[{"_id":"6546","doi_confirm":"1","oa_version":"Published Version","project":[{"_id":"253CDE40-B435-11E9-9278-68D0E5697425","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","grant_number":"24283"}],"doi":"10.15479/AT:ISTA:6546","citation":{"mla":"Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546.","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019.","apa":"Valosková, K. (2019). The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria.","ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546.","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019."},"department":[{"_id":"DaSi"},{"_id":"GradSch"}],"title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","date_updated":"2026-09-03T06:37:27Z","author":[{"last_name":"Valosková","orcid":"0000-0002-7926-0221","first_name":"Katarina","full_name":"Valosková, Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","day":"07","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"544"},{"status":"public","relation":"part_of_dissertation","id":"6187"}]},"file_date_updated":"2021-02-11T11:17:14Z","corr_author":"1","status":"public","ddc":["570"],"month":"06","acknowledged_ssus":[{"_id":"Bio"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2019-06-07T12:49:19Z","abstract":[{"text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2019-06-07T00:00:00Z","publication_status":"published","year":"2019","article_processing_charge":"No","file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14110626,"checksum":"68949c2d96210b45b981a23e9c9cd93c","file_name":"Katarina Valoskova_PhD thesis_final version.docx","creator":"khribikova","date_created":"2019-06-07T13:00:04Z","relation":"source_file","date_updated":"2020-07-14T12:47:33Z","embargo_to":"open_access","file_id":"6549"},{"date_created":"2019-06-07T13:00:08Z","relation":"main_file","file_name":"Katarina Valoskova_PhD thesis_final version.pdf","checksum":"555329cd76e196c96f5278c480ee2e6e","creator":"khribikova","file_size":10054156,"access_level":"open_access","content_type":"application/pdf","file_id":"6550","embargo":"2020-06-07","date_updated":"2021-02-11T11:17:14Z"}],"type":"dissertation","oa":1,"page":"141"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-06-27T00:00:00Z","article_processing_charge":"No","year":"2019","publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:50Z","file_id":"7133","file_size":5054633,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-11-27T09:06:10Z","relation":"source_file","creator":"dernst","checksum":"34d0fe0f6e0af97b5937205a3e350423","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx"},{"file_size":3231837,"access_level":"open_access","content_type":"application/pdf","date_created":"2019-11-27T09:06:10Z","relation":"main_file","creator":"dernst","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","checksum":"140dfb5e3df7edca34f4b6fcc55d876f","date_updated":"2020-07-14T12:47:50Z","file_id":"7134"}],"type":"dissertation","oa":1,"page":"95","month":"06","corr_author":"1","status":"public","ddc":["571","573"],"degree_awarded":"PhD","supervisor":[{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"date_created":"2019-11-27T09:07:14Z","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing.","lang":"eng"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","date_updated":"2026-09-03T06:34:45Z","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","author":[{"first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2020-07-14T12:47:50Z","related_material":{"record":[{"id":"6266","relation":"old_edition","status":"public"}]},"day":"27","_id":"7132","oa_version":"Published Version","doi":"10.15479/at:ista:7132","citation":{"short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:7132.","apa":"Mckenzie, C. (2019). Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:7132","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:7132.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019."},"department":[{"_id":"HaJa"}]},{"_id":"6849","doi_confirm":"1","oa_version":"Published Version","doi":"10.15479/AT:ISTA:6849","citation":{"ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:10.15479/AT:ISTA:6849","apa":"Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6849","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","mla":"Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6849."},"department":[{"_id":"JoCs"},{"_id":"GradSch"}],"title":"The role of CCK-interneurons in regulating hippocampal network dynamics","date_updated":"2026-09-03T06:40:36Z","author":[{"id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Rangel Guerrero, Dámaris K","first_name":"Dámaris K","orcid":"0000-0002-8602-4374","last_name":"Rangel Guerrero"}],"OA_place":"publisher","day":"09","file_date_updated":"2021-02-10T23:30:09Z","publication_identifier":{"isbn":["978-3-99078-003-9"],"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5914"}]},"corr_author":"1","ddc":["570"],"status":"public","month":"09","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"degree_awarded":"PhD","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. ","lang":"eng"}],"has_accepted_license":"1","date_created":"2019-09-06T06:54:16Z","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2019-09-09T00:00:00Z","publication_status":"published","year":"2019","article_processing_charge":"No","file":[{"file_size":18253100,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-09-09T13:09:45Z","relation":"source_file","file_name":"Thesis_Damaris_Rangel_source.docx","creator":"drangel","checksum":"244dc4f74dbfc94f414156092298831f","embargo_to":"open_access","date_updated":"2021-02-10T23:30:09Z","file_id":"6865"},{"content_type":"application/pdf","access_level":"open_access","file_size":2160109,"creator":"drangel","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","checksum":"59c73be40eeaa1c4db24067270151555","relation":"main_file","date_created":"2019-09-09T13:09:52Z","date_updated":"2020-09-11T22:30:04Z","file_id":"6866","embargo":"2020-09-10","request_a_copy":0}],"type":"dissertation","oa":1,"page":"97"},{"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","status":"public","corr_author":"1","month":"03","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k."}],"date_created":"2022-03-18T10:30:32Z","intvolume":" 16","language":[{"iso":"eng"}],"series_title":"OCTR","article_processing_charge":"No","year":"2018","publication_status":"published","date_published":"2018-03-21T00:00:00Z","place":"Cham","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"203-220","editor":[{"first_name":"J","last_name":"Czelakowski","full_name":"Czelakowski, J"}],"oa":1,"type":"book_chapter","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"oa_version":"Preprint","quality_controlled":"1","_id":"10864","volume":16,"department":[{"_id":"VlKo"}],"scopus_import":"1","doi":"10.1007/978-3-319-74772-9_7","citation":{"short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7."},"author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr","last_name":"Kazda","first_name":"Alexandr"},{"full_name":"Kozik, Marcin","last_name":"Kozik","first_name":"Marcin"},{"last_name":"McKenzie","first_name":"Ralph","full_name":"McKenzie, Ralph"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"date_updated":"2024-10-09T21:01:50Z","title":"Absorption and directed Jónsson terms","arxiv":1,"publication_identifier":{"eissn":["2211-2766"],"issn":["2211-2758"],"eisbn":["9783319747729"],"isbn":["9783319747712"]},"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","day":"21","external_id":{"arxiv":["1502.01072"]}},{"_id":"10880","main_file_link":[{"url":"https://doi.org/10.1093/bfgp/ely007","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","citation":{"short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007.","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 2018;17(5):329-338. doi:10.1093/bfgp/ely007","apa":"Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338.","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” Briefings in Functional Genomics, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007."},"doi":"10.1093/bfgp/ely007","scopus_import":"1","department":[{"_id":"CaHe"}],"volume":17,"date_updated":"2026-06-18T10:44:32Z","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","author":[{"id":"4968E7C8-F248-11E8-B48F-1D18A9856A87","full_name":"Yuuta, Moriyama","first_name":"Moriyama","orcid":"0000-0002-2853-8051","last_name":"Yuuta"},{"full_name":"Koshiba-Takeuchi, Kazuko","first_name":"Kazuko","last_name":"Koshiba-Takeuchi"}],"external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"article_type":"original","publication_identifier":{"eissn":["2041-2657"],"issn":["2041-2649"]},"acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","day":"01","month":"09","status":"public","corr_author":"1","ddc":["570"],"publication":"Briefings in Functional Genomics","issue":"5","language":[{"iso":"eng"}],"intvolume":" 17","pmid":1,"date_created":"2022-03-18T12:40:35Z","abstract":[{"lang":"eng","text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation."}],"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-09-01T00:00:00Z","year":"2018","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"article_processing_charge":"No","publication_status":"published","isi":1,"type":"journal_article","oa":1,"page":"329-338"},{"doi":"10.1109/cvpr.2018.00956","citation":{"ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:9175-9184. doi:10.1109/cvpr.2018.00956","apa":"Uijlings, J., Konyushkova, K., Lampert, C., & Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. https://doi.org/10.1109/cvpr.2018.00956","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, United States, 2018, pp. 9175–9184.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–84, doi:10.1109/cvpr.2018.00956.","short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 9175–84. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00956."},"department":[{"_id":"ChLa"}],"scopus_import":"1","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"_id":"10882","external_id":{"isi":["000457843609036"],"arxiv":["1712.08087"]},"conference":{"start_date":"2018-06-18","name":"CVF: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, United States","end_date":"2018-06-23"},"arxiv":1,"day":"17","publication_identifier":{"eissn":["2575-7075"],"isbn":["9781538664209"]},"title":"Learning intelligent dialogs for bounding box annotation","date_updated":"2024-10-09T21:02:26Z","author":[{"first_name":"Jasper","last_name":"Uijlings","full_name":"Uijlings, Jasper"},{"full_name":"Konyushkova, Ksenia","last_name":"Konyushkova","first_name":"Ksenia"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"},{"last_name":"Ferrari","first_name":"Vittorio","full_name":"Ferrari, Vittorio"}],"language":[{"iso":"eng"}],"publisher":"IEEE","date_created":"2022-03-18T12:45:09Z","abstract":[{"text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger.","lang":"eng"}],"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","corr_author":"1","month":"12","status":"public","oa":1,"isi":1,"type":"conference","page":"9175-9184","date_published":"2018-12-17T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","year":"2018","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"intvolume":" 57","has_accepted_license":"1","date_created":"2022-03-18T12:46:32Z","abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"alternative_title":["EPiC Series in Computing"],"publisher":"EasyChair","month":"10","ddc":["000"],"status":"public","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","ec_funded":1,"type":"conference","oa":1,"page":"233-253","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-10-23T00:00:00Z","publication_status":"published","year":"2018","article_processing_charge":"No","file":[{"date_updated":"2022-05-17T07:51:08Z","success":1,"file_id":"11392","access_level":"open_access","content_type":"application/pdf","file_size":720893,"creator":"dernst","file_name":"2018_EPiCs_Chatterjee.pdf","checksum":"1229aa8640bd6db610c85decf2265480","date_created":"2022-05-17T07:51:08Z","relation":"main_file"}],"project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","short":"K. Chatterjee, W. Dvořák, M. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ieee":"K. Chatterjee, W. Dvořák, M. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k.","ama":"Chatterjee K, Dvořák W, Henzinger M, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","apa":"Chatterjee, K., Dvořák, W., Henzinger, M., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","ista":"Chatterjee K, Dvořák W, Henzinger M, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253."},"doi":"10.29007/5z5k","department":[{"_id":"KrCh"}],"scopus_import":"1","volume":57,"_id":"10883","oa_version":"Published Version","quality_controlled":"1","conference":{"name":"LPAR: Logic for Programming, Artificial Intelligence and Reasoning","location":"Awassa, Ethiopia","start_date":"2018-11-17","end_date":"2018-11-21"},"external_id":{"arxiv":["1909.04983"]},"day":"23","publication_identifier":{"issn":["2398-7340"]},"acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","file_date_updated":"2022-05-17T07:51:08Z","arxiv":1,"title":"Quasipolynomial set-based symbolic algorithms for parity games","date_updated":"2025-07-10T11:50:02Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Dvořák, Wolfgang","first_name":"Wolfgang","last_name":"Dvořák"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"first_name":"Alexander","last_name":"Svozil","full_name":"Svozil, Alexander"}]},{"issue":"1","status":"public","quality_controlled":"1","month":"01","publication":"SIAM Journal on Discrete Mathematics","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1606.01814","open_access":"1"}],"extern":"1","_id":"1092","publist_id":"6284","publisher":"SIAM","volume":32,"date_created":"2018-12-11T11:50:06Z","abstract":[{"text":"A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. ","lang":"eng"}],"doi":"10.1137/16M107894X","citation":{"chicago":"Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X.","short":"F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93.","ieee":"F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” SIAM Journal on Discrete Mathematics, vol. 32, no. 1. SIAM, pp. 64–93, 2018.","mla":"Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:10.1137/16M107894X.","ista":"Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93.","ama":"Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93. doi:10.1137/16M107894X","apa":"Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. SIAM. https://doi.org/10.1137/16M107894X"},"intvolume":" 32","language":[{"iso":"eng"}],"author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","first_name":"Fatemeh"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","first_name":"Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler"},{"last_name":"Wang","first_name":"Charles","full_name":"Wang, Charles"},{"last_name":"Yu","first_name":"Josephine","full_name":"Yu, Josephine"}],"publication_status":"published","year":"2018","title":"Generalized permutohedra from probabilistic graphical models","date_published":"2018-01-01T00:00:00Z","date_updated":"2021-01-12T06:48:13Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"64-93","day":"01","oa":1,"type":"journal_article"},{"date_published":"2018-10-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publication_status":"published","oa":1,"ec_funded":1,"type":"conference","page":"185 - 214","status":"public","month":"10","intvolume":" 270","language":[{"iso":"eng"}],"publisher":"Springer","abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"date_created":"2018-12-11T11:44:08Z","date_updated":"2021-01-12T06:48:16Z","title":"Mean-field limits of particles in interaction with quantised radiation fields","author":[{"full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","last_name":"Leopold","orcid":"0000-0002-0495-6822"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"external_id":{"arxiv":["1806.10843"]},"conference":{"start_date":"2017-03-30","name":"MaLiQS: Macroscopic Limits of Quantum Systems","location":"Munich, Germany","end_date":"2017-04-01"},"arxiv":1,"day":"27","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"quality_controlled":"1","oa_version":"Preprint","publist_id":"8045","_id":"11","doi":"10.1007/978-3-030-01602-9_9","citation":{"chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9"},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"volume":270,"scopus_import":1,"department":[{"_id":"RoSe"}]},{"external_id":{"pmid":["30228202"]},"publication_identifier":{"issn":["0890-9369","1549-5477"]},"article_type":"original","day":"18","date_updated":"2024-10-14T11:19:35Z","title":"Tpr regulates the total number of nuclear pore complexes per cell nucleus","author":[{"first_name":"Asako","last_name":"McCloskey","full_name":"McCloskey, Asako"},{"full_name":"Ibarra, Arkaitz","last_name":"Ibarra","first_name":"Arkaitz"},{"orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"}],"citation":{"chicago":"McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development. Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118.","short":"A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.","mla":"McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.","ieee":"A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” Genes & Development, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.","ista":"McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331.","ama":"McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331. doi:10.1101/gad.315523.118","apa":"McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118"},"doi":"10.1101/gad.315523.118","volume":32,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/gad.315523.118","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","extern":"1","_id":"11063","oa":1,"type":"journal_article","page":"1321-1331","date_published":"2018-09-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Developmental Biology","Genetics"],"article_processing_charge":"No","year":"2018","publication_status":"published","intvolume":" 32","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory","date_created":"2022-04-07T07:45:30Z","pmid":1,"abstract":[{"text":"The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.","lang":"eng"}],"month":"09","publication":"Genes & Development","status":"public","issue":"19-20"},{"citation":{"ista":"Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221.","ama":"Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6","apa":"Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6","mla":"Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018, doi:10.1186/s13059-018-1599-6.","ieee":"J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018.","short":"J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).","chicago":"Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6."},"doi":"10.1186/s13059-018-1599-6","volume":19,"scopus_import":"1","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-018-1599-6"}],"_id":"11064","extern":"1","external_id":{"pmid":["30567591"]},"day":"20","article_type":"original","publication_identifier":{"issn":["1474-760X"]},"title":"Predicting age from the transcriptome of human dermal fibroblasts","date_updated":"2024-10-14T11:20:00Z","author":[{"first_name":"Jason G.","last_name":"Fleischer","full_name":"Fleischer, Jason G."},{"full_name":"Schulte, Roberta","last_name":"Schulte","first_name":"Roberta"},{"full_name":"Tsai, Hsiao H.","first_name":"Hsiao H.","last_name":"Tsai"},{"last_name":"Tyagi","first_name":"Swati","full_name":"Tyagi, Swati"},{"full_name":"Ibarra, Arkaitz","last_name":"Ibarra","first_name":"Arkaitz"},{"last_name":"Shokhirev","first_name":"Maxim N.","full_name":"Shokhirev, Maxim N."},{"full_name":"Huang, Ling","first_name":"Ling","last_name":"Huang"},{"last_name":"HETZER","orcid":"0000-0002-2111-992X","first_name":"Martin W","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"last_name":"Navlakha","first_name":"Saket","full_name":"Navlakha, Saket"}],"intvolume":" 19","language":[{"iso":"eng"}],"publisher":"BioMed Central","abstract":[{"text":"Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients.","lang":"eng"}],"date_created":"2022-04-07T07:45:40Z","pmid":1,"status":"public","month":"12","publication":"Genome Biology","oa":1,"type":"journal_article","article_number":"221","date_published":"2018-12-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","year":"2018"},{"intvolume":" 619","language":[{"iso":"eng"}],"publisher":"EDP Sciences","abstract":[{"text":"Distant luminous Lyman-α emitters (LAEs) are excellent targets for spectroscopic observations of galaxies in the epoch of reionisation (EoR). We present deep high-resolution (R = 5000) VLT/X-shooter observations, along with an extensive collection of photometric data of COLA1, a proposed double peaked LAE at z = 6.6. We rule out the possibility that COLA1’s emission line is an [OII] doublet at z = 1.475 on the basis of i) the asymmetric red line-profile and flux ratio of the peaks (blue/red=0.31 ± 0.03) and ii) an unphysical [OII]/Hα ratio ([OII]/Hα > 22). We show that COLA1’s observed B-band flux is explained by a faint extended foreground LAE, for which we detect Lyα and [OIII] at z = 2.142. We thus conclude that COLA1 is a real double-peaked LAE at z = 6.593, the first discovered at z > 6. COLA1 is UV luminous (M1500 = −21.6 ± 0.3), has a high equivalent width (EW0,Lyα = 120−40+50 Å) and very compact Lyα emission (r50,Lyα = 0.33−0.04+0.07 kpc). Relatively weak inferred Hβ+[OIII] line-emission from Spitzer/IRAC indicates an extremely low metallicity of Z < 1/20 Z⊙ or reduced strength of nebular lines due to high escape of ionising photons. The small Lyα peak separation of 220 ± 20 km s−1 implies a low HI column density and an ionising photon escape fraction of ≈15 − 30%, providing the first direct evidence that such galaxies contribute actively to the reionisation of the Universe at z > 6. Based on simple estimates, we find that COLA1 could have provided just enough photons to reionise its own ≈0.3 pMpc (2.3 cMpc) bubble, allowing the blue Lyα line to be observed. However, we also discuss alternative scenarios explaining the detected double peaked nature of COLA1. Our results show that future high-resolution observations of statistical samples of double peaked LAEs at z > 5 are a promising probe of the occurrence of ionised regions around galaxies in the EoR.","lang":"eng"}],"date_created":"2022-07-06T11:14:23Z","publication":"Astronomy & Astrophysics","status":"public","month":"11","oa":1,"type":"journal_article","article_number":"A136","date_published":"2018-11-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / dark ages / reionization / first stars / techniques: spectroscopic / intergalactic medium"],"article_processing_charge":"No","publication_status":"published","doi":"10.1051/0004-6361/201833528","citation":{"ista":"Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. 2018. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 619, A136.","apa":"Matthee, J. J., Sobral, D., Gronke, M., Paulino-Afonso, A., Stefanon, M., & Röttgering, H. (2018). Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833528","ama":"Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201833528","mla":"Matthee, Jorryt J., et al. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics, vol. 619, A136, EDP Sciences, 2018, doi:10.1051/0004-6361/201833528.","ieee":"J. J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, and H. Röttgering, “Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.","short":"J.J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, H. Röttgering, Astronomy & Astrophysics 619 (2018).","chicago":"Matthee, Jorryt J, David Sobral, Max Gronke, Ana Paulino-Afonso, Mauro Stefanon, and Huub Röttgering. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833528."},"volume":619,"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1805.11621","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","_id":"11508","extern":"1","external_id":{"arxiv":["1805.11621"]},"arxiv":1,"article_type":"original","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"acknowledgement":"JM acknowledges the award of a Huygens PhD fellowship from Leiden University. MG acknowledges support from NASA grant NNX17AK58G. APA, PhD::SPACE fellow, acknowledges support from the FCT through the fellowship PD/BD/52706/2014. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 294.A-5018, 098.A-0819, 099.A-0254 and 0100.A-0213. We are grateful for the excellent data-sets from the COSMOS and UltraVISTA survey teams. This research was supported by the Munich Institute for Astro- and Particle Physics (MIAPP) of the DFG cluster of excellence “Origin and Structure of the Universe”. We thank the referee for their comments that improved the paper. We also thank Christoph Behrens, Len Cowie, Koki Kakiichi, Peter Laursen, Charlotte Mason, Eros Vanzella, Lewis Weinberger and Johannes Zabl for discussions. We have benefited from the public available programming language Python, including the numpy, matplotlib, scipy and astropy packages (Hunter 2007; Astropy Collaboration 2013), the astronomical imaging tools Swarp (Bertin 2010) and ds9 and the Topcat analysis tool (Taylor 2013).","day":"19","date_updated":"2024-10-14T11:31:36Z","title":"Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe","author":[{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"first_name":"Max","last_name":"Gronke","full_name":"Gronke, Max"},{"last_name":"Paulino-Afonso","first_name":"Ana","full_name":"Paulino-Afonso, Ana"},{"full_name":"Stefanon, Mauro","last_name":"Stefanon","first_name":"Mauro"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"}]},{"date_published":"2018-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2018","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: formation"],"oa":1,"type":"journal_article","page":"1170-1184","month":"07","status":"public","publication":"Monthly Notices of the Royal Astronomical Society","issue":"1","intvolume":" 478","language":[{"iso":"eng"}],"publisher":"Oxford University Press","abstract":[{"text":"We investigate the morphology of the [C II] emission in a sample of ‘normal’ star-forming galaxies at 5 < z < 7.2 in relation to their UV (rest-frame) counterpart. We use new Atacama Large Millimetre/submillimetre Array (ALMA) observations of galaxies at z ∼ 6–7, as well as a careful re-analysis of archival ALMA data. In total 29 galaxies were analysed, 21 of which are detected in [C II]. For several of the latter the [C II] emission breaks into multiple components. Only a fraction of these [C II] components, if any, is associated with the primary UV systems, while the bulk of the [C II] emission is associated either with fainter UV components, or not associated with any UV counterpart at the current limits. By taking into account the presence of all these components, we find that the L[CII]–SFR (star formation rate) relation at early epochs is fully consistent with the local relation, but it has a dispersion of 0.48 ± 0.07 dex, which is about two times larger than observed locally. We also find that the deviation from the local L[CII]–SFR relation has a weak anticorrelation with the EW(Ly α). The morphological analysis also reveals that [C II] emission is generally much more extended than the UV emission. As a consequence, these primordial galaxies are characterized by a [C II] surface brightness generally much lower than expected from the local Σ[CII]−ΣSFR relation. These properties are likely a consequence of a combination of different effects, namely gas metallicity, [C II] emission from obscured star-forming regions, strong variations of the ionization parameter, and circumgalactic gas in accretion or ejected by these primeval galaxies.","lang":"eng"}],"date_created":"2022-07-11T08:05:42Z","title":"Kiloparsec-scale gaseous clumps and star formation at z = 5–7","date_updated":"2022-08-19T06:58:06Z","author":[{"full_name":"Carniani, S","first_name":"S","last_name":"Carniani"},{"full_name":"Maiolino, R","last_name":"Maiolino","first_name":"R"},{"full_name":"Amorin, R","last_name":"Amorin","first_name":"R"},{"first_name":"L","last_name":"Pentericci","full_name":"Pentericci, L"},{"last_name":"Pallottini","first_name":"A","full_name":"Pallottini, A"},{"full_name":"Ferrara, A","first_name":"A","last_name":"Ferrara"},{"full_name":"Willott, C J","last_name":"Willott","first_name":"C J"},{"full_name":"Smit, R","first_name":"R","last_name":"Smit"},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"first_name":"D","last_name":"Sobral","full_name":"Sobral, D"},{"first_name":"P","last_name":"Santini","full_name":"Santini, P"},{"first_name":"M","last_name":"Castellano","full_name":"Castellano, M"},{"full_name":"De Barros, S","last_name":"De Barros","first_name":"S"},{"first_name":"A","last_name":"Fontana","full_name":"Fontana, A"},{"full_name":"Grazian, A","first_name":"A","last_name":"Grazian"},{"first_name":"L","last_name":"Guaita","full_name":"Guaita, L"}],"external_id":{"arxiv":["1712.03985"]},"arxiv":1,"day":"01","article_type":"original","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"acknowledgement":"This paper makes use of the following ALMA data:\r\nADS/JAO.ALMA#2012.1.00719.S, ADS/JAO.ALMA#2012.A.00040.S,\r\nADS/JAO.ALMA#2013.A.00433.S, ADS/JAO.ALMA#2011.0.00115.S,\r\nADS/JAO.ALMA#2012.1.00033.S, ADS/JAO.ALMA#2012.1.00523.S,\r\nADS/JAO.ALMA#2013.1.00815.S, ADS/JAO.ALMA#2015.1.00834.S.,\r\nADS/JAO.ALMA#2015.1.01105.S, AND ADS/JAO.ALMA#2016.1.01240.S\r\nwhich can be retrieved from the ALMA data archive:\r\nhttps://almascience.eso.org/ alma-data/archive. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. We are grateful to G. Jones to for providing his [C II] flux maps. RM and SC acknowledge support by the Science and Technology Facilities Council (STFC). RM acknowledges ERC Advanced Grant 695671 ‘QUENCH’. AF acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120.","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.03985","open_access":"1"}],"_id":"11555","extern":"1","doi":"10.1093/mnras/sty1088","citation":{"ista":"Carniani S, Maiolino R, Amorin R, Pentericci L, Pallottini A, Ferrara A, Willott CJ, Smit R, Matthee JJ, Sobral D, Santini P, Castellano M, De Barros S, Fontana A, Grazian A, Guaita L. 2018. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 478(1), 1170–1184.","ama":"Carniani S, Maiolino R, Amorin R, et al. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 2018;478(1):1170-1184. doi:10.1093/mnras/sty1088","apa":"Carniani, S., Maiolino, R., Amorin, R., Pentericci, L., Pallottini, A., Ferrara, A., … Guaita, L. (2018). Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1088","ieee":"S. Carniani et al., “Kiloparsec-scale gaseous clumps and star formation at z = 5–7,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1. Oxford University Press, pp. 1170–1184, 2018.","mla":"Carniani, S., et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1, Oxford University Press, 2018, pp. 1170–84, doi:10.1093/mnras/sty1088.","short":"S. Carniani, R. Maiolino, R. Amorin, L. Pentericci, A. Pallottini, A. Ferrara, C.J. Willott, R. Smit, J.J. Matthee, D. Sobral, P. Santini, M. Castellano, S. De Barros, A. Fontana, A. Grazian, L. Guaita, Monthly Notices of the Royal Astronomical Society 478 (2018) 1170–1184.","chicago":"Carniani, S, R Maiolino, R Amorin, L Pentericci, A Pallottini, A Ferrara, C J Willott, et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1088."},"volume":478,"scopus_import":"1"},{"article_type":"original","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"acknowledgement":"We thank the anonymous reviewer for their timely and constructive comments that greatly helped us to improve the manuscript. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. IRS acknowledges support from the ERC Advanced Grant DUSTYGAL (321334), STFC (ST/P000541/1), and a Royal Society/Wolfson Merit Award. PNB is grateful for support from STFC via grant ST/M001229/1. We thank Anne Verhamme, Kimihiko Nakajima, Ryan Trainor, Sangeeta Malhotra, Max Gronke, James Rhoads, Fang Xia An, Matthew Hayes, Takashi Kojima, Mark Dijkstra, and Anne Jaskot for many helpful and engaging discussions, particularly during the SnowCLAW Ly α workshop. We thank Bruno Ribeiro, Stephane Charlot, and Joseph Caruana for comments on the manuscript. The authors would also like to thank Ingrid Tengs, Meg Singleton, Ali Khostovan, and Sara Perez for participating in part of the observations. We also thank Joao Calhau, Leah Morabito, Sergio Santos, and Aayush Saxena for their assistance with the narrow-band observations which allowed to select some of the sour ces. Based on observations obtained with the William Herschel Telescope, program: W16AN004; the Very Large Telescope, programs: 098.A-0819 & 099.A-0254; and the Keck II telescope, program: C267D. 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.A-0943, 098.A-0819, 099.A-0254 and 179.A-2005. The authors acknowledge the award of service time (SW2014b20) on the 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. The authors would also like to thank all the extremely helpful observatory staff that have greatly contributed towards our observations, particularly Fiona Riddick, Lilian Dominguez, Florencia Jimenez, and Ian Skillen. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), 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.","day":"01","arxiv":1,"external_id":{"arxiv":["1802.10102"]},"author":[{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"full_name":"Darvish, Behnam","first_name":"Behnam","last_name":"Darvish"},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"full_name":"Best, Philip N","first_name":"Philip N","last_name":"Best"},{"first_name":"Lara","last_name":"Alegre","full_name":"Alegre, Lara"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"},{"first_name":"Bahram","last_name":"Mobasher","full_name":"Mobasher, Bahram"},{"first_name":"Ana","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana"},{"full_name":"Stroe, Andra","last_name":"Stroe","first_name":"Andra"},{"full_name":"Oteo, Iván","last_name":"Oteo","first_name":"Iván"}],"date_updated":"2022-08-19T07:01:08Z","title":"The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN","scopus_import":"1","volume":477,"citation":{"ista":"Sobral D, Matthee JJ, Darvish B, Smail I, Best PN, Alegre L, Röttgering H, Mobasher B, Paulino-Afonso A, Stroe A, Oteo I. 2018. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 477(2), 2817–2840.","ama":"Sobral D, Matthee JJ, Darvish B, et al. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 2018;477(2):2817-2840. doi:10.1093/mnras/sty782","apa":"Sobral, D., Matthee, J. J., Darvish, B., Smail, I., Best, P. N., Alegre, L., … Oteo, I. (2018). The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty782","mla":"Sobral, David, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2, Oxford University Press, 2018, pp. 2817–40, doi:10.1093/mnras/sty782.","ieee":"D. Sobral et al., “The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN,” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2. Oxford University Press, pp. 2817–2840, 2018.","short":"D. Sobral, J.J. Matthee, B. Darvish, I. Smail, P.N. Best, L. Alegre, H. Röttgering, B. Mobasher, A. Paulino-Afonso, A. Stroe, I. Oteo, Monthly Notices of the Royal Astronomical Society 477 (2018) 2817–2840.","chicago":"Sobral, David, Jorryt J Matthee, Behnam Darvish, Ian Smail, Philip N Best, Lara Alegre, Huub Röttgering, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty782."},"doi":"10.1093/mnras/sty782","_id":"11557","extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.10102","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","page":"2817-2840","type":"journal_article","oa":1,"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: starburst","cosmology: observations"],"article_processing_charge":"No","year":"2018","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-06-01T00:00:00Z","date_created":"2022-07-12T07:18:02Z","abstract":[{"lang":"eng","text":"Deep narrow-band surveys have revealed a large population of faint Ly α emitters (LAEs) in the distant Universe, but relatively little is known about the most luminous sources (LLyα≳1042.7 erg s−1; LLyα≳L∗Lyα). Here we present the spectroscopic follow-up of 21 luminous LAEs at z ∼ 2–3 found with panoramic narrow-band surveys over five independent extragalactic fields (≈4 × 106 Mpc3 surveyed at z ∼ 2.2 and z ∼ 3.1). We use WHT/ISIS, Keck/DEIMOS, and VLT/X-SHOOTER to study these sources using high ionization UV lines. Luminous LAEs at z ∼ 2–3 have blue UV slopes (β=−2.0+0.3−0.1) and high Ly α escape fractions (50+20−15 per cent) and span five orders of magnitude in UV luminosity (MUV ≈ −19 to −24). Many (70 per cent) show at least one high ionization rest-frame UV line such as C IV, N V, C III], He II or O III], typically blue-shifted by ≈100–200 km s−1 relative to Ly α. Their Ly α profiles reveal a wide variety of shapes, including significant blue-shifted components and widths from 200 to 4000 km s−1. Overall, 60 ± 11 per cent appear to be active galactic nucleus (AGN) dominated, and at LLyα > 1043.3 erg s−1 and/or MUV < −21.5 virtually all LAEs are AGNs with high ionization parameters (log U = 0.6 ± 0.5) and with metallicities of ≈0.5 − 1 Z⊙. Those lacking signatures of AGNs (40 ± 11 per cent) have lower ionization parameters (logU=−3.0+1.6−0.9 and log ξion = 25.4 ± 0.2) and are apparently metal-poor sources likely powered by young, dust-poor ‘maximal’ starbursts. Our results show that luminous LAEs at z ∼ 2–3 are a diverse population and that 2×L∗Lyα and 2×M∗UV mark a sharp transition in the nature of LAEs, from star formation dominated to AGN dominated."}],"publisher":"Oxford University Press","language":[{"iso":"eng"}],"intvolume":" 477","issue":"2","status":"public","publication":"Monthly Notices of the Royal Astronomical Society","month":"06"},{"oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.04451","open_access":"1"}],"_id":"11558","extern":"1","citation":{"ieee":"D. Sobral et al., “Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6,” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4. Oxford University Press, pp. 4725–4752, 2018.","mla":"Sobral, David, et al. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4, Oxford University Press, 2018, pp. 4725–52, doi:10.1093/mnras/sty378.","ama":"Sobral D, Santos S, Matthee JJ, et al. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 2018;476(4):4725-4752. doi:10.1093/mnras/sty378","ista":"Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Ribeiro B, Calhau J, Khostovan AA. 2018. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 476(4), 4725–4752.","apa":"Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Ribeiro, B., Calhau, J., & Khostovan, A. A. (2018). Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty378","chicago":"Sobral, David, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Bruno Ribeiro, João Calhau, and Ali A Khostovan. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty378.","short":"D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, B. Ribeiro, J. Calhau, A.A. Khostovan, Monthly Notices of the Royal Astronomical Society 476 (2018) 4725–4752."},"doi":"10.1093/mnras/sty378","volume":476,"scopus_import":"1","title":"Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6","date_updated":"2022-08-19T07:04:45Z","author":[{"full_name":"Sobral, David","first_name":"David","last_name":"Sobral"},{"full_name":"Santos, Sérgio","first_name":"Sérgio","last_name":"Santos"},{"last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Paulino-Afonso, Ana","first_name":"Ana","last_name":"Paulino-Afonso"},{"full_name":"Ribeiro, Bruno","last_name":"Ribeiro","first_name":"Bruno"},{"full_name":"Calhau, João","last_name":"Calhau","first_name":"João"},{"full_name":"Khostovan, Ali A","first_name":"Ali A","last_name":"Khostovan"}],"external_id":{"arxiv":["1712.04451"]},"arxiv":1,"day":"01","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"article_type":"original","acknowledgement":"We thank the anonymous referee for their constructive comments that helped us improve the manuscript. DS acknowledges the hospitality of the IAC and a Severo Ochoa visiting grant. SS and JC acknowledge studentships from the Lancaster University. JM acknowledges a Huygens PhD fellowship from Leiden University. APA acknowledges financial support from the Science and Technology Foundation (FCT, Portugal) through research grants UID/FIS/04434/2013 and fellowship PD/BD/52706/2014. The authors thank Alyssa Drake, Kimihiko Nakajima, Yuichi Harikane, Max Gronke, Irene Shivaei, Helmut Dannerbauer, Huub Rottgering, ¨ Marius Eide, and Masami Ouchi for many engaging and stimulating discussions. We also thank Sara Perez, Alex Bennett, and Tom Rose for their involvement in the early stages of this project. Based on data products from observations made with European Southern Observatory (ESO) Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 097.A 0943,\r\n098.A-0819, 099.A-0254, and 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Based on observations using the WFC on the 2.5 m INT, as part of programmes 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118, and 2016AN001. The INT is 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 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 (CFHTLS), a collaborative project of NRC and CNRS.\r\nWe are grateful to the CFHTLS, COSMOS-UltraVISTA, and COSMOS survey teams. We are also unmeasurably thankful to the pioneering and continuous work from previous Ly α surveys’ teams. Without these previous Ly α and the wider reach legacy surveys, this research would have been impossible. We also thank the VUDS team for making available spectroscopic redshifts from data obtained with VIMOS at the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Programme 185.A-0791. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY and SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2005). We publicly release a catalogue with all LAEs used in this paper (SC4K), so it can be freely explored by the community (see five example entries in Table A1).","publication":"Monthly Notices of the Royal Astronomical Society","status":"public","month":"06","issue":"4","intvolume":" 476","language":[{"iso":"eng"}],"publisher":"Oxford University Press","date_created":"2022-07-12T10:41:08Z","abstract":[{"lang":"eng","text":"We present and explore deep narrow- and medium-band data obtained with the Subaru and the Isaac Newton Telescopes in the ∼2 deg2 COSMOS field. We use these data as an extremely wide, low-resolution (R ∼ 20–80) Integral Field Unit survey to slice through the COSMOS field and obtain a large sample of ∼4000 Ly α emitters (LAEs) from z ∼ 2 to 6 in 16 redshift slices (SC4K). We present new Ly α luminosity functions (LFs) covering a comoving volume of ∼108 Mpc3. SC4K extensively complements ultradeep surveys, jointly covering over 4 dex in Ly α luminosity and revealing a global (2.5 < z < 6) synergy LF with α=−1.93+0.12−0.12, log10Φ∗Lyα=−3.45+0.22−0.29 Mpc−3, and log10L∗Lyα=42.93+0.15−0.11 erg s−1. The Schechter component of the Ly α LF reveals a factor ∼5 rise in L∗Lyα and a ∼7 × decline in Φ∗Lyα from z ∼ 2 to 6. The data reveal an extra power-law (or Schechter) component above LLy α ≈ 1043.3 erg s−1 at z ∼ 2.2–3.5 and we show that it is partially driven by X-ray and radio active galactic nucleus (AGN), as their Ly α LF resembles the excess. The power-law component vanishes and/or is below our detection limits above z > 3.5, likely linked with the evolution of the AGN population. The Ly α luminosity density rises by a factor ∼2 from z ∼ 2 to 3 but is then found to be roughly constant (1.1+0.2−0.2×1040 erg s−1 Mpc−3) to z ∼ 6, despite the ∼0.7 dex drop in ultraviolet (UV) luminosity density. The Ly α/UV luminosity density ratio rises from 4 ± 1 per cent to 30 ± 6 per cent from z ∼ 2.2 to 6. Our results imply a rise of a factor of ≈2 in the global ionization efficiency (ξion) and a factor ≈4 ± 1 in the Ly α escape fraction from z ∼ 2 to 6, hinting for evolution in both the typical burstiness/stellar populations and even more so in the typical interstellar medium conditions allowing Ly α photons to escape."}],"date_published":"2018-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: high-redshift","galaxies: luminosity function","mass function","galaxies: statistics"],"article_processing_charge":"No","year":"2018","oa":1,"type":"journal_article","page":"4725-4752"},{"issue":"1","publication":"Monthly Notices of the Royal Astronomical Society: Letters","status":"public","month":"09","publisher":"Oxford University Press","date_created":"2022-07-14T12:49:47Z","abstract":[{"text":"Observations show that star-forming galaxies reside on a tight 3D plane between mass, gas-phase metallicity, and star formation rate (SFR), which can be explained by the interplay between metal-poor gas inflows, SFR and outflows. However, different metals are released on different time-scales, which may affect the slope of this relation. Here, we use central, star-forming galaxies with Mstar = 109.0–10.5 M⊙ from the EAGLE hydrodynamical simulation to examine 3D relations between mass, SFR, and chemical enrichment using absolute and relative C, N, O, and Fe abundances. We show that the scatter is smaller when gas-phase α-enhancement is used rather than metallicity. A similar plane also exists for stellar α-enhancement, implying that present-day specific SFRs are correlated with long time-scale star formation histories. Between z = 0 and 1, the α-enhancement plane is even more insensitive to redshift than the plane using metallicity. However, it evolves at z > 1 due to lagging iron yields. At fixed mass, galaxies with higher SFRs have star formation histories shifted towards late times, are more α-enhanced, and this α-enhancement increases with redshift as observed. These findings suggest that relations between physical properties inferred from observations may be affected by systematic variations in α-enhancements.","lang":"eng"}],"intvolume":" 479","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: formation","galaxies: star formation"],"year":"2018","date_published":"2018-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"L34 - L39","oa":1,"type":"journal_article","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.06786","open_access":"1"}],"extern":"1","_id":"11584","volume":479,"scopus_import":"1","doi":"10.1093/mnrasl/sly093","citation":{"ieee":"J. J. Matthee and J. Schaye, “Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement,” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1. Oxford University Press, pp. L34–L39, 2018.","mla":"Matthee, Jorryt J., and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1, Oxford University Press, 2018, pp. L34–39, doi:10.1093/mnrasl/sly093.","ista":"Matthee JJ, Schaye J. 2018. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 479(1), L34–L39.","ama":"Matthee JJ, Schaye J. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 2018;479(1):L34-L39. doi:10.1093/mnrasl/sly093","apa":"Matthee, J. J., & Schaye, J. (2018). Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press. https://doi.org/10.1093/mnrasl/sly093","chicago":"Matthee, Jorryt J, and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press, 2018. https://doi.org/10.1093/mnrasl/sly093.","short":"J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society: Letters 479 (2018) L34–L39."},"author":[{"first_name":"Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"first_name":"Joop","last_name":"Schaye","full_name":"Schaye, Joop"}],"title":"Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement","date_updated":"2024-10-14T11:37:53Z","arxiv":1,"day":"01","acknowledgement":"We thank the anonymous referee for their constructive comments. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Jarle Brinchmann, Rob Crain and David Sobral for discussions. We acknowledge the use of the TOPCAT software (Taylor 2013) for assisting in rapid exploration of multidimensional data sets and the use of PYTHON and its NUMPY, MATPLOTLIB, and PANDAS packages.","article_type":"original","publication_identifier":{"eissn":["1745-3933"],"issn":["1745-3925"]},"external_id":{"arxiv":["1802.06786"]}},{"abstract":[{"text":"Asteroseismology provides global stellar parameters such as masses, radii, or surface gravities using mean global seismic parameters and effective temperature for thousands of low-mass stars (0.8 M⊙ < M < 3 M⊙). This methodology has been successfully applied to stars in which acoustic modes excited by turbulent convection are measured. Other methods such as the Flicker technique can also be used to determine stellar surface gravities, but only works for log g above 2.5 dex. In this work, we present a new metric called FliPer (Flicker in spectral power density, in opposition to the standard Flicker measurement which is computed in the time domain); it is able to extend the range for which reliable surface gravities can be obtained (0.1 < log g < 4.6 dex) without performing any seismic analysis for stars brighter than Kp < 14. FliPer takes into account the average variability of a star measured in the power density spectrum in a given range of frequencies. However, FliPer values calculated on several ranges of frequency are required to better characterize a star. Using a large set of asteroseismic targets it is possible to calibrate the behavior of surface gravity with FliPer through machine learning. This calibration made with a random forest regressor covers a wide range of surface gravities from main-sequence stars to subgiants and red giants, with very small uncertainties from 0.04 to 0.1 dex. FliPer values can be inserted in automatic global seismic pipelines to either give an estimation of the stellar surface gravity or to assess the quality of the seismic results by detecting any outliers in the obtained νmax values. FliPer also constrains the surface gravities of main-sequence dwarfs using only long-cadence data for which the Nyquist frequency is too low to measure the acoustic-mode properties.","lang":"eng"}],"date_created":"2022-07-18T14:37:39Z","publisher":"EDP Sciences","language":[{"iso":"eng"}],"intvolume":" 620","status":"public","month":"12","publication":"Astronomy & Astrophysics","type":"journal_article","oa":1,"publication_status":"published","year":"2018","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","asteroseismology / methods","data analysis / stars","oscillations"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-12-01T00:00:00Z","article_number":"A38","scopus_import":"1","volume":620,"doi":"10.1051/0004-6361/201833106","citation":{"chicago":"Bugnet, Lisa Annabelle, R. A. García, G. R. Davies, S. Mathur, E. Corsaro, O. J. Hall, and B. M. Rendle. “FliPer: A Global Measure of Power Density to Estimate Surface Gravities of Main-Sequence Solar-like Stars and Red Giants.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833106.","short":"L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, E. Corsaro, O.J. Hall, B.M. Rendle, Astronomy & Astrophysics 620 (2018).","mla":"Bugnet, Lisa Annabelle, et al. “FliPer: A Global Measure of Power Density to Estimate Surface Gravities of Main-Sequence Solar-like Stars and Red Giants.” Astronomy & Astrophysics, vol. 620, A38, EDP Sciences, 2018, doi:10.1051/0004-6361/201833106.","ieee":"L. A. Bugnet et al., “FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants,” Astronomy & Astrophysics, vol. 620. EDP Sciences, 2018.","ama":"Bugnet LA, García RA, Davies GR, et al. FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. 2018;620. doi:10.1051/0004-6361/201833106","apa":"Bugnet, L. A., García, R. A., Davies, G. R., Mathur, S., Corsaro, E., Hall, O. J., & Rendle, B. M. (2018). FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833106","ista":"Bugnet LA, García RA, Davies GR, Mathur S, Corsaro E, Hall OJ, Rendle BM. 2018. FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. 620, A38."},"extern":"1","_id":"11618","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1809.05105","open_access":"1"}],"day":"01","acknowledgement":"We thank the anonymous referee for the very useful comments. We would also like to thank M. Benbakoura for his help in analyzing the light curves of several binary systems included in our set of stars. L.B. and R.A.G. acknowledge the support from PLATO and GOLF CNES grants. S.M. acknowledges support from the National Aeronautics and Space Administration under Grant NNX15AF13G, the National Science Foundation grant AST-1411685, and the Ramon y Cajal fellowship no. RYC-2015-17697. E.C. is funded by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 664931. O.J.H and B.M.R. acknowledge the support of the UK Science and Technology Facilities Council (STFC). Funding for the Stellar Astrophysics Centre is provided by the Danish National Research Foundation (Grant DNRF106). This research has made use of NASA’s Astrophysics Data System. 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.","article_type":"original","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"arxiv":1,"external_id":{"arxiv":["1809.05105"]},"author":[{"first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle"},{"full_name":"García, R. A.","last_name":"García","first_name":"R. A."},{"last_name":"Davies","first_name":"G. R.","full_name":"Davies, G. R."},{"full_name":"Mathur, S.","last_name":"Mathur","first_name":"S."},{"first_name":"E.","last_name":"Corsaro","full_name":"Corsaro, E."},{"full_name":"Hall, O. J.","first_name":"O. J.","last_name":"Hall"},{"full_name":"Rendle, B. M.","last_name":"Rendle","first_name":"B. M."}],"title":"FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants","date_updated":"2024-10-14T11:40:17Z"},{"oa":1,"type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","planetary systems / planets and satellites","detection / planets and satellites","fundamental parameters / planets and satellites","terrestrial planets / stars","fundamental parameters"],"year":"2018","article_processing_charge":"No","publication_status":"published","article_number":"L10","date_published":"2018-11-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"EDP Sciences","abstract":[{"lang":"eng","text":"We report on the confirmation and mass determination of π Men c, the first transiting planet discovered by NASA’s TESS space mission. π Men is a naked-eye (V = 5.65 mag), quiet G0 V star that was previously known to host a sub-stellar companion (π Men b) on a longperiod (Porb = 2091 days), eccentric (e = 0.64) orbit. Using TESS time-series photometry, combined with Gaia data, published UCLES at AAT Doppler measurements, and archival HARPS at ESO-3.6m radial velocities, we found that π Men c is a close-in planet with an orbital period of Porb = 6.27 days, a mass of Mc = 4.52 ± 0.81 M⊕, and a radius of Rc = 2.06 ± 0.03 R⊕. Based on the planet’s orbital period and size, π Men c is a super-Earth located at, or close to, the radius gap, while its mass and bulk density suggest it may have held on to a significant atmosphere. Because of the brightness of the host star, this system is highly suitable for a wide range of further studies to characterize the planetary atmosphere and dynamical properties. We also performed an asteroseismic analysis of the TESS data and detected a hint of power excess consistent with the seismic values expected for this star, although this result depends on the photometric aperture used to extract the light curve. This marginal detection is expected from pre-launch simulations hinting at the asteroseismic potential of the TESS mission for longer, multi-sector observations and/or for more evolved bright stars."}],"date_created":"2022-07-18T14:41:16Z","intvolume":" 619","language":[{"iso":"eng"}],"publication":"Astronomy & Astrophysics","status":"public","month":"11","arxiv":1,"article_type":"letter_note","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"day":"22","external_id":{"arxiv":["1809.07573"]},"author":[{"last_name":"Gandolfi","first_name":"D.","full_name":"Gandolfi, D."},{"full_name":"Barragán, O.","last_name":"Barragán","first_name":"O."},{"full_name":"Livingston, J. H.","last_name":"Livingston","first_name":"J. H."},{"full_name":"Fridlund, M.","first_name":"M.","last_name":"Fridlund"},{"full_name":"Justesen, A. B.","first_name":"A. B.","last_name":"Justesen"},{"first_name":"S.","last_name":"Redfield","full_name":"Redfield, S."},{"last_name":"Fossati","first_name":"L.","full_name":"Fossati, L."},{"full_name":"Mathur, S.","first_name":"S.","last_name":"Mathur"},{"full_name":"Grziwa, S.","first_name":"S.","last_name":"Grziwa"},{"full_name":"Cabrera, J.","first_name":"J.","last_name":"Cabrera"},{"first_name":"R. A.","last_name":"García","full_name":"García, R. A."},{"first_name":"C. M.","last_name":"Persson","full_name":"Persson, C. M."},{"full_name":"Van Eylen, V.","first_name":"V.","last_name":"Van Eylen"},{"full_name":"Hatzes, A. P.","first_name":"A. P.","last_name":"Hatzes"},{"full_name":"Hidalgo, D.","last_name":"Hidalgo","first_name":"D."},{"full_name":"Albrecht, S.","first_name":"S.","last_name":"Albrecht"},{"last_name":"Bugnet","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"first_name":"W. D.","last_name":"Cochran","full_name":"Cochran, W. D."},{"full_name":"Csizmadia, Sz.","last_name":"Csizmadia","first_name":"Sz."},{"full_name":"Deeg, H.","first_name":"H.","last_name":"Deeg"},{"full_name":"Eigmüller, Ph.","first_name":"Ph.","last_name":"Eigmüller"},{"full_name":"Endl, M.","first_name":"M.","last_name":"Endl"},{"full_name":"Erikson, A.","first_name":"A.","last_name":"Erikson"},{"last_name":"Esposito","first_name":"M.","full_name":"Esposito, M."},{"last_name":"Guenther","first_name":"E.","full_name":"Guenther, E."},{"first_name":"J.","last_name":"Korth","full_name":"Korth, J."},{"last_name":"Luque","first_name":"R.","full_name":"Luque, R."},{"first_name":"P.","last_name":"Montañes Rodríguez","full_name":"Montañes Rodríguez, P."},{"full_name":"Nespral, D.","last_name":"Nespral","first_name":"D."},{"full_name":"Nowak, G.","first_name":"G.","last_name":"Nowak"},{"last_name":"Pätzold","first_name":"M.","full_name":"Pätzold, M."},{"first_name":"J.","last_name":"Prieto-Arranz","full_name":"Prieto-Arranz, J."}],"date_updated":"2022-08-22T07:43:29Z","title":"TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae","volume":619,"scopus_import":"1","doi":"10.1051/0004-6361/201834289","citation":{"chicago":"Gandolfi, D., O. Barragán, J. H. Livingston, M. Fridlund, A. B. Justesen, S. Redfield, L. Fossati, et al. “TESS’s First Planet: A Super-Earth Transiting the Naked-Eye Star π Mensae.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201834289.","short":"D. Gandolfi, O. Barragán, J.H. Livingston, M. Fridlund, A.B. Justesen, S. Redfield, L. Fossati, S. Mathur, S. Grziwa, J. Cabrera, R.A. García, C.M. Persson, V. Van Eylen, A.P. Hatzes, D. Hidalgo, S. Albrecht, L.A. Bugnet, W.D. Cochran, S. Csizmadia, H. Deeg, P. Eigmüller, M. Endl, A. Erikson, M. Esposito, E. Guenther, J. Korth, R. Luque, P. Montañes Rodríguez, D. Nespral, G. Nowak, M. Pätzold, J. Prieto-Arranz, Astronomy & Astrophysics 619 (2018).","ieee":"D. Gandolfi et al., “TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.","mla":"Gandolfi, D., et al. “TESS’s First Planet: A Super-Earth Transiting the Naked-Eye Star π Mensae.” Astronomy & Astrophysics, vol. 619, L10, EDP Sciences, 2018, doi:10.1051/0004-6361/201834289.","apa":"Gandolfi, D., Barragán, O., Livingston, J. H., Fridlund, M., Justesen, A. B., Redfield, S., … Prieto-Arranz, J. (2018). TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834289","ista":"Gandolfi D, Barragán O, Livingston JH, Fridlund M, Justesen AB, Redfield S, Fossati L, Mathur S, Grziwa S, Cabrera J, García RA, Persson CM, Van Eylen V, Hatzes AP, Hidalgo D, Albrecht S, Bugnet LA, Cochran WD, Csizmadia S, Deeg H, Eigmüller P, Endl M, Erikson A, Esposito M, Guenther E, Korth J, Luque R, Montañes Rodríguez P, Nespral D, Nowak G, Pätzold M, Prieto-Arranz J. 2018. TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. 619, L10.","ama":"Gandolfi D, Barragán O, Livingston JH, et al. TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201834289"},"main_file_link":[{"url":"https://arxiv.org/abs/1809.07573","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","extern":"1","_id":"11619"},{"language":[{"iso":"eng"}],"intvolume":" 478","abstract":[{"lang":"eng","text":"We report the discovery and characterization of HD 89345b (K2-234b; EPIC 248777106b), a Saturn-sized planet orbiting a slightly evolved star. HD 89345 is a bright star (V = 9.3 mag) observed by the K2 mission with 1 min time sampling. It exhibits solar-like oscillations. We conducted asteroseismology to determine the parameters of the star, finding the mass and radius to be 1.12+0.04−0.01M⊙ and 1.657+0.020−0.004R⊙, respectively. The star appears to have recently left the main sequence, based on the inferred age, 9.4+0.4−1.3Gyr, and the non-detection of mixed modes. The star hosts a ‘warm Saturn’ (P = 11.8 d, Rp = 6.86 ± 0.14 R⊕). Radial-velocity follow-up observations performed with the FIbre-fed Echelle Spectrograph, HARPS, and HARPS-N spectrographs show that the planet has a mass of 35.7 ± 3.3 M⊕. The data also show that the planet’s orbit is eccentric (e ≈ 0.2). An investigation of the rotational splitting of the oscillation frequencies of the star yields no conclusive evidence on the stellar inclination angle. We further obtained Rossiter–McLaughlin observations, which result in a broad posterior of the stellar obliquity. The planet seems to confirm to the same patterns that have been observed for other sub-Saturns regarding planet mass and multiplicity, orbital eccentricity, and stellar metallicity."}],"date_created":"2022-07-18T14:43:17Z","publisher":"Oxford University Press","status":"public","month":"08","publication":"Monthly Notices of the Royal Astronomical Society","issue":"4","type":"journal_article","oa":1,"page":"4866-4880","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-08-01T00:00:00Z","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","asteroseismology","planets and satellites: composition","planets and satellites: formation","planets and satellites: fundamental parameters"],"year":"2018","publication_status":"published","citation":{"mla":"Van Eylen, V., et al. “HD 89345: A Bright Oscillating Star Hosting a Transiting Warm Saturn-Sized Planet Observed by K2.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 4, Oxford University Press, 2018, pp. 4866–80, doi:10.1093/mnras/sty1390.","ieee":"V. Van Eylen et al., “HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 4. Oxford University Press, pp. 4866–4880, 2018.","ama":"Van Eylen V, Dai F, Mathur S, et al. HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. 2018;478(4):4866-4880. doi:10.1093/mnras/sty1390","apa":"Van Eylen, V., Dai, F., Mathur, S., Gandolfi, D., Albrecht, S., Fridlund, M., … Smith, A. M. S. (2018). HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1390","ista":"Van Eylen V, Dai F, Mathur S, Gandolfi D, Albrecht S, Fridlund M, García RA, Guenther E, Hjorth M, Justesen AB, Livingston J, Lund MN, Pérez Hernández F, Prieto-Arranz J, Regulo C, Bugnet LA, Everett ME, Hirano T, Nespral D, Nowak G, Palle E, Silva Aguirre V, Trifonov T, Winn JN, Barragán O, Beck PG, Chaplin WJ, Cochran WD, Csizmadia S, Deeg H, Endl M, Heeren P, Grziwa S, Hatzes AP, Hidalgo D, Korth J, Mathis S, Montañes Rodriguez P, Narita N, Patzold M, Persson CM, Rodler F, Smith AMS. 2018. HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. 478(4), 4866–4880.","chicago":"Van Eylen, V, F Dai, S Mathur, D Gandolfi, S Albrecht, M Fridlund, R A García, et al. “HD 89345: A Bright Oscillating Star Hosting a Transiting Warm Saturn-Sized Planet Observed by K2.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1390.","short":"V. Van Eylen, F. Dai, S. Mathur, D. Gandolfi, S. Albrecht, M. Fridlund, R.A. García, E. Guenther, M. Hjorth, A.B. Justesen, J. Livingston, M.N. Lund, F. Pérez Hernández, J. Prieto-Arranz, C. Regulo, L.A. Bugnet, M.E. Everett, T. Hirano, D. Nespral, G. Nowak, E. Palle, V. Silva Aguirre, T. Trifonov, J.N. Winn, O. Barragán, P.G. Beck, W.J. Chaplin, W.D. Cochran, S. Csizmadia, H. Deeg, M. Endl, P. Heeren, S. Grziwa, A.P. Hatzes, D. Hidalgo, J. Korth, S. Mathis, P. Montañes Rodriguez, N. Narita, M. Patzold, C.M. Persson, F. Rodler, A.M.S. Smith, Monthly Notices of the Royal Astronomical Society 478 (2018) 4866–4880."},"doi":"10.1093/mnras/sty1390","scopus_import":"1","volume":478,"_id":"11620","extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.01860"}],"oa_version":"Preprint","quality_controlled":"1","external_id":{"arxiv":["1805.01860"]},"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"article_type":"original","acknowledgement":"We gratefully acknowledge many helpful suggestions by the anonymous referee. Based on observations made with a) the Nordic Optical Telescope, operated by the Nordic Optical Telescope Scientific Association at the Observatorio del Roque de los Muchachos; b) the ESO-3.6m telescope at La Silla Observatory under programme ID 0100.C-0808; c) the Italian Telescopio Nazionale Galileo operated on the island of La Palma by the Fundación Galileo Galilei of the Istituto Nazionale di Astrofisica. NESSI was funded by the NASA Exoplanet Exploration Program and the NASA Ames Research Center. NESSI was built at the Ames Research Center by Steve B. Howell, Nic Scott, Elliott P. Horch, and Emmett Quigley. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730890. This material reflects only the authors views and the Commission is not liable for any use that may be made of the information contained therein. DG gratefully acknowledges the financial support of the Programma Giovani Ricercatori – Rita Levi Montalcini – Rientro dei Cervelli (2012) awarded by the Italian Ministry of Education, Universities and Research (MIUR). SaM would like to acknowledge support from the Ramon y Cajal fellowship number RYC-2015-17697. AJ, MH, and SA acknowledge support by the Danish Council for Independent Research, through a DFF Sapere Aude Starting Grant nr. 4181-00487B. SzCs, APH, MP, and HR acknowledge the support of the DFG priority program SPP 1992Exploring the Diversity of Extrasolar Planets (grants HA 3279/12-1, PA 525/18-1, PA5 25/19-1 and PA525/20-1, RA 714/14-1) HD, CR, and FPH acknowledge the financial support from MINECO under grants ESP2015-65712-C5-4-R and AYA2016-76378-P. This paper has made use of the IAC Supercomputing facility HTCondor (http://research.cs.wisc.edu/htcondor/), partly financed by the Ministry of Economy and Competitiveness with FEDER funds, code IACA13-3E-2493. MF and CMP gratefully acknowledge the support of the Swedish National Space Board. RAG and StM thanks the support of the CNES PLATO grant. PGB is a postdoctoral fellow in the MINECO-programme ’Juan de la Cierva Incorporacion’ (IJCI-2015-26034). StM acknowledges support from ERC through SPIRE grant (647383) and from ISSI through the ENCELADE 2.0 team. VSA acknowledges support from VILLUM FONDEN (research grant 10118). MNL acknowledges support from the ESA-PRODEX programme. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (Grant agreement no.: DNRF106) This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. This research was made with the use of NASA’s Astrophysics Data System and 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.","day":"01","arxiv":1,"date_updated":"2022-08-22T07:45:38Z","title":"HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2","author":[{"full_name":"Van Eylen, V","first_name":"V","last_name":"Van Eylen"},{"last_name":"Dai","first_name":"F","full_name":"Dai, F"},{"first_name":"S","last_name":"Mathur","full_name":"Mathur, S"},{"first_name":"D","last_name":"Gandolfi","full_name":"Gandolfi, D"},{"first_name":"S","last_name":"Albrecht","full_name":"Albrecht, S"},{"full_name":"Fridlund, M","first_name":"M","last_name":"Fridlund"},{"last_name":"García","first_name":"R A","full_name":"García, R A"},{"full_name":"Guenther, E","last_name":"Guenther","first_name":"E"},{"last_name":"Hjorth","first_name":"M","full_name":"Hjorth, M"},{"full_name":"Justesen, A B","first_name":"A B","last_name":"Justesen"},{"full_name":"Livingston, J","first_name":"J","last_name":"Livingston"},{"full_name":"Lund, M N","last_name":"Lund","first_name":"M N"},{"last_name":"Pérez Hernández","first_name":"F","full_name":"Pérez Hernández, F"},{"last_name":"Prieto-Arranz","first_name":"J","full_name":"Prieto-Arranz, J"},{"full_name":"Regulo, C","first_name":"C","last_name":"Regulo"},{"first_name":"Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"full_name":"Everett, M E","last_name":"Everett","first_name":"M E"},{"last_name":"Hirano","first_name":"T","full_name":"Hirano, T"},{"first_name":"D","last_name":"Nespral","full_name":"Nespral, D"},{"first_name":"G","last_name":"Nowak","full_name":"Nowak, G"},{"first_name":"E","last_name":"Palle","full_name":"Palle, E"},{"full_name":"Silva Aguirre, V","last_name":"Silva Aguirre","first_name":"V"},{"full_name":"Trifonov, T","first_name":"T","last_name":"Trifonov"},{"first_name":"J N","last_name":"Winn","full_name":"Winn, J N"},{"first_name":"O","last_name":"Barragán","full_name":"Barragán, O"},{"full_name":"Beck, P G","last_name":"Beck","first_name":"P G"},{"full_name":"Chaplin, W J","first_name":"W J","last_name":"Chaplin"},{"full_name":"Cochran, W D","last_name":"Cochran","first_name":"W D"},{"last_name":"Csizmadia","first_name":"S","full_name":"Csizmadia, S"},{"last_name":"Deeg","first_name":"H","full_name":"Deeg, H"},{"first_name":"M","last_name":"Endl","full_name":"Endl, M"},{"full_name":"Heeren, P","first_name":"P","last_name":"Heeren"},{"first_name":"S","last_name":"Grziwa","full_name":"Grziwa, S"},{"full_name":"Hatzes, A P","first_name":"A P","last_name":"Hatzes"},{"full_name":"Hidalgo, D","first_name":"D","last_name":"Hidalgo"},{"full_name":"Korth, J","first_name":"J","last_name":"Korth"},{"full_name":"Mathis, S","first_name":"S","last_name":"Mathis"},{"last_name":"Montañes Rodriguez","first_name":"P","full_name":"Montañes Rodriguez, P"},{"full_name":"Narita, N","last_name":"Narita","first_name":"N"},{"full_name":"Patzold, M","first_name":"M","last_name":"Patzold"},{"last_name":"Persson","first_name":"C M","full_name":"Persson, C M"},{"full_name":"Rodler, F","last_name":"Rodler","first_name":"F"},{"full_name":"Smith, A M S","last_name":"Smith","first_name":"A M S"}]},{"abstract":[{"text":"The recently launched NASA Transiting Exoplanet Survey Satellite (TESS) mission is going to collect lightcurves for a few hundred million of stars and we expect to increase the number of pulsating stars to analyze compared to the few thousand stars observed by the CoRoT, Kepler and K2 missions. However, most of the TESS targets have not yet been properly classified and characterized. In order to improve the analysis of the TESS data, it is crucial to determine the type of stellar pulsations in a timely manner. We propose an automatic method to classify stars attending to their pulsation properties, in particular, to identify solar-like pulsators among all TESS targets. It relies on the use of the global amount of power contained in the power spectrum (already known as the FliPer method) as a key parameter, along with\r\nthe effective temperature, to feed into a machine learning classifier. Our study, based on TESS simulated datasets, shows that we are able to classify pulsators with a 98% accuracy.","lang":"eng"}],"date_created":"2022-07-21T07:05:23Z","language":[{"iso":"eng"}],"citation":{"mla":"Bugnet, Lisa Annabelle, et al. “FliPer: Classifying TESS Pulsating Stars.” ArXiv, 1811.12140, doi:10.48550/arXiv.1811.12140.","ieee":"L. A. Bugnet, R. A. García, G. R. Davies, S. Mathur, O. J. Hall, and B. M. Rendle, “FliPer: Classifying TESS pulsating stars,” arXiv. .","ama":"Bugnet LA, García RA, Davies GR, Mathur S, Hall OJ, Rendle BM. FliPer: Classifying TESS pulsating stars. arXiv. doi:10.48550/arXiv.1811.12140","ista":"Bugnet LA, García RA, Davies GR, Mathur S, Hall OJ, Rendle BM. FliPer: Classifying TESS pulsating stars. arXiv, 1811.12140.","apa":"Bugnet, L. A., García, R. A., Davies, G. R., Mathur, S., Hall, O. J., & Rendle, B. M. (n.d.). FliPer: Classifying TESS pulsating stars. arXiv. https://doi.org/10.48550/arXiv.1811.12140","chicago":"Bugnet, Lisa Annabelle, R. A. García, G. R. Davies, S. Mathur, O. J. Hall, and B. M. Rendle. “FliPer: Classifying TESS Pulsating Stars.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1811.12140.","short":"L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, O.J. Hall, B.M. Rendle, ArXiv (n.d.)."},"doi":"10.48550/arXiv.1811.12140","extern":"1","_id":"11631","status":"public","oa_version":"Preprint","publication":"arXiv","month":"11","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1811.12140"}],"day":"29","arxiv":1,"type":"preprint","oa":1,"external_id":{"arxiv":["1811.12140"]},"publication_status":"submitted","article_processing_charge":"No","year":"2018","keyword":["asteroseismology - methods","data analysis - stars","oscillations"],"author":[{"full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle"},{"full_name":"García, R. A.","last_name":"García","first_name":"R. A."},{"full_name":"Davies, G. R.","last_name":"Davies","first_name":"G. R."},{"first_name":"S.","last_name":"Mathur","full_name":"Mathur, S."},{"last_name":"Hall","first_name":"O. J.","full_name":"Hall, O. J."},{"full_name":"Rendle, B. M.","first_name":"B. M.","last_name":"Rendle"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"FliPer: Classifying TESS pulsating stars","article_number":"1811.12140","date_updated":"2022-08-22T08:41:55Z","date_published":"2018-11-29T00:00:00Z"}]