_name":"R. A.","last_name":"Marino","full_name":"Marino, R. A."},{"first_name":"M. V.","last_name":"Maseda","full_name":"Maseda, M. V."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"first_name":"J.","last_name":"Schaye","full_name":"Schaye, J."},{"full_name":"Soucail, G.","last_name":"Soucail","first_name":"G."}],"volume":628,"date_created":"2022-07-06T10:09:36Z","date_updated":"2022-07-19T09:36:31Z","year":"2019","acknowledgement":"We thank the anonymous referee for their critical review and useful suggestions. This work has been carried out thanks to the support of the OCEVU Labex (ANR-11-LABX-0060) and the A*MIDEX project (ANR-11-IDEX-0001-02) funded by the “Investissements d’Avenir” French government programme managed by the ANR. Partially funded by the ERC starting grant CALENDS (JR, VP, BC, JM), the Agence Nationale de la recherche bearing the reference ANR-13-BS05-0010-02 (FOGHAR), and the “Programme National de Cosmologie and Galaxies” (PNCG) of CNRS/INSU, France. GdV, RP, JR, GM, JM, BC, and VP also acknowledge support by the Programa de Cooperacion Cientifica – ECOS SUD Program C16U02. NL acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 669253), ABD acknowledges support from the ERC advanced grant “Cosmic Gas”. LW acknowledges support by the Competitive Fund of the Leibniz Association through grant SAW-2015-AIP-2, and TG acknowledges support from the European Research Council under grant agreement ERC-stg-757258 (TRIPLE).. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 060.A-9345, 094.A-0115, 095.A-0181, 096.A-0710, 097.A0269, 100.A-0249, and 294.A-5032. Also based on observations obtained with the NASA/ESA Hubble Space Telescope, retrieved from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute (STScI). STScI is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS 5-26555. This research made use of Astropy, a community-developed core Python package for Astronomy (Astropy Collaboration 2013). All plots in this paper were created using Matplotlib (Hunter 2007).","publisher":"EDP Sciences","publication_status":"published","extern":"1","article_number":"A3","date_published":"2019-07-25T00:00:00Z","citation":{"ista":"de La Vieuville G, Bina D, Pello R, Mahler G, Richard J, Drake AB, Herenz EC, Bauer FE, Clément B, Lagattuta D, Laporte N, Martinez J, Patrício V, Wisotzki L, Zabl J, Bouwens RJ, Contini T, Garel T, Guiderdoni B, Marino RA, Maseda MV, Matthee JJ, Schaye J, Soucail G. 2019. Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy & Astrophysics. 628, A3.","ieee":"G. de La Vieuville et al., “Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE,” Astronomy & Astrophysics, vol. 628. EDP Sciences, 2019.","apa":"de La Vieuville, G., Bina, D., Pello, R., Mahler, G., Richard, J., Drake, A. B., … Soucail, G. (2019). Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834471","ama":"de La Vieuville G, Bina D, Pello R, et al. Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy & Astrophysics. 2019;628. doi:10.1051/0004-6361/201834471","chicago":"La Vieuville, G. de, D. Bina, R. Pello, G. Mahler, J. Richard, A. B. Drake, E. C. Herenz, et al. “Faint End of the z ∼ 3–7 Luminosity Function of Lyman-Alpha Emitters behind Lensing Clusters Observed with MUSE.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834471.","mla":"de La Vieuville, G., et al. “Faint End of the z ∼ 3–7 Luminosity Function of Lyman-Alpha Emitters behind Lensing Clusters Observed with MUSE.” Astronomy & Astrophysics, vol. 628, A3, EDP Sciences, 2019, doi:10.1051/0004-6361/201834471.","short":"G. de La Vieuville, D. Bina, R. Pello, G. Mahler, J. Richard, A.B. Drake, E.C. Herenz, F.E. Bauer, B. Clément, D. Lagattuta, N. Laporte, J. Martinez, V. Patrício, L. Wisotzki, J. Zabl, R.J. Bouwens, T. Contini, T. Garel, B. Guiderdoni, R.A. Marino, M.V. Maseda, J.J. Matthee, J. Schaye, G. Soucail, Astronomy & Astrophysics 628 (2019)."},"publication":"Astronomy & Astrophysics","article_type":"original","article_processing_charge":"No","day":"25","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","gravitational lensing: strong / galaxies: high-redshift / dark ages","reionization","first stars / galaxies: clusters: general / galaxies: luminosity function","mass function"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11505","intvolume":" 628","title":"Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE","status":"public","abstract":[{"text":"Contact. This paper presents the results obtained with the Multi-Unit Spectroscopic Explorer (MUSE) at the ESO Very Large Telescope on the faint end of the Lyman-alpha luminosity function (LF) based on deep observations of four lensing clusters. The goal of our project is to set strong constraints on the relative contribution of the Lyman-alpha emitter (LAE) population to cosmic reionization.\r\n\r\nAims. The precise aim of the present study is to further constrain the abundance of LAEs by taking advantage of the magnification provided by lensing clusters to build a blindly selected sample of galaxies which is less biased than current blank field samples in redshift and luminosity. By construction, this sample of LAEs is complementary to those built from deep blank fields, whether observed by MUSE or by other facilities, and makes it possible to determine the shape of the LF at fainter levels, as well as its evolution with redshift.\r\n\r\nMethods. We selected a sample of 156 LAEs with redshifts between 2.9 ≤ z ≤ 6.7 and magnification-corrected luminosities in the range 39 ≲ log LLyα [erg s−1] ≲43. To properly take into account the individual differences in detection conditions between the LAEs when computing the LF, including lensing configurations, and spatial and spectral morphologies, the non-parametric 1/Vmax method was adopted. The price to pay to benefit from magnification is a reduction of the effective volume of the survey, together with a more complex analysis procedure to properly determine the effective volume Vmax for each galaxy. In this paper we present a complete procedure for the determination of the LF based on IFU detections in lensing clusters. This procedure, including some new methods for masking, effective volume integration and (individual) completeness determinations, has been fully automated when possible, and it can be easily generalized to the analysis of IFU observations in blank fields.\r\n\r\nResults. As a result of this analysis, the Lyman-alpha LF has been obtained in four different redshift bins: 2.9 < z < 6, 7, 2.9 < z < 4.0, 4.0 < z < 5.0, and 5.0 < z < 6.7 with constraints down to log LLyα = 40.5. From our data only, no significant evolution of LF mean slope can be found. When performing a Schechter analysis also including data from the literature to complete the present sample towards the brightest luminosities, a steep faint end slope was measured varying from α = −1.69−0.08+0.08 to α = −1.87−0.12+0.12 between the lowest and the highest redshift bins.\r\n\r\nConclusions. The contribution of the LAE population to the star formation rate density at z ∼ 6 is ≲50% depending on the luminosity limit considered, which is of the same order as the Lyman-break galaxy (LBG) contribution. The evolution of the LAE contribution with redshift depends on the assumed escape fraction of Lyman-alpha photons, and appears to slightly increase with increasing redshift when this fraction is conservatively set to one. Depending on the intersection between the LAE/LBG populations, the contribution of the observed galaxies to the ionizing flux may suffice to keep the universe ionized at z ∼ 6.","lang":"eng"}],"type":"journal_article"},{"scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: star formation / galaxies: statistics / galaxies: evolution / galaxies: formation / galaxies: ISM"],"day":"26","article_processing_charge":"No","publication":"Astronomy & Astrophysics","citation":{"chicago":"Sobral, David, and Jorryt J Matthee. “Predicting Lyα Escape Fractions with a Simple Observable: Lyα in Emission as an Empirically Calibrated Star Formation Rate Indicator.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201833075.","mla":"Sobral, David, and Jorryt J. Matthee. “Predicting Lyα Escape Fractions with a Simple Observable: Lyα in Emission as an Empirically Calibrated Star Formation Rate Indicator.” Astronomy & Astrophysics, vol. 623, A157, EDP Sciences, 2019, doi:10.1051/0004-6361/201833075.","short":"D. Sobral, J.J. Matthee, Astronomy & Astrophysics 623 (2019).","ista":"Sobral D, Matthee JJ. 2019. Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator. Astronomy & Astrophysics. 623, A157.","ieee":"D. Sobral and J. J. Matthee, “Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator,” Astronomy & Astrophysics, vol. 623. EDP Sciences, 2019.","apa":"Sobral, D., & Matthee, J. J. (2019). Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833075","ama":"Sobral D, Matthee JJ. Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator. Astronomy & Astrophysics. 2019;623. doi:10.1051/0004-6361/201833075"},"article_type":"original","date_published":"2019-03-26T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Lyman-α (Lyα) is intrinsically the brightest line emitted from active galaxies. While it originates from many physical processes, for star-forming galaxies the intrinsic Lyα luminosity is a direct tracer of the Lyman-continuum (LyC) radiation produced by the most massive O- and early-type B-stars (M⋆ ≳ 10 M⊙) with lifetimes of a few Myrs. As such, Lyα luminosity should be an excellent instantaneous star formation rate (SFR) indicator. However, its resonant nature and susceptibility to dust as a rest-frame UV photon makes Lyα very hard to interpret due to the uncertain Lyα escape fraction, fesc, Lyα. Here we explore results from the CAlibrating LYMan-α with Hα (CALYMHA) survey at z = 2.2, follow-up of Lyα emitters (LAEs) at z = 2.2 − 2.6 and a z ∼ 0−0.3 compilation of LAEs to directly measure fesc, Lyα with Hα. We derive a simple empirical relation that robustly retrieves fesc, Lyα as a function of Lyα rest-frame EW (EW0): fesc,Lyα = 0.0048 EW0[Å] ± 0.05 and we show that it constrains a well-defined anti-correlation between ionisation efficiency (ξion) and dust extinction in LAEs. Observed Lyα luminosities and EW0 are easy measurable quantities at high redshift, thus making our relation a practical tool to estimate intrinsic Lyα and LyC luminosities under well controlled and simple assumptions. Our results allow observed Lyα luminosities to be used to compute SFRs for LAEs at z ∼ 0−2.6 within ±0.2 dex of the Hα dust corrected SFRs. We apply our empirical SFR(Lyα,EW0) calibration to several sources at z ≥ 2.6 to find that star-forming LAEs have SFRs typically ranging from 0.1 to 20 M⊙ yr−1 and that our calibration might be even applicable for the most luminous LAEs within the epoch of re-ionisation. Our results imply high ionisation efficiencies (log10[ξion/Hz erg−1] = 25.4−25.6) and low dust content in LAEs across cosmic time, and will be easily tested with future observations with JWST which can obtain Hα and Hβ measurements for high-redshift LAEs."}],"_id":"11507","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator","status":"public","intvolume":" 623","oa_version":"Published Version","month":"03","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"external_id":{"arxiv":["1803.08923"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1803.08923","open_access":"1"}],"quality_controlled":"1","doi":"10.1051/0004-6361/201833075","language":[{"iso":"eng"}],"article_number":"A157","extern":"1","year":"2019","acknowledgement":"We thank the anonymous referees for multiple comments and suggestions which have improved the manuscript. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt et al. 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007) and ASTROPY (Astropy Collaboration 2013) packages, and the TOPCAT analysis program (Taylor 2013). The results and samples of LAEs used for this paper are publicly available (see e.g. Sobral et al. 2017, 2018a) and we also provide the toy model used as a PYTHON script.","publication_status":"published","publisher":"EDP Sciences","author":[{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"}],"date_updated":"2022-07-19T09:37:20Z","date_created":"2022-07-06T11:08:16Z","volume":623},{"article_number":"140","extern":"1","year":"2019","acknowledgement":"We are grateful to the referee for providing a constructive report. L.A.B. wants to thank Madusha L.P. Gunawardhana for her help with platefit. Based on observations collected at the European Southern Observatory under ESO programme(s): 094.A-2089(B), 095.A-0010(A), 096.A-0045(A), and 096.A-0045(B). This paper makes use of the following ALMA data: ADS/JAO.ALMA#2016.1.00324.L. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), NSC and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.\r\n\r\n\"Este trabajo contó con el apoyo de CONICYT+Programa de Astronomía+ Fondo CHINA-CONICYT\" J.G-L. acknowledges partial support from ALMA-CONICYT project 31160033. F.E.B. acknowledges support from CONICYT grant Basal AFB-170002 (FEB), and the Ministry of Economy, Development, and Tourism's Millennium Science Initiative through grant IC120009, awarded to The Millennium Institute of Astrophysics, MAS (FEB). J.B. acknowledges support by Fundação para a Ciência e a Tecnologia (FCT) through national funds (UID/FIS/04434/2013) and Investigador FCT contract IF/01654/2014/CP1215/CT0003., and by FEDER through COMPETE2020 (POCI-01-0145-FEDER-007672). T.D-S. acknowledges support from ALMA-CONYCIT project 31130005 and FONDECYT project 1151239. J.H. acknowledges support of the VIDI research programme with project number 639.042.611, which is (partly) financed by the Netherlands Organization for Scientific Research (NWO). D.R. acknowledges support from the National Science Foundation under grant No. AST-1614213. I.R.S. acknowledges support from the ERC Advanced Grant DUSTYGAL (321334) and STFC (ST/P000541/1)\r\n\r\nWork on Gnuastro has been funded by the Japanese MEXT scholarship and its Grant-in-Aid for Scientific Research (21244012, 24253003), the ERC advanced grant 339659-MUSICOS, European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement No. 721463 to the SUNDIAL ITN, and from the Spanish MINECO under grant No. AYA2016-76219-P.","publication_status":"published","publisher":"IOP Publishing","author":[{"last_name":"Boogaard","first_name":"Leindert A.","full_name":"Boogaard, Leindert A."},{"last_name":"Decarli","first_name":"Roberto","full_name":"Decarli, Roberto"},{"full_name":"González-López, Jorge","last_name":"González-López","first_name":"Jorge"},{"full_name":"van der Werf, Paul","last_name":"van der Werf","first_name":"Paul"},{"full_name":"Walter, Fabian","first_name":"Fabian","last_name":"Walter"},{"full_name":"Bouwens, Rychard","first_name":"Rychard","last_name":"Bouwens"},{"first_name":"Manuel","last_name":"Aravena","full_name":"Aravena, Manuel"},{"full_name":"Carilli, Chris","first_name":"Chris","last_name":"Carilli"},{"full_name":"Bauer, Franz Erik","first_name":"Franz Erik","last_name":"Bauer"},{"full_name":"Brinchmann, Jarle","last_name":"Brinchmann","first_name":"Jarle"},{"full_name":"Contini, Thierry","first_name":"Thierry","last_name":"Contini"},{"first_name":"Pierre","last_name":"Cox","full_name":"Cox, Pierre"},{"last_name":"da Cunha","first_name":"Elisabete","full_name":"da Cunha, Elisabete"},{"first_name":"Emanuele","last_name":"Daddi","full_name":"Daddi, Emanuele"},{"full_name":"Díaz-Santos, Tanio","last_name":"Díaz-Santos","first_name":"Tanio"},{"full_name":"Hodge, Jacqueline","first_name":"Jacqueline","last_name":"Hodge"},{"last_name":"Inami","first_name":"Hanae","full_name":"Inami, Hanae"},{"first_name":"Rob","last_name":"Ivison","full_name":"Ivison, Rob"},{"first_name":"Michael","last_name":"Maseda","full_name":"Maseda, Michael"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"last_name":"Oesch","first_name":"Pascal","full_name":"Oesch, Pascal"},{"full_name":"Popping, Gergö","last_name":"Popping","first_name":"Gergö"},{"last_name":"Riechers","first_name":"Dominik","full_name":"Riechers, Dominik"},{"full_name":"Schaye, Joop","last_name":"Schaye","first_name":"Joop"},{"full_name":"Schouws, Sander","last_name":"Schouws","first_name":"Sander"},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"first_name":"Axel","last_name":"Weiss","full_name":"Weiss, Axel"},{"last_name":"Wisotzki","first_name":"Lutz","full_name":"Wisotzki, Lutz"},{"full_name":"Bacon, Roland","last_name":"Bacon","first_name":"Roland"},{"first_name":"Paulo C.","last_name":"Cortes","full_name":"Cortes, Paulo C."},{"full_name":"Rix, Hans-Walter","first_name":"Hans-Walter","last_name":"Rix"},{"full_name":"Somerville, Rachel S.","first_name":"Rachel S.","last_name":"Somerville"},{"full_name":"Swinbank, Mark","last_name":"Swinbank","first_name":"Mark"},{"full_name":"Wagg, Jeff","first_name":"Jeff","last_name":"Wagg"}],"date_updated":"2022-07-19T09:50:55Z","date_created":"2022-07-06T13:31:35Z","volume":882,"month":"09","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"oa":1,"external_id":{"arxiv":["1903.09167"]},"main_file_link":[{"url":"https://arxiv.org/abs/1903.09167","open_access":"1"}],"quality_controlled":"1","doi":"10.3847/1538-4357/ab3102","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We discuss the nature and physical properties of gas-mass selected galaxies in the ALMA spectroscopic survey (ASPECS) of the Hubble Ultra Deep Field (HUDF). We capitalize on the deep optical integral-field spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE) HUDF Survey and multiwavelength data to uniquely associate all 16 line emitters, detected in the ALMA data without preselection, with rotational transitions of carbon monoxide (CO). We identify 10 as CO(2–1) at 1 < z < 2, 5 as CO(3–2) at 2 < z < 3, and 1 as CO(4–3) at z = 3.6. Using the MUSE data as a prior, we identify two additional CO(2–1) emitters, increasing the total sample size to 18. We infer metallicities consistent with (super-)solar for the CO-detected galaxies at z ≤ 1.5, motivating our choice of a Galactic conversion factor between CO luminosity and molecular gas mass for these galaxies. Using deep Chandra imaging of the HUDF, we determine an X-ray AGN fraction of 20% and 60% among the CO emitters at z ∼ 1.4 and z ∼ 2.6, respectively. Being a CO-flux-limited survey, ASPECS-LP detects molecular gas in galaxies on, above, and below the main sequence (MS) at z ∼ 1.4. For stellar masses ≥1010 (1010.5) ${M}_{\\odot }$, we detect about 40% (50%) of all galaxies in the HUDF at 1 < z < 2 (2 < z < 3). The combination of ALMA and MUSE integral-field spectroscopy thus enables an unprecedented view of MS galaxies during the peak of galaxy formation."}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11514","status":"public","title":"The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy","intvolume":" 882","oa_version":"Preprint","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"day":"11","article_processing_charge":"No","publication":"The Astrophysical Journal","citation":{"chicago":"Boogaard, Leindert A., Roberto Decarli, Jorge González-López, Paul van der Werf, Fabian Walter, Rychard Bouwens, Manuel Aravena, et al. “The ALMA Spectroscopic Survey in the HUDF: Nature and Physical Properties of Gas-Mass Selected Galaxies Using MUSE Spectroscopy.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab3102.","short":"L.A. Boogaard, R. Decarli, J. González-López, P. van der Werf, F. Walter, R. Bouwens, M. Aravena, C. Carilli, F.E. Bauer, J. Brinchmann, T. Contini, P. Cox, E. da Cunha, E. Daddi, T. Díaz-Santos, J. Hodge, H. Inami, R. Ivison, M. Maseda, J.J. Matthee, P. Oesch, G. Popping, D. Riechers, J. Schaye, S. Schouws, I. Smail, A. Weiss, L. Wisotzki, R. Bacon, P.C. Cortes, H.-W. Rix, R.S. Somerville, M. Swinbank, J. Wagg, The Astrophysical Journal 882 (2019).","mla":"Boogaard, Leindert A., et al. “The ALMA Spectroscopic Survey in the HUDF: Nature and Physical Properties of Gas-Mass Selected Galaxies Using MUSE Spectroscopy.” The Astrophysical Journal, vol. 882, no. 2, 140, IOP Publishing, 2019, doi:10.3847/1538-4357/ab3102.","apa":"Boogaard, L. A., Decarli, R., González-López, J., van der Werf, P., Walter, F., Bouwens, R., … Wagg, J. (2019). The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab3102","ieee":"L. A. Boogaard et al., “The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy,” The Astrophysical Journal, vol. 882, no. 2. IOP Publishing, 2019.","ista":"Boogaard LA, Decarli R, González-López J, van der Werf P, Walter F, Bouwens R, Aravena M, Carilli C, Bauer FE, Brinchmann J, Contini T, Cox P, da Cunha E, Daddi E, Díaz-Santos T, Hodge J, Inami H, Ivison R, Maseda M, Matthee JJ, Oesch P, Popping G, Riechers D, Schaye J, Schouws S, Smail I, Weiss A, Wisotzki L, Bacon R, Cortes PC, Rix H-W, Somerville RS, Swinbank M, Wagg J. 2019. The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. The Astrophysical Journal. 882(2), 140.","ama":"Boogaard LA, Decarli R, González-López J, et al. The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. The Astrophysical Journal. 2019;882(2). doi:10.3847/1538-4357/ab3102"},"article_type":"original","date_published":"2019-09-11T00:00:00Z"},{"article_type":"original","publication":"The Astrophysical Journal","citation":{"chicago":"Marino, Raffaella Anna, Sebastiano Cantalupo, Gabriele Pezzulli, Simon J. Lilly, Sofia Gallego, Ruari Mackenzie, Jorryt J Matthee, et al. “A Giant Lyα Nebula and a Small-Scale Clumpy Outflow in the System of the Exotic Quasar J0952+0114 Unveiled by MUSE.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab2881.","mla":"Marino, Raffaella Anna, et al. “A Giant Lyα Nebula and a Small-Scale Clumpy Outflow in the System of the Exotic Quasar J0952+0114 Unveiled by MUSE.” The Astrophysical Journal, vol. 880, no. 1, 47, IOP Publishing, 2019, doi:10.3847/1538-4357/ab2881.","short":"R.A. Marino, S. Cantalupo, G. Pezzulli, S.J. Lilly, S. Gallego, R. Mackenzie, J.J. Matthee, J. Brinchmann, N. Bouché, A. Feltre, S. Muzahid, I. Schroetter, S.D. Johnson, T. Nanayakkara, The Astrophysical Journal 880 (2019).","ista":"Marino RA, Cantalupo S, Pezzulli G, Lilly SJ, Gallego S, Mackenzie R, Matthee JJ, Brinchmann J, Bouché N, Feltre A, Muzahid S, Schroetter I, Johnson SD, Nanayakkara T. 2019. A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE. The Astrophysical Journal. 880(1), 47.","ieee":"R. A. Marino et al., “A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE,” The Astrophysical Journal, vol. 880, no. 1. IOP Publishing, 2019.","apa":"Marino, R. A., Cantalupo, S., Pezzulli, G., Lilly, S. J., Gallego, S., Mackenzie, R., … Nanayakkara, T. (2019). A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab2881","ama":"Marino RA, Cantalupo S, Pezzulli G, et al. A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE. The Astrophysical Journal. 2019;880(1). doi:10.3847/1538-4357/ab2881"},"date_published":"2019-07-24T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","day":"24","article_processing_charge":"No","title":"A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE","status":"public","intvolume":" 880","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11516","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"The well-known quasar SDSS J095253.83+011421.9 (J0952+0114) at z = 3.02 has one of the most peculiar spectra discovered so far, showing the presence of narrow Lyα and broad metal emission lines. Although recent studies have suggested that a proximate damped Lyα absorption (PDLA) system causes this peculiar spectrum, the origin of the gas associated with the PDLA is unknown. Here we report the results of observations with the Multi Unit Spectroscopic Explorer (MUSE) that reveal a new giant (≈100 physical kpc) Lyα nebula. The detailed analysis of the Lyα velocity, velocity dispersion, and surface brightness profiles suggests that the J0952+0114 Lyα nebula shares similar properties with other QSO nebulae previously detected with MUSE, implying that the PDLA in J0952+0144 is covering only a small fraction of the solid angle of the QSO emission. We also detected bright and spectrally narrow C iv λ1550 and He ii λ1640 extended emission around J0952+0114 with velocity centroids similar to the peak of the extended and central narrow Lyα emission. The presence of a peculiarly bright, unresolved, and relatively broad He ii λ1640 emission in the central region at exactly the same PDLA redshift hints at the possibility that the PDLA originates in a clumpy outflow with a bulk velocity of about 500 km s−1. The smaller velocity dispersion of the large-scale Lyα emission suggests that the high-speed outflow is confined to the central region. Lastly, the derived spatially resolved He ii/Lyα and C iv/Lyα maps show a positive gradient with the distance to the QSO, hinting at a non-homogeneous distribution of the ionization parameter."}],"issue":"1","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1906.06347","open_access":"1"}],"external_id":{"arxiv":["1906.06347"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ab2881","month":"07","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"publication_status":"published","publisher":"IOP Publishing","year":"2019","acknowledgement":"We thank Lutz Wisotzki for stimulating discussions. This work is based on observations taken at ESO/VLT in Paranal and we would like to thank the ESO staff for their assistance and support during the MUSE GTO campaigns. This work was supported by the Swiss National Science Foundation. This research made use of Astropy, a community-developed core PYTHON package for astronomy (Astropy Collaboration et al. 2013), NumPy and SciPy (Oliphant 2007), Matplotlib (Hunter 2007), IPython (Perez & Granger 2007), and of the NASA Astrophysics Data System Bibliographic Services. S.C. and G.P. gratefully acknowledge support from Swiss National Science Foundation grant PP00P2−163824. A.F. acknowledges support from the ERC via Advanced Grant under grants agreement no. 339659-MUSICOS. J.B. acknowledges support by FCT/MCTES through national funds by grant UID/FIS/04434/2019 and through Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. S.D.J. is supported by a NASA Hubble Fellowship (HST-HF2-51375.001-A). T.N. acknowledges the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) top grant TOP1.16.057.","date_created":"2022-07-06T13:50:33Z","date_updated":"2022-08-18T10:20:18Z","volume":880,"author":[{"full_name":"Marino, Raffaella Anna","first_name":"Raffaella Anna","last_name":"Marino"},{"last_name":"Cantalupo","first_name":"Sebastiano","full_name":"Cantalupo, Sebastiano"},{"last_name":"Pezzulli","first_name":"Gabriele","full_name":"Pezzulli, Gabriele"},{"full_name":"Lilly, Simon J.","last_name":"Lilly","first_name":"Simon J."},{"full_name":"Gallego, Sofia","last_name":"Gallego","first_name":"Sofia"},{"full_name":"Mackenzie, Ruari","last_name":"Mackenzie","first_name":"Ruari"},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"},{"full_name":"Brinchmann, Jarle","first_name":"Jarle","last_name":"Brinchmann"},{"last_name":"Bouché","first_name":"Nicolas","full_name":"Bouché, Nicolas"},{"last_name":"Feltre","first_name":"Anna","full_name":"Feltre, Anna"},{"full_name":"Muzahid, Sowgat","last_name":"Muzahid","first_name":"Sowgat"},{"full_name":"Schroetter, Ilane","last_name":"Schroetter","first_name":"Ilane"},{"full_name":"Johnson, Sean D.","first_name":"Sean D.","last_name":"Johnson"},{"last_name":"Nanayakkara","first_name":"Themiya","full_name":"Nanayakkara, Themiya"}],"article_number":"47","extern":"1"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","day":"21","article_processing_charge":"No","article_type":"original","publication":"The Astrophysical Journal","citation":{"apa":"Matthee, J. J., Sobral, D., Boogaard, L. A., Röttgering, H., Vallini, L., Ferrara, A., … Mobasher, B. (2019). Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab2f81","ieee":"J. J. Matthee et al., “Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization,” The Astrophysical Journal, vol. 881, no. 2. IOP Publishing, 2019.","ista":"Matthee JJ, Sobral D, Boogaard LA, Röttgering H, Vallini L, Ferrara A, Paulino-Afonso A, Boone F, Schaerer D, Mobasher B. 2019. Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization. The Astrophysical Journal. 881(2), 124.","ama":"Matthee JJ, Sobral D, Boogaard LA, et al. Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization. The Astrophysical Journal. 2019;881(2). doi:10.3847/1538-4357/ab2f81","chicago":"Matthee, Jorryt J, D. Sobral, L. A. Boogaard, H. Röttgering, L. Vallini, A. Ferrara, A. Paulino-Afonso, F. Boone, D. Schaerer, and B. Mobasher. “Resolved UV and [C Ii] Structures of Luminous Galaxies within the Epoch of Reionization.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab2f81.","short":"J.J. Matthee, D. Sobral, L.A. Boogaard, H. Röttgering, L. Vallini, A. Ferrara, A. Paulino-Afonso, F. Boone, D. Schaerer, B. Mobasher, The Astrophysical Journal 881 (2019).","mla":"Matthee, Jorryt J., et al. “Resolved UV and [C Ii] Structures of Luminous Galaxies within the Epoch of Reionization.” The Astrophysical Journal, vol. 881, no. 2, 124, IOP Publishing, 2019, doi:10.3847/1538-4357/ab2f81."},"date_published":"2019-08-21T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We present new deep ALMA and Hubble Space Telescope (HST)/WFC3 observations of MASOSA and VR7, two luminous Lyα emitters (LAEs) at z = 6.5, for which the UV continuum levels differ by a factor of four. No IR dust continuum emission is detected in either, indicating little amounts of obscured star formation and/or high dust temperatures. MASOSA, with a UV luminosity M1500 = −20.9, compact size, and very high Lyα ${\\mathrm{EW}}_{0}\\approx 145\\,\\mathring{\\rm A} $, is undetected in [C ii] to a limit of L[C ii] < 2.2 × 107 L⊙, implying a metallicity Z ≲ 0.07 Z⊙. Intriguingly, our HST data indicate a red UV slope β = −1.1 ± 0.7, at odds with the low dust content. VR7, which is a bright (M1500 = −22.4) galaxy with moderate color (β = −1.4 ± 0.3) and Lyα EW0 = 34 Å, is clearly detected in [C ii] emission (S/N = 15). VR7's rest-frame UV morphology can be described by two components separated by ≈1.5 kpc and is globally more compact than the [C ii] emission. The global [C ii]/UV ratio indicates Z ≈ 0.2 Z⊙, but there are large variations in the UV/[C ii] ratio on kiloparsec scales. We also identify diffuse, possibly outflowing, [C ii]-emitting gas at ≈100 km s−1 with respect to the peak. VR7 appears to be assembling its components at a slightly more evolved stage than other luminous LAEs, with outflows already shaping its direct environment at z ∼ 7. Our results further indicate that the global [C ii]−UV relation steepens at SFR < 30 M⊙ yr−1, naturally explaining why the [C ii]/UV ratio is anticorrelated with Lyα EW in many, but not all, observed LAEs."}],"issue":"2","status":"public","title":"Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization","intvolume":" 881","_id":"11515","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"08","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1903.08171"]},"main_file_link":[{"url":"https://arxiv.org/abs/1903.08171","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ab2f81","article_number":"124","extern":"1","publication_status":"published","publisher":"IOP Publishing","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions. We thank Max Gronke for comments on an earlier version of this paper. L.V. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 746119. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2017.1.01451.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada), NSC and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. Based on observations obtained with the Very Large Telescope, programs 294.A-5018, 097.A-0943, and 99.A-0462. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained (from the Data Archive) at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program No. 14699.","year":"2019","date_updated":"2022-08-18T10:19:48Z","date_created":"2022-07-06T13:38:15Z","volume":881,"author":[{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"},{"last_name":"Sobral","first_name":"D.","full_name":"Sobral, D."},{"full_name":"Boogaard, L. A.","first_name":"L. A.","last_name":"Boogaard"},{"last_name":"Röttgering","first_name":"H.","full_name":"Röttgering, H."},{"last_name":"Vallini","first_name":"L.","full_name":"Vallini, L."},{"full_name":"Ferrara, A.","last_name":"Ferrara","first_name":"A."},{"full_name":"Paulino-Afonso, A.","first_name":"A.","last_name":"Paulino-Afonso"},{"last_name":"Boone","first_name":"F.","full_name":"Boone, F."},{"last_name":"Schaerer","first_name":"D.","full_name":"Schaerer, D."},{"full_name":"Mobasher, B.","last_name":"Mobasher","first_name":"B."}]},{"date_published":"2019-06-04T00:00:00Z","article_type":"original","publication":"The Astrophysical Journal","citation":{"short":"E. Wang, S.J. Lilly, G. Pezzulli, J.J. Matthee, The Astrophysical Journal 877 (2019).","mla":"Wang, Enci, et al. “On the Elevation and Suppression of Star Formation within Galaxies.” The Astrophysical Journal, vol. 877, no. 2, 132, IOP Publishing, 2019, doi:10.3847/1538-4357/ab1c5b.","chicago":"Wang, Enci, Simon J. Lilly, Gabriele Pezzulli, and Jorryt J Matthee. “On the Elevation and Suppression of Star Formation within Galaxies.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab1c5b.","ama":"Wang E, Lilly SJ, Pezzulli G, Matthee JJ. On the elevation and suppression of star formation within galaxies. The Astrophysical Journal. 2019;877(2). doi:10.3847/1538-4357/ab1c5b","ieee":"E. Wang, S. J. Lilly, G. Pezzulli, and J. J. Matthee, “On the elevation and suppression of star formation within galaxies,” The Astrophysical Journal, vol. 877, no. 2. IOP Publishing, 2019.","apa":"Wang, E., Lilly, S. J., Pezzulli, G., & Matthee, J. J. (2019). On the elevation and suppression of star formation within galaxies. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab1c5b","ista":"Wang E, Lilly SJ, Pezzulli G, Matthee JJ. 2019. On the elevation and suppression of star formation within galaxies. The Astrophysical Journal. 877(2), 132."},"day":"04","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","oa_version":"Preprint","status":"public","title":"On the elevation and suppression of star formation within galaxies","intvolume":" 877","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11517","abstract":[{"lang":"eng","text":"To understand star formation in galaxies, we investigate the star formation rate (SFR) surface density (ΣSFR) profiles for galaxies, based on a well-defined sample of 976 star-forming MaNGA galaxies. We find that the typical ΣSFR profiles within 1.5Re of normal SF galaxies can be well described by an exponential function for different stellar mass intervals, while the sSFR profile shows positive gradients, especially for more massive SF galaxies. This is due to the more pronounced central cores or bulges rather than the onset of a `quenching' process. While galaxies that lie significantly above (or below) the star formation main sequence (SFMS) show overall an elevation (or suppression) of ΣSFR at all radii, this central elevation (or suppression) is more pronounced in more massive galaxies. The degree of central enhancement and suppression is quite symmetric, suggesting that both the elevation and suppression of star formation are following the same physical processes. Furthermore, we find that the dispersion in ΣSFR within and across the population is found to be tightly correlated with the inferred gas depletion time, whether based on the stellar surface mass density or the orbital dynamical time. This suggests that we are seeing the response of a simple gas-regulator system to variations in the accretion rate. This is explored using a heuristic model that can quantitatively explain the dependence of σ(ΣSFR) on gas depletion timescale. Variations in accretion rate are progressively more damped out in regions of low star-formation efficiency leading to a reduced amplitude of variations in star-formation."}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ab1c5b","quality_controlled":"1","external_id":{"arxiv":["1901.10276"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10276"}],"oa":1,"month":"06","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"date_created":"2022-07-07T08:38:24Z","date_updated":"2022-08-18T10:19:08Z","volume":877,"author":[{"full_name":"Wang, Enci","last_name":"Wang","first_name":"Enci"},{"last_name":"Lilly","first_name":"Simon J.","full_name":"Lilly, Simon J."},{"first_name":"Gabriele","last_name":"Pezzulli","full_name":"Pezzulli, Gabriele"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee"}],"publication_status":"published","publisher":"IOP Publishing","acknowledgement":"We are grateful to the anonymous referee for their thoughtful and constructive review of the paper and their several suggestions (including the analysis of Section 3.4), which have improved the paper. This research has been supported by the Swiss National Science Foundation.\r\n\r\nFunding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High-Performance Computing at the University of Utah. The SDSS website is www.sdss.org.\r\n\r\nSDSS-IV is managed by the Astrophysical Research Consortium for the Participating Institutions of the SDSS Collaboration, including the Brazilian Participation Group, the Carnegie Institution for Science, Carnegie Mellon University, the Chilean Participation Group, the French Participation Group, Harvard-Smithsonian Center for Astrophysics, Instituto de Astrofísica de Canarias, the Johns Hopkins University, Kavli Institute for the Physics and Mathematics of the Universe (IPMU)/University of Tokyo, Lawrence Berkeley National Laboratory, Leibniz Institut für Astrophysik Potsdam (AIP), Max-Planck-Institut für Astronomie (MPIA Heidelberg), Max-Planck-Institut für Astrophysik (MPA Garching), Max-Planck-Institut für Extraterrestrische Physik (MPE), National Astronomical Observatory of China, New Mexico State University, New York University, University of Notre Dame, Observatário Nacional/MCTI, the Ohio State University, Pennsylvania State University, Shanghai Astronomical Observatory, United Kingdom Participation Group, Universidad Nacional Autónoma de México, University of Arizona, University of Colorado Boulder, University of Oxford, University of Portsmouth, University of Utah, University of Virginia, University of Washington, University of Wisconsin, Vanderbilt University, and Yale University","year":"2019","extern":"1","article_number":"132"},{"article_type":"original","page":"555-573","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"mla":"Khostovan, A. A., et al. “The Clustering of Typical Ly α Emitters from z ∼ 2.5–6: Host Halo Masses Depend on Ly α and UV Luminosities.” Monthly Notices of the Royal Astronomical Society, vol. 489, no. 1, Oxford University Press, 2019, pp. 555–73, doi:10.1093/mnras/stz2149.","short":"A.A. Khostovan, D. Sobral, B. Mobasher, J.J. Matthee, R.K. Cochrane, N. Chartab, M. Jafariyazani, A. Paulino-Afonso, S. Santos, J. Calhau, Monthly Notices of the Royal Astronomical Society 489 (2019) 555–573.","chicago":"Khostovan, A A, D Sobral, B Mobasher, Jorryt J Matthee, R K Cochrane, N Chartab, M Jafariyazani, A Paulino-Afonso, S Santos, and J Calhau. “The Clustering of Typical Ly α Emitters from z ∼ 2.5–6: Host Halo Masses Depend on Ly α and UV Luminosities.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz2149.","ama":"Khostovan AA, Sobral D, Mobasher B, et al. The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. Monthly Notices of the Royal Astronomical Society. 2019;489(1):555-573. doi:10.1093/mnras/stz2149","ista":"Khostovan AA, Sobral D, Mobasher B, Matthee JJ, Cochrane RK, Chartab N, Jafariyazani M, Paulino-Afonso A, Santos S, Calhau J. 2019. The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. Monthly Notices of the Royal Astronomical Society. 489(1), 555–573.","apa":"Khostovan, A. A., Sobral, D., Mobasher, B., Matthee, J. J., Cochrane, R. K., Chartab, N., … Calhau, J. (2019). The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz2149","ieee":"A. A. Khostovan et al., “The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities,” Monthly Notices of the Royal Astronomical Society, vol. 489, no. 1. Oxford University Press, pp. 555–573, 2019."},"date_published":"2019-10-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: star formation","cosmology: observations","large-scale structure of Universe"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities","intvolume":" 489","_id":"11535","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the clustering and halo properties of ∼5000 Ly α-selected emission-line galaxies (LAEs) from the Slicing COSMOS 4K (SC4K) and from archival NB497 imaging of SA22 split in 15 discrete redshift slices between z ∼ 2.5 and 6. We measure clustering lengths of r0 ∼ 3–6 h−1 Mpc and typical halo masses of ∼1011 M⊙ for our narrowband-selected LAEs with typical LLy α ∼ 1042–43 erg s−1. The intermediate-band-selected LAEs are observed to have r0 ∼ 3.5–15 h−1 Mpc with typical halo masses of ∼1011–12 M⊙ and typical LLy α ∼ 1043–43.6 erg s−1. We find a strong, redshift-independent correlation between halo mass and Ly α luminosity normalized by the characteristic Ly α luminosity, L⋆(z). The faintest LAEs (L ∼ 0.1 L⋆(z)) typically identified by deep narrowband surveys are found in 1010 M⊙ haloes and the brightest LAEs (L ∼ 7 L⋆(z)) are found in ∼5 × 1012 M⊙ haloes. A dependency on the rest-frame 1500 Å UV luminosity, MUV, is also observed where the halo masses increase from 1011 to 1013 M⊙ for MUV ∼ −19 to −23.5 mag. Halo mass is also observed to increase from 109.8 to 1012 M⊙ for dust-corrected UV star formation rates from ∼0.6 to 10 M⊙ yr−1 and continues to increase up to 1013 M⊙ in halo mass, where the majority of those sources are active galactic nuclei. All the trends we observe are found to be redshift independent. Our results reveal that LAEs are the likely progenitors of a wide range of galaxies depending on their luminosity, from dwarf-like, to Milky Way-type, to bright cluster galaxies. LAEs therefore provide unique insight into the early formation and evolution of the galaxies we observe in the local Universe."}],"issue":"1","quality_controlled":"1","external_id":{"arxiv":["1811.00556"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.00556","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stz2149","month":"10","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous referee for their useful comments and suggestions that helped improve this study. AAK acknowledges that this work was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX16AO92H. JM acknowledges support from the ETH Zwicky fellowship. RKC acknowledges funding from STFC via a studentship. APA acknowledges support from the Fundac¸ao para a Ci ˜ encia e a Tecnologia FCT through the fellowship PD/BD/52706/2014 and the research grant UID/FIS/04434/2013. JC and SS both acknowledge their support from the Lancaster University PhD Fellowship. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY, SCIPY, MATPLOTLIB, SCIKIT-LEARN, and ASTROPY packages, as well as the TOPCAT analysis program. The SC4K samples used in this paper are all publicly available for use by the community (Sobral et al. 2018a). The catalogue is also available on the COSMOS IPAC website (https://irsa.ipac.caltech.edu/data/COSMOS/overview.html).","year":"2019","date_created":"2022-07-07T13:01:03Z","date_updated":"2022-08-19T06:38:42Z","volume":489,"author":[{"full_name":"Khostovan, A A","last_name":"Khostovan","first_name":"A A"},{"last_name":"Sobral","first_name":"D","full_name":"Sobral, D"},{"full_name":"Mobasher, B","last_name":"Mobasher","first_name":"B"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee"},{"full_name":"Cochrane, R K","first_name":"R K","last_name":"Cochrane"},{"first_name":"N","last_name":"Chartab","full_name":"Chartab, N"},{"last_name":"Jafariyazani","first_name":"M","full_name":"Jafariyazani, M"},{"last_name":"Paulino-Afonso","first_name":"A","full_name":"Paulino-Afonso, A"},{"first_name":"S","last_name":"Santos","full_name":"Santos, S"},{"last_name":"Calhau","first_name":"J","full_name":"Calhau, J"}],"extern":"1"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11541","title":"On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components","status":"public","intvolume":" 482","abstract":[{"lang":"eng","text":"We present new Hubble Space Telescope (HST)/WFC3 observations and re-analyse VLT data to unveil the continuum, variability, and rest-frame ultraviolet (UV) lines of the multiple UV clumps of the most luminous Lyα emitter at z = 6.6, CR7 (COSMOS Redshift 7). Our re-reduced, flux-calibrated X-SHOOTER spectra of CR7 reveal an He II emission line in observations obtained along the major axis of Lyα emission with the best seeing conditions. He II is spatially offset by ≈+0.8 arcsec from the peak of Lyα emission, and it is found towards clump B. Our WFC3 grism spectra detects the UV continuum of CR7’s clump A, yielding a power law with β=−2.5+0.6−0.7 and MUV=−21.87+0.25−0.20. No significant variability is found for any of the UV clumps on their own, but there is tentative (≈2.2 σ) brightening of CR7 in F110W as a whole from 2012 to 2017. HST grism data fail to robustly detect rest-frame UV lines in any of the clumps, implying fluxes ≲2×10−17 erg s−1 cm−2 (3σ). We perform CLOUDY modelling to constrain the metallicity and the ionizing nature of CR7. CR7 seems to be actively forming stars without any clear active galactic nucleus activity in clump A, consistent with a metallicity of ∼0.05–0.2 Z⊙. Component C or an interclump component between B and C may host a high ionization source. Our results highlight the need for spatially resolved information to study the formation and assembly of early galaxies."}],"issue":"2","type":"journal_article","date_published":"2019-01-01T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"ama":"Sobral D, Matthee JJ, Brammer G, et al. On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components. Monthly Notices of the Royal Astronomical Society. 2019;482(2):2422-2441. doi:10.1093/mnras/sty2779","ieee":"D. Sobral et al., “On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components,” Monthly Notices of the Royal Astronomical Society, vol. 482, no. 2. Oxford University Press, pp. 2422–2441, 2019.","apa":"Sobral, D., Matthee, J. J., Brammer, G., Ferrara, A., Alegre, L., Röttgering, H., … Darvish, B. (2019). On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty2779","ista":"Sobral D, Matthee JJ, Brammer G, Ferrara A, Alegre L, Röttgering H, Schaerer D, Mobasher B, Darvish B. 2019. On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components. Monthly Notices of the Royal Astronomical Society. 482(2), 2422–2441.","short":"D. Sobral, J.J. Matthee, G. Brammer, A. Ferrara, L. Alegre, H. Röttgering, D. Schaerer, B. Mobasher, B. Darvish, Monthly Notices of the Royal Astronomical Society 482 (2019) 2422–2441.","mla":"Sobral, David, et al. “On the Nature and Physical Conditions of the Luminous Ly α Emitter CR7 and Its Rest-Frame UV Components.” Monthly Notices of the Royal Astronomical Society, vol. 482, no. 2, Oxford University Press, 2019, pp. 2422–41, doi:10.1093/mnras/sty2779.","chicago":"Sobral, David, Jorryt J Matthee, Gabriel Brammer, Andrea Ferrara, Lara Alegre, Huub Röttgering, Daniel Schaerer, Bahram Mobasher, and Behnam Darvish. “On the Nature and Physical Conditions of the Luminous Ly α Emitter CR7 and Its Rest-Frame UV Components.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/sty2779."},"article_type":"original","page":"2422-2441","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","cosmology: observations","dark ages","reionization","first stars","early Universe"],"author":[{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"full_name":"Brammer, Gabriel","first_name":"Gabriel","last_name":"Brammer"},{"last_name":"Ferrara","first_name":"Andrea","full_name":"Ferrara, Andrea"},{"first_name":"Lara","last_name":"Alegre","full_name":"Alegre, Lara"},{"full_name":"Röttgering, Huub","first_name":"Huub","last_name":"Röttgering"},{"first_name":"Daniel","last_name":"Schaerer","full_name":"Schaerer, Daniel"},{"full_name":"Mobasher, Bahram","first_name":"Bahram","last_name":"Mobasher"},{"full_name":"Darvish, Behnam","first_name":"Behnam","last_name":"Darvish"}],"date_created":"2022-07-08T10:40:05Z","date_updated":"2022-08-19T06:49:36Z","volume":482,"acknowledgement":"We thank the anonymous reviewer for the numerous detailed comments that led us to greatly improve the quality, extent, and statistical robustness of this work. DS acknowledges financial support from the Netherlands Organisation for Scientific research through a Veni fellowship. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. AF acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program, grant number NNX12AE20G and the National Science Foundation, grant number 1716907. We are thankful for several discussions and constructive comments from Johannes Zabl, Eros Vanzella, Bo Milvang-Jensen, Henry McCracken, Max Gronke, Mark Dijkstra, Richard Ellis, and Nicolas Laporte. We also thank Umar Burhanudin and Izzy Garland for taking part in the XGAL internship in Lancaster and for exploring the HST grism data independently. Based on observations obtained with HST/WFC3 programs 12578, 14495, and 14596. Based on observations of the National Japanese Observatory with the Suprime-Cam on the Subaru telescope (S14A-086) on the big island of Hawaii. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, 092.A 0786, 093.A-0561, 097.A0043, 097.A-0943, 098.A-0819, 298.A-5012, and 179.A-2005, and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. The authors acknowledge the award of service time (SW2014b20) on the William Herschel Telescope (WHT). WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. This research was supported by the Munich Institute for Astro- and Particle Physics of the DFG cluster of excellence ‘Origin and Structure of the Universe’. We have benefitted immensely from the public available programming language PYTHON, including NUMPY and SCIPY (Jones et al. 2001; Van Der Walt, Colbert & Varoquaux 2011), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2013). This research has made use of the VizieR catalogue access tool, CDS, Strasbourg, France. All data used for this paper are publicly available, and we make all reduced data available with the refereed paper.","year":"2019","publication_status":"published","publisher":"Oxford University Press","extern":"1","doi":"10.1093/mnras/sty2779","language":[{"iso":"eng"}],"external_id":{"arxiv":["1710.08422"]},"main_file_link":[{"url":"https://arxiv.org/abs/1710.08422","open_access":"1"}],"oa":1,"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]}},{"extern":"1","volume":484,"date_created":"2022-07-08T07:48:31Z","date_updated":"2022-08-19T06:42:43Z","author":[{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"},{"full_name":"Schaye, Joop","last_name":"Schaye","first_name":"Joop"}],"publisher":"Oxford University Press","publication_status":"published","acknowledgement":"JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Camila Correa for help analysing snipshot merger trees. We thank the anonymous referee for constructive comments. We also thank Jarle Brinchmann, Rob Crain, Antonios Katsianis, Paola Popesso, and David Sobral for discussions and suggestions. We also thank the participants of the Lorentz Center workshop ‘A Decade of the Star-Forming Main Sequence’ held on 2017 September 4–8, for discussions and ideas. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, and SCIPY (Hunter 2007) packages and the TOPCAT analysis tool (Taylor 2013).","year":"2019","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1093/mnras/stz030","quality_controlled":"1","external_id":{"arxiv":["1805.05956"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.05956"}],"issue":"1","abstract":[{"lang":"eng","text":"Observations have revealed that the star formation rate (SFR) and stellar mass (Mstar) of star-forming galaxies follow a tight relation known as the galaxy main sequence. However, what physical information is encoded in this relation is under debate. Here, we use the EAGLE cosmological hydrodynamical simulation to study the mass dependence, evolution, and origin of scatter in the SFR–Mstar relation. At z = 0, we find that the scatter decreases slightly with stellar mass from 0.35 dex at Mstar ≈ 109 M⊙ to 0.30 dex at Mstar ≳ 1010.5 M⊙. The scatter decreases from z = 0 to z = 5 by 0.05 dex at Mstar ≳ 1010 M⊙ and by 0.15 dex for lower masses. We show that the scatter at z = 0.1 originates from a combination of fluctuations on short time-scales (ranging from 0.2–2 Gyr) that are presumably associated with self-regulation from cooling, star formation, and outflows, but is dominated by long time-scale (∼10 Gyr) variations related to differences in halo formation times. Shorter time-scale fluctuations are relatively more important for lower mass galaxies. At high masses, differences in black hole formation efficiency cause additional scatter, but also diminish the scatter caused by different halo formation times. While individual galaxies cross the main sequence multiple times during their evolution, they fluctuate around tracks associated with their halo properties, i.e. galaxies above/below the main sequence at z = 0.1 tend to have been above/below the main sequence for ≫1 Gyr."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 484","status":"public","title":"The origin of scatter in the star formation rate–stellar mass relation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11540","article_processing_charge":"No","day":"01","keyword":["Space and Planetary Science","Astronomy and Astrophysics : galaxies: evolution","galaxies: formation","galaxies: star formation","cosmology: theory"],"scopus_import":"1","date_published":"2019-03-01T00:00:00Z","page":"915-932","article_type":"original","citation":{"chicago":"Matthee, Jorryt J, and Joop Schaye. “The Origin of Scatter in the Star Formation Rate–Stellar Mass Relation.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz030.","mla":"Matthee, Jorryt J., and Joop Schaye. “The Origin of Scatter in the Star Formation Rate–Stellar Mass Relation.” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 1, Oxford University Press, 2019, pp. 915–32, doi:10.1093/mnras/stz030.","short":"J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society 484 (2019) 915–932.","ista":"Matthee JJ, Schaye J. 2019. The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. 484(1), 915–932.","ieee":"J. J. Matthee and J. Schaye, “The origin of scatter in the star formation rate–stellar mass relation,” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 1. Oxford University Press, pp. 915–932, 2019.","apa":"Matthee, J. J., & Schaye, J. (2019). The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz030","ama":"Matthee JJ, Schaye J. The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. 2019;484(1):915-932. doi:10.1093/mnras/stz030"},"publication":"Monthly Notices of the Royal Astronomical Society"},{"citation":{"ama":"Huber D, Chaplin WJ, Chontos A, et al. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. 2019;157(6). doi:10.3847/1538-3881/ab1488","ista":"Huber D et al. 2019. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. 157(6), 245.","apa":"Huber, D., Chaplin, W. J., Chontos, A., Kjeldsen, H., Christensen-Dalsgaard, J., Bedding, T. R., … Zohrabi, F. (2019). A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. IOP Publishing. https://doi.org/10.3847/1538-3881/ab1488","ieee":"D. Huber et al., “A hot Saturn orbiting an oscillating late subgiant discovered by TESS,” The Astronomical Journal, vol. 157, no. 6. IOP Publishing, 2019.","mla":"Huber, Daniel, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” The Astronomical Journal, vol. 157, no. 6, 245, IOP Publishing, 2019, doi:10.3847/1538-3881/ab1488.","short":"D. Huber, W.J. Chaplin, A. Chontos, H. Kjeldsen, J. Christensen-Dalsgaard, T.R. Bedding, W. Ball, R. Brahm, N. Espinoza, T. Henning, A. Jordán, P. Sarkis, E. Knudstrup, S. Albrecht, F. Grundahl, M.F. Andersen, P.L. Pallé, I. Crossfield, B. Fulton, A.W. Howard, H.T. Isaacson, L.M. Weiss, R. Handberg, M.N. Lund, A.M. Serenelli, J. Rørsted Mosumgaard, A. Stokholm, A. Bieryla, L.A. Buchhave, D.W. Latham, S.N. Quinn, E. Gaidos, T. Hirano, G.R. Ricker, R.K. Vanderspek, S. Seager, J.M. Jenkins, J.N. Winn, H.M. Antia, T. Appourchaux, S. Basu, K.J. Bell, O. Benomar, A. Bonanno, D.L. Buzasi, T.L. Campante, Z. Çelik Orhan, E. Corsaro, M.S. Cunha, G.R. Davies, S. Deheuvels, S.K. Grunblatt, A. Hasanzadeh, M.P. Di Mauro, R. A. García, P. Gaulme, L. Girardi, J.A. Guzik, M. Hon, C. Jiang, T. Kallinger, S.D. Kawaler, J.S. Kuszlewicz, Y. Lebreton, T. Li, M. Lucas, M.S. Lundkvist, A.W. Mann, S. Mathis, S. Mathur, A. Mazumdar, T.S. Metcalfe, A. Miglio, M.J.P. F. G. Monteiro, B. Mosser, A. Noll, B. Nsamba, J.M. Joel Ong, S. Örtel, F. Pereira, P. Ranadive, C. Régulo, T.S. Rodrigues, I.W. Roxburgh, V.S. Aguirre, B. Smalley, M. Schofield, S.G. Sousa, K.G. Stassun, D. Stello, J. Tayar, T.R. White, K. Verma, M. Vrard, M. Yıldız, D. Baker, M. Bazot, C. Beichmann, C. Bergmann, L.A. Bugnet, B. Cale, R. Carlino, S.M. Cartwright, J.L. Christiansen, D.R. Ciardi, O. Creevey, J.A. Dittmann, J.-D.D. Nascimento, V.V. Eylen, G. Fürész, J. Gagné, P. Gao, K. Gazeas, F. Giddens, O.J. Hall, S. Hekker, M.J. Ireland, N. Latouf, D. LeBrun, A.M. Levine, W. Matzko, E. Natinsky, E. Page, P. Plavchan, M. Mansouri-Samani, S. McCauliff, S.E. Mullally, B. Orenstein, A.G. Soto, M. Paegert, J.L. van Saders, C. Schnaible, D.R. Soderblom, R. Szabó, A. Tanner, C.G. Tinney, J. Teske, A. Thomas, R. Trampedach, D. Wright, T.T. Yuan, F. Zohrabi, The Astronomical Journal 157 (2019).","chicago":"Huber, Daniel, William J. Chaplin, Ashley Chontos, Hans Kjeldsen, Jørgen Christensen-Dalsgaard, Timothy R. Bedding, Warrick Ball, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” The Astronomical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-3881/ab1488."},"publication":"The Astronomical Journal","article_type":"original","date_published":"2019-05-30T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_processing_charge":"No","day":"30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11616","intvolume":" 157","status":"public","title":"A hot Saturn orbiting an oscillating late subgiant discovered by TESS","oa_version":"Preprint","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We present the discovery of HD 221416 b, the first transiting planet identified by the Transiting Exoplanet Survey Satellite (TESS) for which asteroseismology of the host star is possible. HD 221416 b (HIP 116158, TOI-197) is a bright (V = 8.2 mag), spectroscopically classified subgiant that oscillates with an average frequency of about 430 μHz and displays a clear signature of mixed modes. The oscillation amplitude confirms that the redder TESS bandpass compared to Kepler has a small effect on the oscillations, supporting the expected yield of thousands of solar-like oscillators with TESS 2 minute cadence observations. Asteroseismic modeling yields a robust determination of the host star radius (R⋆ = 2.943 ± 0.064 R⊙), mass (M⋆ = 1.212 ± 0.074 M⊙), and age (4.9 ± 1.1 Gyr), and demonstrates that it has just started ascending the red-giant branch. Combining asteroseismology with transit modeling and radial-velocity observations, we show that the planet is a \"hot Saturn\" (Rp = 9.17 ± 0.33 R⊕) with an orbital period of ∼14.3 days, irradiance of F = 343 ± 24 F⊕, and moderate mass (Mp = 60.5 ± 5.7 M⊕) and density (ρp = 0.431 ± 0.062 g cm−3). The properties of HD 221416 b show that the host-star metallicity–planet mass correlation found in sub-Saturns (4–8 R⊕) does not extend to larger radii, indicating that planets in the transition between sub-Saturns and Jupiters follow a relatively narrow range of densities. With a density measured to ∼15%, HD 221416 b is one of the best characterized Saturn-size planets to date, augmenting the small number of known transiting planets around evolved stars and demonstrating the power of TESS to characterize exoplanets and their host stars using asteroseismology."}],"main_file_link":[{"url":"https://arxiv.org/abs/1901.01643","open_access":"1"}],"external_id":{"arxiv":["1901.01643"]},"oa":1,"quality_controlled":"1","doi":"10.3847/1538-3881/ab1488","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-6256"]},"month":"05","acknowledgement":"The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the indigenous Hawai'ian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We thank Andrei Tokovinin for helpful information on the Speckle observations obtained with SOAR. D.H. acknowledges support by the National Aeronautics and Space Administration through the TESS Guest Investigator Program (80NSSC18K1585) and by the National Science Foundation (AST-1717000). A.C. acknowledges support by the National Science Foundation under the Graduate Research Fellowship Program. W.J.C., W.H.B., A.M., O.J.H., and G.R.D. acknowledge support from the Science and Technology Facilities Council and UK Space Agency. H.K. and F.G. acknowledge support from the European Social Fund via the Lithuanian Science Council grant No. 09.3.3-LMT-K-712-01-0103. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (grant DNRF106). A.J. acknowledges support from FONDECYT project 1171208, CONICYT project BASAL AFB-170002, and by the Ministry for the Economy, Development, and Tourism's Programa Iniciativa Científica Milenio through grant IC 120009, awarded to the Millennium Institute of Astrophysics (MAS). R.B. acknowledges support from FONDECYT Post-doctoral Fellowship Project 3180246, and from the Millennium Institute of Astrophysics (MAS). A.M.S. is supported by grants ESP2017-82674-R (MINECO) and SGR2017-1131 (AGAUR). R.A.G. and L.B. acknowledge the support of the PLATO grant from the CNES. The research leading to the presented results has received funding from the European Research Council under the European Community's Seventh Framework Programme (FP72007-2013)ERC grant agreement No. 338251 (StellarAges). S.M. acknowledges support from the European Research Council through the SPIRE grant 647383. This work was also supported by FCT (Portugal) through national funds and by FEDER through COMPETE2020 by these grants: UID/FIS/04434/2013 and POCI-01-0145-FEDER-007672, PTDC/FIS-AST/30389/2017, and POCI-01-0145-FEDER-030389. T.L.C. acknowledges support from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 792848 (PULSATION). E.C. is funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 664931. V.S.A. acknowledges support from the Independent Research Fund Denmark (Research grant 7027-00096B). D.S. acknowledges support from the Australian Research Council. S.B. acknowledges NASA grant NNX16AI09G and NSF grant AST-1514676. T.R.W. acknowledges support from the Australian Research Council through grant DP150100250. A.M. acknowledges support from the ERC Consolidator Grant funding scheme (project ASTEROCHRONOMETRY, G.A. n. 772293). S.M. acknowledges support from the Ramon y Cajal fellowship number RYC-2015-17697. M.S.L. is supported by the Carlsberg Foundation (grant agreement No. CF17-0760). A.M. and P.R. acknowledge support from the HBCSE-NIUS programme. J.K.T. and J.T. acknowledge that support for this work was provided by NASA through Hubble Fellowship grants HST-HF2-51399.001 and HST-HF2-51424.001 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. T.S.R. acknowledges financial support from Premiale 2015 MITiC (PI B. Garilli). This project has been supported by the NKFIH K-115709 grant and the Lendület Program of the Hungarian Academy of Sciences, project No. LP2018-7/2018.\r\n\r\nBased on observations made with the Hertzsprung SONG telescope operated on the Spanish Observatorio del Teide on the island of Tenerife by the Aarhus and Copenhagen Universities and by the Instituto de Astrofísica de Canarias. Funding for the TESS mission is provided by NASA's Science Mission directorate. We acknowledge the use of public TESS Alert data from pipelines at the TESS Science Office and at the TESS Science Processing Operations Center. This research has made use of the Exoplanet Follow-up Observation Program website, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program. This paper includes data collected by the TESS mission, which are publicly available from the Mikulski Archive for Space Telescopes (MAST).\r\n\r\nSoftware: Astropy (Astropy Collaboration et al. 2018), Matplotlib (Hunter 2007), DIAMONDS (Corsaro & De Ridder 2014), isoclassify (Huber et al. 2017), EXOFASTv2 (Eastman 2017), ktransit (Barclay 2018).","year":"2019","publisher":"IOP Publishing","publication_status":"published","author":[{"full_name":"Huber, Daniel","last_name":"Huber","first_name":"Daniel"},{"first_name":"William J.","last_name":"Chaplin","full_name":"Chaplin, William J."},{"last_name":"Chontos","first_name":"Ashley","full_name":"Chontos, Ashley"},{"full_name":"Kjeldsen, Hans","last_name":"Kjeldsen","first_name":"Hans"},{"first_name":"Jørgen","last_name":"Christensen-Dalsgaard","full_name":"Christensen-Dalsgaard, Jørgen"},{"first_name":"Timothy R.","last_name":"Bedding","full_name":"Bedding, Timothy R."},{"first_name":"Warrick","last_name":"Ball","full_name":"Ball, Warrick"},{"full_name":"Brahm, Rafael","last_name":"Brahm","first_name":"Rafael"},{"full_name":"Espinoza, Nestor","last_name":"Espinoza","first_name":"Nestor"},{"last_name":"Henning","first_name":"Thomas","full_name":"Henning, Thomas"},{"first_name":"Andrés","last_name":"Jordán","full_name":"Jordán, Andrés"},{"first_name":"Paula","last_name":"Sarkis","full_name":"Sarkis, Paula"},{"last_name":"Knudstrup","first_name":"Emil","full_name":"Knudstrup, Emil"},{"last_name":"Albrecht","first_name":"Simon","full_name":"Albrecht, Simon"},{"last_name":"Grundahl","first_name":"Frank","full_name":"Grundahl, Frank"},{"last_name":"Andersen","first_name":"Mads Fredslund","full_name":"Andersen, Mads Fredslund"},{"last_name":"Pallé","first_name":"Pere L.","full_name":"Pallé, Pere L."},{"full_name":"Crossfield, Ian","first_name":"Ian","last_name":"Crossfield"},{"full_name":"Fulton, Benjamin","last_name":"Fulton","first_name":"Benjamin"},{"full_name":"Howard, Andrew W.","last_name":"Howard","first_name":"Andrew W."},{"last_name":"Isaacson","first_name":"Howard T.","full_name":"Isaacson, Howard T."},{"last_name":"Weiss","first_name":"Lauren M.","full_name":"Weiss, Lauren M."},{"last_name":"Handberg","first_name":"Rasmus","full_name":"Handberg, Rasmus"},{"full_name":"Lund, Mikkel N.","last_name":"Lund","first_name":"Mikkel N."},{"full_name":"Serenelli, Aldo M.","first_name":"Aldo M.","last_name":"Serenelli"},{"full_name":"Rørsted Mosumgaard, Jakob","last_name":"Rørsted Mosumgaard","first_name":"Jakob"},{"first_name":"Amalie","last_name":"Stokholm","full_name":"Stokholm, Amalie"},{"full_name":"Bieryla, Allyson","first_name":"Allyson","last_name":"Bieryla"},{"last_name":"Buchhave","first_name":"Lars A.","full_name":"Buchhave, Lars A."},{"full_name":"Latham, David W.","first_name":"David W.","last_name":"Latham"},{"first_name":"Samuel N.","last_name":"Quinn","full_name":"Quinn, Samuel N."},{"first_name":"Eric","last_name":"Gaidos","full_name":"Gaidos, Eric"},{"full_name":"Hirano, Teruyuki","first_name":"Teruyuki","last_name":"Hirano"},{"first_name":"George R.","last_name":"Ricker","full_name":"Ricker, George R."},{"full_name":"Vanderspek, Roland K.","last_name":"Vanderspek","first_name":"Roland K."},{"full_name":"Seager, Sara","first_name":"Sara","last_name":"Seager"},{"first_name":"Jon M.","last_name":"Jenkins","full_name":"Jenkins, Jon M."},{"last_name":"Winn","first_name":"Joshua N.","full_name":"Winn, Joshua N."},{"full_name":"Antia, H. M.","first_name":"H. M.","last_name":"Antia"},{"full_name":"Appourchaux, Thierry","first_name":"Thierry","last_name":"Appourchaux"},{"first_name":"Sarbani","last_name":"Basu","full_name":"Basu, Sarbani"},{"full_name":"Bell, Keaton J.","first_name":"Keaton J.","last_name":"Bell"},{"last_name":"Benomar","first_name":"Othman","full_name":"Benomar, Othman"},{"full_name":"Bonanno, Alfio","first_name":"Alfio","last_name":"Bonanno"},{"full_name":"Buzasi, Derek L.","first_name":"Derek L.","last_name":"Buzasi"},{"last_name":"Campante","first_name":"Tiago L.","full_name":"Campante, Tiago L."},{"last_name":"Çelik Orhan","first_name":"Z.","full_name":"Çelik Orhan, Z."},{"last_name":"Corsaro","first_name":"Enrico","full_name":"Corsaro, Enrico"},{"last_name":"Cunha","first_name":"Margarida S.","full_name":"Cunha, Margarida S."},{"first_name":"Guy R.","last_name":"Davies","full_name":"Davies, Guy R."},{"full_name":"Deheuvels, Sebastien","first_name":"Sebastien","last_name":"Deheuvels"},{"full_name":"Grunblatt, Samuel K.","last_name":"Grunblatt","first_name":"Samuel K."},{"full_name":"Hasanzadeh, Amir","last_name":"Hasanzadeh","first_name":"Amir"},{"full_name":"Di Mauro, Maria Pia","first_name":"Maria Pia","last_name":"Di Mauro"},{"full_name":"A. García, Rafael","last_name":"A. García","first_name":"Rafael"},{"last_name":"Gaulme","first_name":"Patrick","full_name":"Gaulme, Patrick"},{"first_name":"Léo","last_name":"Girardi","full_name":"Girardi, Léo"},{"full_name":"Guzik, Joyce A.","first_name":"Joyce A.","last_name":"Guzik"},{"first_name":"Marc","last_name":"Hon","full_name":"Hon, Marc"},{"first_name":"Chen","last_name":"Jiang","full_name":"Jiang, Chen"},{"full_name":"Kallinger, Thomas","first_name":"Thomas","last_name":"Kallinger"},{"first_name":"Steven D.","last_name":"Kawaler","full_name":"Kawaler, Steven D."},{"full_name":"Kuszlewicz, James S.","last_name":"Kuszlewicz","first_name":"James S."},{"first_name":"Yveline","last_name":"Lebreton","full_name":"Lebreton, Yveline"},{"full_name":"Li, Tanda","last_name":"Li","first_name":"Tanda"},{"last_name":"Lucas","first_name":"Miles","full_name":"Lucas, Miles"},{"full_name":"Lundkvist, Mia S.","last_name":"Lundkvist","first_name":"Mia S."},{"full_name":"Mann, Andrew W.","last_name":"Mann","first_name":"Andrew W."},{"last_name":"Mathis","first_name":"Stéphane","full_name":"Mathis, Stéphane"},{"full_name":"Mathur, Savita","first_name":"Savita","last_name":"Mathur"},{"first_name":"Anwesh","last_name":"Mazumdar","full_name":"Mazumdar, Anwesh"},{"full_name":"Metcalfe, Travis S.","first_name":"Travis S.","last_name":"Metcalfe"},{"last_name":"Miglio","first_name":"Andrea","full_name":"Miglio, Andrea"},{"full_name":"F. G. Monteiro, Mário J. P.","last_name":"F. G. Monteiro","first_name":"Mário J. P."},{"first_name":"Benoit","last_name":"Mosser","full_name":"Mosser, Benoit"},{"full_name":"Noll, Anthony","last_name":"Noll","first_name":"Anthony"},{"full_name":"Nsamba, Benard","last_name":"Nsamba","first_name":"Benard"},{"full_name":"Joel Ong, Jia Mian","last_name":"Joel Ong","first_name":"Jia Mian"},{"full_name":"Örtel, S.","first_name":"S.","last_name":"Örtel"},{"first_name":"Filipe","last_name":"Pereira","full_name":"Pereira, Filipe"},{"full_name":"Ranadive, Pritesh","last_name":"Ranadive","first_name":"Pritesh"},{"first_name":"Clara","last_name":"Régulo","full_name":"Régulo, Clara"},{"full_name":"Rodrigues, Thaíse S.","last_name":"Rodrigues","first_name":"Thaíse S."},{"full_name":"Roxburgh, Ian W.","first_name":"Ian W.","last_name":"Roxburgh"},{"first_name":"Victor Silva","last_name":"Aguirre","full_name":"Aguirre, Victor Silva"},{"last_name":"Smalley","first_name":"Barry","full_name":"Smalley, Barry"},{"full_name":"Schofield, Mathew","first_name":"Mathew","last_name":"Schofield"},{"full_name":"Sousa, Sérgio G.","first_name":"Sérgio G.","last_name":"Sousa"},{"last_name":"Stassun","first_name":"Keivan G.","full_name":"Stassun, Keivan G."},{"full_name":"Stello, Dennis","last_name":"Stello","first_name":"Dennis"},{"full_name":"Tayar, Jamie","first_name":"Jamie","last_name":"Tayar"},{"full_name":"White, Timothy R.","first_name":"Timothy R.","last_name":"White"},{"last_name":"Verma","first_name":"Kuldeep","full_name":"Verma, Kuldeep"},{"full_name":"Vrard, Mathieu","first_name":"Mathieu","last_name":"Vrard"},{"first_name":"M.","last_name":"Yıldız","full_name":"Yıldız, M."},{"full_name":"Baker, David","first_name":"David","last_name":"Baker"},{"full_name":"Bazot, Michaël","first_name":"Michaël","last_name":"Bazot"},{"first_name":"Charles","last_name":"Beichmann","full_name":"Beichmann, Charles"},{"full_name":"Bergmann, Christoph","first_name":"Christoph","last_name":"Bergmann"},{"orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle"},{"full_name":"Cale, Bryson","last_name":"Cale","first_name":"Bryson"},{"full_name":"Carlino, Roberto","last_name":"Carlino","first_name":"Roberto"},{"last_name":"Cartwright","first_name":"Scott M.","full_name":"Cartwright, Scott M."},{"last_name":"Christiansen","first_name":"Jessie L.","full_name":"Christiansen, Jessie L."},{"first_name":"David R.","last_name":"Ciardi","full_name":"Ciardi, David R."},{"first_name":"Orlagh","last_name":"Creevey","full_name":"Creevey, Orlagh"},{"full_name":"Dittmann, Jason A.","first_name":"Jason A.","last_name":"Dittmann"},{"last_name":"Nascimento","first_name":"Jose-Dias Do","full_name":"Nascimento, Jose-Dias Do"},{"first_name":"Vincent Van","last_name":"Eylen","full_name":"Eylen, Vincent Van"},{"full_name":"Fürész, Gabor","first_name":"Gabor","last_name":"Fürész"},{"full_name":"Gagné, Jonathan","last_name":"Gagné","first_name":"Jonathan"},{"full_name":"Gao, Peter","last_name":"Gao","first_name":"Peter"},{"full_name":"Gazeas, Kosmas","last_name":"Gazeas","first_name":"Kosmas"},{"full_name":"Giddens, Frank","first_name":"Frank","last_name":"Giddens"},{"last_name":"Hall","first_name":"Oliver J.","full_name":"Hall, Oliver J."},{"last_name":"Hekker","first_name":"Saskia","full_name":"Hekker, Saskia"},{"last_name":"Ireland","first_name":"Michael J.","full_name":"Ireland, Michael J."},{"last_name":"Latouf","first_name":"Natasha","full_name":"Latouf, Natasha"},{"last_name":"LeBrun","first_name":"Danny","full_name":"LeBrun, Danny"},{"full_name":"Levine, Alan M.","first_name":"Alan M.","last_name":"Levine"},{"full_name":"Matzko, William","first_name":"William","last_name":"Matzko"},{"first_name":"Eva","last_name":"Natinsky","full_name":"Natinsky, Eva"},{"first_name":"Emma","last_name":"Page","full_name":"Page, Emma"},{"full_name":"Plavchan, Peter","first_name":"Peter","last_name":"Plavchan"},{"first_name":"Masoud","last_name":"Mansouri-Samani","full_name":"Mansouri-Samani, Masoud"},{"last_name":"McCauliff","first_name":"Sean","full_name":"McCauliff, Sean"},{"first_name":"Susan E.","last_name":"Mullally","full_name":"Mullally, Susan E."},{"full_name":"Orenstein, Brendan","last_name":"Orenstein","first_name":"Brendan"},{"full_name":"Soto, Aylin Garcia","last_name":"Soto","first_name":"Aylin Garcia"},{"first_name":"Martin","last_name":"Paegert","full_name":"Paegert, Martin"},{"first_name":"Jennifer L.","last_name":"van Saders","full_name":"van Saders, Jennifer L."},{"full_name":"Schnaible, Chloe","last_name":"Schnaible","first_name":"Chloe"},{"full_name":"Soderblom, David R.","first_name":"David R.","last_name":"Soderblom"},{"full_name":"Szabó, Róbert","first_name":"Róbert","last_name":"Szabó"},{"first_name":"Angelle","last_name":"Tanner","full_name":"Tanner, Angelle"},{"full_name":"Tinney, C. G.","last_name":"Tinney","first_name":"C. G."},{"full_name":"Teske, Johanna","last_name":"Teske","first_name":"Johanna"},{"full_name":"Thomas, Alexandra","first_name":"Alexandra","last_name":"Thomas"},{"full_name":"Trampedach, Regner","last_name":"Trampedach","first_name":"Regner"},{"full_name":"Wright, Duncan","last_name":"Wright","first_name":"Duncan"},{"full_name":"Yuan, Thomas T.","first_name":"Thomas T.","last_name":"Yuan"},{"first_name":"Farzaneh","last_name":"Zohrabi","full_name":"Zohrabi, Farzaneh"}],"volume":157,"date_created":"2022-07-18T14:29:07Z","date_updated":"2022-08-22T07:38:34Z","article_number":"245","extern":"1"},{"oa_version":"Preprint","_id":"11613","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler","intvolume":" 6","abstract":[{"lang":"eng","text":"Over 2,000 stars were observed for 1 month with a high enough cadence in order to look for acoustic modes during the survey phase of the Kepler mission. Solar-like oscillations have been detected in about 540 stars. The question of why no oscillations were detected in the remaining stars is still open. Previous works explained the non-detection of modes with the high level of magnetic activity of the stars. However, the sample of stars studied contained some classical pulsators and red giants that could have biased the results. In this work, we revisit this analysis on a cleaner sample of main-sequence solar-like stars that consists of 1,014 stars. First we compute the predicted amplitude of the modes of that sample and for the stars with detected oscillation and compare it to the noise at high frequency in the power spectrum. We find that the stars with detected modes have an amplitude to noise ratio larger than 0.94. We measure reliable rotation periods and the associated photometric magnetic index for 684 stars out of the full sample and in particular for 323 stars where the amplitude of the modes is predicted to be high enough to be detected. We find that among these 323 stars 32% of them have a level of magnetic activity larger than the Sun during its maximum activity, explaining the non-detection of acoustic modes. Interestingly, magnetic activity cannot be the primary reason responsible for the absence of detectable modes in the remaining 68% of the stars without acoustic modes detected and with reliable rotation periods. Thus, we investigate metallicity, inclination angle of the rotation axis, and binarity as possible causes of low mode amplitudes. Using spectroscopic observations for a subsample, we find that a low metallicity could be the reason for suppressed modes. No clear correlation with binarity nor inclination is found. We also derive the lower limit for our photometric activity index (of 20–30 ppm) below which rotation and magnetic activity are not detected. Finally, with our analysis we conclude that stars with a photometric activity index larger than 2,000 ppm have 98.3% probability of not having oscillations detected."}],"type":"journal_article","date_published":"2019-07-10T00:00:00Z","publication":"Frontiers in Astronomy and Space Sciences","citation":{"ama":"Mathur S, García RA, Bugnet LA, Santos ÂRG, Santiago N, Beck PG. Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler. Frontiers in Astronomy and Space Sciences. 2019;6. doi:10.3389/fspas.2019.00046","ieee":"S. Mathur, R. A. García, L. A. Bugnet, Â. R. G. Santos, N. Santiago, and P. G. Beck, “Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler,” Frontiers in Astronomy and Space Sciences, vol. 6. Frontiers Media, 2019.","apa":"Mathur, S., García, R. A., Bugnet, L. A., Santos, Â. R. G., Santiago, N., & Beck, P. G. (2019). Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler. Frontiers in Astronomy and Space Sciences. Frontiers Media. https://doi.org/10.3389/fspas.2019.00046","ista":"Mathur S, García RA, Bugnet LA, Santos ÂRG, Santiago N, Beck PG. 2019. Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler. Frontiers in Astronomy and Space Sciences. 6, 46.","short":"S. Mathur, R.A. García, L.A. Bugnet, Â.R.G. Santos, N. Santiago, P.G. Beck, Frontiers in Astronomy and Space Sciences 6 (2019).","mla":"Mathur, Savita, et al. “Revisiting the Impact of Stellar Magnetic Activity on the Detectability of Solar-like Oscillations by Kepler.” Frontiers in Astronomy and Space Sciences, vol. 6, 46, Frontiers Media, 2019, doi:10.3389/fspas.2019.00046.","chicago":"Mathur, Savita, Rafael A. García, Lisa Annabelle Bugnet, Ângela R.G. Santos, Netsha Santiago, and Paul G. Beck. “Revisiting the Impact of Stellar Magnetic Activity on the Detectability of Solar-like Oscillations by Kepler.” Frontiers in Astronomy and Space Sciences. Frontiers Media, 2019. https://doi.org/10.3389/fspas.2019.00046."},"article_type":"original","day":"10","article_processing_charge":"No","scopus_import":"1","keyword":["Astronomy and Astrophysics"],"author":[{"full_name":"Mathur, Savita","first_name":"Savita","last_name":"Mathur"},{"first_name":"Rafael A.","last_name":"García","full_name":"García, Rafael A."},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle"},{"full_name":"Santos, Ângela R.G.","last_name":"Santos","first_name":"Ângela R.G."},{"first_name":"Netsha","last_name":"Santiago","full_name":"Santiago, Netsha"},{"full_name":"Beck, Paul G.","first_name":"Paul G.","last_name":"Beck"}],"date_created":"2022-07-18T14:00:36Z","date_updated":"2022-08-22T07:29:55Z","volume":6,"year":"2019","acknowledgement":"This paper includes data collected by the Kepler mission. Funding for the Kepler mission is provided by the NASA Science Mission directorate. Some of the data presented in this paper were obtained from the Mikulski Archive for Space Telescopes (MAST). STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Partly Based on observations obtained with the HERMES spectrograph on the Mercator Telescope, which was supported by the Research Foundation—Flanders (FWO), Belgium, the Research Council of KU Leuven, Belgium, the Fonds National de la Recherche Scientifique (F.R.S.-FNRS), Belgium, the Royal Observatory of Belgium, the Observatoire de Genève, Switzerland, and the Thüringer Landessternwarte Tautenburg, Germany. SM acknowledges support by the National Aeronautics and Space Administration under Grant NNX15AF13G, by the National Science Foundation grant AST-1411685, and the Ramon y Cajal fellowship number RYC-2015-17697. RG acknowledges the support from PLATO and GOLF CNES grants. ÂS acknowledges the support from National Aeronautics and Space Administration under Grant NNX17AF27G. PB acknowledges the support of the MINECO under the fellowship program Juan de la Cierva Incorporacion (IJCI-2015-26034).","publication_status":"published","publisher":"Frontiers Media","extern":"1","article_number":"46","doi":"10.3389/fspas.2019.00046","language":[{"iso":"eng"}],"external_id":{"arxiv":["1907.01415"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.01415","open_access":"1"}],"quality_controlled":"1","month":"07","publication_identifier":{"eissn":["2296-987X"]}},{"extern":"1","acknowledgement":"Funding for this Discovery mission is provided by NASA’s Science mission Directorate. We thank the entire Kepler team without whom this investigation would not be possible. DS is the recipient of an Australian Research Council Future Fellowship (project number FT1400147). RAG acknowledges the support from CNES. SM acknowledges support from NASA grant NNX15AF13G, NSF grant AST-1411685, and the Ramon y Cajal fellowship number RYC-2015-17697. ILC acknowledges scholarship support from the University of Sydney. We would like to thank Nicholas Barbara and Timothy Bedding for providing us with a list of variable stars that helped to validate a number of detections in this study. We also thank the group at the University of Sydney for fruitful discussions. Finally, we gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan Xp GPU used for this research.","year":"2019","publication_status":"published","publisher":"Oxford University Press","author":[{"full_name":"Hon, Marc","first_name":"Marc","last_name":"Hon"},{"first_name":"Dennis","last_name":"Stello","full_name":"Stello, Dennis"},{"first_name":"Rafael A","last_name":"García","full_name":"García, Rafael A"},{"last_name":"Mathur","first_name":"Savita","full_name":"Mathur, Savita"},{"first_name":"Sanjib","last_name":"Sharma","full_name":"Sharma, Sanjib"},{"first_name":"Isabel L","last_name":"Colman","full_name":"Colman, Isabel L"},{"full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet"}],"date_created":"2022-07-18T14:26:03Z","date_updated":"2022-08-22T07:35:19Z","volume":485,"month":"06","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"external_id":{"arxiv":["1903.00115"]},"main_file_link":[{"url":"https://arxiv.org/abs/1903.00115","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1093/mnras/stz622","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The recently published Kepler mission Data Release 25 (DR25) reported on ∼197 000 targets observed during the mission. Despite this, no wide search for red giants showing solar-like oscillations have been made across all stars observed in Kepler’s long-cadence mode. In this work, we perform this task using custom apertures on the Kepler pixel files and detect oscillations in 21 914 stars, representing the largest sample of solar-like oscillating stars to date. We measure their frequency at maximum power, νmax, down to νmax≃4μHz and obtain log (g) estimates with a typical uncertainty below 0.05 dex, which is superior to typical measurements from spectroscopy. Additionally, the νmax distribution of our detections show good agreement with results from a simulated model of the Milky Way, with a ratio of observed to predicted stars of 0.992 for stars with 10<νmax<270μHz. Among our red giant detections, we find 909 to be dwarf/subgiant stars whose flux signal is polluted by a neighbouring giant as a result of using larger photometric apertures than those used by the NASA Kepler science processing pipeline. We further find that only 293 of the polluting giants are known Kepler targets. The remainder comprises over 600 newly identified oscillating red giants, with many expected to belong to the Galactic halo, serendipitously falling within the Kepler pixel files of targeted stars.","lang":"eng"}],"issue":"4","_id":"11615","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"A search for red giant solar-like oscillations in all Kepler data","intvolume":" 485","oa_version":"Preprint","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","asteroseismology","methods: data analysis","techniques: image processing","stars: oscillations","stars: statistics"],"day":"01","article_processing_charge":"No","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"mla":"Hon, Marc, et al. “A Search for Red Giant Solar-like Oscillations in All Kepler Data.” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 4, Oxford University Press, 2019, pp. 5616–30, doi:10.1093/mnras/stz622.","short":"M. Hon, D. Stello, R.A. García, S. Mathur, S. Sharma, I.L. Colman, L.A. Bugnet, Monthly Notices of the Royal Astronomical Society 485 (2019) 5616–5630.","chicago":"Hon, Marc, Dennis Stello, Rafael A García, Savita Mathur, Sanjib Sharma, Isabel L Colman, and Lisa Annabelle Bugnet. “A Search for Red Giant Solar-like Oscillations in All Kepler Data.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz622.","ama":"Hon M, Stello D, García RA, et al. A search for red giant solar-like oscillations in all Kepler data. Monthly Notices of the Royal Astronomical Society. 2019;485(4):5616-5630. doi:10.1093/mnras/stz622","ista":"Hon M, Stello D, García RA, Mathur S, Sharma S, Colman IL, Bugnet LA. 2019. A search for red giant solar-like oscillations in all Kepler data. Monthly Notices of the Royal Astronomical Society. 485(4), 5616–5630.","ieee":"M. Hon et al., “A search for red giant solar-like oscillations in all Kepler data,” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 4. Oxford University Press, pp. 5616–5630, 2019.","apa":"Hon, M., Stello, D., García, R. A., Mathur, S., Sharma, S., Colman, I. L., & Bugnet, L. A. (2019). A search for red giant solar-like oscillations in all Kepler data. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz622"},"article_type":"original","page":"5616-5630","date_published":"2019-06-01T00:00:00Z"},{"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"month":"04","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.09854","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1902.09854"]},"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201834780","article_number":"A79","extern":"1","publisher":"EDP Science","publication_status":"published","year":"2019","acknowledgement":"We thank the enitre T’DA team for useful comments and discussions, in particular Andrew Tkachenko. We also acknowledge Marc Hon, Keaton Bell, and James Kuszlewicz for useful comments on the manuscript. L.B. and R.A.G. acknowledge the support from PLATO and GOLF CNES grants. S.M. acknowledges support by the Ramon y Cajal fellowship number RYC-2015-17697. O.J.H. and B.M.R. acknowledge the support of the UK Science and Technology Facilities Council (STFC). M.N.L. acknowledges the support of the ESA PRODEX programme (PEA 4000119301). Funding for the Stellar Astrophysics Centre is provided by the Danish National Research Foundation (Grant DNRF106).","volume":624,"date_updated":"2022-08-22T07:32:51Z","date_created":"2022-07-18T14:13:34Z","author":[{"full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet"},{"full_name":"García, R. A.","first_name":"R. A.","last_name":"García"},{"full_name":"Mathur, S.","last_name":"Mathur","first_name":"S."},{"full_name":"Davies, G. R.","last_name":"Davies","first_name":"G. R."},{"full_name":"Hall, O. J.","first_name":"O. J.","last_name":"Hall"},{"full_name":"Lund, M. N.","last_name":"Lund","first_name":"M. N."},{"full_name":"Rendle, B. M.","last_name":"Rendle","first_name":"B. M."}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","article_processing_charge":"No","day":"19","article_type":"original","citation":{"chicago":"Bugnet, Lisa Annabelle, R. A. García, S. Mathur, G. R. Davies, O. J. Hall, M. N. Lund, and B. M. Rendle. “FliPerClass: In Search of Solar-like Pulsators among TESS Targets.” Astronomy & Astrophysics. EDP Science, 2019. https://doi.org/10.1051/0004-6361/201834780.","short":"L.A. Bugnet, R.A. García, S. Mathur, G.R. Davies, O.J. Hall, M.N. Lund, B.M. Rendle, Astronomy & Astrophysics 624 (2019).","mla":"Bugnet, Lisa Annabelle, et al. “FliPerClass: In Search of Solar-like Pulsators among TESS Targets.” Astronomy & Astrophysics, vol. 624, A79, EDP Science, 2019, doi:10.1051/0004-6361/201834780.","ieee":"L. A. Bugnet et al., “FliPerClass: In search of solar-like pulsators among TESS targets,” Astronomy & Astrophysics, vol. 624. EDP Science, 2019.","apa":"Bugnet, L. A., García, R. A., Mathur, S., Davies, G. R., Hall, O. J., Lund, M. N., & Rendle, B. M. (2019). FliPerClass: In search of solar-like pulsators among TESS targets. Astronomy & Astrophysics. EDP Science. https://doi.org/10.1051/0004-6361/201834780","ista":"Bugnet LA, García RA, Mathur S, Davies GR, Hall OJ, Lund MN, Rendle BM. 2019. FliPerClass: In search of solar-like pulsators among TESS targets. Astronomy & Astrophysics. 624, A79.","ama":"Bugnet LA, García RA, Mathur S, et al. FliPerClass: In search of solar-like pulsators among TESS targets. Astronomy & Astrophysics. 2019;624. doi:10.1051/0004-6361/201834780"},"publication":"Astronomy & Astrophysics","date_published":"2019-04-19T00:00:00Z","type":"journal_article","abstract":[{"text":"The NASA Transiting Exoplanet Survey Satellite (TESS) is about to provide full-frame images of almost the entire sky. The amount of stellar data to be analysed represents hundreds of millions stars, which is several orders of magnitude more than the number of stars observed by the Convection, Rotation and planetary Transits satellite (CoRoT), and NASA Kepler and K2 missions. We aim at automatically classifying the newly observed stars with near real-time algorithms to better guide the subsequent detailed studies. In this paper, we present a classification algorithm built to recognise solar-like pulsators among classical pulsators. This algorithm relies on the global amount of power contained in the power spectral density (PSD), also known as the flicker in spectral power density (FliPer). Because each type of pulsating star has a characteristic background or pulsation pattern, the shape of the PSD at different frequencies can be used to characterise the type of pulsating star. The FliPer classifier (FliPerClass) uses different FliPer parameters along with the effective temperature as input parameters to feed a ML algorithm in order to automatically classify the pulsating stars observed by TESS. Using noisy TESS-simulated data from the TESS Asteroseismic Science Consortium (TASC), we classify pulsators with a 98% accuracy. Among them, solar-like pulsating stars are recognised with a 99% accuracy, which is of great interest for a further seismic analysis of these stars, which are like our Sun. Similar results are obtained when we trained our classifier and applied it to 27-day subsets of real Kepler data. FliPerClass is part of the large TASC classification pipeline developed by the TESS Data for Asteroseismology (T’DA) classification working group.","lang":"eng"}],"intvolume":" 624","title":"FliPerClass: In search of solar-like pulsators among TESS targets","status":"public","_id":"11614","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"volume":244,"date_created":"2022-07-19T09:21:58Z","date_updated":"2022-08-22T08:10:38Z","author":[{"last_name":"Santos","first_name":"A. R. G.","full_name":"Santos, A. R. G."},{"full_name":"García, R. A.","first_name":"R. A.","last_name":"García"},{"full_name":"Mathur, S.","first_name":"S.","last_name":"Mathur"},{"full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet"},{"last_name":"van Saders","first_name":"J. L.","full_name":"van Saders, J. L."},{"full_name":"Metcalfe, T. S.","last_name":"Metcalfe","first_name":"T. S."},{"first_name":"G. V. A.","last_name":"Simonian","full_name":"Simonian, G. V. A."},{"first_name":"M. H.","last_name":"Pinsonneault","full_name":"Pinsonneault, M. H."}],"publisher":"IOP Publishing","publication_status":"published","acknowledgement":"The authors thank Róbert Szabó Paul G. Beck, Katrien Kolenberg, and Isabel L. Colman for helping on the classification of stars. This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the National Aeronautics and Space Administration (NASA) Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555. A.R.G.S. acknowledges the support from NASA under grant NNX17AF27G. R.A.G. and L.B. acknowledge the support from PLATO and GOLF CNES grants. S.M. acknowledges the support from the Ramon y Cajal fellowship number RYC-2015-17697. T.S.M. acknowledges support from a Visiting Fellowship at the Max Planck Institute for Solar System Research. This research has made use of the NASA Exoplanet Archive, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program.\r\n\r\nSoftware: KADACS (García et al. 2011), NumPy (van der Walt et al. 2011), SciPy (Jones et al. 2001), Matplotlib (Hunter 2007).\r\n\r\nFacilities: MAST - , Kepler Eclipsing Binary Catalog - , Exoplanet Archive. -","year":"2019","extern":"1","article_number":"21","language":[{"iso":"eng"}],"doi":"10.3847/1538-4365/ab3b56","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.05222","open_access":"1"}],"external_id":{"arxiv":["1908.05222"]},"publication_identifier":{"issn":["0067-0049"]},"month":"09","oa_version":"Preprint","intvolume":" 244","title":"Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11623","issue":"1","abstract":[{"lang":"eng","text":"Brightness variations due to dark spots on the stellar surface encode information about stellar surface rotation and magnetic activity. In this work, we analyze the Kepler long-cadence data of 26,521 main-sequence stars of spectral types M and K in order to measure their surface rotation and photometric activity level. Rotation-period estimates are obtained by the combination of a wavelet analysis and autocorrelation function of the light curves. Reliable rotation estimates are determined by comparing the results from the different rotation diagnostics and four data sets. We also measure the photometric activity proxy Sph using the amplitude of the flux variations on an appropriate timescale. We report rotation periods and photometric activity proxies for about 60% of the sample, including 4431 targets for which McQuillan et al. did not report a rotation period. For the common targets with rotation estimates in this study and in McQuillan et al., our rotation periods agree within 99%. In this work, we also identify potential polluters, such as misclassified red giants and classical pulsator candidates. Within the parameter range we study, there is a mild tendency for hotter stars to have shorter rotation periods. The photometric activity proxy spans a wider range of values with increasing effective temperature. The rotation period and photometric activity proxy are also related, with Sph being larger for fast rotators. Similar to McQuillan et al., we find a bimodal distribution of rotation periods."}],"type":"journal_article","date_published":"2019-09-19T00:00:00Z","article_type":"original","citation":{"chicago":"Santos, A. R. G., R. A. García, S. Mathur, Lisa Annabelle Bugnet, J. L. van Saders, T. S. Metcalfe, G. V. A. Simonian, and M. H. Pinsonneault. “Surface Rotation and Photometric Activity for Kepler Targets. I. M and K Main-Sequence Stars.” The Astrophysical Journal Supplement Series. IOP Publishing, 2019. https://doi.org/10.3847/1538-4365/ab3b56.","mla":"Santos, A. R. G., et al. “Surface Rotation and Photometric Activity for Kepler Targets. I. M and K Main-Sequence Stars.” The Astrophysical Journal Supplement Series, vol. 244, no. 1, 21, IOP Publishing, 2019, doi:10.3847/1538-4365/ab3b56.","short":"A.R.G. Santos, R.A. García, S. Mathur, L.A. Bugnet, J.L. van Saders, T.S. Metcalfe, G.V.A. Simonian, M.H. Pinsonneault, The Astrophysical Journal Supplement Series 244 (2019).","ista":"Santos ARG, García RA, Mathur S, Bugnet LA, van Saders JL, Metcalfe TS, Simonian GVA, Pinsonneault MH. 2019. Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars. The Astrophysical Journal Supplement Series. 244(1), 21.","apa":"Santos, A. R. G., García, R. A., Mathur, S., Bugnet, L. A., van Saders, J. L., Metcalfe, T. S., … Pinsonneault, M. H. (2019). Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars. The Astrophysical Journal Supplement Series. IOP Publishing. https://doi.org/10.3847/1538-4365/ab3b56","ieee":"A. R. G. Santos et al., “Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars,” The Astrophysical Journal Supplement Series, vol. 244, no. 1. IOP Publishing, 2019.","ama":"Santos ARG, García RA, Mathur S, et al. Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars. The Astrophysical Journal Supplement Series. 2019;244(1). doi:10.3847/1538-4365/ab3b56"},"publication":"The Astrophysical Journal Supplement Series","article_processing_charge":"No","day":"19","keyword":["Space and Planetary Science","Astronomy and Astrophysics","methods: data analysis","stars: activity","stars: low-mass","stars: rotation","starspots","techniques: photometric"],"scopus_import":"1"},{"abstract":[{"lang":"eng","text":"For a solar-like star, the surface rotation evolves with time, allowing in principle to estimate the age of a star from its surface rotation period. Here we are interested in measuring surface rotation periods of solar-like stars observed by the NASA mission Kepler. Different methods have been developed to track rotation signals in Kepler photometric light curves: time-frequency analysis based on wavelet techniques, autocorrelation and composite spectrum. We use the learning abilities of random forest classifiers to take decisions during two crucial steps of the analysis. First, given some input parameters, we discriminate the considered Kepler targets between rotating MS stars, non-rotating MS stars, red giants, binaries and pulsators. We then use a second classifier only on the MS rotating targets to decide the best data analysis treatment."}],"extern":"1","article_number":"1906.09609","type":"preprint","author":[{"first_name":"S. N.","last_name":"Breton","full_name":"Breton, S. N."},{"last_name":"Bugnet","first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle"},{"full_name":"Santos, A. R. G.","first_name":"A. R. G.","last_name":"Santos"},{"full_name":"Saux, A. Le","first_name":"A. Le","last_name":"Saux"},{"first_name":"S.","last_name":"Mathur","full_name":"Mathur, S."},{"full_name":"Palle, P. L.","first_name":"P. L.","last_name":"Palle"},{"first_name":"R. A.","last_name":"Garcia","full_name":"Garcia, R. A."}],"date_created":"2022-07-20T11:18:53Z","date_updated":"2022-08-22T08:16:53Z","oa_version":"Preprint","_id":"11627","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","status":"public","publication_status":"submitted","title":"Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques","month":"06","day":"23","article_processing_charge":"No","keyword":["asteroseismology","rotation","solar-like stars","kepler","machine learning","random forest"],"date_published":"2019-06-23T00:00:00Z","doi":"10.48550/arXiv.1906.09609","language":[{"iso":"eng"}],"publication":"arXiv","external_id":{"arxiv":["1906.09609"]},"citation":{"short":"S.N. Breton, L.A. Bugnet, A.R.G. Santos, A.L. Saux, S. Mathur, P.L. Palle, R.A. Garcia, ArXiv (n.d.).","mla":"Breton, S. N., et al. “Determining Surface Rotation Periods of Solar-like Stars Observed by the Kepler Mission Using Machine Learning Techniques.” ArXiv, 1906.09609, doi:10.48550/arXiv.1906.09609.","chicago":"Breton, S. N., Lisa Annabelle Bugnet, A. R. G. Santos, A. Le Saux, S. Mathur, P. L. Palle, and R. A. Garcia. “Determining Surface Rotation Periods of Solar-like Stars Observed by the Kepler Mission Using Machine Learning Techniques.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1906.09609.","ama":"Breton SN, Bugnet LA, Santos ARG, et al. Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques. arXiv. doi:10.48550/arXiv.1906.09609","ieee":"S. N. Breton et al., “Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques,” arXiv. .","apa":"Breton, S. N., Bugnet, L. A., Santos, A. R. G., Saux, A. L., Mathur, S., Palle, P. L., & Garcia, R. A. (n.d.). Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques. arXiv. https://doi.org/10.48550/arXiv.1906.09609","ista":"Breton SN, Bugnet LA, Santos ARG, Saux AL, Mathur S, Palle PL, Garcia RA. Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques. arXiv, 1906.09609."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1906.09609","open_access":"1"}]},{"keyword":["asteroseismology - methods","data analysis - thecniques","machine learning - stars","oscillations"],"article_processing_charge":"No","day":"23","month":"06","citation":{"chicago":"Saux, A. Le, Lisa Annabelle Bugnet, S. Mathur, S. N. Breton, and R. A. Garcia. “Automatic Classification of K2 Pulsating Stars Using Machine Learning Techniques.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1906.09611.","mla":"Saux, A. Le, et al. “Automatic Classification of K2 Pulsating Stars Using Machine Learning Techniques.” ArXiv, 1906.09611, doi:10.48550/arXiv.1906.09611.","short":"A.L. Saux, L.A. Bugnet, S. Mathur, S.N. Breton, R.A. Garcia, ArXiv (n.d.).","ista":"Saux AL, Bugnet LA, Mathur S, Breton SN, Garcia RA. Automatic classification of K2 pulsating stars using machine learning techniques. arXiv, 1906.09611.","ieee":"A. L. Saux, L. A. Bugnet, S. Mathur, S. N. Breton, and R. A. Garcia, “Automatic classification of K2 pulsating stars using machine learning techniques,” arXiv. .","apa":"Saux, A. L., Bugnet, L. A., Mathur, S., Breton, S. N., & Garcia, R. A. (n.d.). Automatic classification of K2 pulsating stars using machine learning techniques. arXiv. https://doi.org/10.48550/arXiv.1906.09611","ama":"Saux AL, Bugnet LA, Mathur S, Breton SN, Garcia RA. Automatic classification of K2 pulsating stars using machine learning techniques. arXiv. doi:10.48550/arXiv.1906.09611"},"oa":1,"external_id":{"arxiv":["1906.09611"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1906.09611"}],"publication":"arXiv","doi":"10.48550/arXiv.1906.09611","date_published":"2019-06-23T00:00:00Z","language":[{"iso":"eng"}],"type":"preprint","article_number":"1906.09611","abstract":[{"lang":"eng","text":"The second mission of NASA’s Kepler satellite, K2, has collected hundreds of thousands of lightcurves for stars close to the ecliptic plane. This new sample could increase the number of known pulsating stars and then improve our understanding of those stars. For the moment only a few stars have been properly classified and published. In this work, we present a method to automaticly classify K2 pulsating stars using a Machine Learning technique called Random Forest. The objective is to sort out the stars in four classes: red giant (RG), main-sequence Solar-like stars (SL), classical pulsators (PULS) and Other. To do this we use the effective temperatures and the luminosities of the stars as well as the FliPer features, that measures the amount of power contained in the power spectral density. The classifier now retrieves the right classification for more than 80% of the stars."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11630","year":"2019","status":"public","title":"Automatic classification of K2 pulsating stars using machine learning techniques","publication_status":"submitted","author":[{"full_name":"Saux, A. Le","first_name":"A. Le","last_name":"Saux"},{"full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"first_name":"S.","last_name":"Mathur","full_name":"Mathur, S."},{"last_name":"Breton","first_name":"S. N.","full_name":"Breton, S. N."},{"last_name":"Garcia","first_name":"R. A.","full_name":"Garcia, R. A."}],"oa_version":"Preprint","date_created":"2022-07-21T06:57:10Z","date_updated":"2022-08-22T08:20:29Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ICALP.2019.13"}],"external_id":{"arxiv":["811.12527"]},"oa":1,"quality_controlled":"1","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2019-07-12","start_date":"2019-07-09","location":"Patras, Greece"},"doi":"10.4230/LIPICS.ICALP.2019.13","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"isbn":["978-3-95977-109-2"],"issn":["1868-8969"]},"year":"2019","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Ancona, Bertie","first_name":"Bertie","last_name":"Ancona"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Roditty, Liam","last_name":"Roditty","first_name":"Liam"},{"full_name":"Williams, Virginia Vassilevska","first_name":"Virginia Vassilevska","last_name":"Williams"},{"first_name":"Nicole","last_name":"Wein","full_name":"Wein, Nicole"}],"date_updated":"2023-02-16T10:48:24Z","date_created":"2022-08-12T08:14:51Z","volume":132,"article_number":"13","extern":"1","publication":"46th International Colloquium on Automata, Languages, and Programming","citation":{"ama":"Ancona B, Henzinger MH, Roditty L, Williams VV, Wein N. Algorithms and hardness for diameter in dynamic graphs. In: 46th International Colloquium on Automata, Languages, and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.ICALP.2019.13","ieee":"B. Ancona, M. H. Henzinger, L. Roditty, V. V. Williams, and N. Wein, “Algorithms and hardness for diameter in dynamic graphs,” in 46th International Colloquium on Automata, Languages, and Programming, Patras, Greece, 2019, vol. 132.","apa":"Ancona, B., Henzinger, M. H., Roditty, L., Williams, V. V., & Wein, N. (2019). Algorithms and hardness for diameter in dynamic graphs. In 46th International Colloquium on Automata, Languages, and Programming (Vol. 132). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.13","ista":"Ancona B, Henzinger MH, Roditty L, Williams VV, Wein N. 2019. Algorithms and hardness for diameter in dynamic graphs. 46th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 132, 13.","short":"B. Ancona, M.H. Henzinger, L. Roditty, V.V. Williams, N. Wein, in:, 46th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Ancona, Bertie, et al. “Algorithms and Hardness for Diameter in Dynamic Graphs.” 46th International Colloquium on Automata, Languages, and Programming, vol. 132, 13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.ICALP.2019.13.","chicago":"Ancona, Bertie, Monika H Henzinger, Liam Roditty, Virginia Vassilevska Williams, and Nicole Wein. “Algorithms and Hardness for Diameter in Dynamic Graphs.” In 46th International Colloquium on Automata, Languages, and Programming, Vol. 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.13."},"date_published":"2019-07-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","_id":"11826","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Algorithms and hardness for diameter in dynamic graphs","status":"public","intvolume":" 132","oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"The diameter, radius and eccentricities are natural graph parameters. While these problems have been studied extensively, there are no known dynamic algorithms for them beyond the ones that follow from trivial recomputation after each update or from solving dynamic All-Pairs Shortest Paths (APSP), which is very computationally intensive. This is the situation for dynamic approximation algorithms as well, and even if only edge insertions or edge deletions need to be supported.\r\nThis paper provides a comprehensive study of the dynamic approximation of Diameter, Radius and Eccentricities, providing both conditional lower bounds, and new algorithms whose bounds are optimal under popular hypotheses in fine-grained complexity. Some of the highlights include:\r\n- Under popular hardness hypotheses, there can be no significantly better fully dynamic approximation algorithms than recomputing the answer after each update, or maintaining full APSP.\r\n- Nearly optimal partially dynamic (incremental/decremental) algorithms can be achieved via efficient reductions to (incremental/decremental) maintenance of Single-Source Shortest Paths. For instance, a nearly (3/2+epsilon)-approximation to Diameter in directed or undirected n-vertex, m-edge graphs can be maintained decrementally in total time m^{1+o(1)}sqrt{n}/epsilon^2. This nearly matches the static 3/2-approximation algorithm for the problem that is known to be conditionally optimal.","lang":"eng"}]},{"date_updated":"2023-02-17T09:41:45Z","date_created":"2022-08-16T07:14:57Z","oa_version":"Preprint","author":[{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"Neumann, Stefan","last_name":"Neumann","first_name":"Stefan"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"title":"Efficient distributed workload (re-)embedding","publication_status":"published","status":"public","publisher":"Association for Computing Machinery","_id":"11850","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"text":"Modern networked systems are increasingly reconfigurable, enabling demand-aware infrastructures whose resources can be adjusted according to the workload they currently serve. Such dynamic adjustments can be exploited to improve network utilization and hence performance, by moving frequently interacting communication partners closer, e.g., collocating them in the same server or datacenter. However, dynamically changing the embedding of workloads is algorithmically challenging: communication patterns are often not known ahead of time, but must be learned. During the learning process, overheads related to unnecessary moves (i.e., re-embeddings) should be minimized. This paper studies a fundamental model which captures the tradeoff between the benefits and costs of dynamically collocating communication partners on l servers, in an online manner. Our main contribution is a distributed online algorithm which is asymptotically almost optimal, i.e., almost matches the lower bound (also derived in this paper) on the competitive ratio of any (distributed or centralized) online algorithm.","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"conference":{"end_date":"2019-06-28","location":"Phoenix, AZ, United States","start_date":"2019-06-24","name":"SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems"},"doi":"10.1145/3309697.3331503","date_published":"2019-06-20T00:00:00Z","quality_controlled":"1","page":"43–44","publication":"SIGMETRICS'19: International Conference on Measurement and Modeling of Computer Systems","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.05474"}],"citation":{"mla":"Henzinger, Monika H., et al. “Efficient Distributed Workload (Re-)Embedding.” SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2019, pp. 43–44, doi:10.1145/3309697.3331503.","short":"M.H. Henzinger, S. Neumann, S. Schmid, in:, SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2019, pp. 43–44.","chicago":"Henzinger, Monika H, Stefan Neumann, and Stefan Schmid. “Efficient Distributed Workload (Re-)Embedding.” In SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, 43–44. Association for Computing Machinery, 2019. https://doi.org/10.1145/3309697.3331503.","ama":"Henzinger MH, Neumann S, Schmid S. Efficient distributed workload (re-)embedding. In: SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems. Association for Computing Machinery; 2019:43–44. doi:10.1145/3309697.3331503","ista":"Henzinger MH, Neumann S, Schmid S. 2019. Efficient distributed workload (re-)embedding. SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems, 43–44.","ieee":"M. H. Henzinger, S. Neumann, and S. Schmid, “Efficient distributed workload (re-)embedding,” in SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Phoenix, AZ, United States, 2019, pp. 43–44.","apa":"Henzinger, M. H., Neumann, S., & Schmid, S. (2019). Efficient distributed workload (re-)embedding. In SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems (pp. 43–44). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3309697.3331503"},"oa":1,"external_id":{"arxiv":["1904.05474"]},"day":"20","month":"06","publication_identifier":{"isbn":["978-1-4503-6678-6"]},"article_processing_charge":"No","scopus_import":"1"},{"scopus_import":"1","day":"01","month":"11","publication_identifier":{"eisbn":["978-1-7281-4952-3"],"issn":["2575-8454"],"isbn":["978-1-7281-4953-0"]},"article_processing_charge":"No","quality_controlled":"1","page":"406-423","publication":"60th Annual Symposium on Foundations of Computer Science","citation":{"chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “A New Deterministic Algorithm for Dynamic Set Cover.” In 60th Annual Symposium on Foundations of Computer Science, 406–23. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/focs.2019.00033.","short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 60th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2019, pp. 406–423.","mla":"Bhattacharya, Sayan, et al. “A New Deterministic Algorithm for Dynamic Set Cover.” 60th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2019, pp. 406–23, doi:10.1109/focs.2019.00033.","ieee":"S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “A new deterministic algorithm for dynamic set cover,” in 60th Annual Symposium on Foundations of Computer Science, Baltimore, MD, United States, 2019, pp. 406–423.","apa":"Bhattacharya, S., Henzinger, M. H., & Nanongkai, D. (2019). A new deterministic algorithm for dynamic set cover. In 60th Annual Symposium on Foundations of Computer Science (pp. 406–423). Baltimore, MD, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2019.00033","ista":"Bhattacharya S, Henzinger MH, Nanongkai D. 2019. A new deterministic algorithm for dynamic set cover. 60th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 406–423.","ama":"Bhattacharya S, Henzinger MH, Nanongkai D. A new deterministic algorithm for dynamic set cover. In: 60th Annual Symposium on Foundations of Computer Science. Institute of Electrical and Electronics Engineers; 2019:406-423. doi:10.1109/focs.2019.00033"},"main_file_link":[{"url":"https://arxiv.org/abs/1909.11600","open_access":"1"}],"external_id":{"arxiv":["1909.11600"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"FOCS: Annual Symposium on Foundations of Computer Science","end_date":"2019-11-12","location":"Baltimore, MD, United States","start_date":"2019-11-09"},"doi":"10.1109/focs.2019.00033","date_published":"2019-11-01T00:00:00Z","type":"conference","extern":"1","abstract":[{"text":"We present a deterministic dynamic algorithm for maintaining a (1+ε)f-approximate minimum cost set cover with O(f log(Cn)/ε^2) amortized update time, when the input set system is undergoing element insertions and deletions. Here, n denotes the number of elements, each element appears in at most f sets, and the cost of each set lies in the range [1/C, 1]. Our result, together with that of Gupta~et~al.~[STOC'17], implies that there is a deterministic algorithm for this problem with O(f log(Cn)) amortized update time and O(min(log n, f)) -approximation ratio, which nearly matches the polynomial-time hardness of approximation for minimum set cover in the static setting. Our update time is only O(log (Cn)) away from a trivial lower bound. Prior to our work, the previous best approximation ratio guaranteed by deterministic algorithms was O(f^2), which was due to Bhattacharya~et~al.~[ICALP`15]. In contrast, the only result that guaranteed O(f) -approximation was obtained very recently by Abboud~et~al.~[STOC`19], who designed a dynamic algorithm with (1+ε)f-approximation ratio and O(f^2 log n/ε) amortized update time. Besides the extra O(f) factor in the update time compared to our and Gupta~et~al.'s results, the Abboud~et~al.~algorithm is randomized, and works only when the adversary is oblivious and the sets are unweighted (each set has the same cost). We achieve our result via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. This approach was pursued previously by Bhattacharya~et~al.~and Gupta~et~al., but not in the recent paper by Abboud~et~al. Unlike previous primal-dual algorithms that try to satisfy some local constraints for individual sets at all time, our algorithm basically waits until the dual solution changes significantly globally, and fixes the solution only where the fix is needed.","lang":"eng"}],"status":"public","title":"A new deterministic algorithm for dynamic set cover","publication_status":"published","publisher":"Institute of Electrical and Electronics Engineers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11853","year":"2019","date_created":"2022-08-16T08:00:00Z","date_updated":"2023-02-17T09:50:37Z","oa_version":"Preprint","author":[{"last_name":"Bhattacharya","first_name":"Sayan","full_name":"Bhattacharya, Sayan"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}]},{"scopus_import":"1","month":"06","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["0737-8017"],"isbn":["978-1-4503-6705-9"]},"publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","citation":{"apa":"Daga, M., Henzinger, M. H., Nanongkai, D., & Saranurak, T. (2019). Distributed edge connectivity in sublinear time. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 343–354). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3313276.3316346","ieee":"M. Daga, M. H. Henzinger, D. Nanongkai, and T. Saranurak, “Distributed edge connectivity in sublinear time,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 343–354.","ista":"Daga M, Henzinger MH, Nanongkai D, Saranurak T. 2019. Distributed edge connectivity in sublinear time. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 343–354.","ama":"Daga M, Henzinger MH, Nanongkai D, Saranurak T. Distributed edge connectivity in sublinear time. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. Association for Computing Machinery; 2019:343–354. doi:10.1145/3313276.3316346","chicago":"Daga, Mohit, Monika H Henzinger, Danupon Nanongkai, and Thatchaphol Saranurak. “Distributed Edge Connectivity in Sublinear Time.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 343–354. Association for Computing Machinery, 2019. https://doi.org/10.1145/3313276.3316346.","short":"M. Daga, M.H. Henzinger, D. Nanongkai, T. Saranurak, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2019, pp. 343–354.","mla":"Daga, Mohit, et al. “Distributed Edge Connectivity in Sublinear Time.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2019, pp. 343–354, doi:10.1145/3313276.3316346."},"oa":1,"external_id":{"arxiv":["1904.04341"]},"main_file_link":[{"url":"https://arxiv.org/abs/1904.04341","open_access":"1"}],"quality_controlled":"1","page":"343–354","conference":{"name":"STOC: Symposium on Theory of Computing","start_date":"2019-06-23","location":"Phoenix, AZ, United States","end_date":"2019-06-26"},"date_published":"2019-06-01T00:00:00Z","doi":"10.1145/3313276.3316346","language":[{"iso":"eng"}],"type":"conference","abstract":[{"lang":"eng","text":"We present the first sublinear-time algorithm that can compute the edge connectivity λ of a network exactly on distributed message-passing networks (the CONGEST model), as long as the network contains no multi-edge. We present the first sublinear-time algorithm for a distributed message-passing network sto compute its edge connectivity λ exactly in the CONGEST model, as long as there are no parallel edges. Our algorithm takes Õ(n1−1/353D1/353+n1−1/706) time to compute λ and a cut of cardinality λ with high probability, where n and D are the number of nodes and the diameter of the network, respectively, and Õ hides polylogarithmic factors. This running time is sublinear in n (i.e. Õ(n1−є)) whenever D is. Previous sublinear-time distributed algorithms can solve this problem either (i) exactly only when λ=O(n1/8−є) [Thurimella PODC’95; Pritchard, Thurimella, ACM Trans. Algorithms’11; Nanongkai, Su, DISC’14] or (ii) approximately [Ghaffari, Kuhn, DISC’13; Nanongkai, Su, DISC’14]. To achieve this we develop and combine several new techniques. First, we design the first distributed algorithm that can compute a k-edge connectivity certificate for any k=O(n1−є) in time Õ(√nk+D). The previous sublinear-time algorithm can do so only when k=o(√n) [Thurimella PODC’95]. In fact, our algorithm can be turned into the first parallel algorithm with polylogarithmic depth and near-linear work. Previous near-linear work algorithms are essentially sequential and previous polylogarithmic-depth algorithms require Ω(mk) work in the worst case (e.g. [Karger, Motwani, STOC’93]). Second, we show that by combining the recent distributed expander decomposition technique of [Chang, Pettie, Zhang, SODA’19] with techniques from the sequential deterministic edge connectivity algorithm of [Kawarabayashi, Thorup, STOC’15], we can decompose the network into a sublinear number of clusters with small average diameter and without any mincut separating a cluster (except the “trivial” ones). This leads to a simplification of the Kawarabayashi-Thorup framework (except that we are randomized while they are deterministic). This might make this framework more useful in other models of computation. Finally, by extending the tree packing technique from [Karger STOC’96], we can find the minimum cut in time proportional to the number of components. As a byproduct of this technique, we obtain an Õ(n)-time algorithm for computing exact minimum cut for weighted graphs."}],"extern":"1","_id":"11865","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Distributed edge connectivity in sublinear time","status":"public","publisher":"Association for Computing Machinery","author":[{"full_name":"Daga, Mohit","last_name":"Daga","first_name":"Mohit"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"},{"full_name":"Saranurak, Thatchaphol","last_name":"Saranurak","first_name":"Thatchaphol"}],"date_created":"2022-08-16T09:11:17Z","date_updated":"2023-02-17T10:26:25Z","oa_version":"Preprint"},{"publication_identifier":{"eisbn":["978-1-61197-548-2"]},"month":"01","quality_controlled":"1","external_id":{"arxiv":["1810.10932"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.10932"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1137/1.9781611975482.115","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2019-01-06","location":"San Diego, CA, United States","end_date":"2019-01-09"},"extern":"1","publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","year":"2019","date_created":"2022-08-16T09:50:33Z","date_updated":"2023-02-21T16:31:21Z","related_material":{"record":[{"id":"11871","status":"public","relation":"earlier_version"}]},"author":[{"last_name":"Bernstein","first_name":"Aaron","full_name":"Bernstein, Aaron"},{"full_name":"Forster, Sebastian","last_name":"Forster","first_name":"Sebastian"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"1899-1918","citation":{"ista":"Bernstein A, Forster S, Henzinger MH. 2019. A deamortization approach for dynamic spanner and dynamic maximal matching. 30th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1899–1918.","apa":"Bernstein, A., Forster, S., & Henzinger, M. H. (2019). A deamortization approach for dynamic spanner and dynamic maximal matching. In 30th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1899–1918). San Diego, CA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975482.115","ieee":"A. Bernstein, S. Forster, and M. H. Henzinger, “A deamortization approach for dynamic spanner and dynamic maximal matching,” in 30th Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2019, pp. 1899–1918.","ama":"Bernstein A, Forster S, Henzinger MH. A deamortization approach for dynamic spanner and dynamic maximal matching. In: 30th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2019:1899-1918. doi:10.1137/1.9781611975482.115","chicago":"Bernstein, Aaron, Sebastian Forster, and Monika H Henzinger. “A Deamortization Approach for Dynamic Spanner and Dynamic Maximal Matching.” In 30th Annual ACM-SIAM Symposium on Discrete Algorithms, 1899–1918. Society for Industrial and Applied Mathematics, 2019. https://doi.org/10.1137/1.9781611975482.115.","mla":"Bernstein, Aaron, et al. “A Deamortization Approach for Dynamic Spanner and Dynamic Maximal Matching.” 30th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2019, pp. 1899–918, doi:10.1137/1.9781611975482.115.","short":"A. Bernstein, S. Forster, M.H. Henzinger, in:, 30th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2019, pp. 1899–1918."},"publication":"30th Annual ACM-SIAM Symposium on Discrete Algorithms","date_published":"2019-01-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Many dynamic graph algorithms have an amortized update time, rather than a stronger worst-case guarantee. But amortized data structures are not suitable for real-time systems, where each individual operation has to be executed quickly. For this reason, there exist many recent randomized results that aim to provide a guarantee stronger than amortized expected. The strongest possible guarantee for a randomized algorithm is that it is always correct (Las Vegas), and has high-probability worst-case update time, which gives a bound on the time for each individual operation that holds with high probability.\r\n\r\nIn this paper we present the first polylogarithmic high-probability worst-case time bounds for the dynamic spanner and the dynamic maximal matching problem.\r\n\r\n1.\t\r\nFor dynamic spanner, the only known o(n) worst-case bounds were O(n3/4) high-probability worst-case update time for maintaining a 3-spanner, and O(n5/9) for maintaining a 5-spanner. We give a O(1)k log3(n) high-probability worst-case time bound for maintaining a (2k – 1)-spanner, which yields the first worst-case polylog update time for all constant k. (All the results above maintain the optimal tradeoff of stretch 2k – 1 and Õ(n1+1/k) edges.)\r\n\r\n2.\t\r\nFor dynamic maximal matching, or dynamic 2-approximate maximum matching, no algorithm with o(n) worst-case time bound was known and we present an algorithm with O(log5 (n)) high-probability worst-case time; similar worst-case bounds existed only for maintaining a matching that was (2 + ∊)-approximate, and hence not maximal.\r\n\r\nOur results are achieved using a new approach for converting amortized guarantees to worst-case ones for randomized data structures by going through a third type of guarantee, which is a middle ground between the two above: an algorithm is said to have worst-case expected update time α if for every update σ, the expected time to process σ is at most α. Although stronger than amortized expected, the worst-case expected guarantee does not resolve the fundamental problem of amortization: a worst-case expected update time of O(1) still allows for the possibility that every 1/f(n) updates requires Θ(f(n)) time to process, for arbitrarily high f(n). In this paper we present a black-box reduction that converts any data structure with worst-case expected update time into one with a high-probability worst-case update time: the query time remains the same, while the update time increases by a factor of O(log2(n)).\r\n\r\nThus we achieve our results in two steps: (1) First we show how to convert existing dynamic graph algorithms with amortized expected polylogarithmic running times into algorithms with worst-case expected polylogarithmic running times. (2) Then we use our black-box reduction to achieve the polylogarithmic high-probability worst-case time bound. All our algorithms are Las-Vegas-type algorithms."}],"status":"public","title":"A deamortization approach for dynamic spanner and dynamic maximal matching","_id":"11871","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"}]