[{"scopus_import":"1","intvolume":" 8","month":"06","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"license":"https://creativecommons.org/licenses/by/4.0/","volume":8,"related_material":{"record":[{"relation":"research_data","id":"9804","status":"public"},{"relation":"dissertation_contains","id":"11388","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6721","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","creator":"apreinsp","date_updated":"2020-07-14T12:47:38Z","file_size":6748249,"date_created":"2019-07-29T07:41:18Z","file_name":"2019_eLife_Castro.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"6713","file_date_updated":"2020-07-14T12:47:38Z","department":[{"_id":"NiBa"}],"date_updated":"2024-03-27T23:30:22Z","ddc":["576"],"oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_created":"2019-07-28T21:59:17Z","doi":"10.7554/eLife.42014","date_published":"2019-06-06T00:00:00Z","year":"2019","isi":1,"has_accepted_license":"1","publication":"eLife","day":"06","article_number":"e42014","external_id":{"isi":["000473588700001"],"pmid":["31169497"]},"article_processing_charge":"No","author":[{"first_name":"João Pl","full_name":"Castro, João Pl","last_name":"Castro"},{"first_name":"Michelle N.","last_name":"Yancoskie","full_name":"Yancoskie, Michelle N."},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, Marta"},{"first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X"},{"first_name":"Layla","full_name":"Hiramatsu, Layla","last_name":"Hiramatsu"},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"first_name":"William H.","full_name":"Beluch, William H.","last_name":"Beluch"},{"first_name":"Ronald","full_name":"Naumann, Ronald","last_name":"Naumann"},{"full_name":"Skuplik, Isabella","last_name":"Skuplik","first_name":"Isabella"},{"full_name":"Cobb, John","last_name":"Cobb","first_name":"John"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Rolian","full_name":"Rolian, Campbell","first_name":"Campbell"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"}],"title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","citation":{"mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","oa_version":"Preprint","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"text":"We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit.","lang":"eng"}],"month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.05841"}],"oa":1,"publication":"arXiv","language":[{"iso":"eng"}],"day":"13","year":"2019","publication_status":"submitted","date_created":"2021-10-01T12:14:51Z","ec_funded":1,"date_published":"2019-10-13T00:00:00Z","related_material":{"record":[{"status":"public","id":"10058","relation":"dissertation_contains"}]},"doi":"10.48550/arXiv.1910.05841","article_number":"1910.05841","_id":"10065","project":[{"call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"status":"public","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, 1910.05841, doi:10.48550/arXiv.1910.05841.","short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","ieee":"A. C. Hofmann et al., “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” arXiv. .","apa":"Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. https://doi.org/10.48550/arXiv.1910.05841","ama":"Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. doi:10.48550/arXiv.1910.05841","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1910.05841.","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841."},"date_updated":"2024-03-27T23:30:26Z","department":[{"_id":"GeKa"}],"title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","article_processing_charge":"No","external_id":{"arxiv":["1910.05841"]},"author":[{"first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801"},{"last_name":"Borovkov","full_name":"Borovkov, Maxim","first_name":"Maxim"},{"last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ballabio, Andrea","last_name":"Ballabio","first_name":"Andrea"},{"full_name":"Frigerio, Jacopo","last_name":"Frigerio","first_name":"Jacopo"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}]},{"citation":{"ista":"Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh A, Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. 2019. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.","chicago":"Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.41801.","ieee":"K. Valosková et al., “A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” eLife, vol. 8. eLife Sciences Publications, 2019.","short":"K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A. Ratheesh, P. Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen, D.E. Siekhaus, ELife 8 (2019).","apa":"Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M., … Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.41801","ama":"Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 2019;8. doi:10.7554/elife.41801","mla":"Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife, vol. 8, e41801, eLife Sciences Publications, 2019, doi:10.7554/elife.41801."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000462530200001"]},"article_processing_charge":"No","author":[{"last_name":"Valosková","full_name":"Valosková, Katarina","first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","last_name":"Biebl","full_name":"Biebl, Julia"},{"first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek","full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389"},{"first_name":"Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi","last_name":"Emtenani"},{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György"},{"id":"495A3C32-F248-11E8-B48F-1D18A9856A87","first_name":"Michaela","orcid":"0000-0003-2427-6856","full_name":"Misova, Michaela","last_name":"Misova"},{"last_name":"Ratheesh","orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna","first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rodrigues","full_name":"Rodrigues, Patricia","id":"2CE4065A-F248-11E8-B48F-1D18A9856A87","first_name":"Patricia"},{"last_name":"Shkarina","full_name":"Shkarina, Katerina","first_name":"Katerina"},{"full_name":"Larsen, Ida Signe Bohse","last_name":"Larsen","first_name":"Ida Signe Bohse"},{"first_name":"Sergey Y","last_name":"Vakhrushev","full_name":"Vakhrushev, Sergey Y"},{"first_name":"Henrik","last_name":"Clausen","full_name":"Clausen, Henrik"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"}],"title":"A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion","article_number":"e41801","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"},{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion"},{"call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"},{"_id":"25388084-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Breaking barriers: Investigating the junctional and mechanobiological changes underlying the ability of Drosophila immune cells to invade an epithelium","grant_number":"329540"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"year":"2019","has_accepted_license":"1","isi":1,"publication":"eLife","day":"26","date_created":"2019-03-28T13:37:45Z","doi":"10.7554/elife.41801","date_published":"2019-03-26T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_updated":"2024-03-27T23:30:29Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:23Z","department":[{"_id":"DaSi"}],"_id":"6187","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":4496017,"date_updated":"2020-07-14T12:47:23Z","file_name":"2019_eLife_Valoskova.pdf","date_created":"2019-03-28T14:00:41Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6188","checksum":"cc0d1a512559d52e7e7cb0e9b9854b40"}],"ec_funded":1,"volume":8,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/","relation":"press_release"}],"record":[{"id":"6530","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"8983","status":"public"},{"id":"6546","status":"public","relation":"dissertation_contains"}]},"abstract":[{"text":"Aberrant 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 a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"03"},{"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"Katarina Valoskova_PhD thesis_final version.docx","date_created":"2019-06-07T13:00:04Z","file_size":14110626,"date_updated":"2020-07-14T12:47:33Z","creator":"khribikova","file_id":"6549","checksum":"68949c2d96210b45b981a23e9c9cd93c","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"},{"file_name":"Katarina Valoskova_PhD thesis_final version.pdf","date_created":"2019-06-07T13:00:08Z","creator":"khribikova","file_size":10054156,"date_updated":"2021-02-11T11:17:14Z","embargo":"2020-06-07","file_id":"6550","checksum":"555329cd76e196c96f5278c480ee2e6e","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"6187","status":"public"},{"id":"544","status":"public","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"Bio"}],"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"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","supervisor":[{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-19T10:15:54Z","ddc":["570"],"department":[{"_id":"DaSi"}],"file_date_updated":"2021-02-11T11:17:14Z","_id":"6546","type":"dissertation","status":"public","has_accepted_license":"1","year":"2019","day":"07","page":"141","date_published":"2019-06-07T00:00:00Z","doi":"10.15479/AT:ISTA:6546","date_created":"2019-06-07T12:49:19Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Valosková","full_name":"Valosková, Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"}],"article_processing_charge":"No","title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","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"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2019-04-30T11:56:10Z","date_published":"2019-04-30T00:00:00Z","doi":"10.15479/AT:ISTA:6363","page":"140","day":"30","year":"2019","has_accepted_license":"1","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","article_processing_charge":"No","author":[{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363.","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363","apa":"Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6363","mla":"Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6363."},"month":"04","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Distinguishing between similar experiences is achieved by the brain in a process called pattern separation. In the hippocampus, pattern separation reduces the interference of memories and increases the storage capacity by decorrelating similar inputs patterns of neuronal activity into non-overlapping output firing patterns. Winners-take-all (WTA) mechanism is a theoretical model for pattern separation in which a \"winner\" cell suppresses the activity of the neighboring neurons through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of feedback inhibition in which a GC inhibits other GCs but not itself through the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron connectivity was more spatially confined but less abundant than PV+interneurons–GC connectivity, leading to an asymmetrical distribution of excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the primary mechanism. This process relied on lateral inhibition, fast-signaling properties of PV+interneurons and the asymmetrical distribution of excitatory and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in vivoleads to acute deficits in discrimination between similar environments, suggesting that PV+interneuron networks are necessary for behavioral relevant computations. Our results demonstrate that PV+interneurons possess unique connectivity and fast signaling properties that confer to the dentate gyrus network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n"}],"related_material":{"record":[{"id":"21","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2020-05-09","file_id":"6389","checksum":"77c6c05cfe8b58c8abcf1b854375d084","file_size":13966891,"date_updated":"2021-02-11T11:17:15Z","creator":"cespinoza","file_name":"Espinozathesis_all2.pdf","date_created":"2019-05-07T16:00:39Z"},{"date_created":"2019-05-07T16:00:48Z","file_name":"Espinoza_Thesis.docx","date_updated":"2020-07-14T12:47:28Z","file_size":11159900,"creator":"cespinoza","checksum":"f6aa819f127691a2b0fc21c76eb09746","file_id":"6390","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-000-8"]},"status":"public","type":"dissertation","_id":"6363","department":[{"_id":"PeJo"}],"file_date_updated":"2021-02-11T11:17:15Z","ddc":["570"],"date_updated":"2023-09-15T12:03:48Z","supervisor":[{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}]},{"article_number":"129","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification for almost-sure termination of probabilistic programs,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , Athens, Greece, 2019, vol. 3.","short":"M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , ACM, 2019.","ama":"Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure termination of probabilistic programs. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . Vol 3. ACM; 2019. doi:10.1145/3360555","apa":"Huang, M., Fu, H., Chatterjee, K., & Goharshady, A. K. (2019). Modular verification for almost-sure termination of probabilistic programs. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360555","mla":"Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , vol. 3, 129, ACM, 2019, doi:10.1145/3360555.","ista":"Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for almost-sure termination of probabilistic programs. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 129.","chicago":"Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , Vol. 3. ACM, 2019. https://doi.org/10.1145/3360555."},"title":"Modular verification for almost-sure termination of probabilistic programs","article_processing_charge":"No","external_id":{"arxiv":["1901.06087"]},"author":[{"first_name":"Mingzhang","full_name":"Huang, Mingzhang","last_name":"Huang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"}],"oa":1,"quality_controlled":"1","publisher":"ACM","publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications ","day":"01","year":"2019","has_accepted_license":"1","date_created":"2019-08-09T09:54:20Z","date_published":"2019-10-01T00:00:00Z","doi":"10.1145/3360555","_id":"6780","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"conference":{"location":"Athens, Greece","end_date":"2019-10-25","start_date":"2019-10-23","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications"},"type":"conference","ddc":["000"],"date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:40Z","oa_version":"Published Version","abstract":[{"text":"In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a\r\ngiven probabilistic program terminates with probability 1. Scalable approaches for program analysis often\r\nrely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure\r\ntermination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic programs.\r\nBesides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a\r\nsound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel\r\nnotion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat are linear and show that they can be synthesized in polynomial time. Finally, we present experimental\r\nresults on a variety of benchmarks and several natural examples that model various types of nested while\r\nloops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination property","lang":"eng"}],"intvolume":" 3","month":"10","language":[{"iso":"eng"}],"file":[{"creator":"akafshda","file_size":1024643,"date_updated":"2020-07-14T12:47:40Z","file_name":"oopsla-2019.pdf","date_created":"2019-08-12T15:40:57Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6807","checksum":"3482d8ace6fb4991eb7810e3b70f1b9f"},{"file_name":"2019_ACM_Huang.pdf","date_created":"2020-05-12T15:15:14Z","file_size":538579,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst","checksum":"4e5a6fb2b59a75222a4e8335a5a60eac","file_id":"7821","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"volume":3},{"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"article_number":"53","title":"Efficient parameterized algorithms for data packing","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nastaran","full_name":"Okati, Nastaran","last_name":"Okati"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019).","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” Proceedings of the ACM on Programming Languages, vol. 3, no. POPL. ACM, 2019.","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. ACM. https://doi.org/10.1145/3290366","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 2019;3(POPL). doi:10.1145/3290366","mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no. POPL, 53, ACM, 2019, doi:10.1145/3290366."},"oa":1,"publisher":"ACM","quality_controlled":"1","date_created":"2019-05-06T12:18:17Z","date_published":"2019-01-01T00:00:00Z","doi":"10.1145/3290366","publication":"Proceedings of the ACM on Programming Languages","day":"01","year":"2019","has_accepted_license":"1","pubrep_id":"1056","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6380","file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"KrCh"}],"ddc":["004"],"date_updated":"2024-03-27T23:30:33Z","intvolume":" 3","month":"01","oa_version":"Published Version","abstract":[{"lang":"eng","text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. "}],"ec_funded":1,"volume":3,"related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"issue":"POPL","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c157752f96877b36685ad7063ada4524","file_id":"6381","date_updated":"2020-07-14T12:47:29Z","file_size":1294962,"creator":"dernst","date_created":"2019-05-06T12:23:11Z","file_name":"2019_ACM_POPL_Chatterjee.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2475-1421"]}},{"date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"_id":"6056","conference":{"end_date":"2019-05-17","location":"Seoul, Korea","start_date":"2019-05-14","name":"IEEE International Conference on Blockchain and Cryptocurrency"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"abstract":[{"text":"In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07986"}],"scopus_import":1,"month":"05","citation":{"ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts: Secure randomness on the blockchain. IEEE International Conference on Blockchain and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency, 8751326.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In IEEE International Conference on Blockchain and Cryptocurrency. IEEE, 2019. https://doi.org/10.1109/BLOC.2019.8751326.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart contracts: Secure randomness on the blockchain,” in IEEE International Conference on Blockchain and Cryptocurrency, Seoul, Korea, 2019.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International Conference on Blockchain and Cryptocurrency, IEEE, 2019.","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Probabilistic smart contracts: Secure randomness on the blockchain. In IEEE International Conference on Blockchain and Cryptocurrency. Seoul, Korea: IEEE. https://doi.org/10.1109/BLOC.2019.8751326","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts: Secure randomness on the blockchain. In: IEEE International Conference on Blockchain and Cryptocurrency. IEEE; 2019. doi:10.1109/BLOC.2019.8751326","mla":"Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” IEEE International Conference on Blockchain and Cryptocurrency, 8751326, IEEE, 2019, doi:10.1109/BLOC.2019.8751326."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1902.07986"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"full_name":"Pourdamghani, Arash","last_name":"Pourdamghani","first_name":"Arash"}],"title":"Probabilistic smart contracts: Secure randomness on the blockchain","article_number":"8751326","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"year":"2019","publication":"IEEE International Conference on Blockchain and Cryptocurrency","day":"01","date_created":"2019-02-26T09:03:15Z","date_published":"2019-05-01T00:00:00Z","doi":"10.1109/BLOC.2019.8751326","oa":1,"quality_controlled":"1","publisher":"IEEE"},{"abstract":[{"text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","month":"04","publication_status":"published","publication_identifier":{"isbn":["9781450359337"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:29Z","file_size":1023934,"date_created":"2019-05-06T12:09:27Z","file_name":"2019_ACM_Chatterjee.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6379","checksum":"fbfbcd5a0c7a743862bfc3045539a614"}],"ec_funded":1,"volume":"Part F147772","related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"_id":"6378","conference":{"name":"ACM Symposium on Applied Computing","start_date":"2019-04-08","end_date":"2019-04-12","location":"Limassol, Cyprus"},"type":"conference","pubrep_id":"1069","status":"public","date_updated":"2024-03-27T23:30:33Z","ddc":["004"],"file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"KrCh"}],"oa":1,"quality_controlled":"1","publisher":"ACM","year":"2019","has_accepted_license":"1","isi":1,"publication":"Proceedings of the 34th ACM Symposium on Applied Computing","day":"01","page":"374-381","date_created":"2019-05-06T12:11:36Z","doi":"10.1145/3297280.3297319","date_published":"2019-04-01T00:00:00Z","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"citation":{"ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381. doi:10.1145/3297280.3297319","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000474685800049"]},"article_processing_charge":"No","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arash","full_name":"Pourdamghani, Arash","last_name":"Pourdamghani"}],"title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving"},{"scopus_import":"1","month":"06","abstract":[{"text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs,\r\nwhich aims at automated methods for analyzing the resource-usage of such programs.\r\nPrevious approaches for this problem could only handle nonnegative bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,\r\nboth positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the\r\nexpected accumulated cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a) general positive and negative costs with bounded updates in\r\nvariables; and (b) nonnegative costs with general updates to variables.\r\nWe show that several natural examples which could not be\r\nhandled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"5457","status":"public"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"paper.pdf","date_created":"2019-03-25T10:11:22Z","creator":"akafshda","file_size":4051066,"date_updated":"2020-07-14T12:47:20Z","checksum":"703a5e9b8c8587f2a44085ffd9a4db64","file_id":"6176","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"conference":{"start_date":"2019-06-22","end_date":"2019-06-26","location":"Phoenix, AZ, United States","name":"PLDI: Conference on Programming Language Design and Implementation"},"type":"conference","keyword":["Program Cost Analysis","Program Termination","Probabilistic Programs","Martingales"],"status":"public","_id":"6175","file_date_updated":"2020-07-14T12:47:20Z","department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:33Z","ddc":["000"],"oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","page":"204-220","date_created":"2019-03-25T10:13:25Z","doi":"10.1145/3314221.3314581","date_published":"2019-06-08T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation","day":"08","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1902.04659"],"isi":["000523190300014"]},"article_processing_charge":"No","author":[{"first_name":"Peixin","full_name":"Wang, Peixin","last_name":"Wang"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","full_name":"Fu, Hongfei","last_name":"Fu"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Qin","full_name":"Qin, Xudong","first_name":"Xudong"},{"last_name":"Shi","full_name":"Shi, Wenjun","first_name":"Wenjun"}],"title":"Cost analysis of nondeterministic probabilistic programs","citation":{"short":"P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–220.","ieee":"P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost analysis of nondeterministic probabilistic programs,” in PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Phoenix, AZ, United States, 2019, pp. 204–220.","apa":"Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., & Shi, W. (2019). Cost analysis of nondeterministic probabilistic programs. In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 204–220). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3314221.3314581","ama":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of nondeterministic probabilistic programs. In: PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2019:204-220. doi:10.1145/3314221.3314581","mla":"Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.” PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–20, doi:10.1145/3314221.3314581.","ista":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Conference on Programming Language Design and Implementation, 204–220.","chicago":"Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee, Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.” In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, 204–20. Association for Computing Machinery, 2019. https://doi.org/10.1145/3314221.3314581."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"day":"01","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","has_accepted_license":"1","isi":1,"year":"2019","date_published":"2019-04-01T00:00:00Z","doi":"10.1145/3297280.3297322","date_created":"2019-05-26T21:59:15Z","page":"400-408","quality_controlled":"1","publisher":"ACM","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “The Treewidth of Smart Contracts.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:400–408. ACM, n.d. https://doi.org/10.1145/3297280.3297322.","ista":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium on Applied Computing vol. Part F147772, 400–408.","mla":"Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, pp. 400–08, doi:10.1145/3297280.3297322.","apa":"Chatterjee, K., Goharshady, A. K., & Goharshady, E. K. (n.d.). The treewidth of smart contracts. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297322","ama":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; :400-408. doi:10.1145/3297280.3297322","ieee":"K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart contracts,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, vol. Part F147772, pp. 400–408.","short":"K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, n.d., pp. 400–408."},"title":"The treewidth of smart contracts","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"}],"article_processing_charge":"No","external_id":{"isi":["000474685800052"]},"file":[{"file_id":"7827","checksum":"dddc20f6d9881f23b8755eb720ec9d6f","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-05-14T09:50:11Z","file_name":"2019_ACM_Chatterjee.pdf","date_updated":"2020-07-14T12:47:32Z","file_size":6937138,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450359337"]},"publication_status":"submitted","volume":"Part F147772","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.\r\n\r\nTwo classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.\r\n"}],"month":"04","scopus_import":"1","ddc":["000"],"date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:32Z","_id":"6490","status":"public","pubrep_id":"1070","type":"conference","conference":{"name":"SAC: Symposium on Applied Computing","location":"Limassol, Cyprus","end_date":"2019-04-12","start_date":"2019-04-08"}},{"article_number":"23","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ama":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3363525","apa":"Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., & Pavlogiannis, A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3363525","short":"K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 41 (2019).","ieee":"K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 23, ACM, 2019, doi:10.1145/3363525.","ista":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 41(4), 23.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3363525."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goyal","full_name":"Goyal, Prateesh","first_name":"Prateesh"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"article_processing_charge":"No","external_id":{"isi":["000564108400004"]},"title":"Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth","quality_controlled":"1","publisher":"ACM","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"ACM Transactions on Programming Languages and Systems","doi":"10.1145/3363525","date_published":"2019-11-01T00:00:00Z","date_created":"2019-12-09T08:33:33Z","_id":"7158","type":"journal_article","article_type":"original","status":"public","date_updated":"2024-03-27T23:30:34Z","ddc":["000"],"file_date_updated":"2020-10-08T12:58:10Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.\r\n\r\nOur main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.\r\n"}],"oa_version":"Submitted Version","scopus_import":"1","month":"11","intvolume":" 41","publication_identifier":{"issn":["0164-0925"]},"publication_status":"published","file":[{"file_name":"2019_ACMTransactions_Chatterjee.pdf","date_created":"2020-10-08T12:58:10Z","file_size":667357,"date_updated":"2020-10-08T12:58:10Z","creator":"dernst","success":1,"file_id":"8632","checksum":"291cc86a07bd010d4815e177dac57b70","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":41,"related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"issue":"4","ec_funded":1},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"639","status":"public"},{"relation":"dissertation_contains","id":"8934","status":"public"}]},"volume":41,"issue":"4","abstract":[{"text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}],"scopus_import":"1","intvolume":" 41","month":"10","date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"_id":"7014","article_type":"original","type":"journal_article","status":"public","year":"2019","isi":1,"publication":"ACM Transactions on Programming Languages and Systems","day":"01","date_created":"2019-11-13T08:33:43Z","doi":"10.1145/3339984","date_published":"2019-10-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","citation":{"mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019).","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3339984","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3339984","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984.","ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000564108400001"],"arxiv":["1705.00317"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"}],"title":"Non-polynomial worst-case analysis of recursive programs","article_number":"20","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}]},{"oa":1,"quality_controlled":"1","publisher":"ASME","year":"2019","isi":1,"publication":"Journal of Fluids Engineering","day":"01","date_created":"2019-05-26T21:59:13Z","doi":"10.1115/1.4043494","date_published":"2019-11-01T00:00:00Z","article_number":"111105","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering. ASME, 2019. https://doi.org/10.1115/1.4043494.","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141, no. 11. ASME, 2019.","apa":"Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. ASME. https://doi.org/10.1115/1.4043494","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105, ASME, 2019, doi:10.1115/1.4043494."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1809.07625"],"isi":["000487748600005"]},"author":[{"first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","last_name":"Kühnen"},{"full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","abstract":[{"lang":"eng","text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.07625"}],"scopus_import":"1","intvolume":" 141","month":"11","publication_status":"published","publication_identifier":{"eissn":["1528901X"],"issn":["00982202"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":141,"related_material":{"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"issue":"11","_id":"6486","type":"journal_article","article_type":"original","status":"public","date_updated":"2024-03-27T23:30:35Z","department":[{"_id":"BjHo"}]},{"isi":1,"year":"2019","day":"25","publication":"Journal of Fluid Mechanics","page":"934-948","doi":"10.1017/jfm.2019.191","date_published":"2019-05-25T00:00:00Z","date_created":"2019-04-07T21:59:14Z","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"citation":{"chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2019.191.","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948.","mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:10.1017/jfm.2019.191.","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948, 2019.","apa":"Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2019.191","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","last_name":"Scarselli"},{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","last_name":"Kühnen"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"external_id":{"isi":["000462606100001"],"arxiv":["1807.05357"]},"article_processing_charge":"No","title":"Relaminarising pipe flow by wall movement","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"},{"call_identifier":"H2020","_id":"25104D44-B435-11E9-9278-68D0E5697425","name":"Eliminating turbulence in oil pipelines","grant_number":"737549"}],"publication_identifier":{"issn":["00221120"],"eissn":["14697645"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":867,"related_material":{"link":[{"relation":"supplementary_material","url":"https://doi.org/10.1017/jfm.2019.191"}],"record":[{"status":"public","id":"7258","relation":"dissertation_contains"}]},"ec_funded":1,"abstract":[{"text":"Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05357"}],"month":"05","intvolume":" 867","date_updated":"2024-03-27T23:30:35Z","department":[{"_id":"BjHo"}],"_id":"6228","type":"journal_article","status":"public"},{"date_updated":"2024-03-27T23:30:37Z","department":[{"_id":"JiFr"}],"_id":"6260","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"11626","status":"public"},{"relation":"dissertation_contains","id":"8822","status":"public"}]},"volume":180,"issue":"2","ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.","lang":"eng"}],"month":"06","intvolume":" 180","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.19.00201"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165. doi:10.1104/pp.19.00201","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","ieee":"A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:10.1104/pp.19.00201."},"title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","author":[{"full_name":"Oochi, A","last_name":"Oochi","first_name":"A"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","last_name":"Hajny"},{"first_name":"K","full_name":"Fukui, K","last_name":"Fukui"},{"first_name":"Y","full_name":"Nakao, Y","last_name":"Nakao"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei"},{"first_name":"M","last_name":"Quareshy","full_name":"Quareshy, M"},{"last_name":"Takahashi","full_name":"Takahashi, K","first_name":"K"},{"first_name":"T","full_name":"Kinoshita, T","last_name":"Kinoshita"},{"first_name":"SR","last_name":"Harborough","full_name":"Harborough, SR"},{"full_name":"Kepinski, S","last_name":"Kepinski","first_name":"S"},{"last_name":"Kasahara","full_name":"Kasahara, H","first_name":"H"},{"full_name":"Napier, RM","last_name":"Napier","first_name":"RM"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Hayashi, KI","last_name":"Hayashi","first_name":"KI"}],"article_processing_charge":"No","external_id":{"pmid":["30936248"],"isi":["000470086100045"]},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"01","publication":"Plant Physiology","isi":1,"year":"2019","date_published":"2019-06-01T00:00:00Z","doi":"10.1104/pp.19.00201","date_created":"2019-04-09T08:38:20Z","page":"1152-1165","acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","publisher":"ASPB","quality_controlled":"1","oa":1},{"page":"1463-1479.e18","date_created":"2019-06-02T21:59:12Z","date_published":"2019-05-30T00:00:00Z","doi":"10.1016/j.cell.2019.04.030","year":"2019","has_accepted_license":"1","isi":1,"publication":"Cell","day":"30","oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","article_processing_charge":"No","external_id":{"isi":["000469415100013"],"pmid":["31080065"]},"author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland","full_name":"Kardos, Roland","last_name":"Kardos"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","last_name":"Xue","full_name":"Xue, Shi-lei"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","citation":{"ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18. doi:10.1016/j.cell.2019.04.030","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"ec_funded":1,"issue":"6","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/"}],"record":[{"relation":"dissertation_contains","id":"8350","status":"public"}]},"volume":177,"publication_status":"published","publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-10-21T07:22:34Z","file_size":3356292,"date_created":"2020-10-21T07:22:34Z","file_name":"2019_Cell_Shamipour_accepted.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8686","checksum":"aea43726d80e35ce3885073a5f05c3e3","success":1}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"scopus_import":"1","intvolume":" 177","month":"05","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-10-21T07:22:34Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:38Z","ddc":["570"],"article_type":"original","type":"journal_article","status":"public","_id":"6508"},{"department":[{"_id":"CaHe"},{"_id":"BjHo"}],"file_date_updated":"2020-10-21T07:09:45Z","date_updated":"2024-03-27T23:30:38Z","ddc":["570"],"article_type":"original","type":"journal_article","status":"public","_id":"7001","ec_funded":1,"issue":"4","related_material":{"record":[{"id":"7186","status":"public","relation":"dissertation_contains"},{"status":"public","id":"8350","relation":"dissertation_contains"}],"link":[{"description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release"}]},"volume":179,"publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_Cell_Schwayer_accepted.pdf","date_created":"2020-10-21T07:09:45Z","creator":"dernst","file_size":8805878,"date_updated":"2020-10-21T07:09:45Z","success":1,"checksum":"33dac4bb77ee630e2666e936b4d57980","file_id":"8684","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 179","month":"10","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"pmid":1,"oa_version":"Submitted Version","article_processing_charge":"No","external_id":{"pmid":["31675500"],"isi":["000493898000012"]},"author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer"},{"full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra"},{"first_name":"M","last_name":"Balda","full_name":"Balda, M"},{"first_name":"M","full_name":"Tada, M","last_name":"Tada"},{"first_name":"K","last_name":"Matter","full_name":"Matter, K"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","citation":{"apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","ieee":"C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006.","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"page":"937-952.e18","date_created":"2019-11-12T12:51:06Z","doi":"10.1016/j.cell.2019.10.006","date_published":"2019-10-31T00:00:00Z","year":"2019","isi":1,"has_accepted_license":"1","publication":"Cell","day":"31","oa":1,"publisher":"Cell Press","quality_controlled":"1"},{"file_date_updated":"2020-10-17T22:30:03Z","department":[{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2023-10-18T08:49:17Z","supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"status":"public","type":"dissertation","_id":"6891","related_material":{"link":[{"url":"https://ist.ac.at/en/news/feeling-like-a-cell/","relation":"press_release"}],"record":[{"relation":"part_of_dissertation","id":"6328","status":"public"},{"relation":"part_of_dissertation","id":"15","status":"public"},{"status":"public","id":"6877","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"6950","checksum":"00d100d6468e31e583051e0a006b640c","date_updated":"2020-10-17T22:30:03Z","file_size":74735267,"creator":"akopf","date_created":"2019-10-15T05:28:42Z","file_name":"Kopf_PhD_Thesis.docx"},{"file_id":"6951","checksum":"5d1baa899993ae6ca81aebebe1797000","embargo":"2020-10-16","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-10-15T05:28:47Z","file_name":"Kopf_PhD_Thesis1.pdf","creator":"akopf","date_updated":"2020-10-17T22:30:03Z","file_size":52787224}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n"}],"title":"The implication of cytoskeletal dynamics on leukocyte migration","article_processing_charge":"No","author":[{"orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:10.15479/AT:ISTA:6891","apa":"Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria."},"project":[{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2019-09-19T08:19:44Z","date_published":"2019-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:6891","page":"171","day":"24","year":"2019","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","call_identifier":"FWF","_id":"265FAEBA-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","ieee":"J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["30944468"],"isi":["000465594200050"]},"article_processing_charge":"No","author":[{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","last_name":"Kopf","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656"},{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"full_name":"de Vries, Ingrid","last_name":"de Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"full_name":"Driscoll, Meghan K.","last_name":"Driscoll","first_name":"Meghan K."},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Erik S.","full_name":"Welf, Erik S.","last_name":"Welf"},{"full_name":"Danuser, Gaudenz","last_name":"Danuser","first_name":"Gaudenz"},{"first_name":"Reto","last_name":"Fiolka","full_name":"Fiolka, Reto"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2019","isi":1,"publication":"Nature","day":"25","page":"546-550","date_created":"2019-04-17T06:52:28Z","doi":"10.1038/s41586-019-1087-5","date_published":"2019-04-25T00:00:00Z","_id":"6328","article_type":"letter_note","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"scopus_import":"1","intvolume":" 568","month":"04","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"14697","status":"public"},{"relation":"dissertation_contains","id":"6891","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/","description":"News on IST Homepage"}]},"volume":568},{"month":"09","intvolume":" 179","scopus_import":"1","pmid":1,"oa_version":"None","volume":179,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6891"}]},"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"6877","department":[{"_id":"MiSi"}],"date_updated":"2024-03-27T23:30:40Z","quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.cell.2019.08.047","date_published":"2019-09-19T00:00:00Z","date_created":"2019-09-15T22:00:46Z","page":"51-53","day":"19","publication":"Cell","isi":1,"year":"2019","title":"The neural crest pitches in to remove apoptotic debris","author":[{"first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"pmid":["31539498"],"isi":["000486618500011"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047.","apa":"Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047."}},{"date_updated":"2024-03-27T23:30:41Z","department":[{"_id":"SiHi"}],"_id":"6830","status":"public","article_type":"letter_note","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"issue":"5","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"volume":103,"pmid":1,"oa_version":"Published Version","intvolume":" 103","month":"09","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.021","open_access":"1"}],"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021."},"title":"Memo1 tiles the radial glial cell grid","external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"article_processing_charge":"No","author":[{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"publication":"Neuron","day":"04","year":"2019","isi":1,"date_created":"2019-08-25T22:00:50Z","doi":"10.1016/j.neuron.2019.08.021","date_published":"2019-09-04T00:00:00Z","page":"750-752","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"intvolume":" 20","month":"07","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation."}],"ec_funded":1,"issue":"13","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"volume":20,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_id":"6645","creator":"dernst","date_updated":"2020-07-14T12:47:34Z","file_size":3330291,"date_created":"2019-07-17T06:17:15Z","file_name":"2019_JournalMolecularScience_Adamowski.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1422-0067"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"6627","file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2024-03-27T23:30:43Z","oa":1,"publisher":"MDPI","quality_controlled":"1","date_created":"2019-07-11T12:00:32Z","date_published":"2019-07-07T00:00:00Z","doi":"10.3390/ijms20133337","publication":"International Journal of Molecular Sciences","day":"07","year":"2019","has_accepted_license":"1","isi":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"3337","title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","external_id":{"isi":["000477041100221"],"pmid":["31284661"]},"article_processing_charge":"Yes","author":[{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337.","chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337."}},{"month":"11","intvolume":" 38","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"issue":"6","volume":38,"related_material":{"record":[{"status":"public","id":"12897","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"file_name":"xcad_sup_mat_siga19.pdf","date_created":"2019-11-26T14:24:26Z","title":"X-CAD Supplemental Material","creator":"bbickel","file_size":1673176,"date_updated":"2020-07-14T12:47:49Z","file_id":"7119","checksum":"56a2fb019adcb556d2b022f5e5acb68c","relation":"supplementary_material","access_level":"open_access","content_type":"application/pdf"},{"checksum":"5f29d76aceb5102e766cbab9b17d776e","file_id":"7120","content_type":"application/pdf","description":"This is the author's version of the work.","relation":"main_file","access_level":"open_access","file_name":"XCAD_authors_version.pdf","date_created":"2019-11-26T14:24:27Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_size":14563618,"date_updated":"2020-07-14T12:47:49Z","creator":"bbickel"},{"file_id":"7121","checksum":"0d31e123286cbec9e28b2001c2bb0d55","content_type":"video/mp4","relation":"main_file","access_level":"open_access","file_name":"XCAD_video.mp4","date_created":"2019-11-26T14:27:37Z","file_size":259979129,"date_updated":"2020-07-14T12:47:49Z","creator":"bbickel"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"7117","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:49Z","ddc":["000"],"date_updated":"2024-03-27T23:30:46Z","quality_controlled":"1","publisher":"ACM","oa":1,"doi":"10.1145/3355089.3356576","date_published":"2019-11-06T00:00:00Z","date_created":"2019-11-26T14:22:09Z","day":"06","publication":"ACM Transactions on Graphics","has_accepted_license":"1","isi":1,"year":"2019","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"article_number":"157","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schumacher, Christian","last_name":"Schumacher","first_name":"Christian"},{"first_name":"Espen","last_name":"Knoop","full_name":"Knoop, Espen"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"},{"first_name":"Moritz","last_name":"Bächer","full_name":"Bächer, Moritz"}],"article_processing_charge":"No","external_id":{"isi":["000498397300007"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157."}},{"_id":"6189","status":"public","type":"journal_article","date_updated":"2024-03-27T23:30:47Z","department":[{"_id":"BjHo"}],"oa_version":"Preprint","abstract":[{"text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations.","lang":"eng"}],"month":"03","intvolume":" 122","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.06358"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication_status":"published","volume":122,"issue":"11","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9728"}]},"article_number":"114502","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502"},"title":"Transition to turbulence in particle laden flows","author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","first_name":"Nishchal","last_name":"Agrawal","full_name":"Agrawal, Nishchal"},{"full_name":"Choueiri, George H","last_name":"Choueiri","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"external_id":{"isi":["000461922000006"],"arxiv":["1809.06358"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"22","publication":"Physical Review Letters","isi":1,"year":"2019","date_published":"2019-03-22T00:00:00Z","doi":"10.1103/PhysRevLett.122.114502","date_created":"2019-03-31T21:59:12Z"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n"}],"month":"05","alternative_title":["ISTA Thesis"],"file":[{"creator":"cigler","file_size":12597663,"date_updated":"2021-02-11T11:17:13Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","date_created":"2019-05-03T11:54:52Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2020-05-02","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_id":"6373"},{"date_updated":"2020-07-14T12:47:28Z","file_size":34644426,"creator":"cigler","date_created":"2019-05-03T11:54:54Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"6374","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"id":"67","status":"public","relation":"part_of_dissertation"},{"id":"5585","status":"public","relation":"popular_science"}]},"_id":"6371","status":"public","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"type":"dissertation","ddc":["576","579"],"supervisor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"date_updated":"2024-02-21T13:45:52Z","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:13Z","publisher":"Institute of Science and Technology Austria","oa":1,"day":"03","has_accepted_license":"1","year":"2019","doi":"10.15479/AT:ISTA:6371","date_published":"2019-05-03T00:00:00Z","date_created":"2019-05-03T11:55:51Z","page":"152","project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria."},"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","author":[{"id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","last_name":"Igler","full_name":"Igler, Claudia"}],"article_processing_charge":"No"},{"file_date_updated":"2021-11-15T10:27:29Z","department":[{"_id":"KrPi"}],"date_updated":"2021-11-15T10:48:49Z","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10286","issue":"3","volume":2018,"publication_status":"published","publication_identifier":{"eissn":["2569-2925"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10289","checksum":"b816b848f046c48a8357700d9305dce5","file_size":955755,"date_updated":"2021-11-15T10:27:29Z","creator":"cchlebak","file_name":"2018_IACR_Allini.pdf","date_created":"2021-11-15T10:27:29Z"}],"scopus_import":"1","intvolume":" 2018","month":"01","abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Allini, Elie Noumon","last_name":"Allini","first_name":"Elie Noumon"},{"full_name":"Skórski, Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"},{"first_name":"Oto","full_name":"Petura, Oto","last_name":"Petura"},{"first_name":"Florent","full_name":"Bernard, Florent","last_name":"Bernard"},{"full_name":"Laban, Marek","last_name":"Laban","first_name":"Marek"},{"first_name":"Viktor","last_name":"Fischer","full_name":"Fischer, Viktor"}],"title":"Evaluation and monitoring of free running oscillators serving as source of randomness","citation":{"ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"214-242","date_created":"2021-11-14T23:01:25Z","date_published":"2018-01-01T00:00:00Z","doi":"10.13154/tches.v2018.i3.214-242","year":"2018","has_accepted_license":"1","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","day":"01","oa":1,"publisher":"International Association for Cryptologic Research","quality_controlled":"1"},{"pmid":1,"oa_version":"None","abstract":[{"text":"Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.","lang":"eng"}],"month":"01","intvolume":" 12","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"publication_status":"published","issue":"2","volume":12,"_id":"10362","status":"public","keyword":["general physics and astronomy"],"type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-11-26T15:57:02Z","acknowledgement":"We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1).","publisher":"American Chemical Society","quality_controlled":"1","day":"19","publication":"ACS Nano","year":"2018","date_published":"2018-01-19T00:00:00Z","doi":"10.1021/acsnano.7b08044","date_created":"2021-11-26T15:15:00Z","page":"1508-1518","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044","apa":"Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.7b08044","ieee":"P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.","short":"P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.","mla":"Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044.","ista":"Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518.","chicago":"Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044."},"title":"A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement","author":[{"last_name":"Fisher","full_name":"Fisher, Patrick D. Ellis","first_name":"Patrick D. Ellis"},{"last_name":"Shen","full_name":"Shen, Qi","first_name":"Qi"},{"first_name":"Bernice","last_name":"Akpinar","full_name":"Akpinar, Bernice"},{"full_name":"Davis, Luke K.","last_name":"Davis","first_name":"Luke K."},{"first_name":"Kenny Kwok Hin","full_name":"Chung, Kenny Kwok Hin","last_name":"Chung"},{"first_name":"David","full_name":"Baddeley, David","last_name":"Baddeley"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"first_name":"Thomas J.","last_name":"Melia","full_name":"Melia, Thomas J."},{"first_name":"Bart W.","last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W."},{"last_name":"Lin","full_name":"Lin, Chenxiang","first_name":"Chenxiang"},{"last_name":"Lusk","full_name":"Lusk, C. Patrick","first_name":"C. Patrick"}],"external_id":{"pmid":["29350911"]},"article_processing_charge":"No"},{"scopus_import":"1","intvolume":" 10","month":"03","abstract":[{"lang":"eng","text":"Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation."}],"oa_version":"None","pmid":1,"issue":"5","volume":10,"publication_status":"published","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["general chemical engineering","general chemistry"],"status":"public","_id":"10360","date_updated":"2021-11-26T15:14:00Z","extern":"1","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).","page":"523-531","date_created":"2021-11-26T12:41:38Z","doi":"10.1038/s41557-018-0023-x","date_published":"2018-03-26T00:00:00Z","year":"2018","publication":"Nature Chemistry","day":"26","article_processing_charge":"No","external_id":{"pmid":["29581486"]},"author":[{"first_name":"Samuel I. A.","last_name":"Cohen","full_name":"Cohen, Samuel I. A."},{"last_name":"Cukalevski","full_name":"Cukalevski, Risto","first_name":"Risto"},{"last_name":"Michaels","full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T."},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Mattias","full_name":"Törnquist, Mattias","last_name":"Törnquist"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"last_name":"Dobson","full_name":"Dobson, Christopher M.","first_name":"Christopher M."},{"full_name":"Buell, Alexander K.","last_name":"Buell","first_name":"Alexander K."},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"}],"title":"Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide","citation":{"chicago":"Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry. Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x.","ista":"Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531.","mla":"Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x.","ieee":"S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” Nature Chemistry, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.","short":"S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531.","apa":"Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-018-0023-x","ama":"Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"status":"public","keyword":["materials chemistry"],"article_type":"original","type":"journal_article","_id":"10357","extern":"1","date_updated":"2021-11-26T12:40:02Z","month":"10","intvolume":" 122","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"text":"The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.","lang":"eng"}],"volume":122,"issue":"49","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"publication_status":"published","title":"Statistical mechanics of globular oligomer formation by protein molecules","author":[{"first_name":"Alexander J.","full_name":"Dear, Alexander J.","last_name":"Dear"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"external_id":{"pmid":["30336667"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805.","ista":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730.","mla":"Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805.","ieee":"A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” The Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018.","short":"A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730.","ama":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805","apa":"Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.8b07805"},"quality_controlled":"1","publisher":"American Chemical Society","acknowledgement":"We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions.","date_published":"2018-10-18T00:00:00Z","doi":"10.1021/acs.jpcb.8b07805","date_created":"2021-11-26T11:55:12Z","page":"11721-11730","day":"18","publication":"The Journal of Physical Chemistry B","year":"2018"},{"year":"2018","day":"18","publication":"Nano Letters","page":"5350-5356","date_published":"2018-04-18T00:00:00Z","doi":"10.1021/acs.nanolett.8b00786","date_created":"2021-11-26T12:15:47Z","acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"citation":{"ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786","apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356.","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:10.1021/acs.nanolett.8b00786.","ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Tine","full_name":"Curk, Tine","last_name":"Curk"},{"full_name":"Wirnsberger, Peter","last_name":"Wirnsberger","first_name":"Peter"},{"last_name":"Dobnikar","full_name":"Dobnikar, Jure","first_name":"Jure"},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"article_processing_charge":"No","external_id":{"pmid":["29667410"]},"title":"Controlling cargo trafficking in multicomponent membranes","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":18,"issue":"9","abstract":[{"text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.10147","open_access":"1"}],"month":"04","intvolume":" 18","date_updated":"2021-11-26T15:14:08Z","extern":"1","_id":"10359","article_type":"original","type":"journal_article","status":"public","keyword":["mechanical engineering","condensed matter physics"]},{"author":[{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"first_name":"Lucie X.","last_name":"Liu","full_name":"Liu, Lucie X."},{"last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"last_name":"Bolhuis","full_name":"Bolhuis, Peter G.","first_name":"Peter G."},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."}],"external_id":{"arxiv":["1803.04851"]},"article_processing_charge":"No","title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation","citation":{"chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics. Taylor & Francis, 2018. https://doi.org/10.1080/00268976.2018.1474280.","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065.","mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22, Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor & Francis, pp. 3055–3065, 2018.","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., & Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","quality_controlled":"1","publisher":"Taylor & Francis","oa":1,"acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","page":"3055-3065","date_published":"2018-05-24T00:00:00Z","doi":"10.1080/00268976.2018.1474280","date_created":"2021-11-26T12:08:02Z","year":"2018","day":"24","publication":"Molecular Physics","type":"journal_article","article_type":"original","status":"public","keyword":["physical chemistry"],"_id":"10358","date_updated":"2021-11-26T12:39:58Z","extern":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.04851"}],"month":"05","intvolume":" 116","abstract":[{"lang":"eng","text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements."}],"oa_version":"Preprint","volume":116,"issue":"21-22","publication_identifier":{"issn":["0026-8976"],"eissn":["1362-3028"]},"publication_status":"published","language":[{"iso":"eng"}]},{"date_updated":"2021-11-26T15:58:19Z","extern":"1","_id":"10361","type":"journal_article","article_type":"original","status":"public","keyword":["physical and theoretical chemistry"],"publication_identifier":{"eissn":["1545-1593"],"issn":["0066-426X"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":69,"abstract":[{"text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"02","intvolume":" 69","citation":{"apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322","ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322","ieee":"T. C. T. Michaels et al., “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” Annual Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018.","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298.","chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews, 2018. https://doi.org/10.1146/annurev-physchem-050317-021322."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"full_name":"Habchi, Johnny","last_name":"Habchi","first_name":"Johnny"},{"first_name":"Sean","full_name":"Chia, Sean","last_name":"Chia"},{"last_name":"Meisl","full_name":"Meisl, Georg","first_name":"Georg"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"first_name":"Christopher M.","full_name":"Dobson, Christopher M.","last_name":"Dobson"},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."}],"external_id":{"pmid":["29490200"]},"article_processing_charge":"No","title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation","year":"2018","day":"28","publication":"Annual Review of Physical Chemistry","page":"273-298","doi":"10.1146/annurev-physchem-050317-021322","date_published":"2018-02-28T00:00:00Z","date_created":"2021-11-26T12:52:12Z","acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","publisher":"Annual Reviews","quality_controlled":"1"},{"_id":"10626","article_type":"original","type":"journal_article","keyword":["general physics and astronomy"],"status":"public","date_updated":"2022-01-14T13:48:35Z","extern":"1","abstract":[{"lang":"eng","text":"Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1805.04199","open_access":"1"}],"scopus_import":"1","intvolume":" 121","month":"11","publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"language":[{"iso":"eng"}],"volume":121,"issue":"22","article_number":"226801","citation":{"chicago":"Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.226801.","ista":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801.","mla":"Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801.","short":"H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018).","ieee":"H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22. American Physical Society, 2018.","ama":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801","apa":"Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.226801"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["1805.04199"]},"article_processing_charge":"No","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"H.","full_name":"Zhou, H.","last_name":"Zhou"},{"last_name":"Spanton","full_name":"Spanton, E. M.","first_name":"E. M."},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"title":"Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices","acknowledgement":"We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2018","publication":"Physical Review Letters","day":"28","date_created":"2022-01-14T12:15:47Z","doi":"10.1103/physrevlett.121.226801","date_published":"2018-11-28T00:00:00Z"},{"extern":"1","date_updated":"2022-01-14T13:58:24Z","_id":"10627","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"volume":97,"issue":"18","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures."}],"intvolume":" 97","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.08184"}],"scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:10.1103/physrevb.97.184501.","short":"H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).","ieee":"H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” Physical Review B, vol. 97, no. 18. American Physical Society, 2018.","ama":"Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501","apa":"Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.184501","chicago":"Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.","ista":"Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501."},"title":"Imaging phase slip dynamics in micron-size superconducting rings","article_processing_charge":"No","external_id":{"arxiv":["1703.08184"]},"author":[{"last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"full_name":"Naibert, Tyler R.","last_name":"Naibert","first_name":"Tyler R."},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"article_number":"184501","publication":"Physical Review B","day":"08","year":"2018","date_created":"2022-01-14T13:48:47Z","doi":"10.1103/physrevb.97.184501","date_published":"2018-05-08T00:00:00Z","acknowledgement":"We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"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.","oa":1,"quality_controlled":"1","publisher":"EasyChair","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","day":"23","year":"2018","has_accepted_license":"1","date_created":"2022-03-18T12:46:32Z","doi":"10.29007/5z5k","date_published":"2018-10-23T00:00:00Z","page":"233-253","project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"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 MH, 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. H., & 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","short":"K. Chatterjee, W. Dvořák, M.H. 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. H. 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.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H 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.","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253."},"title":"Quasipolynomial set-based symbolic algorithms for parity games","article_processing_charge":"No","external_id":{"arxiv":["1909.04983"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Wolfgang","last_name":"Dvořák","full_name":"Dvořák, Wolfgang"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Svozil","full_name":"Svozil, Alexander","first_name":"Alexander"}],"oa_version":"Published Version","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"}],"intvolume":" 57","month":"10","alternative_title":["EPiC Series in Computing"],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2022-05-17T07:51:08Z","file_size":720893,"date_created":"2022-05-17T07:51:08Z","file_name":"2018_EPiCs_Chatterjee.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1229aa8640bd6db610c85decf2265480","file_id":"11392","success":1}],"publication_status":"published","publication_identifier":{"issn":["2398-7340"]},"ec_funded":1,"volume":57,"_id":"10883","status":"public","conference":{"location":"Awassa, Ethiopia","end_date":"2018-11-21","start_date":"2018-11-17","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning"},"type":"conference","ddc":["000"],"date_updated":"2022-07-29T09:24:31Z","file_date_updated":"2022-05-17T07:51:08Z","department":[{"_id":"KrCh"}]},{"date_created":"2018-12-11T11:50:06Z","volume":32,"date_published":"2018-01-01T00:00:00Z","doi":"10.1137/16M107894X","issue":"1","page":"64-93","language":[{"iso":"eng"}],"publication":"SIAM Journal on Discrete Mathematics","day":"01","year":"2018","publication_status":"published","intvolume":" 32","month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.01814"}],"publisher":"SIAM","quality_controlled":"1","oa_version":"Preprint","abstract":[{"lang":"eng","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. "}],"title":"Generalized permutohedra from probabilistic graphical models","author":[{"first_name":"Fatemeh","id":"2C29581E-F248-11E8-B48F-1D18A9856A87","full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler"},{"full_name":"Wang, Charles","last_name":"Wang","first_name":"Charles"},{"last_name":"Yu","full_name":"Yu, Josephine","first_name":"Josephine"}],"publist_id":"6284","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T06:48:13Z","citation":{"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.","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.","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","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","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."},"status":"public","type":"journal_article","_id":"1092"},{"oa":1,"quality_controlled":"1","publisher":"Springer","year":"2018","day":"27","page":"185 - 214","date_created":"2018-12-11T11:44:08Z","doi":"10.1007/978-3-030-01602-9_9","date_published":"2018-10-27T00:00:00Z","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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.","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1806.10843"]},"author":[{"last_name":"Leopold","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"publist_id":"8045","title":"Mean-field limits of particles in interaction with quantised radiation fields","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"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"scopus_import":1,"intvolume":" 270","month":"10","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":270,"_id":"11","conference":{"name":"MaLiQS: Macroscopic Limits of Quantum Systems","location":"Munich, Germany","end_date":"2017-04-01","start_date":"2017-03-30"},"type":"conference","status":"public","date_updated":"2021-01-12T06:48:16Z","department":[{"_id":"RoSe"}]},{"external_id":{"pmid":["30228202"]},"article_processing_charge":"No","author":[{"first_name":"Asako","last_name":"McCloskey","full_name":"McCloskey, Asako"},{"last_name":"Ibarra","full_name":"Ibarra, Arkaitz","first_name":"Arkaitz"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"title":"Tpr regulates the total number of nuclear pore complexes per cell nucleus","citation":{"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.","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","short":"A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.","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.","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.","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."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa":1,"publisher":"Cold Spring Harbor Laboratory","quality_controlled":"1","page":"1321-1331","date_created":"2022-04-07T07:45:30Z","date_published":"2018-09-18T00:00:00Z","doi":"10.1101/gad.315523.118","year":"2018","publication":"Genes & Development","day":"18","article_type":"original","type":"journal_article","keyword":["Developmental Biology","Genetics"],"status":"public","_id":"11063","date_updated":"2022-07-18T08:32:32Z","extern":"1","main_file_link":[{"url":"https://doi.org/10.1101/gad.315523.118","open_access":"1"}],"scopus_import":"1","intvolume":" 32","month":"09","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"}],"pmid":1,"oa_version":"Published Version","volume":32,"issue":"19-20","publication_status":"published","publication_identifier":{"issn":["0890-9369","1549-5477"]},"language":[{"iso":"eng"}]},{"date_created":"2022-04-07T07:45:40Z","doi":"10.1186/s13059-018-1599-6","date_published":"2018-12-20T00:00:00Z","year":"2018","publication":"Genome Biology","day":"20","oa":1,"quality_controlled":"1","publisher":"BioMed Central","article_processing_charge":"No","external_id":{"pmid":["30567591"]},"author":[{"first_name":"Jason G.","last_name":"Fleischer","full_name":"Fleischer, Jason G."},{"last_name":"Schulte","full_name":"Schulte, Roberta","first_name":"Roberta"},{"last_name":"Tsai","full_name":"Tsai, Hsiao H.","first_name":"Hsiao H."},{"first_name":"Swati","full_name":"Tyagi, Swati","last_name":"Tyagi"},{"last_name":"Ibarra","full_name":"Ibarra, Arkaitz","first_name":"Arkaitz"},{"full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev","first_name":"Maxim N."},{"last_name":"Huang","full_name":"Huang, Ling","first_name":"Ling"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"},{"first_name":"Saket","last_name":"Navlakha","full_name":"Navlakha, Saket"}],"title":"Predicting age from the transcriptome of human dermal fibroblasts","citation":{"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).","ieee":"J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018.","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","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","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.","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.","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."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_number":"221","volume":19,"publication_status":"published","publication_identifier":{"issn":["1474-760X"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-018-1599-6"}],"scopus_import":"1","intvolume":" 19","month":"12","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"}],"oa_version":"Published Version","pmid":1,"date_updated":"2022-07-18T08:32:34Z","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"11064"},{"quality_controlled":"1","publisher":"EDP Sciences","oa":1,"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).","doi":"10.1051/0004-6361/201833528","date_published":"2018-11-19T00:00:00Z","date_created":"2022-07-06T11:14:23Z","day":"19","publication":"Astronomy & Astrophysics","year":"2018","article_number":"A136","title":"Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe","author":[{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"first_name":"Max","last_name":"Gronke","full_name":"Gronke, Max"},{"first_name":"Ana","full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso"},{"last_name":"Stefanon","full_name":"Stefanon, Mauro","first_name":"Mauro"},{"last_name":"Röttgering","full_name":"Röttgering, Huub","first_name":"Huub"}],"external_id":{"arxiv":["1805.11621"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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","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).","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."},"month":"11","intvolume":" 619","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1805.11621","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":619,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / dark ages / reionization / first stars / techniques: spectroscopic / intergalactic medium"],"article_type":"original","type":"journal_article","_id":"11508","extern":"1","date_updated":"2022-07-19T09:32:08Z"},{"page":"2999-3015","date_published":"2018-08-01T00:00:00Z","doi":"10.1093/mnras/sty925","date_created":"2022-07-08T11:48:48Z","year":"2018","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"We thank the anonymous referee for their useful comments and suggestions that improved this study. AAK thanks Anahita Alavi and Irene Shivaei for useful discussion in the making of this paper. AAK acknowledges that this work was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX16AO92H. 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. PNB is grateful for support from STFC via grant STM001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Grant DUSTYGAL (321334), and a Royal Society/Wolfson Merit award. 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.","author":[{"full_name":"Khostovan, A A","last_name":"Khostovan","first_name":"A A"},{"first_name":"D","full_name":"Sobral, D","last_name":"Sobral"},{"first_name":"B","last_name":"Mobasher","full_name":"Mobasher, B"},{"first_name":"P N","full_name":"Best, P N","last_name":"Best"},{"first_name":"I","full_name":"Smail, I","last_name":"Smail"},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Darvish, B","last_name":"Darvish","first_name":"B"},{"full_name":"Nayyeri, H","last_name":"Nayyeri","first_name":"H"},{"full_name":"Hemmati, S","last_name":"Hemmati","first_name":"S"},{"full_name":"Stott, J P","last_name":"Stott","first_name":"J P"}],"external_id":{"arxiv":["1705.01101"]},"article_processing_charge":"No","title":"The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass","citation":{"short":"A.A. Khostovan, D. Sobral, B. Mobasher, P.N. Best, I. Smail, J.J. Matthee, B. Darvish, H. Nayyeri, S. Hemmati, J.P. Stott, Monthly Notices of the Royal Astronomical Society 478 (2018) 2999–3015.","ieee":"A. A. Khostovan et al., “The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3. Oxford University Press, pp. 2999–3015, 2018.","apa":"Khostovan, A. A., Sobral, D., Mobasher, B., Best, P. N., Smail, I., Matthee, J. J., … Stott, J. P. (2018). The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty925","ama":"Khostovan AA, Sobral D, Mobasher B, et al. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 2018;478(3):2999-3015. doi:10.1093/mnras/sty925","mla":"Khostovan, A. A., et al. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3, Oxford University Press, 2018, pp. 2999–3015, doi:10.1093/mnras/sty925.","ista":"Khostovan AA, Sobral D, Mobasher B, Best PN, Smail I, Matthee JJ, Darvish B, Nayyeri H, Hemmati S, Stott JP. 2018. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 478(3), 2999–3015.","chicago":"Khostovan, A A, D Sobral, B Mobasher, P N Best, I Smail, Jorryt J Matthee, B Darvish, H Nayyeri, S Hemmati, and J P Stott. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty925."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","volume":478,"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.01101"}],"month":"08","intvolume":" 478","abstract":[{"text":"We investigate the clustering properties of ∼7000 H β + [O III] and [O II] narrowband-selected emitters at z ∼ 0.8–4.7 from the High-z Emission Line Survey. We find clustering lengths, r0, of 1.5–4.0 h−1 Mpc and minimum dark matter halo masses of 1010.7–12.1 M⊙ for our z = 0.8–3.2 H β + [O III] emitters and r0 ∼ 2.0–8.3 h−1 Mpc and halo masses of 1011.5–12.6 M⊙ for our z = 1.5–4.7 [O II] emitters. We find r0 to strongly increase both with increasing line luminosity and redshift. By taking into account the evolution of the characteristic line luminosity, L⋆(z), and using our model predictions of halo mass given r0, we find a strong, redshift-independent increasing trend between L/L⋆(z) and minimum halo mass. The faintest H β + [O III] emitters are found to reside in 109.5 M⊙ haloes and the brightest emitters in 1013.0 M⊙ haloes. For [O II] emitters, the faintest emitters are found in 1010.5 M⊙ haloes and the brightest emitters in 1012.6 M⊙ haloes. A redshift-independent stellar mass dependency is also observed where the halo mass increases from 1011 to 1012.5 M⊙ for stellar masses of 108.5 to 1011.5 M⊙, respectively. We investigate the interdependencies of these trends by repeating our analysis in a Lline−Mstar grid space for our most populated samples (H β + [O III] z = 0.84 and [O II] z = 1.47) and find that the line luminosity dependency is stronger than the stellar mass dependency on halo mass. For L > L⋆ emitters at all epochs, we find a relatively flat trend with halo masses of 1012.5–13 M⊙, which may be due to quenching mechanisms in massive haloes that is consistent with a transitional halo mass predicted by models.","lang":"eng"}],"oa_version":"Published Version","date_updated":"2022-08-19T06:53:39Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: star formation","cosmology: observations","large-scale structure of Universe"],"_id":"11549"},{"author":[{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"last_name":"Darvish","full_name":"Darvish, Behnam","first_name":"Behnam"},{"first_name":"Ian","last_name":"Smail","full_name":"Smail, Ian"},{"first_name":"Philip N","last_name":"Best","full_name":"Best, Philip N"},{"last_name":"Alegre","full_name":"Alegre, Lara","first_name":"Lara"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"},{"first_name":"Bahram","last_name":"Mobasher","full_name":"Mobasher, Bahram"},{"first_name":"Ana","full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso"},{"first_name":"Andra","full_name":"Stroe, Andra","last_name":"Stroe"},{"last_name":"Oteo","full_name":"Oteo, Iván","first_name":"Iván"}],"article_processing_charge":"No","external_id":{"arxiv":["1802.10102"]},"title":"The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN","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.","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.","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"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.","page":"2817-2840","date_published":"2018-06-01T00:00:00Z","doi":"10.1093/mnras/sty782","date_created":"2022-07-12T07:18:02Z","year":"2018","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: starburst","cosmology: observations"],"_id":"11557","date_updated":"2022-08-19T07:01:08Z","extern":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.10102"}],"month":"06","intvolume":" 477","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."}],"oa_version":"Preprint","volume":477,"issue":"2","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","language":[{"iso":"eng"}]},{"article_processing_charge":"No","external_id":{"arxiv":["1712.04451"]},"author":[{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"full_name":"Santos, Sérgio","last_name":"Santos","first_name":"Sérgio"},{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"first_name":"Ana","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana"},{"full_name":"Ribeiro, Bruno","last_name":"Ribeiro","first_name":"Bruno"},{"first_name":"João","full_name":"Calhau, João","last_name":"Calhau"},{"full_name":"Khostovan, Ali A","last_name":"Khostovan","first_name":"Ali A"}],"title":"Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6","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.","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","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).","page":"4725-4752","date_created":"2022-07-12T10:41:08Z","doi":"10.1093/mnras/sty378","date_published":"2018-06-01T00:00:00Z","year":"2018","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: high-redshift","galaxies: luminosity function","mass function","galaxies: statistics"],"status":"public","_id":"11558","date_updated":"2022-08-19T07:04:45Z","extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.04451","open_access":"1"}],"scopus_import":"1","intvolume":" 476","month":"06","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."}],"oa_version":"Preprint","volume":476,"issue":"4","publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}]},{"intvolume":" 478","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1712.03985","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","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"}],"volume":478,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: formation"],"status":"public","type":"journal_article","article_type":"original","_id":"11555","extern":"1","date_updated":"2022-08-19T06:58:06Z","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","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.","date_created":"2022-07-11T08:05:42Z","date_published":"2018-07-01T00:00:00Z","doi":"10.1093/mnras/sty1088","page":"1170-1184","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","year":"2018","title":"Kiloparsec-scale gaseous clumps and star formation at z = 5–7","external_id":{"arxiv":["1712.03985"]},"article_processing_charge":"No","author":[{"first_name":"S","last_name":"Carniani","full_name":"Carniani, S"},{"full_name":"Maiolino, R","last_name":"Maiolino","first_name":"R"},{"last_name":"Amorin","full_name":"Amorin, R","first_name":"R"},{"first_name":"L","last_name":"Pentericci","full_name":"Pentericci, L"},{"first_name":"A","last_name":"Pallottini","full_name":"Pallottini, A"},{"full_name":"Ferrara, A","last_name":"Ferrara","first_name":"A"},{"first_name":"C J","full_name":"Willott, C J","last_name":"Willott"},{"full_name":"Smit, R","last_name":"Smit","first_name":"R"},{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"last_name":"Sobral","full_name":"Sobral, D","first_name":"D"},{"first_name":"P","full_name":"Santini, P","last_name":"Santini"},{"first_name":"M","full_name":"Castellano, M","last_name":"Castellano"},{"last_name":"De Barros","full_name":"De Barros, S","first_name":"S"},{"last_name":"Fontana","full_name":"Fontana, A","first_name":"A"},{"full_name":"Grazian, A","last_name":"Grazian","first_name":"A"},{"first_name":"L","last_name":"Guaita","full_name":"Guaita, L"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","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."}},{"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","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.","page":"L34 - L39","date_created":"2022-07-14T12:49:47Z","date_published":"2018-09-01T00:00:00Z","doi":"10.1093/mnrasl/sly093","year":"2018","publication":"Monthly Notices of the Royal Astronomical Society: Letters","day":"01","external_id":{"arxiv":["1802.06786"]},"article_processing_charge":"No","author":[{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"last_name":"Schaye","full_name":"Schaye, Joop","first_name":"Joop"}],"title":"Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement","citation":{"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.","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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1802.06786","open_access":"1"}],"scopus_import":"1","intvolume":" 479","month":"09","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"}],"oa_version":"Preprint","volume":479,"issue":"1","publication_status":"published","publication_identifier":{"eissn":["1745-3933"],"issn":["1745-3925"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: formation","galaxies: star formation"],"status":"public","_id":"11584","date_updated":"2022-08-19T08:35:45Z","extern":"1"},{"article_number":"L10","title":"TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae","external_id":{"arxiv":["1809.07573"]},"article_processing_charge":"No","author":[{"first_name":"D.","last_name":"Gandolfi","full_name":"Gandolfi, D."},{"first_name":"O.","last_name":"Barragán","full_name":"Barragán, O."},{"full_name":"Livingston, J. H.","last_name":"Livingston","first_name":"J. H."},{"full_name":"Fridlund, M.","last_name":"Fridlund","first_name":"M."},{"first_name":"A. B.","full_name":"Justesen, A. B.","last_name":"Justesen"},{"first_name":"S.","last_name":"Redfield","full_name":"Redfield, S."},{"first_name":"L.","full_name":"Fossati, L.","last_name":"Fossati"},{"first_name":"S.","last_name":"Mathur","full_name":"Mathur, S."},{"first_name":"S.","last_name":"Grziwa","full_name":"Grziwa, S."},{"first_name":"J.","full_name":"Cabrera, J.","last_name":"Cabrera"},{"full_name":"García, R. A.","last_name":"García","first_name":"R. A."},{"first_name":"C. M.","last_name":"Persson","full_name":"Persson, C. M."},{"full_name":"Van Eylen, V.","last_name":"Van Eylen","first_name":"V."},{"full_name":"Hatzes, A. P.","last_name":"Hatzes","first_name":"A. P."},{"first_name":"D.","last_name":"Hidalgo","full_name":"Hidalgo, D."},{"last_name":"Albrecht","full_name":"Albrecht, S.","first_name":"S."},{"last_name":"Bugnet","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"first_name":"W. D.","full_name":"Cochran, W. D.","last_name":"Cochran"},{"last_name":"Csizmadia","full_name":"Csizmadia, Sz.","first_name":"Sz."},{"last_name":"Deeg","full_name":"Deeg, H.","first_name":"H."},{"first_name":"Ph.","last_name":"Eigmüller","full_name":"Eigmüller, Ph."},{"last_name":"Endl","full_name":"Endl, M.","first_name":"M."},{"full_name":"Erikson, A.","last_name":"Erikson","first_name":"A."},{"first_name":"M.","full_name":"Esposito, M.","last_name":"Esposito"},{"last_name":"Guenther","full_name":"Guenther, E.","first_name":"E."},{"full_name":"Korth, J.","last_name":"Korth","first_name":"J."},{"first_name":"R.","full_name":"Luque, R.","last_name":"Luque"},{"first_name":"P.","full_name":"Montañes Rodríguez, P.","last_name":"Montañes Rodríguez"},{"full_name":"Nespral, D.","last_name":"Nespral","first_name":"D."},{"first_name":"G.","full_name":"Nowak, G.","last_name":"Nowak"},{"first_name":"M.","full_name":"Pätzold, M.","last_name":"Pätzold"},{"first_name":"J.","last_name":"Prieto-Arranz","full_name":"Prieto-Arranz, J."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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).","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","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","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.","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.","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."},"oa":1,"publisher":"EDP Sciences","quality_controlled":"1","date_created":"2022-07-18T14:41:16Z","doi":"10.1051/0004-6361/201834289","date_published":"2018-11-22T00:00:00Z","publication":"Astronomy & Astrophysics","day":"22","year":"2018","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"],"status":"public","type":"journal_article","article_type":"letter_note","_id":"11619","extern":"1","date_updated":"2022-08-22T07:43:29Z","intvolume":" 619","month":"11","main_file_link":[{"url":"https://arxiv.org/abs/1809.07573","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"volume":619,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]}},{"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1809.05105","open_access":"1"}],"scopus_import":"1","intvolume":" 620","month":"12","publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"language":[{"iso":"eng"}],"volume":620,"_id":"11618","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics","asteroseismology / methods","data analysis / stars","oscillations"],"status":"public","date_updated":"2022-08-22T07:41:07Z","extern":"1","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.","oa":1,"publisher":"EDP Sciences","quality_controlled":"1","year":"2018","publication":"Astronomy & Astrophysics","day":"01","date_created":"2022-07-18T14:37:39Z","date_published":"2018-12-01T00:00:00Z","doi":"10.1051/0004-6361/201833106","article_number":"A38","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.","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.","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.","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","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","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.","short":"L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, E. Corsaro, O.J. Hall, B.M. Rendle, Astronomy & Astrophysics 620 (2018)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1809.05105"]},"author":[{"id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle"},{"last_name":"García","full_name":"García, R. A.","first_name":"R. A."},{"first_name":"G. R.","full_name":"Davies, G. R.","last_name":"Davies"},{"first_name":"S.","full_name":"Mathur, S.","last_name":"Mathur"},{"first_name":"E.","full_name":"Corsaro, E.","last_name":"Corsaro"},{"first_name":"O. J.","full_name":"Hall, O. J.","last_name":"Hall"},{"first_name":"B. M.","last_name":"Rendle","full_name":"Rendle, B. M."}],"title":"FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants"},{"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.","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"day":"01","publication":"Monthly Notices of the Royal Astronomical Society","year":"2018","doi":"10.1093/mnras/sty1390","date_published":"2018-08-01T00:00:00Z","date_created":"2022-07-18T14:43:17Z","page":"4866-4880","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","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.","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."},"title":"HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2","author":[{"first_name":"V","full_name":"Van Eylen, V","last_name":"Van Eylen"},{"full_name":"Dai, F","last_name":"Dai","first_name":"F"},{"first_name":"S","last_name":"Mathur","full_name":"Mathur, S"},{"last_name":"Gandolfi","full_name":"Gandolfi, D","first_name":"D"},{"first_name":"S","full_name":"Albrecht, S","last_name":"Albrecht"},{"first_name":"M","full_name":"Fridlund, M","last_name":"Fridlund"},{"full_name":"García, R A","last_name":"García","first_name":"R A"},{"last_name":"Guenther","full_name":"Guenther, E","first_name":"E"},{"full_name":"Hjorth, M","last_name":"Hjorth","first_name":"M"},{"last_name":"Justesen","full_name":"Justesen, A B","first_name":"A B"},{"first_name":"J","full_name":"Livingston, J","last_name":"Livingston"},{"first_name":"M N","full_name":"Lund, M N","last_name":"Lund"},{"first_name":"F","last_name":"Pérez Hernández","full_name":"Pérez Hernández, F"},{"full_name":"Prieto-Arranz, J","last_name":"Prieto-Arranz","first_name":"J"},{"last_name":"Regulo","full_name":"Regulo, C","first_name":"C"},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000"},{"first_name":"M E","full_name":"Everett, M E","last_name":"Everett"},{"full_name":"Hirano, T","last_name":"Hirano","first_name":"T"},{"last_name":"Nespral","full_name":"Nespral, D","first_name":"D"},{"first_name":"G","full_name":"Nowak, G","last_name":"Nowak"},{"first_name":"E","full_name":"Palle, E","last_name":"Palle"},{"full_name":"Silva Aguirre, V","last_name":"Silva Aguirre","first_name":"V"},{"first_name":"T","full_name":"Trifonov, 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"},{"first_name":"W J","full_name":"Chaplin, W J","last_name":"Chaplin"},{"last_name":"Cochran","full_name":"Cochran, W D","first_name":"W D"},{"last_name":"Csizmadia","full_name":"Csizmadia, S","first_name":"S"},{"last_name":"Deeg","full_name":"Deeg, H","first_name":"H"},{"full_name":"Endl, M","last_name":"Endl","first_name":"M"},{"last_name":"Heeren","full_name":"Heeren, P","first_name":"P"},{"last_name":"Grziwa","full_name":"Grziwa, S","first_name":"S"},{"last_name":"Hatzes","full_name":"Hatzes, A P","first_name":"A P"},{"full_name":"Hidalgo, D","last_name":"Hidalgo","first_name":"D"},{"first_name":"J","last_name":"Korth","full_name":"Korth, J"},{"first_name":"S","full_name":"Mathis, S","last_name":"Mathis"},{"last_name":"Montañes Rodriguez","full_name":"Montañes Rodriguez, P","first_name":"P"},{"first_name":"N","full_name":"Narita, N","last_name":"Narita"},{"first_name":"M","last_name":"Patzold","full_name":"Patzold, M"},{"last_name":"Persson","full_name":"Persson, C M","first_name":"C M"},{"full_name":"Rodler, F","last_name":"Rodler","first_name":"F"},{"last_name":"Smith","full_name":"Smith, A M S","first_name":"A M S"}],"article_processing_charge":"No","external_id":{"arxiv":["1805.01860"]},"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"08","intvolume":" 478","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.01860"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","issue":"4","volume":478,"_id":"11620","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","asteroseismology","planets and satellites: composition","planets and satellites: formation","planets and satellites: fundamental parameters"],"article_type":"original","type":"journal_article","extern":"1","date_updated":"2022-08-22T07:45:38Z"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bugnet LA, García RA, Davies GR, Mathur S, Hall OJ, Rendle BM. FliPer: Classifying TESS pulsating stars. 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.","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","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","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. .","short":"L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, O.J. Hall, B.M. Rendle, ArXiv (n.d.).","mla":"Bugnet, Lisa Annabelle, et al. “FliPer: Classifying TESS Pulsating Stars.” ArXiv, 1811.12140, doi:10.48550/arXiv.1811.12140."},"date_updated":"2022-08-22T08:41:55Z","title":"FliPer: Classifying TESS pulsating stars","author":[{"first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet"},{"first_name":"R. A.","last_name":"García","full_name":"García, R. A."},{"first_name":"G. R.","full_name":"Davies, G. R.","last_name":"Davies"},{"last_name":"Mathur","full_name":"Mathur, S.","first_name":"S."},{"full_name":"Hall, O. J.","last_name":"Hall","first_name":"O. J."},{"full_name":"Rendle, B. M.","last_name":"Rendle","first_name":"B. M."}],"external_id":{"arxiv":["1811.12140"]},"article_processing_charge":"No","article_number":"1811.12140","_id":"11631","status":"public","keyword":["asteroseismology - methods","data analysis - stars","oscillations"],"type":"preprint","day":"29","publication":"arXiv","language":[{"iso":"eng"}],"year":"2018","publication_status":"submitted","date_published":"2018-11-29T00:00:00Z","doi":"10.48550/arXiv.1811.12140","date_created":"2022-07-21T07:05:23Z","oa_version":"Preprint","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"}],"month":"11","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1811.12140"}],"oa":1}]