[{"article_processing_charge":"No","author":[{"full_name":"Valentini, Marco","last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"}],"file_date_updated":"2021-05-14T11:56:48Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","date_updated":"2024-02-21T12:40:09Z","citation":{"chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.","ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9389.","mla":"Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389.","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389","apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","short":"M. Valentini, (2021)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public","_id":"9389","date_created":"2021-05-14T12:07:53Z","contributor":[{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","contributor_type":"contact_person"}],"doi":"10.15479/AT:ISTA:9389","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8910"}]},"date_published":"2021-01-01T00:00:00Z","year":"2021","has_accepted_license":"1","file":[{"file_id":"9390","checksum":"80a905c4eef24dab6fb247e81a3d67f5","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Notebook_Valentini.pdf","date_created":"2021-05-14T11:42:23Z","file_size":10572981,"date_updated":"2021-05-14T11:42:23Z","creator":"mvalenti"},{"file_name":"Experimental_data.zip","date_created":"2021-05-14T11:56:48Z","creator":"mvalenti","file_size":99076111,"date_updated":"2021-05-14T11:56:48Z","file_id":"9391","checksum":"1e61a7e63949448a8db0091cdac23570","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"}],"oa":1,"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"."}],"acknowledged_ssus":[{"_id":"NanoFab"}],"oa_version":"Published Version"},{"file":[{"creator":"cchlebak","file_size":1917512,"date_updated":"2021-12-17T08:12:37Z","file_name":"2021_PhysRevResearch_Aggarwal.pdf","date_created":"2021-12-17T08:12:37Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10561","checksum":"60a1bc9c9b616b1b155044bb8cfc6484"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","id":"8831","status":"public"},{"status":"public","id":"8834","relation":"research_data"}]},"volume":3,"issue":"2","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Hole gases in planar germanium can have high mobilities in combination with strong spin-orbit interaction and electrically tunable g factors, and are therefore emerging as a promising platform for creating hybrid superconductor-semiconductor devices. A key challenge towards hybrid Ge-based quantum technologies is the design of high-quality interfaces and superconducting contacts that are robust against magnetic fields. In this work, by combining the assets of aluminum, which provides good contact to the Ge, and niobium, which has a significant superconducting gap, we demonstrate highly transparent low-disordered JoFETs with relatively large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs, opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip."}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"month":"04","intvolume":" 3","scopus_import":"1","ddc":["620"],"date_updated":"2024-02-21T12:41:26Z","file_date_updated":"2021-12-17T08:12:37Z","department":[{"_id":"GeKa"}],"_id":"10559","status":"public","keyword":["general engineering"],"article_type":"original","type":"journal_article","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)"},"day":"15","publication":"Physical Review Research","has_accepted_license":"1","year":"2021","doi":"10.1103/physrevresearch.3.l022005","date_published":"2021-04-15T00:00:00Z","date_created":"2021-12-16T18:50:57Z","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant agreement No. 844511 Grant Agreement No. 862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autnoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 823717 ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. G.S. and M.V. acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO). J.D. acknowledges support through FRIPRO-project 274853, which is funded by the Research Council of Norway.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. 2021;3(2). doi:10.1103/physrevresearch.3.l022005","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (2021). Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.3.l022005","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Martí-Sánchez, M. Veldhorst, J. Arbiol, G. Scappucci, J. Danon, G. Katsaros, Physical Review Research 3 (2021).","ieee":"K. Aggarwal et al., “Enhancement of proximity-induced superconductivity in a planar Ge hole gas,” Physical Review Research, vol. 3, no. 2. American Physical Society, 2021.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” Physical Review Research, vol. 3, no. 2, L022005, American Physical Society, 2021, doi:10.1103/physrevresearch.3.l022005.","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Martí-Sánchez S, Veldhorst M, Arbiol J, Scappucci G, Danon J, Katsaros G. 2021. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. 3(2), L022005.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Martí-Sánchez, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” Physical Review Research. American Physical Society, 2021. https://doi.org/10.1103/physrevresearch.3.l022005."},"title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","author":[{"last_name":"Aggarwal","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra","first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb"},{"last_name":"Hofmann","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez"},{"last_name":"Sammak","full_name":"Sammak, Amir","first_name":"Amir"},{"first_name":"Marc","full_name":"Botifoll, Marc","last_name":"Botifoll"},{"full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez","first_name":"Sara"},{"first_name":"Menno","full_name":"Veldhorst, Menno","last_name":"Veldhorst"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Scappucci","full_name":"Scappucci, Giordano","first_name":"Giordano"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"article_processing_charge":"No","external_id":{"arxiv":["2012.00322"]},"article_number":"L022005","project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}]},{"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","keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"status":"public","_id":"10166","file_date_updated":"2021-10-22T11:48:02Z","department":[{"_id":"BeVi"}],"date_updated":"2024-02-21T12:40:29Z","ddc":["595"],"scopus_import":"1","intvolume":" 288","month":"09","abstract":[{"text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"volume":288,"related_material":{"link":[{"url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1","relation":"supplementary_material"}],"record":[{"id":"9949","status":"public","relation":"research_data"}]},"issue":"1959","publication_status":"published","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-10-22T11:48:02Z","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","date_updated":"2021-10-22T11:48:02Z","file_size":995806,"creator":"cchlebak","file_id":"10172","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"article_number":"20211720","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","last_name":"Huylmans"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana"},{"full_name":"Hontoria, Francisco","last_name":"Hontoria","first_name":"Francisco"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","citation":{"ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2021. https://doi.org/10.1098/rspb.2021.1720.","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society, 2021.","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720","apa":"Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"The Royal Society","quality_controlled":"1","acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","date_created":"2021-10-21T07:46:06Z","doi":"10.1098/rspb.2021.1720","date_published":"2021-09-22T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"Proceedings of the Royal Society B: Biological Sciences","day":"22"},{"_id":"9192","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":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9192.","mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192.","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021).","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192"},"date_updated":"2024-02-21T12:41:09Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2021-02-24T17:45:13Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","article_processing_charge":"No","author":[{"last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"},{"last_name":"Arathoon","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document."}],"month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"success":1,"checksum":"f85537815809a8a4b7da9d01163f88c0","file_id":"9193","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"Data_Code.zip","date_created":"2021-02-24T17:45:13Z","creator":"larathoo","file_size":5934452,"date_updated":"2021-02-24T17:45:13Z"}],"day":"26","year":"2021","has_accepted_license":"1","date_created":"2021-02-24T17:49:21Z","contributor":[{"last_name":"Surendranadh","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","contributor_type":"project_member","last_name":"Baskett"},{"last_name":"Field","orcid":"0000-0002-4014-8478","contributor_type":"project_member","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","contributor_type":"project_member"},{"contributor_type":"project_leader","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11411"},{"relation":"later_version","id":"11321","status":"public"},{"relation":"earlier_version","id":"8254","status":"public"}]},"doi":"10.15479/AT:ISTA:9192","date_published":"2021-02-26T00:00:00Z"},{"day":"24","file":[{"file_id":"9950","checksum":"90461837eed66beac6fa302993cf0ca9","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2021-08-21T13:43:59Z","file_name":"Data.zip","creator":"bvicoso","date_updated":"2021-08-21T13:43:59Z","file_size":139188306}],"year":"2021","has_accepted_license":"1","date_created":"2021-08-21T13:44:22Z","date_published":"2021-08-24T00:00:00Z","doi":"10.15479/AT:ISTA:9949","related_material":{"record":[{"relation":"used_in_publication","id":"10166","status":"public"}]},"oa_version":"None","month":"08","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:40:30Z","citation":{"mla":"Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949.","ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949","short":"B. Vicoso, (2021).","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949.","ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9949."},"department":[{"_id":"BeVi"}],"title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","file_date_updated":"2021-08-21T13:43:59Z","article_processing_charge":"No","author":[{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"_id":"9949","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":"research_data"},{"day":"07","publication":"PLOS Computational Biology","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-01-07T00:00:00Z","doi":"10.1371/journal.pcbi.1008529","date_created":"2021-01-08T07:16:18Z","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008529","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” PLOS Computational Biology, vol. 17. Public Library of Science, 2021.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529."},"title":"Minimal biophysical model of combined antibiotic action","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"isi":["000608045000010"]},"article_number":"e1008529","project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"file":[{"file_size":3690053,"date_updated":"2021-02-04T12:30:48Z","creator":"dernst","file_name":"2021_PlosComBio_Kavcic.pdf","date_created":"2021-02-04T12:30:48Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"e29f2b42651bef8e034781de8781ffac","file_id":"9092"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","volume":17,"related_material":{"record":[{"relation":"earlier_version","id":"7673","status":"public"},{"status":"public","id":"8930","relation":"research_data"}]},"oa_version":"Published Version","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"month":"01","intvolume":" 17","ddc":["570"],"date_updated":"2024-02-21T12:41:41Z","department":[{"_id":"GaTk"}],"file_date_updated":"2021-02-04T12:30:48Z","_id":"8997","status":"public","keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"type":"journal_article","article_type":"original","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)"}},{"article_number":"e65993","project":[{"grant_number":"628377","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","call_identifier":"FP7","_id":"2517526A-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03901","name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks","call_identifier":"FWF","_id":"268BFA92-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993.","chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.65993.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993","ieee":"A. A. Nagy-Staron et al., “Local genetic context shapes the function of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications, 2021, doi:10.7554/elife.65993."},"title":"Local genetic context shapes the function of a gene regulatory network","author":[{"first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A","orcid":"0000-0002-1391-8377","last_name":"Nagy-Staron"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek"},{"last_name":"Caruso Carter","full_name":"Caruso Carter, Caroline","first_name":"Caroline"},{"full_name":"Sonnleitner, Elisabeth","last_name":"Sonnleitner","first_name":"Elisabeth"},{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic"},{"full_name":"Paixão, Tiago","last_name":"Paixão","first_name":"Tiago"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"isi":["000631050900001"]},"acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"day":"08","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-03-08T00:00:00Z","doi":"10.7554/elife.65993","date_created":"2021-03-23T10:11:46Z","_id":"9283","status":"public","keyword":["Genetics and Molecular Biology"],"type":"journal_article","article_type":"original","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)"},"ddc":["570"],"date_updated":"2024-02-21T12:41:57Z","file_date_updated":"2021-03-23T10:12:58Z","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs."}],"month":"03","intvolume":" 10","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"3c2f44058c2dd45a5a1027f09d263f8e","file_id":"9284","file_size":1390469,"date_updated":"2021-03-23T10:12:58Z","creator":"bkavcic","file_name":"elife-65993-v2.pdf","date_created":"2021-03-23T10:12:58Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"8951","relation":"research_data"}]},"volume":10,"ec_funded":1},{"issue":"6","volume":40,"ec_funded":1,"file":[{"date_updated":"2021-10-27T07:08:07Z","file_size":107708317,"creator":"bbickel","date_created":"2021-10-27T07:08:07Z","file_name":"rigidmolds-authorversion.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"384ece7a9ad1026787ba9560b04336d5","file_id":"10185"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368 "]},"publication_status":"published","month":"12","intvolume":" 40","main_file_link":[{"open_access":"1","url":"http://vcg.isti.cnr.it/Publications/2021/AMBCP21"}],"oa_version":"Submitted Version","abstract":[{"text":"We introduce a novel technique to automatically decompose an input object’s volume into a set of parts that can be represented by two opposite height fields. Such decomposition enables the manufacturing of individual parts using two-piece reusable rigid molds. Our decomposition strategy relies on a new energy formulation that utilizes a pre-computed signal on the mesh volume representing the accessibility for a predefined set of extraction directions. Thanks to this novel formulation, our method allows for efficient optimization of a fabrication-aware partitioning of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our approach by generating valid volume partitionings for a wide range of complex objects and physically reproducing several of them.","lang":"eng"}],"department":[{"_id":"BeBi"}],"file_date_updated":"2021-10-27T07:08:07Z","ddc":["000"],"date_updated":"2024-02-28T12:52:48Z","status":"public","article_type":"original","type":"journal_article","_id":"10184","date_published":"2021-12-01T00:00:00Z","doi":"10.1145/3478513.3480555","date_created":"2021-10-27T07:08:19Z","day":"01","publication":"ACM Transactions on Graphics","isi":1,"has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"The authors thank Marco Callieri for all his precious help with the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent fabrication-oriented computational design and modeling (grant no. 715767).","title":"Volume decomposition for two-piece rigid casting","author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"last_name":"Malomo","full_name":"Malomo, Luigi","first_name":"Luigi"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cignoni","full_name":"Cignoni, Paolo","first_name":"Paolo"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"}],"article_processing_charge":"No","external_id":{"isi":["000729846700077"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3478513.3480555.","ista":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.","mla":"Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions on Graphics, vol. 40, no. 6, 272, Association for Computing Machinery, 2021, doi:10.1145/3478513.3480555.","ama":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 2021;40(6). doi:10.1145/3478513.3480555","apa":"Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., & Pietroni, N. (2021). Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3478513.3480555","short":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 40 (2021).","ieee":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition for two-piece rigid casting,” ACM Transactions on Graphics, vol. 40, no. 6. Association for Computing Machinery, 2021."},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"272"},{"abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model that distills core aspects of distributed and parallel computation, developed as a tool to solve combinatorial (typically graph) problems in systems of many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in n, the number of nodes in the input graph) space, with randomized algorithms presented for the fundamental problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all edges incident to a single node. This poses a considerable obstacle compared to classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier, we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph, with the additional property that solving the problem on this subgraph provides significant progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic MPC algorithms for solving the problems of Maximal Matching and Maximal Independent Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel et al. [DISC’17].","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.05390"}],"intvolume":" 17","month":"06","publication_status":"published","publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"language":[{"iso":"eng"}],"file":[{"file_name":"MISMM-arxiv.pdf","date_created":"2021-06-10T19:33:56Z","file_size":587404,"date_updated":"2021-06-10T19:33:56Z","creator":"pdavies","success":1,"file_id":"9542","checksum":"a21c627683890c309a68f6389302c408","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"related_material":{"record":[{"id":"7802","status":"public","relation":"earlier_version"}]},"volume":17,"issue":"2","_id":"9541","type":"journal_article","article_type":"original","status":"public","date_updated":"2024-02-28T12:53:09Z","ddc":["000"],"file_date_updated":"2021-06-10T19:33:56Z","department":[{"_id":"DaAl"}],"acknowledgement":"Institute of Science and Technology Austria (IST Austria). Email: peter.davies@ist.ac.at. Work partially\r\ndone at the Department of Computer Science and Centre for Discrete Mathematics and its Applications (DIMAP),University of Warwick. Research partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411, the Centre for Discrete Mathematics and its Applications, a Weizmann-UK Making Connections Grant, and EPSRC award EP/N011163/1.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"ACM Transactions on Algorithms","day":"01","date_created":"2021-06-10T19:31:05Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1145/3451992","article_number":"16","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” ACM Transactions on Algorithms, vol. 17, no. 2. Association for Computing Machinery, 2021.","short":"A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).","apa":"Czumaj, A., Davies, P., & Parter, M. (2021). Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3451992","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 2021;17(2). doi:10.1145/3451992","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms, vol. 17, no. 2, 16, Association for Computing Machinery, 2021, doi:10.1145/3451992.","ista":"Czumaj A, Davies P, Parter M. 2021. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 17(2), 16.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms. Association for Computing Machinery, 2021. https://doi.org/10.1145/3451992."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000661311300006"],"arxiv":["1912.05390"]},"article_processing_charge":"No","author":[{"last_name":"Czumaj","full_name":"Czumaj, Artur","first_name":"Artur"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","last_name":"Davies","first_name":"Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"first_name":"Merav","last_name":"Parter","full_name":"Parter, Merav"}],"title":"Graph sparsification for derandomizing massively parallel computation with low space"},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"article_number":"160602","title":"Anderson localization of composite particles","article_processing_charge":"No","external_id":{"isi":["000707495700001"],"arxiv":["2011.06279"]},"author":[{"orcid":"0000-0003-4982-5970","full_name":"Suzuki, Fumika","last_name":"Suzuki","first_name":"Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"full_name":"Zurek, Wojciech H.","last_name":"Zurek","first_name":"Wojciech H."},{"first_name":"Roman V.","last_name":"Krems","full_name":"Krems, Roman V."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems. “Anderson Localization of Composite Particles.” Physical Review Letters. American Physical Society , 2021. https://doi.org/10.1103/physrevlett.127.160602.","ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","mla":"Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” Physical Review Letters, vol. 127, no. 16, 160602, American Physical Society , 2021, doi:10.1103/physrevlett.127.160602.","short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021).","ieee":"F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization of composite particles,” Physical Review Letters, vol. 127, no. 16. American Physical Society , 2021.","apa":"Suzuki, F., Lemeshko, M., Zurek, W. H., & Krems, R. V. (2021). Anderson localization of composite particles. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.127.160602","ama":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite particles. Physical Review Letters. 2021;127(16). doi:10.1103/physrevlett.127.160602"},"oa":1,"publisher":"American Physical Society ","quality_controlled":"1","acknowledgement":"We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez. F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z. is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program. R. V. K. is supported by NSERC of Canada.\r\n","date_created":"2021-10-13T09:21:33Z","date_published":"2021-10-12T00:00:00Z","doi":"10.1103/physrevlett.127.160602","publication":"Physical Review Letters","day":"12","year":"2021","isi":1,"keyword":["General Physics and Astronomy"],"status":"public","article_type":"original","type":"journal_article","_id":"10134","department":[{"_id":"MiLe"}],"date_updated":"2024-02-29T12:34:10Z","intvolume":" 127","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/2011.06279","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics."}],"ec_funded":1,"volume":127,"issue":"16","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}},{"project":[{"name":"Coordination in constrained and natural distributed systems","grant_number":"840605","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"title":"Efficient load-balancing through distributed token dropping","author":[{"last_name":"Brandt","full_name":"Brandt, Sebastian","first_name":"Sebastian"},{"last_name":"Keller","full_name":"Keller, Barbara","first_name":"Barbara"},{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646"},{"last_name":"Suomela","full_name":"Suomela, Jukka","first_name":"Jukka"},{"last_name":"Uitto","full_name":"Uitto, Jara","first_name":"Jara"}],"article_processing_charge":"No","external_id":{"arxiv":["2005.07761"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event, United States. https://doi.org/10.1145/3409964.3461785","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2021, pp. 129–139.","mla":"Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–39, doi:10.1145/3409964.3461785.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021. https://doi.org/10.1145/3409964.3461785."},"quality_controlled":"1","oa":1,"acknowledgement":"We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.","doi":"10.1145/3409964.3461785","date_published":"2021-07-06T00:00:00Z","date_created":"2021-07-18T22:01:22Z","page":"129-139","day":"06","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","year":"2021","status":"public","type":"conference","conference":{"location":" Virtual Event, United States","end_date":"2021-07-08","start_date":"2021-07-06","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures "},"_id":"9678","department":[{"_id":"DaAl"}],"date_updated":"2024-03-05T07:13:12Z","month":"07","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2005.07761","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively."}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"15074"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450380706"]},"publication_status":"published"},{"_id":"8286","status":"public","type":"journal_article","article_type":"original","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)"},"conference":{"start_date":"2020-07-08","location":"Virtual, Online; Germany","end_date":"2020-07-11","name":"ICALP: International Colloquium on Automata, Languages, and Programming "},"ddc":["000"],"date_updated":"2024-03-05T07:35:53Z","department":[{"_id":"DaAl"}],"file_date_updated":"2021-12-27T10:36:40Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. "}],"month":"12","scopus_import":"1","file":[{"creator":"cchlebak","date_updated":"2021-12-27T10:36:40Z","file_size":525950,"date_created":"2021-12-27T10:36:40Z","file_name":"2021_Algorithmica_Alistarh.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10577","checksum":"21169b25b0c8e17b21e12af22bff9870","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"publication_status":"published","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.4230/LIPIcs.ICALP.2020.7"}],"record":[{"status":"public","id":"15077","relation":"earlier_version"}]},"ec_funded":1,"project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2021. https://doi.org/10.1007/s00453-021-00905-9.","ista":"Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing on cycles. Algorithmica.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica, Springer Nature, 2021, doi:10.1007/s00453-021-00905-9.","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2021). Dynamic averaging load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer Nature. https://doi.org/10.1007/s00453-021-00905-9","ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. Algorithmica. 2021. doi:10.1007/s00453-021-00905-9","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” Algorithmica. Springer Nature, 2021.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021)."},"title":"Dynamic averaging load balancing on cycles","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"},{"full_name":"Sabour, Amirmojtaba","last_name":"Sabour","first_name":"Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67"}],"external_id":{"isi":["000734004600001"],"arxiv":["2003.09297"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"24","publication":"Algorithmica","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1007/s00453-021-00905-9","date_published":"2021-12-24T00:00:00Z","date_created":"2020-08-24T06:24:04Z"},{"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"oa_version":"Published Version","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","id":"9787","status":"public"},{"status":"public","id":"9792","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9225","status":"public"},{"status":"public","id":"9781","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9791","status":"public"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-08-19T14:03:48Z","file_name":"Thesis_FeliciangeliA.pdf","creator":"dfelicia","date_updated":"2021-09-06T09:28:56Z","file_size":1958710,"checksum":"e88bb8ca43948abe060eb2d2fa719881","file_id":"9944","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_size":3771669,"date_updated":"2022-03-10T12:13:57Z","creator":"dfelicia","file_name":"thesis.7z","date_created":"2021-08-19T14:06:35Z","content_type":"application/octet-stream","relation":"source_file","access_level":"closed","file_id":"9945","checksum":"72810843abee83705853505b3f8348aa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"dissertation","status":"public","_id":"9733","file_date_updated":"2022-03-10T12:13:57Z","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"date_updated":"2024-03-06T12:30:44Z","supervisor":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"ddc":["515","519","539"],"oa":1,"publisher":"Institute of Science and Technology Austria","page":"180","date_created":"2021-07-27T15:48:30Z","doi":"10.15479/at:ista:9733","date_published":"2021-08-20T00:00:00Z","year":"2021","has_accepted_license":"1","day":"20","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"article_processing_charge":"No","author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli"}],"title":"The polaron at strong coupling","citation":{"ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"intvolume":" 22","month":"04","main_file_link":[{"open_access":"1","url":"https://www.jmlr.org/papers/v22/20-255.html"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods."}],"volume":22,"issue":"114","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"9595","checksum":"6428aa8bcb67768b6949c99b55d5281d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf","date_created":"2021-06-23T07:09:41Z","file_size":11237154,"date_updated":"2021-06-23T07:09:41Z","creator":"asandaue"}],"publication_status":"published","publication_identifier":{"eissn":["15337928"],"issn":["15324435"]},"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":"9571","file_date_updated":"2021-06-23T07:09:41Z","department":[{"_id":"DaAl"}],"ddc":["000"],"date_updated":"2024-03-06T12:22:07Z","oa":1,"publisher":"Journal of Machine Learning Research","quality_controlled":"1","date_created":"2021-06-20T22:01:33Z","date_published":"2021-04-01T00:00:00Z","page":"1−43","publication":"Journal of Machine Learning Research","day":"01","year":"2021","has_accepted_license":"1","title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","article_processing_charge":"No","external_id":{"arxiv":["1908.06077"]},"author":[{"last_name":"Ramezani-Kebrya","full_name":"Ramezani-Kebrya, Ali","first_name":"Ali"},{"last_name":"Faghri","full_name":"Faghri, Fartash","first_name":"Fartash"},{"last_name":"Markov","full_name":"Markov, Ilya","first_name":"Ilya"},{"full_name":"Aksenov, Vitalii","last_name":"Aksenov","id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Daniel M.","last_name":"Roy","full_name":"Roy, Daniel M."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43.","chicago":"Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2021.","ama":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 2021;22(114):1−43.","apa":"Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., & Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. Journal of Machine Learning Research.","ieee":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” Journal of Machine Learning Research, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021.","short":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43.","mla":"Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43."}},{"article_type":"original","type":"journal_article","status":"public","_id":"8544","department":[{"_id":"SiHi"}],"date_updated":"2024-03-06T12:12:48Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.06.14.151258","open_access":"1"}],"month":"02","intvolume":" 109","abstract":[{"text":"The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.","lang":"eng"}],"oa_version":"Preprint","issue":"4","volume":109,"ec_funded":1,"publication_identifier":{"eissn":["1097-4199"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Takeo, Yukari H.","last_name":"Takeo","first_name":"Yukari H."},{"full_name":"Shuster, S. Andrew","last_name":"Shuster","first_name":"S. Andrew"},{"full_name":"Jiang, Linnie","last_name":"Jiang","first_name":"Linnie"},{"full_name":"Hu, Miley","last_name":"Hu","first_name":"Miley"},{"last_name":"Luginbuhl","full_name":"Luginbuhl, David J.","first_name":"David J."},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"first_name":"Mark J.","full_name":"Wagner, Mark J.","last_name":"Wagner"},{"first_name":"Surya","full_name":"Ganguli, Surya","last_name":"Ganguli"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"}],"article_processing_charge":"No","title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","citation":{"ista":"Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8.","chicago":"Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2020.11.028.","apa":"Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.11.028","ama":"Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 2021;109(4):P629-644.E8. doi:10.1016/j.neuron.2020.11.028","short":"Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8.","ieee":"Y. H. Takeo et al., “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” Neuron, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021.","mla":"Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:10.1016/j.neuron.2020.11.028."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator.","page":"P629-644.E8","date_published":"2021-02-17T00:00:00Z","doi":"10.1016/j.neuron.2020.11.028","date_created":"2020-09-21T11:59:47Z","year":"2021","day":"17","publication":"Neuron"},{"title":"The effective mass problem for the Landau-Pekar equations","department":[{"_id":"RoSe"}],"article_processing_charge":"No","external_id":{"arxiv":["2107.03720"]},"author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli"},{"last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"date_updated":"2024-03-06T12:30:45Z","citation":{"chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, n.d.","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, 2107.03720.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv.","apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. arXiv.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” arXiv. ."},"status":"public","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"type":"preprint","article_number":"2107.03720 ","_id":"9791","ec_funded":1,"date_created":"2021-08-06T08:49:45Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"10755"},{"status":"public","id":"9733","relation":"dissertation_contains"}]},"date_published":"2021-07-08T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","day":"08","publication_status":"submitted","year":"2021","month":"07","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2107.03720","open_access":"1"}],"acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged..","oa_version":"Preprint","abstract":[{"text":"We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar.","lang":"eng"}]},{"acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","oa":1,"publisher":"Cell Press","quality_controlled":"1","publication":"Neuron","day":"07","year":"2021","isi":1,"date_created":"2020-02-28T11:00:12Z","doi":"10.1016/j.neuron.2021.01.020","date_published":"2021-04-07T00:00:00Z","page":"1227-1241.e5","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/10.1016/j.neuron.2021.01.020.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020"},"title":"Statistical analysis and optimality of neural systems","external_id":{"isi":["000637809600006"]},"article_processing_charge":"No","author":[{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"last_name":"Hledik","full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems."}],"intvolume":" 109","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/848374"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":109,"issue":"7","related_material":{"record":[{"status":"public","id":"15020","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/"}]},"_id":"7553","status":"public","type":"journal_article","date_updated":"2024-03-06T14:22:51Z","department":[{"_id":"GaTk"}]},{"date_published":"2021-04-01T00:00:00Z","date_created":"2022-01-03T11:34:22Z","page":"397-405","day":"01","publication":"Proceedings of The 24th International Conference on Artificial Intelligence and Statistics","year":"2021","quality_controlled":"1","publisher":"ML Research Press","oa":1,"acknowledgement":"The authors would like to thank Andrea Montanari for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.","editor":[{"last_name":"Banerjee","full_name":"Banerjee, Arindam","first_name":"Arindam"},{"first_name":"Kenji","full_name":"Fukumizu, Kenji","last_name":"Fukumizu"}],"title":"Approximate message passing with spectral initialization for generalized linear models","author":[{"last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"},{"last_name":"Venkataramanan","full_name":"Venkataramanan, Ramji","first_name":"Ramji"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2010.03460"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Mondelli, M., & Venkataramanan, R. (2021). Approximate message passing with spectral initialization for generalized linear models. In A. Banerjee & K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics (Vol. 130, pp. 397–405). Virtual, San Diego, CA, United States: ML Research Press.","ama":"Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization for generalized linear models. In: Banerjee A, Fukumizu K, eds. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. Vol 130. ML Research Press; 2021:397-405.","short":"M. Mondelli, R. Venkataramanan, in:, A. Banerjee, K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2021, pp. 397–405.","ieee":"M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral initialization for generalized linear models,” in Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Virtual, San Diego, CA, United States, 2021, vol. 130, pp. 397–405.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, vol. 130, ML Research Press, 2021, pp. 397–405.","ista":"Mondelli M, Venkataramanan R. 2021. Approximate message passing with spectral initialization for generalized linear models. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, vol. 130, 397–405.","chicago":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” In Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, 130:397–405. ML Research Press, 2021."},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"volume":130,"related_material":{"record":[{"status":"public","id":"12480","relation":"later_version"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2640-3498"]},"publication_status":"published","month":"04","intvolume":" 130","scopus_import":"1","alternative_title":["Proceedings of Machine Learning Research"],"main_file_link":[{"url":"https://proceedings.mlr.press/v130/mondelli21a.html","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":" We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach. ","lang":"eng"}],"department":[{"_id":"MaMo"}],"date_updated":"2024-03-07T10:36:53Z","status":"public","type":"conference","conference":{"name":"AISTATS: Artificial Intelligence and Statistics","start_date":"2021-04-13","end_date":"2021-04-15","location":"Virtual, San Diego, CA, United States"},"_id":"10598"},{"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000559345400001"]},"author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"last_name":"Dong","full_name":"Dong, Qiao-Li","first_name":"Qiao-Li"},{"first_name":"Lu-Lu","full_name":"Liu, Lu-Lu","last_name":"Liu"},{"first_name":"Jen-Chih","last_name":"Yao","full_name":"Yao, Jen-Chih"}],"title":"New strong convergence method for the sum of two maximal monotone operators","citation":{"chicago":"Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering. Springer Nature, 2021. https://doi.org/10.1007/s11081-020-09544-5.","ista":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653.","mla":"Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering, vol. 22, Springer Nature, 2021, pp. 2627–53, doi:10.1007/s11081-020-09544-5.","ieee":"Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method for the sum of two maximal monotone operators,” Optimization and Engineering, vol. 22. Springer Nature, pp. 2627–2653, 2021.","short":"Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering 22 (2021) 2627–2653.","apa":"Shehu, Y., Dong, Q.-L., Liu, L.-L., & Yao, J.-C. (2021). New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. Springer Nature. https://doi.org/10.1007/s11081-020-09544-5","ama":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 2021;22:2627-2653. doi:10.1007/s11081-020-09544-5"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"page":"2627-2653","date_created":"2020-08-03T14:29:57Z","date_published":"2021-02-25T00:00:00Z","doi":"10.1007/s11081-020-09544-5","year":"2021","isi":1,"has_accepted_license":"1","publication":"Optimization and Engineering","day":"25","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7—2007–2013) (Grant Agreement No. 616160). The authors are grateful to the anonymous referees and the handling Editor for their comments and suggestions which have improved the earlier version of the manuscript greatly.","file_date_updated":"2020-08-03T15:24:39Z","department":[{"_id":"VlKo"}],"date_updated":"2024-03-07T14:39:29Z","ddc":["510"],"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)"},"article_type":"original","type":"journal_article","status":"public","_id":"8196","ec_funded":1,"volume":22,"publication_status":"published","publication_identifier":{"issn":["1389-4420"],"eissn":["1573-2924"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-08-03T15:24:39Z","file_size":2137860,"creator":"dernst","date_created":"2020-08-03T15:24:39Z","file_name":"2020_OptimizationEngineering_Shehu.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8197","success":1}],"scopus_import":"1","intvolume":" 22","month":"02","abstract":[{"lang":"eng","text":"This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis."}],"oa_version":"Published Version"},{"intvolume":" 6","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.08133"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. ","lang":"eng"}],"ec_funded":1,"volume":6,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2058-8437"]},"status":"public","type":"journal_article","article_type":"original","_id":"8911","department":[{"_id":"GeKa"}],"date_updated":"2024-03-07T14:48:57Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT.","date_created":"2020-12-02T10:52:51Z","date_published":"2021-10-01T00:00:00Z","doi":"10.1038/s41578-020-00262-z","page":"926–943 ","publication":"Nature Reviews Materials","day":"01","year":"2021","isi":1,"project":[{"call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497"},{"name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","grant_number":"Y00715","call_identifier":"FWF","_id":"2552F888-B435-11E9-9278-68D0E5697425"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"title":"The germanium quantum information route","article_processing_charge":"No","external_id":{"isi":["000600826100003"],"arxiv":["2004.08133"]},"author":[{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"last_name":"Kloeffel","full_name":"Kloeffel, Christoph","first_name":"Christoph"},{"full_name":"Zwanenburg, Floris A.","last_name":"Zwanenburg","first_name":"Floris A."},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"first_name":"Maksym","full_name":"Myronov, Maksym","last_name":"Myronov"},{"last_name":"Zhang","full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun"},{"full_name":"Franceschi, Silvano De","last_name":"Franceschi","first_name":"Silvano De"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” Nature Reviews Materials. Springer Nature, 2021. https://doi.org/10.1038/s41578-020-00262-z.","ista":"Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943.","mla":"Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” Nature Reviews Materials, vol. 6, Springer Nature, 2021, pp. 926–943, doi:10.1038/s41578-020-00262-z.","short":"G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943.","ieee":"G. Scappucci et al., “The germanium quantum information route,” Nature Reviews Materials, vol. 6. Springer Nature, pp. 926–943, 2021.","apa":"Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. Nature Reviews Materials. Springer Nature. https://doi.org/10.1038/s41578-020-00262-z","ama":"Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. Nature Reviews Materials. 2021;6:926–943. doi:10.1038/s41578-020-00262-z"}},{"_id":"8338","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-07T14:51:11Z","department":[{"_id":"HeEd"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory."}],"month":"10","intvolume":" 66","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.00856"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"publication_status":"published","volume":66,"ec_funded":1,"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976.","chicago":"Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00240-w.","ieee":"A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 938–976, 2021.","short":"A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976.","apa":"Akopyan, A., Bobenko, A. I., Schief, W. K., & Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00240-w","ama":"Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 2021;66:938-976. doi:10.1007/s00454-020-00240-w","mla":"Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 938–76, doi:10.1007/s00454-020-00240-w."},"title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"last_name":"Bobenko","full_name":"Bobenko, Alexander I.","first_name":"Alexander I."},{"first_name":"Wolfgang K.","full_name":"Schief, Wolfgang K.","last_name":"Schief"},{"first_name":"Jan","full_name":"Techter, Jan","last_name":"Techter"}],"external_id":{"arxiv":["1908.00856"],"isi":["000564488500002"]},"article_processing_charge":"No","acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Discrete and Computational Geometry","isi":1,"year":"2021","doi":"10.1007/s00454-020-00240-w","date_published":"2021-10-01T00:00:00Z","date_created":"2020-09-06T22:01:13Z","page":"938-976"},{"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing 34 (2021) 463–487.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” Distributed Computing, vol. 34. Springer Nature, pp. 463–487, 2021.","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. Distributed Computing. 2021;34:463-487. doi:10.1007/s00446-020-00380-5","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2021). Fast approximate shortest paths in the congested clique. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-020-00380-5","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing, vol. 34, Springer Nature, 2021, pp. 463–87, doi:10.1007/s00446-020-00380-5.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate shortest paths in the congested clique. Distributed Computing. 34, 463–487.","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing. Springer Nature, 2021. https://doi.org/10.1007/s00446-020-00380-5."},"title":"Fast approximate shortest paths in the congested clique","author":[{"last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren","first_name":"Keren"},{"last_name":"Dory","full_name":"Dory, Michal","first_name":"Michal"},{"last_name":"Korhonen","full_name":"Korhonen, Janne","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"last_name":"Leitersdorf","full_name":"Leitersdorf, Dean","first_name":"Dean"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1903.05956"],"isi":["000556444600001"]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful discussions. This project has received funding from the European Union’s Horizon 2020 Research And Innovation Program under Grant Agreement No. 755839.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"01","publication":"Distributed Computing","isi":1,"year":"2021","date_published":"2021-12-01T00:00:00Z","doi":"10.1007/s00446-020-00380-5","date_created":"2020-06-07T22:00:54Z","page":"463-487","_id":"7939","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-03-07T14:43:39Z","department":[{"_id":"DaAl"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:\r\n A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. "}],"month":"12","intvolume":" 34","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00446-020-00380-5"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"publication_status":"published","volume":34,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6933"}]}},{"ec_funded":1,"volume":66,"publication_status":"published","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00233-9"}],"scopus_import":"1","intvolume":" 66","month":"09","abstract":[{"text":"We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"HeEd"}],"date_updated":"2024-03-07T14:54:59Z","ddc":["510"],"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":"8248","page":"666-686","date_created":"2020-08-11T07:11:51Z","doi":"10.1007/s00454-020-00233-9","date_published":"2021-09-01T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Discrete and Computational Geometry","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000558119300001"]},"author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"last_name":"Dyer","full_name":"Dyer, Ramsay","first_name":"Ramsay"},{"full_name":"Ghosh, Arijit","last_name":"Ghosh","first_name":"Arijit"},{"first_name":"Andre","full_name":"Lieutier, Andre","last_name":"Lieutier"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs"}],"title":"Local conditions for triangulating submanifolds of Euclidean space","citation":{"mla":"Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 666–86, doi:10.1007/s00454-020-00233-9.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., & Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00233-9","ama":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 2021;66:666-686. doi:10.1007/s00454-020-00233-9","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 666–686, 2021.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00233-9.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}]},{"title":"Regulation of size and scale in vertebrate spinal cord development","external_id":{"pmid":["32391980"],"isi":["000531419400001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021. https://doi.org/10.1002/wdev.383.","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology, e383, Wiley, 2021, doi:10.1002/wdev.383.","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. 2021. doi:10.1002/wdev.383","apa":"Kuzmicz-Kowalska, K., & Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. Wiley. https://doi.org/10.1002/wdev.383"},"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"grant_number":"F07802","name":"Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"article_number":"e383","date_created":"2020-05-24T22:01:00Z","doi":"10.1002/wdev.383","date_published":"2021-04-15T00:00:00Z","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","day":"15","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","department":[{"_id":"AnKi"}],"file_date_updated":"2020-11-24T13:11:39Z","ddc":["570"],"date_updated":"2024-03-07T15:03:00Z","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)"},"article_type":"original","type":"journal_article","_id":"7883","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14323"}]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"f0a7745d48afa09ea7025e876a0145a8","file_id":"8800","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","date_created":"2020-11-24T13:11:39Z","creator":"dernst","file_size":2527276,"date_updated":"2020-11-24T13:11:39Z"}],"publication_status":"published","publication_identifier":{"eissn":["17597692"],"issn":["17597684"]},"month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern."}]},{"_id":"7905","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)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-07T15:01:58Z","ddc":["510"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-11-25T09:06:41Z","abstract":[{"lang":"eng","text":"We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 65","month":"06","publication_status":"published","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8803","checksum":"487a84ea5841b75f04f66d7ebd71b67e","success":1,"date_updated":"2020-11-25T09:06:41Z","file_size":1013730,"creator":"dernst","date_created":"2020-11-25T09:06:41Z","file_name":"2020_DiscreteCompGeometry_Brown.pdf"}],"volume":65,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"citation":{"chicago":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00206-y.","ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.","mla":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:10.1007/s00454-020-00206-y.","ieee":"A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” Discrete and Computational Geometry, vol. 65. Springer Nature, pp. 1166–1198, 2021.","short":"A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.","apa":"Brown, A., & Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00206-y","ama":"Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 2021;65:1166-1198. doi:10.1007/s00454-020-00206-y"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1712.07734"],"isi":["000536324700001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam","last_name":"Brown","full_name":"Brown, Adam"},{"last_name":"Wang","full_name":"Wang, Bei","first_name":"Bei"}],"title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2021","has_accepted_license":"1","isi":1,"publication":"Discrete and Computational Geometry","day":"01","page":"1166-1198","date_created":"2020-05-30T10:26:04Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1007/s00454-020-00206-y"},{"_id":"8601","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","ddc":["510"],"date_updated":"2024-03-07T15:07:53Z","department":[{"_id":"LaEr"}],"file_date_updated":"2020-10-05T14:53:40Z","oa_version":"Published Version","abstract":[{"text":"We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble.","lang":"eng"}],"month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":497032,"date_updated":"2020-10-05T14:53:40Z","creator":"dernst","file_name":"2020_ProbTheory_Cipolloni.pdf","date_created":"2020-10-05T14:53:40Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"611ae28d6055e1e298d53a57beb05ef4","file_id":"8612"}],"publication_status":"published","publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"ec_funded":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields. Springer Nature, 2021. https://doi.org/10.1007/s00440-020-01003-7.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields.","mla":"Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2021, doi:10.1007/s00440-020-01003-7.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2021.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021).","ama":"Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. 2021. doi:10.1007/s00440-020-01003-7","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-020-01003-7"},"title":"Edge universality for non-Hermitian random matrices","external_id":{"arxiv":["1908.00969"],"isi":["000572724600002"]},"article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Probability Theory and Related Fields","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2020-10-04T22:01:37Z","date_published":"2021-02-01T00:00:00Z","doi":"10.1007/s00440-020-01003-7"},{"file":[{"file_size":2148882,"date_updated":"2024-03-07T14:58:51Z","creator":"kschuh","file_name":"2021_OptimizationLetters_Shehu.pdf","date_created":"2024-03-07T14:58:51Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"63c5f31cd04626152a19f97a2476281b","file_id":"15089"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1862-4480"],"issn":["1862-4472"]},"publication_status":"published","volume":15,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method.","lang":"eng"}],"month":"09","intvolume":" 15","scopus_import":"1","ddc":["510"],"date_updated":"2024-03-07T15:00:43Z","file_date_updated":"2024-03-07T14:58:51Z","department":[{"_id":"VlKo"}],"_id":"7925","status":"public","type":"journal_article","article_type":"original","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)"},"day":"01","publication":"Optimization Letters","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-09-01T00:00:00Z","doi":"10.1007/s11590-020-01603-1","date_created":"2020-06-04T11:28:33Z","page":"2109-2126","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are grateful to the referees for their insightful comments which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,” Optimization Letters, vol. 15. Springer Nature, pp. 2109–2126, 2021.","short":"Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126.","apa":"Shehu, Y., & Gibali, A. (2021). New inertial relaxed method for solving split feasibilities. Optimization Letters. Springer Nature. https://doi.org/10.1007/s11590-020-01603-1","ama":"Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities. Optimization Letters. 2021;15:2109-2126. doi:10.1007/s11590-020-01603-1","mla":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters, vol. 15, Springer Nature, 2021, pp. 2109–26, doi:10.1007/s11590-020-01603-1.","ista":"Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126.","chicago":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters. Springer Nature, 2021. https://doi.org/10.1007/s11590-020-01603-1."},"title":"New inertial relaxed method for solving split feasibilities","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"first_name":"Aviv","full_name":"Gibali, Aviv","last_name":"Gibali"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000537342300001"]},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair."}],"month":"07","intvolume":" 184","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2021.05.029","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"]},"publication_status":"published","volume":184,"issue":"14","_id":"15151","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"type":"journal_article","article_type":"review","extern":"1","date_updated":"2024-03-25T12:31:39Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"08","publication":"Cell","year":"2021","doi":"10.1016/j.cell.2021.05.029","date_published":"2021-07-08T00:00:00Z","date_created":"2024-03-21T07:54:19Z","page":"3599-3611","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14), 3599–3611.","chicago":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.05.029.","ama":"Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021;184(14):3599-3611. doi:10.1016/j.cell.2021.05.029","apa":"Michael, A. K., & Thomä, N. H. (2021). Reading the chromatinized genome. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.05.029","ieee":"A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” Cell, vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021.","short":"A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611.","mla":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:10.1016/j.cell.2021.05.029."},"title":"Reading the chromatinized genome","author":[{"full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","last_name":"Michael","first_name":"Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"first_name":"Nicolas H.","full_name":"Thomä, Nicolas H.","last_name":"Thomä"}],"article_processing_charge":"No"},{"project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967."},"title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","author":[{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","first_name":"Yuji","last_name":"Okamoto","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji"},{"last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina"},{"first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M","last_name":"Vargas Barroso"},{"last_name":"Suter","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"external_id":{"isi":["000650528700003"],"pmid":["33990799"]},"article_processing_charge":"No","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Nature Protocols","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-06-01T00:00:00Z","doi":"10.1038/s41596-021-00526-0","date_created":"2021-05-30T22:01:24Z","page":"2947–2967","_id":"9438","status":"public","article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-08-10T22:30:51Z","file_date_updated":"2021-12-02T23:30:05Z","department":[{"_id":"PeJo"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"month":"06","intvolume":" 16","scopus_import":"1","file":[{"creator":"cziletti","date_updated":"2021-12-02T23:30:05Z","file_size":38574802,"date_created":"2021-07-08T12:27:55Z","file_name":"VandaeletalAuthorVersion2021.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9639","checksum":"7eb580abd8893cdb0b410cf41bc8c263","embargo":"2021-12-01"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["17542189"],"eissn":["17502799"]},"publication_status":"published","issue":"6","volume":16,"ec_funded":1},{"_id":"9992","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"date_updated":"2023-09-07T13:38:33Z","ddc":["575"],"file_date_updated":"2021-09-15T22:30:26Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"9993","checksum":"c763064adaa720e16066c1a4f9682bbb","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2021-09-09T07:29:48Z","file_name":"Thesis_vupload.docx","creator":"lhoermaye","date_updated":"2021-09-15T22:30:26Z","file_size":25179004},{"checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","file_id":"9996","embargo":"2021-09-09","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-09-09T14:25:08Z","file_name":"Thesis_vfinal_pdfa.pdf","creator":"lhoermaye","date_updated":"2021-09-15T22:30:26Z","file_size":6246900}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"6351","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6943","status":"public"},{"id":"8002","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"project":[{"grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"citation":{"mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"}],"article_processing_charge":"No","title":"Wound healing in the Arabidopsis root meristem","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","day":"13","page":"168","date_published":"2021-09-13T00:00:00Z","doi":"10.15479/at:ista:9992","date_created":"2021-09-09T07:37:20Z"},{"publication_identifier":{"issn":["2662-8457"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"11430","checksum":"9fec5b667909ef52be96d502e4f8c2ae","embargo":"2022-06-17","date_updated":"2022-06-18T22:30:03Z","file_size":1699466,"creator":"patrickd","date_created":"2022-06-02T12:51:07Z","file_name":"Guzmanetal2021.pdf"},{"file_name":"Guzmanetal2021Suppl.pdf","date_created":"2022-06-02T12:53:47Z","title":"Supplementary Material","creator":"patrickd","file_size":3005651,"date_updated":"2022-06-18T22:30:03Z","embargo":"2022-06-17","file_id":"11431","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","relation":"supplementary_material","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"12","related_material":{"link":[{"url":"https://ista.ac.at/en/news/spot-the-difference/","relation":"press_release"}],"record":[{"relation":"software","id":"10110","status":"public"}]},"volume":1,"ec_funded":1,"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/647800"}],"month":"12","intvolume":" 1","date_updated":"2023-08-10T22:30:10Z","ddc":["610"],"department":[{"_id":"PeJo"}],"file_date_updated":"2022-06-18T22:30:03Z","_id":"10816","article_type":"original","type":"journal_article","status":"public","keyword":["general medicine"],"has_accepted_license":"1","year":"2021","day":"16","publication":"Nature Computational Science","page":"830-842","date_published":"2021-12-16T00:00:00Z","doi":"10.1038/s43588-021-00157-1","date_created":"2022-03-04T08:32:36Z","acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","last_name":"Guzmán"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia ","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez"},{"last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","last_name":"Suter"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"article_processing_charge":"No","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"}]},{"month":"12","publisher":"IST Austria","oa":1,"abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/spot-the-difference/","relation":"press_release","description":"News on IST Webpage"}],"record":[{"relation":"used_for_analysis_in","id":"10816","status":"public"}]},"date_published":"2021-12-16T00:00:00Z","doi":"10.15479/AT:ISTA:10110","license":"https://opensource.org/licenses/GPL-3.0","date_created":"2021-10-08T06:44:22Z","file":[{"file_name":"patternseparation-main (1).zip","date_created":"2021-10-08T08:46:04Z","creator":"cchlebak","file_size":332990101,"date_updated":"2021-10-08T08:46:04Z","success":1,"file_id":"10114","checksum":"f92f8931cad0aa7e411c1715337bf408","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"}],"day":"16","has_accepted_license":"1","year":"2021","status":"public","type":"software","tmp":{"name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","short":"GPL 3.0"},"_id":"10110","file_date_updated":"2021-10-08T08:46:04Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","author":[{"orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","last_name":"Guzmán","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia "},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin"},{"orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","last_name":"Suter","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"ddc":["005"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-03-27T23:30:11Z","citation":{"chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.","mla":"Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. https://doi.org/10.15479/AT:ISTA:10110","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021."}},{"oa_version":"Preprint","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"month":"09","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"day":"29","publication":"bioRxiv","language":[{"iso":"eng"}],"year":"2021","publication_status":"submitted","date_published":"2021-09-29T00:00:00Z","doi":"10.1101/2021.09.28.460602","related_material":{"record":[{"status":"public","id":"11932","relation":"dissertation_contains"}]},"ec_funded":1,"date_created":"2021-10-04T06:23:34Z","_id":"10077","status":"public","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"type":"preprint","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-03-27T23:30:16Z","citation":{"chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602"},"department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","author":[{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"full_name":"Savin, Cristina","last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"file":[{"date_created":"2021-03-22T11:46:00Z","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","creator":"dernst","date_updated":"2021-09-16T22:30:03Z","file_size":1811448,"checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","file_id":"9276","embargo":"2021-09-15","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"publication_status":"published","volume":13,"issue":"5","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"month":"03","intvolume":" 13","scopus_import":"1","ddc":["540"],"date_updated":"2023-09-05T15:34:44Z","file_date_updated":"2021-09-16T22:30:03Z","department":[{"_id":"StFr"}],"_id":"9250","status":"public","keyword":["General Chemistry","General Chemical Engineering"],"article_type":"original","type":"journal_article","day":"15","publication":"Nature Chemistry","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1038/s41557-021-00643-z","date_published":"2021-03-15T00:00:00Z","date_created":"2021-03-16T11:12:20Z","page":"465-471","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-021-00643-z","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 2021;13(5):465-471. doi:10.1038/s41557-021-00643-z","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z."},"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","author":[{"first_name":"Yann K.","last_name":"Petit","full_name":"Petit, Yann K."},{"full_name":"Mourad, Eléonore","last_name":"Mourad","first_name":"Eléonore"},{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"first_name":"Christian","full_name":"Leypold, Christian","last_name":"Leypold"},{"full_name":"Windischbacher, Andreas","last_name":"Windischbacher","first_name":"Andreas"},{"full_name":"Mijailovic, Daniel","last_name":"Mijailovic","first_name":"Daniel"},{"first_name":"Christian","full_name":"Slugovc, Christian","last_name":"Slugovc"},{"full_name":"Borisov, Sergey M.","last_name":"Borisov","first_name":"Sergey M."},{"full_name":"Zojer, Egbert","last_name":"Zojer","first_name":"Egbert"},{"first_name":"Sergio","last_name":"Brutti","full_name":"Brutti, Sergio"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"}],"article_processing_charge":"No","external_id":{"isi":["000629296400001"],"pmid":["33723377"]}},{"file_date_updated":"2022-07-02T22:30:06Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"ddc":["570"],"date_updated":"2023-09-07T13:33:27Z","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","_id":"9623","related_material":{"record":[{"id":"9750","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9006","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-07-01T14:48:54Z","file_name":"PhDThesis_SCM.docx","creator":"scaballe","date_updated":"2022-07-02T22:30:06Z","file_size":131946790,"file_id":"9624","checksum":"e039225a47ef32666d59bf35ddd30ecf","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2022-07-01","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_id":"9625","file_size":17094958,"date_updated":"2022-07-02T22:30:06Z","creator":"scaballe","file_name":"PhDThesis_SCM.pdf","date_created":"2021-07-01T14:46:25Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-012-1"]},"month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","article_processing_charge":"No","author":[{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623","mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623."},"date_created":"2021-07-01T14:50:17Z","doi":"10.15479/at:ista:9623","date_published":"2021-07-01T00:00:00Z","page":"111","year":"2021","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"year":"2021","isi":1,"publication":"Developmental Cell","day":"25","page":"P213-226","date_created":"2021-01-17T23:01:10Z","doi":"10.1016/j.devcel.2020.12.002","date_published":"2021-01-25T00:00:00Z","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","oa":1,"quality_controlled":"1","publisher":"Elsevier","citation":{"chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002.","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002.","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002","apa":"Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"author":[{"last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"title":"Cytoplasm's got moves","publication_status":"published","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"language":[{"iso":"eng"}],"issue":"2","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9623"}]},"volume":56,"abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"scopus_import":"1","intvolume":" 56","month":"01","date_updated":"2024-03-27T23:30:18Z","department":[{"_id":"CaHe"}],"_id":"9006","article_type":"original","type":"journal_article","status":"public"},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"337e0f7959c35ec959984cacdcb472ba","file_id":"9430","success":1,"date_updated":"2021-05-28T12:39:43Z","file_size":9358599,"creator":"kschuh","date_created":"2021-05-28T12:39:43Z","file_name":"2021_NatureCommunications_Morandell.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"7800","relation":"earlier_version"},{"id":"12401","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}]},"volume":12,"issue":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"}],"abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"intvolume":" 12","month":"05","ddc":["572"],"date_updated":"2024-03-27T23:30:23Z","file_date_updated":"2021-05-28T12:39:43Z","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"_id":"9429","keyword":["General Biochemistry","Genetics and Molecular Biology"],"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)"},"article_type":"original","type":"journal_article","publication":"Nature Communications","day":"24","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-05-28T11:49:46Z","doi":"10.1038/s41467-021-23123-x","date_published":"2021-05-24T00:00:00Z","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x."},"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","article_processing_charge":"No","external_id":{"isi":["000658769900010"]},"author":[{"last_name":"Morandell","full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin"},{"id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","last_name":"Schwarz","full_name":"Schwarz, Lena A"},{"first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173"},{"last_name":"Tasciyan","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","full_name":"Knaus, Lisa","last_name":"Knaus"},{"id":"D23090A2-9057-11EA-883A-A8396FC7A38F","first_name":"Zoe","full_name":"Dobler, Zoe","last_name":"Dobler"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"article_number":"3058","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy","grant_number":"F07807"},{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"page":"151","date_published":"2021-10-05T00:00:00Z","doi":"10.15479/at:ista:10058","date_created":"2021-09-30T07:53:49Z","has_accepted_license":"1","year":"2021","day":"05","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","author":[{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","citation":{"mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8831","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10065"},{"relation":"part_of_dissertation","id":"10066","status":"public"},{"relation":"part_of_dissertation","id":"8909","status":"public"},{"id":"5816","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","file_id":"10061","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_name":"PHD_Thesis_Jirovec_Source.zip","date_created":"2021-09-30T14:29:14Z","creator":"djirovec","file_size":32397600,"date_updated":"2022-12-20T23:30:07Z"},{"file_name":"PHD_Thesis_pdfa2b_1.pdf","date_created":"2021-10-05T07:56:49Z","creator":"djirovec","file_size":26910829,"date_updated":"2022-12-20T23:30:07Z","embargo":"2022-10-06","file_id":"10087","checksum":"5fbe08d4f66d1153e04c47971538fae8","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"10","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments."}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"file_date_updated":"2022-12-20T23:30:07Z","supervisor":[{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-08T11:41:08Z","ddc":["621","539"],"type":"dissertation","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)"},"status":"public","keyword":["qubits","quantum computing","holes"],"_id":"10058"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","date_created":"2020-12-02T10:50:47Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1038/s41563-021-01022-2","page":"1106–1112","publication":"Nature Materials","day":"01","year":"2021","isi":1,"project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"title":"A singlet triplet hole spin qubit in planar Ge","external_id":{"arxiv":["2011.13755"],"isi":["000657596400001"]},"article_processing_charge":"No","author":[{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C","last_name":"Hofmann"},{"first_name":"Andrea","full_name":"Ballabio, Andrea","last_name":"Ballabio"},{"first_name":"Philipp M.","last_name":"Mutter","full_name":"Mutter, Philipp M."},{"full_name":"Tavani, Giulio","last_name":"Tavani","first_name":"Giulio"},{"first_name":"Marc","last_name":"Botifoll","full_name":"Botifoll, Marc"},{"first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro","last_name":"Crippa"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"last_name":"Sagi","full_name":"Sagi, Oliver","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"},{"first_name":"Frederico","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","last_name":"Martins","orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez"},{"last_name":"Borovkov","full_name":"Borovkov, Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","first_name":"Maksim"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2.","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","ieee":"D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,” Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021."},"intvolume":" 20","month":"08","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.13755"}],"scopus_import":"1","oa_version":"Preprint","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}],"record":[{"status":"public","id":"9323","relation":"research_data"},{"id":"10058","status":"public","relation":"dissertation_contains"}]},"volume":20,"issue":"8","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"status":"public","type":"journal_article","article_type":"original","_id":"8909","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"date_updated":"2024-03-27T23:30:26Z"},{"file_date_updated":"2022-05-21T22:30:04Z","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:32:32Z","ddc":["571"],"type":"dissertation","status":"public","_id":"9397","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"9398","checksum":"7f98532f5324a0b2f3fa8de2967baa19","date_updated":"2022-05-21T22:30:04Z","file_size":47799741,"creator":"khuljev","date_created":"2021-05-17T12:29:12Z","file_name":"KHuljev_Thesis_corrections.docx"},{"embargo":"2022-05-20","file_id":"9401","checksum":"bf512f8a1e572a543778fc4b227c01ba","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"new_KHuljev_Thesis_corrections.pdf","date_created":"2021-05-18T14:50:28Z","file_size":16542131,"date_updated":"2022-05-21T22:30:04Z","creator":"khuljev"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"oa_version":"Published Version","author":[{"last_name":"Huljev","full_name":"Huljev, Karla","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","citation":{"chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"101","doi":"10.15479/at:ista:9397","date_published":"2021-05-18T00:00:00Z","date_created":"2021-05-17T12:31:30Z","has_accepted_license":"1","year":"2021","day":"18","publisher":"Institute of Science and Technology Austria","oa":1},{"_id":"10066","article_number":"2107.12975","type":"preprint","status":"public","project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"citation":{"apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. https://doi.org/10.48550/arXiv.2107.12975","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. doi:10.48550/arXiv.2107.12975","short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.).","ieee":"B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” arXiv. .","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, 2107.12975, doi:10.48550/arXiv.2107.12975.","ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975.","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.12975."},"date_updated":"2024-03-27T23:30:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"B.","full_name":"Severin, B.","last_name":"Severin"},{"first_name":"D. T.","last_name":"Lennon","full_name":"Lennon, D. T."},{"first_name":"L. C.","full_name":"Camenzind, L. C.","last_name":"Camenzind"},{"first_name":"F.","last_name":"Vigneau","full_name":"Vigneau, F."},{"first_name":"F.","last_name":"Fedele","full_name":"Fedele, F."},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801"},{"full_name":"Ballabio, A.","last_name":"Ballabio","first_name":"A."},{"full_name":"Chrastina, D.","last_name":"Chrastina","first_name":"D."},{"first_name":"G.","last_name":"Isella","full_name":"Isella, G."},{"full_name":"Kruijf, M. de","last_name":"Kruijf","first_name":"M. de"},{"last_name":"Carballido","full_name":"Carballido, M. J.","first_name":"M. J."},{"last_name":"Svab","full_name":"Svab, S.","first_name":"S."},{"first_name":"A. V.","last_name":"Kuhlmann","full_name":"Kuhlmann, A. V."},{"full_name":"Braakman, F. R.","last_name":"Braakman","first_name":"F. R."},{"last_name":"Geyer","full_name":"Geyer, S.","first_name":"S."},{"first_name":"F. N. M.","last_name":"Froning","full_name":"Froning, F. N. M."},{"last_name":"Moon","full_name":"Moon, H.","first_name":"H."},{"full_name":"Osborne, M. A.","last_name":"Osborne","first_name":"M. A."},{"first_name":"D.","last_name":"Sejdinovic","full_name":"Sejdinovic, D."},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"},{"first_name":"D. M.","full_name":"Zumbühl, D. M.","last_name":"Zumbühl"},{"full_name":"Briggs, G. A. D.","last_name":"Briggs","first_name":"G. A. D."},{"first_name":"N.","last_name":"Ares","full_name":"Ares, N."}],"external_id":{"arxiv":["2107.12975"]},"article_processing_charge":"No","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","department":[{"_id":"GeKa"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning."}],"oa_version":"Preprint","acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations.","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12975","open_access":"1"}],"oa":1,"month":"07","year":"2021","publication_status":"submitted","day":"27","language":[{"iso":"eng"}],"publication":"arXiv","doi":"10.48550/arXiv.2107.12975","related_material":{"record":[{"status":"public","id":"10058","relation":"dissertation_contains"}]},"date_published":"2021-07-27T00:00:00Z","date_created":"2021-10-01T12:40:22Z"},{"_id":"9437","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)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:30Z","ddc":["570"],"file_date_updated":"2021-05-31T09:43:09Z","department":[{"_id":"RySh"},{"_id":"PeJo"}],"abstract":[{"text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"04","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-05-31T09:43:09Z","file_name":"2021_eLife_Bhandari.pdf","creator":"cziletti","date_updated":"2021-05-31T09:43:09Z","file_size":8174719,"checksum":"6ebcb79999f889766f7cd79ee134ad28","file_id":"9440","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}],"record":[{"relation":"dissertation_contains","id":"9562","status":"public"}]},"volume":10,"article_number":"e68274","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000651761700001"]},"article_processing_charge":"No","author":[{"last_name":"Bhandari","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676"},{"full_name":"Fernández-Fernández, Diego","last_name":"Fernández-Fernández","first_name":"Diego"},{"first_name":"Thorsten","last_name":"Fritzius","full_name":"Fritzius, Thorsten"},{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C","last_name":"Önal"},{"last_name":"Montanaro-Punzengruber","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","first_name":"Jacqueline-Claire"},{"first_name":"Martin","full_name":"Gassmann, Martin","last_name":"Gassmann"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"first_name":"Akos","full_name":"Kulik, Akos","last_name":"Kulik"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"}],"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","year":"2021","has_accepted_license":"1","isi":1,"publication":"eLife","day":"29","date_created":"2021-05-30T22:01:23Z","doi":"10.7554/ELIFE.68274","date_published":"2021-04-29T00:00:00Z"},{"publisher":"Institute of Science and Technology Austria","oa":1,"day":"01","has_accepted_license":"1","year":"2021","date_published":"2021-06-01T00:00:00Z","doi":"10.15479/at:ista:9562","date_created":"2021-06-17T14:10:47Z","page":"124","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562"},"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","author":[{"first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","last_name":"Kleindienst"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"06","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2021-06-17T14:03:14Z","file_name":"Thesis.pdf","date_updated":"2022-07-02T22:30:04Z","file_size":77299142,"creator":"dkleindienst","file_id":"9563","checksum":"659df5518db495f679cb1df9e9bd1d94","embargo":"2022-07-01","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"checksum":"3bcf63a2b19e5b6663be051bea332748","file_id":"9564","content_type":"application/zip","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2021-06-17T14:04:30Z","file_name":"Thesis_source.zip","date_updated":"2022-07-02T22:30:04Z","file_size":369804895,"creator":"dkleindienst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"status":"public","id":"9756","relation":"part_of_dissertation"},{"status":"public","id":"9437","relation":"part_of_dissertation"},{"status":"public","id":"8532","relation":"part_of_dissertation"},{"status":"public","id":"612","relation":"part_of_dissertation"}]},"_id":"9562","status":"public","type":"dissertation","ddc":["570"],"supervisor":[{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"}],"date_updated":"2023-09-11T12:55:53Z","file_date_updated":"2022-07-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"RySh"}]},{"_id":"8934","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"dissertation","status":"public","date_updated":"2023-09-22T10:03:21Z","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"ddc":["005"],"file_date_updated":"2021-12-23T23:30:04Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"01","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":5251507,"date_updated":"2021-12-23T23:30:04Z","creator":"akafshda","file_name":"Thesis-pdfa.pdf","date_created":"2020-12-22T20:08:44Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2021-12-22","checksum":"d1b9db3725aed34dadd81274aeb9426c","file_id":"8969"},{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","checksum":"1661df7b393e6866d2460eba3c905130","file_id":"8970","creator":"akafshda","file_size":10636756,"date_updated":"2021-03-04T23:30:04Z","file_name":"source.zip","date_created":"2020-12-22T20:08:50Z"}],"related_material":{"record":[{"id":"1386","status":"public","relation":"part_of_dissertation"},{"id":"1437","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"311"},{"id":"6056","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6380","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"639"},{"relation":"part_of_dissertation","status":"public","id":"66"},{"relation":"part_of_dissertation","status":"public","id":"6780"},{"id":"6918","status":"public","relation":"part_of_dissertation"},{"id":"7810","status":"public","relation":"part_of_dissertation"},{"id":"6175","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6378","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6490","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7014"},{"id":"8089","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8728","status":"public"},{"id":"7158","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5977","status":"public"},{"status":"public","id":"6009","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6340"},{"status":"public","id":"949","relation":"part_of_dissertation"}]},"project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"title":"Parameterized and algebro-geometric advances in static program analysis","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","day":"01","page":"278","date_created":"2020-12-10T12:17:07Z","date_published":"2021-01-01T00:00:00Z","doi":"10.15479/AT:ISTA:8934"},{"citation":{"mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Tomasek","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin"}],"article_processing_charge":"No","title":"Pathogenic Escherichia coli hijack the host immune response","has_accepted_license":"1","year":"2021","day":"18","page":"73","doi":"10.15479/at:ista:10307","date_published":"2021-11-18T00:00:00Z","date_created":"2021-11-18T15:05:06Z","publisher":"Institute of Science and Technology Austria","oa":1,"supervisor":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","last_name":"Sixt"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"date_updated":"2023-09-07T13:34:38Z","ddc":["570"],"file_date_updated":"2022-12-20T23:30:05Z","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"_id":"10307","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_name":"ThesisTomasekKathrin.pdf","date_created":"2021-11-18T15:07:31Z","file_size":13266088,"date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek","embargo":"2022-11-18","checksum":"b39c9e0ef18d0484d537a67551effd02","file_id":"10308","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","file_size":7539509,"date_created":"2021-11-18T15:07:46Z","file_name":"ThesisTomasekKathrin.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"10309","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10316"}]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11"},{"month":"10","oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","oa_version":"Preprint","abstract":[{"text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"date_created":"2021-11-19T12:24:16Z","ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"11843","status":"public"},{"relation":"dissertation_contains","id":"10307","status":"public"}]},"doi":"10.1101/2021.10.18.464770","date_published":"2021-10-18T00:00:00Z","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"18","publication_status":"submitted","year":"2021","project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","type":"preprint","_id":"10316","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"article_processing_charge":"No","author":[{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek"},{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","last_name":"Glatzová","full_name":"Glatzová, Ivana"},{"last_name":"Lukesch","full_name":"Lukesch, Michael S.","first_name":"Michael S."},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","last_name":"Sixt"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. doi:10.1101/2021.10.18.464770","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, 10.1101/2021.10.18.464770."},"date_updated":"2024-03-27T23:30:35Z"},{"project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"article_number":"e106862","author":[{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marco","last_name":"Marconi","full_name":"Marconi, Marco"},{"first_name":"Andrea","last_name":"Vega","full_name":"Vega, Andrea"},{"first_name":"Jose","last_name":"O’Brien","full_name":"O’Brien, Jose"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed"},{"first_name":"Livio","last_name":"Antonielli","full_name":"Antonielli, Livio"},{"last_name":"Montesinos López","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C"},{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang"},{"last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"last_name":"Cuesta","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Artner, Christina","last_name":"Artner","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina"},{"first_name":"Eleonore","full_name":"Bouguyon, Eleonore","last_name":"Bouguyon"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez","first_name":"Rodrigo A."},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"article_processing_charge":"Yes (via OA deal)","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","citation":{"apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3). doi:10.15252/embj.2020106862","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ieee":"K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo Press, 2021.","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862, Embo Press, 2021, doi:10.15252/embj.2020106862.","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2020106862."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Embo Press","oa":1,"acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","date_published":"2021-02-01T00:00:00Z","doi":"10.15252/embj.2020106862","date_created":"2021-01-17T23:01:12Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"EMBO Journal","type":"journal_article","article_type":"original","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)"},"status":"public","_id":"9010","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2021-02-11T12:28:29Z","date_updated":"2024-03-27T23:30:39Z","ddc":["580"],"scopus_import":"1","month":"02","intvolume":" 40","abstract":[{"text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"volume":40,"issue":"3","related_material":{"record":[{"id":"10303","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","relation":"press_release","description":"News on IST Homepage"}]},"publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9110","checksum":"dc55c900f3b061d6c2790b8813d759a3","success":1,"creator":"dernst","date_updated":"2021-02-11T12:28:29Z","file_size":2358617,"date_created":"2021-02-11T12:28:29Z","file_name":"2021_Embo_Otvos.pdf"}],"language":[{"iso":"eng"}]},{"acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"06","publication":"EMBO Reports","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.15252/embr.202051813","date_published":"2021-09-06T00:00:00Z","date_created":"2021-08-15T22:01:30Z","article_number":"e51813","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","ieee":"A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813."},"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","author":[{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"last_name":"Fredes","full_name":"Fredes, Isabel","first_name":"Isabel"},{"first_name":"José","last_name":"O’Brien","full_name":"O’Brien, José"},{"last_name":"Shen","full_name":"Shen, Zhouxin","first_name":"Zhouxin"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983"},{"last_name":"Abualia","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Briggs, Steven P.","last_name":"Briggs","first_name":"Steven P."},{"first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez"}],"external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"article_processing_charge":"Yes","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate."}],"month":"09","intvolume":" 22","scopus_import":"1","file":[{"success":1,"checksum":"750de03dc3b715c37090126c1548ba13","file_id":"10090","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_EmboR_Vega.pdf","date_created":"2021-10-05T13:36:42Z","creator":"cchlebak","file_size":3144854,"date_updated":"2021-10-05T13:36:42Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"publication_status":"published","volume":22,"related_material":{"record":[{"relation":"dissertation_contains","id":"10303","status":"public"}]},"issue":"9","_id":"9913","status":"public","type":"journal_article","article_type":"original","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)"},"ddc":["580"],"date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"file_date_updated":"2021-10-05T13:36:42Z"},{"file":[{"creator":"rabualia","file_size":28005730,"date_updated":"2022-12-20T23:30:06Z","file_name":"AbualiaPhDthesisfinalv3.pdf","date_created":"2021-11-22T14:48:21Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-11-23","file_id":"10331","checksum":"dea38b98aa4da1cea03dcd0f10862818"},{"creator":"rabualia","file_size":62841883,"date_updated":"2022-12-20T23:30:06Z","file_name":"AbualiaPhDthesisfinalv3.docx","date_created":"2021-11-22T14:48:34Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10332","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"9010","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9913"},{"status":"public","id":"47","relation":"part_of_dissertation"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"month":"11","alternative_title":["ISTA Thesis"],"ddc":["580","581"],"supervisor":[{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"date_updated":"2023-09-19T14:42:45Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:06Z","_id":"10303","status":"public","type":"dissertation","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)"},"day":"22","has_accepted_license":"1","year":"2021","doi":"10.15479/at:ista:10303","date_published":"2021-11-22T00:00:00Z","date_created":"2021-11-18T11:20:59Z","page":"139","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria."},"title":"Role of hormones in nitrate regulated growth","author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","last_name":"Abualia"}],"article_processing_charge":"No"},{"day":"02","has_accepted_license":"1","year":"2021","doi":"10.15479/at:ista:9962","date_published":"2021-09-02T00:00:00Z","date_created":"2021-08-29T12:36:50Z","page":"182","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962."},"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","author":[{"last_name":"Hansen","full_name":"Hansen, Andi H","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"file":[{"date_updated":"2022-09-03T22:30:04Z","file_size":10629190,"creator":"ahansen","date_created":"2021-08-30T09:17:39Z","file_name":"Thesis_Hansen.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","file_id":"9971"},{"creator":"ahansen","file_size":13457469,"date_updated":"2022-09-03T22:30:04Z","file_name":"Thesis_Hansen_PDFA-1a.pdf","date_created":"2021-08-30T09:29:44Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-09-02","checksum":"204fa40321a1c6289b68c473634c4bf3","file_id":"9972"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8569"},{"relation":"part_of_dissertation","id":"960","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.","lang":"eng"}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["570"],"supervisor":[{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-22T09:58:30Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"file_date_updated":"2022-09-03T22:30:04Z","_id":"9962","status":"public","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"type":"dissertation","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)"}},{"citation":{"chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2.","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000655563800002"],"arxiv":["2011.09486"]},"article_processing_charge":"No","author":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"}],"title":"Quantum many-body scars and weak breaking of ergodicity","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"year":"2021","has_accepted_license":"1","isi":1,"publication":"Nature Physics","day":"01","page":"675–685","date_created":"2021-05-28T09:03:50Z","doi":"10.1038/s41567-021-01230-2","date_published":"2021-06-01T00:00:00Z","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","oa":1,"quality_controlled":"1","publisher":"Nature Research","date_updated":"2023-10-18T08:20:59Z","ddc":["539"],"department":[{"_id":"MaSe"}],"file_date_updated":"2021-12-02T23:30:03Z","_id":"9428","type":"journal_article","article_type":"review","status":"public","publication_status":"published","publication_identifier":{"eissn":["1745-2481"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-20T09:27:43Z","file_name":"RevisedQMBSreview.pdf","creator":"patrickd","date_updated":"2021-12-02T23:30:03Z","file_size":10028836,"file_id":"10026","checksum":"316ed42ea1b42b0f1a3025bb476266fc","embargo":"2021-12-01","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"issue":"6","volume":17,"abstract":[{"text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology.","lang":"eng"}],"oa_version":"Preprint","intvolume":" 17","month":"06"},{"doi":"10.1016/j.plantsci.2020.110750","date_published":"2021-02-01T00:00:00Z","date_created":"2020-12-09T14:48:28Z","day":"01","publication":"Plant Science","isi":1,"has_accepted_license":"1","year":"2021","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","author":[{"last_name":"Gelová","orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana"},{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"full_name":"Brunoud, Géraldine","last_name":"Brunoud","first_name":"Géraldine"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","last_name":"Zhang"},{"last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","full_name":"Michalko, Jaroslav","last_name":"Michalko"},{"first_name":"Zlata","full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","last_name":"Hajny"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"last_name":"Vernoux","full_name":"Vernoux, Teva","first_name":"Teva"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750","ieee":"Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750."},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"article_number":"110750","related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"volume":303,"ec_funded":1,"file":[{"date_updated":"2021-02-04T07:49:25Z","file_size":12563728,"creator":"dernst","date_created":"2021-02-04T07:49:25Z","file_name":"2021_PlantScience_Gelova.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9083","checksum":"a7f2562bdca62d67dfa88e271b62a629","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0168-9452"]},"publication_status":"published","month":"02","intvolume":" 303","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"file_date_updated":"2021-02-04T07:49:25Z","ddc":["580"],"date_updated":"2024-03-27T23:30:43Z","status":"public","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"article_type":"original","type":"journal_article","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)"},"_id":"8931"},{"date_created":"2021-03-26T12:08:38Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1093/plphys/kiab134","page":"1122–1142","publication":"Plant Physiology","day":"01","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000671555900031"],"pmid":["33734402"]},"author":[{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li"},{"last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin"},{"first_name":"E","full_name":"Himschoot, E","last_name":"Himschoot"},{"full_name":"Wang, R","last_name":"Wang","first_name":"R"},{"last_name":"Vanneste","full_name":"Vanneste, S","first_name":"S"},{"full_name":"Sánchez-Simarro, J","last_name":"Sánchez-Simarro","first_name":"J"},{"last_name":"Aniento","full_name":"Aniento, F","first_name":"F"},{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:10.1093/plphys/kiab134.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 2021;186(2):1122–1142. doi:10.1093/plphys/kiab134","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiab134","ieee":"M. Narasimhan et al., “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” Plant Physiology, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology. Oxford University Press, 2021. https://doi.org/10.1093/plphys/kiab134.","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142."},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"ec_funded":1,"volume":186,"issue":"2","related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"},{"status":"public","id":"10083","relation":"dissertation_contains"}],"link":[{"relation":"erratum","url":"10.1093/plphys/kiab380"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_PlantPhysio_Narasimhan.pdf","date_created":"2021-11-11T15:07:51Z","creator":"cziletti","file_size":2289127,"date_updated":"2021-11-11T15:07:51Z","success":1,"file_id":"10273","checksum":"532bb9469d3b665907f06df8c383eade","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"intvolume":" 186","month":"06","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. "}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-11-11T15:07:51Z","ddc":["580"],"date_updated":"2024-03-27T23:30:43Z","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":"9287"},{"date_updated":"2023-10-31T19:30:02Z","supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"ddc":["575"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2022-12-20T23:30:03Z","_id":"10083","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","status":"public","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10138","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","embargo":"2022-10-14","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-14T08:00:07Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","date_updated":"2022-12-20T23:30:03Z","file_size":8616142,"creator":"cchlebak"},{"date_updated":"2022-12-20T23:30:03Z","file_size":15058499,"creator":"cchlebak","date_created":"2021-10-14T08:00:13Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"10139","checksum":"f23ed258ca894f6aabf58b0c128bf242"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"442","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8931"},{"status":"public","id":"9287","relation":"part_of_dissertation"},{"id":"8283","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8986"},{"id":"6627","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10095","status":"public"},{"relation":"part_of_dissertation","id":"10015","status":"public"}]},"abstract":[{"text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","citation":{"ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083","apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"title":"Rapid cell growth regulation in Arabidopsis","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"year":"2021","has_accepted_license":"1","day":"06","date_created":"2021-10-04T13:33:10Z","doi":"10.15479/at:ista:10083","date_published":"2021-10-06T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria"},{"author":[{"first_name":"N","full_name":"Nikonorova, N","last_name":"Nikonorova"},{"first_name":"E","last_name":"Murphy","full_name":"Murphy, E"},{"first_name":"CF","full_name":"Fonseca de Lima, CF","last_name":"Fonseca de Lima"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"full_name":"van de Cotte, B","last_name":"van de Cotte","first_name":"B"},{"last_name":"Vu","full_name":"Vu, LD","first_name":"LD"},{"first_name":"D","last_name":"Balcerowicz","full_name":"Balcerowicz, D"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"last_name":"Kong","full_name":"Kong, X","first_name":"X"},{"first_name":"G","full_name":"De Rop, G","last_name":"De Rop"},{"first_name":"T","full_name":"Beeckman, T","last_name":"Beeckman"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"last_name":"Vissenberg","full_name":"Vissenberg, K","first_name":"K"},{"first_name":"PC","last_name":"Morris","full_name":"Morris, PC"},{"first_name":"Z","last_name":"Ding","full_name":"Ding, Z"},{"first_name":"I","full_name":"De Smet, I","last_name":"De Smet"}],"external_id":{"pmid":["34359847"],"isi":["000676604700001"]},"article_processing_charge":"Yes","title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","citation":{"ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665.","chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071665.","apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. MDPI. https://doi.org/10.3390/cells10071665","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 2021;10. doi:10.3390/cells10071665","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).","ieee":"N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” Cells, vol. 10. MDPI, 2021.","mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells, vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"article_number":"1665 ","date_published":"2021-07-02T00:00:00Z","doi":"10.3390/cells10071665","date_created":"2021-09-14T11:36:20Z","isi":1,"has_accepted_license":"1","year":"2021","day":"02","publication":"Cells","quality_controlled":"1","publisher":"MDPI","oa":1,"acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","file_date_updated":"2021-09-16T09:07:06Z","department":[{"_id":"JiFr"}],"date_updated":"2024-03-27T23:30:43Z","ddc":["575"],"article_type":"original","type":"journal_article","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)"},"status":"public","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"_id":"10015","volume":10,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"ec_funded":1,"publication_identifier":{"issn":["2073-4409"]},"publication_status":"published","file":[{"file_name":"2021_Cells_Nikonorova.pdf","date_created":"2021-09-16T09:07:06Z","creator":"cchlebak","file_size":2667848,"date_updated":"2021-09-16T09:07:06Z","success":1,"checksum":"2a9f534b9c2200e72e2cde95afaf4eed","file_id":"10021","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"month":"07","intvolume":" 10","abstract":[{"lang":"eng","text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip."}],"oa_version":"Published Version","pmid":1},{"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","oa":1,"year":"2021","publication":"Research Square","day":"09","date_created":"2021-10-06T08:56:22Z","doi":"10.21203/rs.3.rs-266395/v3","date_published":"2021-09-09T00:00:00Z","article_number":"266395","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. .","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jian","full_name":"Chen, Jian","last_name":"Chen"},{"last_name":"Shabala","full_name":"Shabala, Lana","first_name":"Lana"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Shabala, Sergey","last_name":"Shabala","first_name":"Sergey"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"last_name":"Kinoshita","full_name":"Kinoshita, Toshinori","first_name":"Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"oa_version":"Preprint","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"month":"09","publication_status":"accepted","publication_identifier":{"issn":["2693-5015"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"10223"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"_id":"10095","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":"preprint","status":"public","date_updated":"2024-03-27T23:30:43Z","department":[{"_id":"JiFr"},{"_id":"NanoFab"}]},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9997"},{"relation":"part_of_dissertation","status":"public","id":"2"},{"relation":"part_of_dissertation","id":"9402","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_name":"submission_new.zip","date_created":"2021-11-18T12:41:46Z","file_size":29703124,"date_updated":"2022-12-20T23:30:08Z","creator":"lschmid","file_id":"10305","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","embargo_to":"open_access","content_type":"application/zip","relation":"source_file","access_level":"closed"},{"embargo":"2022-10-18","file_id":"10306","checksum":"d940af042e94660c6b6a7b4f0b184d47","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"thesis_new_upload.pdf","date_created":"2021-11-18T12:59:15Z","file_size":8320985,"date_updated":"2022-12-20T23:30:08Z","creator":"lschmid"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"11","abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"oa_version":"Published Version","file_date_updated":"2022-12-20T23:30:08Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-11-07T08:28:29Z","ddc":["519","576"],"type":"dissertation","status":"public","_id":"10293","page":"171","doi":"10.15479/at:ista:10293","date_published":"2021-11-17T00:00:00Z","date_created":"2021-11-15T17:12:57Z","has_accepted_license":"1","year":"2021","day":"17","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"}],"article_processing_charge":"No","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","citation":{"ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293","mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}]},{"doi":"10.1038/s41598-021-96932-1","date_published":"2021-08-31T00:00:00Z","date_created":"2021-09-11T16:22:02Z","day":"31","publication":"Scientific Reports","isi":1,"has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","title":"The evolution of indirect reciprocity under action and assessment generosity","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid"},{"first_name":"Pouya","full_name":"Shati, Pouya","last_name":"Shati"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"isi":["000692406400018"],"pmid":["34465830"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-96932-1","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:10.1038/s41598-021-96932-1.","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1."},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"article_number":"17443","volume":11,"related_material":{"record":[{"id":"10293","status":"public","relation":"dissertation_contains"}]},"issue":"1","ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10006","checksum":"19df8816cf958b272b85841565c73182","success":1,"creator":"cchlebak","date_updated":"2021-09-13T10:31:21Z","file_size":2424943,"date_created":"2021-09-13T10:31:21Z","file_name":"2021_ScientificReports_Schmid.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","month":"08","intvolume":" 11","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms.","lang":"eng"}],"file_date_updated":"2021-09-13T10:31:21Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"ddc":["003"],"date_updated":"2024-03-27T23:30:44Z","status":"public","keyword":["Multidisciplinary"],"article_type":"original","type":"journal_article","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)"},"_id":"9997"},{"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability."}],"month":"05","intvolume":" 5","scopus_import":"1","file":[{"date_created":"2023-11-07T08:27:23Z","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","creator":"dernst","date_updated":"2023-11-07T08:27:23Z","file_size":5232761,"file_id":"14496","checksum":"34f55e173f90dc1dab731063458ac780","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2397-3374"]},"publication_status":"published","volume":5,"related_material":{"record":[{"status":"public","id":"10293","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","description":"News on IST Homepage"}]},"issue":"10","ec_funded":1,"_id":"9402","status":"public","article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2024-03-27T23:30:44Z","file_date_updated":"2023-11-07T08:27:23Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"13","publication":"Nature Human Behaviour","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-05-13T00:00:00Z","doi":"10.1038/s41562-021-01114-8","date_created":"2021-05-18T16:56:57Z","page":"1292–1302","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour. Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8.","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302.","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:10.1038/s41562-021-01114-8.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-021-01114-8","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302."},"title":"A unified framework of direct and indirect reciprocity","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","last_name":"Schmid"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"article_processing_charge":"No","external_id":{"pmid":["33986519"],"isi":["000650304000002"]}},{"acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"19","publication":"ACM Transactions on Graphics","doi":"10.1145/3450626.3459800","date_published":"2021-07-19T00:00:00Z","date_created":"2021-08-08T22:01:26Z","article_number":"126","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459800.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459800","apa":"Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves. ACM Transactions on Graphics. Virtual: Association for Computing Machinery. https://doi.org/10.1145/3450626.3459800","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459800.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"article_processing_charge":"No","external_id":{"isi":["000674930900091"]},"title":"The design space of plane elastic curves","abstract":[{"lang":"eng","text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements."}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 40","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10150","checksum":"7e5d08ce46b0451b3102eacd3d00f85f","success":1,"creator":"chafner","date_updated":"2021-10-18T10:42:15Z","file_size":17064290,"date_created":"2021-10-18T10:42:15Z","file_name":"elastic-curves-paper.pdf"},{"creator":"chafner","file_size":547156,"date_updated":"2021-10-18T10:42:22Z","file_name":"elastic-curves-supp.pdf","date_created":"2021-10-18T10:42:22Z","relation":"supplementary_material","access_level":"open_access","content_type":"application/pdf","checksum":"0088643478be7c01a703b5b10767348f","file_id":"10151"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","description":"News on IST Website"}],"record":[{"status":"public","id":"12897","relation":"dissertation_contains"}]},"issue":"4","volume":40,"ec_funded":1,"_id":"9817","article_type":"original","type":"journal_article","conference":{"name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2021-08-13","location":"Virtual","start_date":"2021-08-09"},"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)"},"status":"public","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"date_updated":"2024-03-27T23:30:45Z","ddc":["516"],"file_date_updated":"2021-10-18T10:42:22Z","department":[{"_id":"BeBi"}]},{"month":"10","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects."}],"related_material":{"record":[{"id":"9160","status":"public","relation":"part_of_dissertation"}]},"file":[{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"10186","checksum":"ce7108853e6cec6224f17cd6429b51fe","creator":"cziletti","date_updated":"2022-12-20T23:30:05Z","file_size":28508629,"date_created":"2021-10-27T07:45:37Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx"},{"creator":"cziletti","file_size":10623525,"date_updated":"2022-12-20T23:30:05Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","date_created":"2021-10-27T07:45:57Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-10-28","file_id":"10187","checksum":"0d7afb846e8e31ec794de47bf44e12ef"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","_id":"10135","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:05Z","ddc":["570"],"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"date_updated":"2024-01-25T10:53:29Z","publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/at:ista:10135","date_published":"2021-10-13T00:00:00Z","date_created":"2021-10-13T13:42:48Z","day":"13","has_accepted_license":"1","year":"2021","project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746"}],"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","author":[{"last_name":"Semerádová","full_name":"Semerádová, Hana","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","mla":"Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135","apa":"Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135"}},{"_id":"9728","status":"public","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"type":"dissertation","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)"},"ddc":["532"],"supervisor":[{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"date_updated":"2024-02-28T13:14:39Z","file_date_updated":"2022-07-29T22:30:05Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"month":"07","alternative_title":["ISTA Thesis"],"file":[{"checksum":"77436be3563a90435024307b1b5ee7e8","file_id":"9744","content_type":"application/x-zip-compressed","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2021-07-28T13:32:02Z","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","date_updated":"2022-07-29T22:30:05Z","file_size":22859658,"creator":"nagrawal"},{"embargo":"2022-07-28","file_id":"9745","checksum":"72a891d7daba85445c29b868c22575ed","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","date_created":"2021-07-28T13:32:05Z","creator":"nagrawal","file_size":18658048,"date_updated":"2022-07-29T22:30:05Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6189"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","mla":"Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728","apa":"Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728"},"title":"Transition to turbulence and drag reduction in particle-laden pipe flows","author":[{"first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","last_name":"Agrawal","full_name":"Agrawal, Nishchal"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"29","has_accepted_license":"1","year":"2021","doi":"10.15479/at:ista:9728","date_published":"2021-07-29T00:00:00Z","date_created":"2021-07-27T13:40:30Z","page":"118"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"issue":"52","volume":117,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context.","lang":"eng"}],"intvolume":" 117","month":"12","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2"}],"scopus_import":"1","extern":"1","date_updated":"2021-11-25T15:35:58Z","_id":"10336","status":"public","article_type":"original","type":"journal_article","publication":"Proceedings of the National Academy of Sciences","day":"16","year":"2020","date_created":"2021-11-25T15:07:09Z","date_published":"2020-12-16T00:00:00Z","doi":"10.1073/pnas.2007694117","page":"33090-33098","acknowledgement":"We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098.","chicago":"Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117.","apa":"Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117","ama":"Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098. doi:10.1073/pnas.2007694117","short":"J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098.","ieee":"J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” Proceedings of the National Academy of Sciences, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.","mla":"Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117."},"title":"Physical mechanisms of amyloid nucleation on fluid membranes","article_processing_charge":"No","external_id":{"pmid":["33328273"]},"author":[{"last_name":"Krausser","full_name":"Krausser, Johannes","first_name":"Johannes"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"}]},{"author":[{"first_name":"Xiaohe","last_name":"Tian","full_name":"Tian, Xiaohe"},{"full_name":"Leite, Diana M.","last_name":"Leite","first_name":"Diana M."},{"first_name":"Edoardo","full_name":"Scarpa, Edoardo","last_name":"Scarpa"},{"last_name":"Nyberg","full_name":"Nyberg, Sophie","first_name":"Sophie"},{"first_name":"Gavin","full_name":"Fullstone, Gavin","last_name":"Fullstone"},{"first_name":"Joe","full_name":"Forth, Joe","last_name":"Forth"},{"full_name":"Matias, Diana","last_name":"Matias","first_name":"Diana"},{"first_name":"Azzurra","full_name":"Apriceno, Azzurra","last_name":"Apriceno"},{"first_name":"Alessandro","last_name":"Poma","full_name":"Poma, Alessandro"},{"last_name":"Duro-Castano","full_name":"Duro-Castano, Aroa","first_name":"Aroa"},{"first_name":"Manish","full_name":"Vuyyuru, Manish","last_name":"Vuyyuru"},{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Zhongping","last_name":"Zhang","full_name":"Zhang, Zhongping"},{"first_name":"Pan","last_name":"Xiang","full_name":"Xiang, Pan"},{"last_name":"Fang","full_name":"Fang, Bin","first_name":"Bin"},{"full_name":"Tian, Yupeng","last_name":"Tian","first_name":"Yupeng"},{"first_name":"Lei","last_name":"Luo","full_name":"Luo, Lei"},{"first_name":"Loris","full_name":"Rizzello, Loris","last_name":"Rizzello"},{"last_name":"Battaglia","full_name":"Battaglia, Giuseppe","first_name":"Giuseppe"}],"article_processing_charge":"No","external_id":{"pmid":["33246953"]},"title":"On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias","citation":{"ista":"Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 6(48), eabc4397.","chicago":"Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone, Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.abc4397.","ieee":"X. Tian et al., “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” Science Advances, vol. 6, no. 48. American Association for the Advancement of Science, 2020.","short":"X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias, A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić, Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science Advances 6 (2020).","apa":"Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J., … Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abc4397","ama":"Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 2020;6(48). doi:10.1126/sciadv.abc4397","mla":"Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.abc4397."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"eabc4397 ","date_published":"2020-11-27T00:00:00Z","doi":"10.1126/sciadv.abc4397","date_created":"2021-11-26T06:40:28Z","has_accepted_license":"1","year":"2020","day":"27","publication":"Science Advances","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"Funding: G.B. thanks the ERC for the starting grant (MEViC 278793) and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1), EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227). X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author contributions: X.T. prepared and characterized POs, performed all the fast imaging in both conventional and STED microscopy, set up the initial BBB model, encapsulated the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized POs; performed all the permeability studies, PLA assays, WB and associated data analysis, and part of the colocalization assays; and performed experiments with the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared and characterized POs and performed part of the colocalization and inhibition assays. G.F. designed, performed, and analyzed the agent-based simulations of transcytosis. J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed all fast imaging and supervised and coordinated the overall work. X.T., D.M.L., E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.","file_date_updated":"2021-11-26T06:50:09Z","date_updated":"2021-11-26T07:00:24Z","extern":"1","ddc":["611"],"type":"journal_article","article_type":"original","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)"},"status":"public","keyword":["multidisciplinary"],"_id":"10342","issue":"48","volume":6,"publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","file":[{"file_size":10381298,"date_updated":"2021-11-26T06:50:09Z","creator":"cchlebak","file_name":"2020_SciAdv_Tian.pdf","date_created":"2021-11-26T06:50:09Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10343","checksum":"3ba2eca975930cdb0b1ce1ae876885a7"}],"language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1","open_access":"1"}],"month":"11","intvolume":" 6","abstract":[{"lang":"eng","text":"The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across."}],"pmid":1,"oa_version":"Published Version"},{"title":"Exploring the design rules for efficient membrane-reshaping nanostructures","external_id":{"pmid":["33315453"]},"article_processing_charge":"No","author":[{"last_name":"Forster","full_name":"Forster, Joel C.","first_name":"Joel C."},{"last_name":"Krausser","full_name":"Krausser, Johannes","first_name":"Johannes"},{"full_name":"Vuyyuru, Manish R.","last_name":"Vuyyuru","first_name":"Manish R."},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” Physical Review Letters, vol. 125, no. 22. American Physical Society, 2020.","short":"J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020).","ama":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 2020;125(22). doi:10.1103/physrevlett.125.228101","apa":"Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., & Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.228101","mla":"Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:10.1103/physrevlett.125.228101.","ista":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 125(22), 228101.","chicago":"Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.228101."},"article_number":"228101","date_created":"2021-11-26T07:10:43Z","doi":"10.1103/physrevlett.125.228101","date_published":"2020-11-23T00:00:00Z","publication":"Physical Review Letters","day":"23","year":"2020","has_accepted_license":"1","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.), the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the United Kingdom Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1).","file_date_updated":"2021-11-26T07:16:49Z","ddc":["530"],"extern":"1","date_updated":"2021-11-30T08:33:14Z","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":"10344","issue":"22","volume":125,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"10345","checksum":"fbf2e1415e332d6add90222d60401a1d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PhysRevLett_Forster.pdf","date_created":"2021-11-26T07:16:49Z","creator":"cchlebak","file_size":844353,"date_updated":"2021-11-26T07:16:49Z"}],"publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"intvolume":" 125","month":"11","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry."}]},{"abstract":[{"text":"Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1"}],"scopus_import":"1","intvolume":" 16","month":"10","publication_status":"published","publication_identifier":{"issn":["1744-683X","1744-6848"]},"language":[{"iso":"eng"}],"volume":16,"issue":"47","_id":"10341","type":"journal_article","article_type":"original","keyword":["condensed matter physics","general chemistry"],"status":"public","date_updated":"2021-11-26T07:00:33Z","extern":"1","acknowledgement":"We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.).","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","year":"2020","publication":"Soft Matter","day":"06","page":"10628-10639","date_created":"2021-11-26T06:29:41Z","doi":"10.1039/d0sm00712a","date_published":"2020-10-06T00:00:00Z","citation":{"mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:10.1039/d0sm00712a.","ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” Soft Matter, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 2020;16(47):10628-10639. doi:10.1039/d0sm00712a","apa":"Debets, V. E., Janssen, L. M. C., & Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm00712a","chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter. Royal Society of Chemistry, 2020. https://doi.org/10.1039/d0sm00712a.","ista":"Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"pmid":["33084724"]},"article_processing_charge":"No","author":[{"last_name":"Debets","full_name":"Debets, V. E.","first_name":"V. E."},{"first_name":"L. M. C.","full_name":"Janssen, L. M. C.","last_name":"Janssen"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes"},{"acknowledgement":"We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu, Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.), Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).","oa":1,"publisher":"Cell Press","quality_controlled":"1","publication":"Biophysical Journal","day":"23","year":"2020","date_created":"2021-11-26T07:27:24Z","doi":"10.1016/j.bpj.2020.09.013","date_published":"2020-09-23T00:00:00Z","page":"1791-1799","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.","chicago":"Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal. Cell Press, 2020. https://doi.org/10.1016/j.bpj.2020.09.013.","ama":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 2020;119(9):1791-1799. doi:10.1016/j.bpj.2020.09.013","apa":"Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., & Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. Cell Press. https://doi.org/10.1016/j.bpj.2020.09.013","ieee":"A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” Biophysical Journal, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020.","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799.","mla":"Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:10.1016/j.bpj.2020.09.013."},"title":"Modeling fibrillogenesis of collagen-mimetic molecules","article_processing_charge":"No","external_id":{"pmid":["33049216"]},"author":[{"first_name":"Anne E.","full_name":"Hafner, Anne E.","last_name":"Hafner"},{"full_name":"Gyori, Noemi G.","last_name":"Gyori","first_name":"Noemi G."},{"first_name":"Ciaran A.","last_name":"Bench","full_name":"Bench, Ciaran A."},{"first_name":"Luke K.","full_name":"Davis, Luke K.","last_name":"Davis"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications.","lang":"eng"}],"intvolume":" 119","month":"09","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0006-3495"]},"volume":119,"issue":"9","_id":"10346","keyword":["biophysics"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-11-26T07:45:24Z"},{"abstract":[{"text":"The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f","open_access":"1"}],"scopus_import":"1","intvolume":" 11","month":"06","publication_status":"published","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/3.0/","volume":11,"issue":"24","_id":"10350","tmp":{"short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png"},"type":"journal_article","article_type":"original","keyword":["general chemistry"],"status":"public","date_updated":"2021-11-26T11:21:20Z","extern":"1","acknowledgement":"We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge (TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship, Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation (MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus Newman Foundation (TPJK) for financial support. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL).","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","year":"2020","publication":"Chemical Science","day":"08","page":"6236-6247","date_created":"2021-11-26T09:08:19Z","date_published":"2020-06-08T00:00:00Z","doi":"10.1039/c9sc06501f","citation":{"ista":"Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. 2020. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 11(24), 6236–6247.","chicago":"Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” Chemical Science. Royal Society of Chemistry, 2020. https://doi.org/10.1039/c9sc06501f.","ama":"Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 2020;11(24):6236-6247. doi:10.1039/c9sc06501f","apa":"Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., & Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c9sc06501f","short":"A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse, T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247.","ieee":"A. J. Dear et al., “Identification of on- and off-pathway oligomers in amyloid fibril formation,” Chemical Science, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020.","mla":"Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” Chemical Science, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:10.1039/c9sc06501f."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["32953019"]},"author":[{"last_name":"Dear","full_name":"Dear, Alexander J.","first_name":"Alexander J."},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"first_name":"Magnus","full_name":"Kjaergaard, Magnus","last_name":"Kjaergaard"},{"first_name":"Sara","full_name":"Linse, Sara","last_name":"Linse"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."}],"title":"Identification of on- and off-pathway oligomers in amyloid fibril formation"},{"acknowledgement":"We thank the MRC LMCB at UCL for their support; the flow cytometry STP at the Francis Crick Institute for assistance, with special thanks to S. Purewal and D. Davis; C. Bertoli for mentorship\r\nand advice; J. M. Garcia-Arcos for help early on in this project; the entire Baum lab for their input throughout the project; the Albers lab for advice and reagents, with special thanks to M. Van Wolferen and S. Albers; the members of the Wellcome consortium for archaeal cytoskeleton studies for advice and comments; and J. Löwe, S. Oliferenko, M. Balasubramanian, and D. Gerlich for discussions and advice on the manuscript. N.P.R. and S.B. would like to thank N. Rzechorzek, A. Simon, and S. Anjum for discussion and advice.","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","year":"2020","publication":"Science","day":"07","date_created":"2021-11-26T08:21:34Z","doi":"10.1126/science.aaz2532","date_published":"2020-08-07T00:00:00Z","citation":{"ieee":"G. Tarrason Risa et al., “The proteasome controls ESCRT-III–mediated cell division in an archaeon,” Science, vol. 369, no. 6504. American Association for the Advancement of Science, 2020.","short":"G. Tarrason Risa, F. Hurtig, S. Bray, A.E. Hafner, L. Harker-Kirschneck, P. Faull, C. Davis, D. Papatziamou, D.R. Mutavchiev, C. Fan, L. Meneguello, A. Arashiro Pulschen, G. Dey, S. Culley, M. Kilkenny, D.P. Souza, L. Pellegrini, R.A.M. de Bruin, R. Henriques, A.P. Snijders, A. Šarić, A.-C. Lindås, N.P. Robinson, B. Baum, Science 369 (2020).","apa":"Tarrason Risa, G., Hurtig, F., Bray, S., Hafner, A. E., Harker-Kirschneck, L., Faull, P., … Baum, B. (2020). The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaz2532","ama":"Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 2020;369(6504). doi:10.1126/science.aaz2532","mla":"Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” Science, vol. 369, no. 6504, American Association for the Advancement of Science, 2020, doi:10.1126/science.aaz2532.","ista":"Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås A-C, Robinson NP, Baum B. 2020. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 369(6504).","chicago":"Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aaz2532."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["32764038"]},"author":[{"last_name":"Tarrason Risa","full_name":"Tarrason Risa, Gabriel","first_name":"Gabriel"},{"full_name":"Hurtig, Fredrik","last_name":"Hurtig","first_name":"Fredrik"},{"last_name":"Bray","full_name":"Bray, Sian","first_name":"Sian"},{"last_name":"Hafner","full_name":"Hafner, Anne E.","first_name":"Anne E."},{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"last_name":"Faull","full_name":"Faull, Peter","first_name":"Peter"},{"full_name":"Davis, Colin","last_name":"Davis","first_name":"Colin"},{"last_name":"Papatziamou","full_name":"Papatziamou, Dimitra","first_name":"Dimitra"},{"full_name":"Mutavchiev, Delyan R.","last_name":"Mutavchiev","first_name":"Delyan R."},{"last_name":"Fan","full_name":"Fan, Catherine","first_name":"Catherine"},{"full_name":"Meneguello, Leticia","last_name":"Meneguello","first_name":"Leticia"},{"first_name":"Andre","full_name":"Arashiro Pulschen, Andre","last_name":"Arashiro Pulschen"},{"last_name":"Dey","full_name":"Dey, Gautam","first_name":"Gautam"},{"first_name":"Siân","full_name":"Culley, Siân","last_name":"Culley"},{"full_name":"Kilkenny, Mairi","last_name":"Kilkenny","first_name":"Mairi"},{"full_name":"Souza, Diorge P.","last_name":"Souza","first_name":"Diorge P."},{"last_name":"Pellegrini","full_name":"Pellegrini, Luca","first_name":"Luca"},{"first_name":"Robertus A. M.","full_name":"de Bruin, Robertus A. M.","last_name":"de Bruin"},{"first_name":"Ricardo","last_name":"Henriques","full_name":"Henriques, Ricardo"},{"first_name":"Ambrosius P.","full_name":"Snijders, Ambrosius P.","last_name":"Snijders"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Lindås","full_name":"Lindås, Ann-Christin","first_name":"Ann-Christin"},{"first_name":"Nicholas P.","full_name":"Robinson, Nicholas P.","last_name":"Robinson"},{"last_name":"Baum","full_name":"Baum, Buzz","first_name":"Buzz"}],"title":"The proteasome controls ESCRT-III–mediated cell division in an archaeon","abstract":[{"text":"Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/774273v1"}],"scopus_import":"1","intvolume":" 369","month":"08","publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"volume":369,"issue":"6504","_id":"10349","article_type":"original","type":"journal_article","keyword":["multidisciplinary"],"status":"public","date_updated":"2021-11-26T08:58:33Z","extern":"1"},{"citation":{"chicago":"Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller, Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006684117.","ista":"Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 117(39), 24251–24257.","mla":"Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:10.1073/pnas.2006684117.","ieee":"T. C. T. Michaels et al., “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” Proceedings of the National Academy of Sciences, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020.","short":"T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S. Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences 117 (2020) 24251–24257.","ama":"Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 2020;117(39):24251-24257. doi:10.1073/pnas.2006684117","apa":"Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio, P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2006684117"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Meisl","full_name":"Meisl, Georg","first_name":"Georg"},{"first_name":"Gabriella T.","last_name":"Heller","full_name":"Heller, Gabriella T."},{"first_name":"Samo","full_name":"Curk, Samo","last_name":"Curk"},{"first_name":"Paolo","full_name":"Arosio, Paolo","last_name":"Arosio"},{"first_name":"Sara","full_name":"Linse, Sara","last_name":"Linse"},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"external_id":{"pmid":["32929030"]},"article_processing_charge":"No","title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","acknowledgement":"We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.); the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.); Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation (T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through the ERC Grant PhysProt (Agreement 337969).","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"year":"2020","day":"14","publication":"Proceedings of the National Academy of Sciences","page":"24251-24257","doi":"10.1073/pnas.2006684117","date_published":"2020-09-14T00:00:00Z","date_created":"2021-11-26T07:48:27Z","_id":"10347","type":"journal_article","article_type":"original","status":"public","keyword":["multidisciplinary"],"date_updated":"2021-11-26T08:59:06Z","extern":"1","abstract":[{"lang":"eng","text":"Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716","open_access":"1"}],"month":"09","intvolume":" 117","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":117,"issue":"39"},{"publication_status":"published","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"language":[{"iso":"eng"}],"issue":"5","volume":12,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41557-020-0468-6","relation":"erratum"}]},"abstract":[{"text":"Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases.","lang":"eng"}],"oa_version":"None","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.01.08.897488"}],"scopus_import":"1","intvolume":" 12","month":"04","date_updated":"2021-11-26T11:21:08Z","extern":"1","_id":"10351","article_type":"original","type":"journal_article","keyword":["general chemical engineering","general chemistry"],"status":"public","year":"2020","publication":"Nature Chemistry","day":"13","page":"445-451","date_created":"2021-11-26T09:15:13Z","doi":"10.1038/s41557-020-0452-1","date_published":"2020-04-13T00:00:00Z","acknowledgement":"We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V., C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant MAMBA (S.L., agreement no. 340890). The research that led to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"apa":"Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G., … Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-020-0452-1","ama":"Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 2020;12(5):445-451. doi:10.1038/s41557-020-0452-1","ieee":"T. C. T. Michaels et al., “Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide,” Nature Chemistry, vol. 12, no. 5. Springer Nature, pp. 445–451, 2020.","short":"T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J. Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Chemistry 12 (2020) 445–451.","mla":"Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry, vol. 12, no. 5, Springer Nature, 2020, pp. 445–51, doi:10.1038/s41557-020-0452-1.","ista":"Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 12(5), 445–451.","chicago":"Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio, Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry. Springer Nature, 2020. https://doi.org/10.1038/s41557-020-0452-1."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["32303714"]},"author":[{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Curk, Samo","last_name":"Curk","first_name":"Samo"},{"full_name":"Bernfur, Katja","last_name":"Bernfur","first_name":"Katja"},{"last_name":"Arosio","full_name":"Arosio, Paolo","first_name":"Paolo"},{"last_name":"Meisl","full_name":"Meisl, Georg","first_name":"Georg"},{"first_name":"Alexander J.","last_name":"Dear","full_name":"Dear, Alexander J."},{"last_name":"Cohen","full_name":"Cohen, Samuel I. A.","first_name":"Samuel I. A."},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"}],"title":"Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.07.021.","ista":"Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18.","mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” Cell, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:10.1016/j.cell.2020.07.021.","apa":"Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., & Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.07.021","ama":"Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 2020;182(5):1140-1155.e18. doi:10.1016/j.cell.2020.07.021","ieee":"A.-K. Pfitzner et al., “An ESCRT-III polymerization sequence drives membrane deformation and fission,” Cell, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020.","short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18."},"title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","author":[{"last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina","first_name":"Anna-Katharina"},{"last_name":"Mercier","full_name":"Mercier, Vincent","first_name":"Vincent"},{"first_name":"Xiuyun","full_name":"Jiang, Xiuyun","last_name":"Jiang"},{"last_name":"Moser von Filseck","full_name":"Moser von Filseck, Joachim","first_name":"Joachim"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"},{"last_name":"Roux","full_name":"Roux, Aurélien","first_name":"Aurélien"}],"external_id":{"pmid":["32814015"]},"article_processing_charge":"No","acknowledgement":"The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck for careful correction of this manuscript and helpful discussions. The authors want to thank the NCCR Chemical Biology for constant support during this project. A.R. acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975, and 31003A_173087) and the European Research Council Consolidator (311536). A.Š. acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1) and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship (2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA 160728/1 [leader, Sophie Martin]).","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"18","publication":"Cell","year":"2020","doi":"10.1016/j.cell.2020.07.021","date_published":"2020-08-18T00:00:00Z","date_created":"2021-11-26T08:02:27Z","page":"1140-1155.e18","_id":"10348","status":"public","keyword":["general biochemistry","genetics and molecular biology"],"article_type":"original","type":"journal_article","extern":"1","date_updated":"2021-11-26T08:58:37Z","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity.","lang":"eng"}],"month":"08","intvolume":" 182","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"]},"publication_status":"published","volume":182,"issue":"5"},{"_id":"10352","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-11-26T11:21:16Z","extern":"1","abstract":[{"text":"In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/571687","open_access":"1"}],"month":"02","intvolume":" 101","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":101,"article_number":"022420","citation":{"ista":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 101(2), 022420.","chicago":"Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E. American Physical Society, 2020. https://doi.org/10.1103/physreve.101.022420.","ieee":"L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” Physical Review E, vol. 101, no. 2. American Physical Society, 2020.","short":"L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).","apa":"Davis, L. K., Ford, I. J., Šarić, A., & Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.101.022420","ama":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 2020;101(2). doi:10.1103/physreve.101.022420","mla":"Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:10.1103/physreve.101.022420."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Luke K.","full_name":"Davis, Luke K.","last_name":"Davis"},{"first_name":"Ian J.","last_name":"Ford","full_name":"Ford, Ian J."},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Bart W.","last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W."}],"article_processing_charge":"No","external_id":{"pmid":["32168597"]},"title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","acknowledgement":"We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos (Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto) for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering and Physical Sciences Research Council (EP/L504889/1, B.W.H.).","quality_controlled":"1","publisher":"American Physical Society","oa":1,"year":"2020","day":"28","publication":"Physical Review E","doi":"10.1103/physreve.101.022420","date_published":"2020-02-28T00:00:00Z","date_created":"2021-11-26T09:41:04Z"},{"date_created":"2021-11-26T09:57:01Z","doi":"10.1103/physrevlett.124.048102","date_published":"2020-01-31T00:00:00Z","year":"2020","publication":"Physical Review Letters","day":"31","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"We thank Samantha Miller, Bert Poolman, and the members of Šarić and Pilizota laboratories for useful discussion. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P. and A.Š.), Darwin Trust of University of Edinburgh (H.S.), Industrial Biotechnology Innovation Centre (H.S. and T.P.), BBSRC Council Crossing Biological Membrane Network (H.S. and T.P.), BBSRC/EPSRC/MRC Synthetic Biology Research Centre (T.P.), and the Royal Society (A.Š.).","external_id":{"pmid":["32058787"]},"article_processing_charge":"No","author":[{"first_name":"Alexandru","last_name":"Paraschiv","full_name":"Paraschiv, Alexandru"},{"last_name":"Hegde","full_name":"Hegde, Smitha","first_name":"Smitha"},{"full_name":"Ganti, Raman","last_name":"Ganti","first_name":"Raman"},{"first_name":"Teuta","full_name":"Pilizota, Teuta","last_name":"Pilizota"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"title":"Dynamic clustering regulates activity of mechanosensitive membrane channels","citation":{"ama":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 2020;124(4). doi:10.1103/physrevlett.124.048102","apa":"Paraschiv, A., Hegde, S., Ganti, R., Pilizota, T., & Šarić, A. (2020). Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.124.048102","short":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, A. Šarić, Physical Review Letters 124 (2020).","ieee":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, and A. Šarić, “Dynamic clustering regulates activity of mechanosensitive membrane channels,” Physical Review Letters, vol. 124, no. 4. American Physical Society, 2020.","mla":"Paraschiv, Alexandru, et al. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters, vol. 124, no. 4, 048102, American Physical Society, 2020, doi:10.1103/physrevlett.124.048102.","ista":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. 2020. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 124(4), 048102.","chicago":"Paraschiv, Alexandru, Smitha Hegde, Raman Ganti, Teuta Pilizota, and Anđela Šarić. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.124.048102."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"048102","issue":"4","volume":124,"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/553248"}],"scopus_import":"1","intvolume":" 124","month":"01","abstract":[{"text":"Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content.","lang":"eng"}],"pmid":1,"oa_version":"Preprint","date_updated":"2021-11-26T11:21:12Z","extern":"1","type":"journal_article","article_type":"original","keyword":["general physics and astronomy"],"status":"public","_id":"10353"},{"type":"patent","status":"public","_id":"10557","applicant":["Ecole Polytechnique Federale de Lausanne"],"author":[{"last_name":"Ford","full_name":"Ford, Bryan","first_name":"Bryan"},{"full_name":"Gasse, Linus","last_name":"Gasse","first_name":"Linus"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Jovanovic, Philipp","last_name":"Jovanovic","first_name":"Philipp"}],"article_processing_charge":"No","department":[{"_id":"ElKo"}],"title":"Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods","date_updated":"2021-12-21T10:04:50Z","citation":{"mla":"Ford, Bryan, et al. Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods. 2020.","apa":"Ford, B., Gasse, L., Kokoris Kogias, E., & Jovanovic, P. (2020). Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.","ama":"Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. 2020.","short":"B. Ford, L. Gasse, E. Kokoris Kogias, P. Jovanovic, (2020).","ieee":"B. Ford, L. Gasse, E. Kokoris Kogias, and P. Jovanovic, “Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.” 2020.","chicago":"Ford, Bryan, Linus Gasse, Eleftherios Kokoris Kogias, and Philipp Jovanovic. “Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods,” 2020.","ista":"Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. 2020. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods."},"ipn":"10581613","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://patents.google.com/patent/US10581613B2/en","open_access":"1"}],"oa":1,"month":"03","abstract":[{"lang":"eng","text":"Data storage and retrieval systems, methods, and computer-readable media utilize a cryptographically verifiable data structure that facilitates verification of a transaction in a decentralized peer-to-peer environment using multi-hop backwards and forwards links. Backward links are cryptographic hashes of past records. Forward links are cryptographic signatures of future records that are added retroactively to records once the target block has been appended to the data structure."}],"application_date":"2017-06-09","oa_version":"Published Version","publication_date":"2020-03-03","date_published":"2020-03-03T00:00:00Z","related_material":{"link":[{"url":"https://patents.google.com/patent/US20180359096A1/en","relation":"earlier_version"}]},"date_created":"2021-12-16T13:28:59Z","year":"2020","ipc":" H04L9/3247 ; G06Q20/29 ; G06Q20/382 ; H04L9/3236","day":"03"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We acknowledge discussions with J. Checkelsky, S. Chen, C. Dean, M. Yankowitz, D. Reilly, I. Sodemann and M. Zaletel. Work at UCSB was primarily supported by the ARO under MURI W911NF-16-1-0361. Measurements of twisted bilayer graphene (Extended Data Fig. 8) and measurements at elevated temperatures (Extended Data Fig. 3) were supported by a SEED grant and made use of shared facilities of the UCSB MRSEC (NSF DMR 1720256), a member of the Materials Research Facilities Network (www.mrfn.org). A.F.Y. acknowledges the support of the David and Lucille Packard Foundation under award 2016-65145. A.H.M. and J.Z. were supported by the National Science Foundation through the Center for Dynamics and Control of Materials, an NSF MRSEC under Cooperative Agreement number DMR-1720595, and by the Welch Foundation under grant TBF1473. C.L.T. acknowledges support from the Hertz Foundation and from the National Science Foundation Graduate Research Fellowship Program under grant 1650114. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant Number JPMXP0112101001, JSPS KAKENHI grant numbers JP20H00354 and the CREST(JPMJCR15F3), JST.","page":"66-70","doi":"10.1038/s41586-020-2963-8","date_published":"2020-11-23T00:00:00Z","date_created":"2022-01-13T14:12:17Z","year":"2020","day":"23","publication":"Nature","author":[{"last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy"},{"first_name":"J.","last_name":"Zhu","full_name":"Zhu, J."},{"full_name":"Kumar, M. A.","last_name":"Kumar","first_name":"M. A."},{"full_name":"Zhang, Y.","last_name":"Zhang","first_name":"Y."},{"first_name":"F.","full_name":"Yang, F.","last_name":"Yang"},{"full_name":"Tschirhart, C. L.","last_name":"Tschirhart","first_name":"C. L."},{"full_name":"Serlin, M.","last_name":"Serlin","first_name":"M."},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"last_name":"Taniguchi","full_name":"Taniguchi, T.","first_name":"T."},{"first_name":"A. H.","last_name":"MacDonald","full_name":"MacDonald, A. H."},{"first_name":"A. F.","full_name":"Young, A. F.","last_name":"Young"}],"article_processing_charge":"No","external_id":{"arxiv":["2004.11353"],"pmid":["33230333"]},"title":"Electrical switching of magnetic order in an orbital Chern insulator","citation":{"mla":"Polshyn, Hryhoriy, et al. “Electrical Switching of Magnetic Order in an Orbital Chern Insulator.” Nature, vol. 588, no. 7836, Springer Nature, 2020, pp. 66–70, doi:10.1038/s41586-020-2963-8.","apa":"Polshyn, H., Zhu, J., Kumar, M. A., Zhang, Y., Yang, F., Tschirhart, C. L., … Young, A. F. (2020). Electrical switching of magnetic order in an orbital Chern insulator. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2963-8","ama":"Polshyn H, Zhu J, Kumar MA, et al. Electrical switching of magnetic order in an orbital Chern insulator. Nature. 2020;588(7836):66-70. doi:10.1038/s41586-020-2963-8","short":"H. Polshyn, J. Zhu, M.A. Kumar, Y. Zhang, F. Yang, C.L. Tschirhart, M. Serlin, K. Watanabe, T. Taniguchi, A.H. MacDonald, A.F. Young, Nature 588 (2020) 66–70.","ieee":"H. Polshyn et al., “Electrical switching of magnetic order in an orbital Chern insulator,” Nature, vol. 588, no. 7836. Springer Nature, pp. 66–70, 2020.","chicago":"Polshyn, Hryhoriy, J. Zhu, M. A. Kumar, Y. Zhang, F. Yang, C. L. Tschirhart, M. Serlin, et al. “Electrical Switching of Magnetic Order in an Orbital Chern Insulator.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2963-8.","ista":"Polshyn H, Zhu J, Kumar MA, Zhang Y, Yang F, Tschirhart CL, Serlin M, Watanabe K, Taniguchi T, MacDonald AH, Young AF. 2020. Electrical switching of magnetic order in an orbital Chern insulator. Nature. 588(7836), 66–70."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.11353"}],"month":"11","intvolume":" 588","abstract":[{"text":"Magnetism typically arises from the joint effect of Fermi statistics and repulsive Coulomb interactions, which favours ground states with non-zero electron spin. As a result, controlling spin magnetism with electric fields—a longstanding technological goal in spintronics and multiferroics1,2—can be achieved only indirectly. Here we experimentally demonstrate direct electric-field control of magnetic states in an orbital Chern insulator3,4,5,6, a magnetic system in which non-trivial band topology favours long-range order of orbital angular momentum but the spins are thought to remain disordered7,8,9,10,11,12,13,14. We use van der Waals heterostructures consisting of a graphene monolayer rotationally faulted with respect to a Bernal-stacked bilayer to realize narrow and topologically non-trivial valley-projected moiré minibands15,16,17. At fillings of one and three electrons per moiré unit cell within these bands, we observe quantized anomalous Hall effects18 with transverse resistance approximately equal to h/2e2 (where h is Planck’s constant and e is the charge on the electron), which is indicative of spontaneous polarization of the system into a single-valley-projected band with a Chern number equal to two. At a filling of three electrons per moiré unit cell, we find that the sign of the quantum anomalous Hall effect can be reversed via field-effect control of the chemical potential; moreover, this transition is hysteretic, which we use to demonstrate non-volatile electric-field-induced reversal of the magnetic state. A theoretical analysis19 indicates that the effect arises from the topological edge states, which drive a change in sign of the magnetization and thus a reversal in the favoured magnetic state. Voltage control of magnetic states can be used to electrically pattern non-volatile magnetic-domain structures hosting chiral edge states, with applications ranging from reconfigurable microwave circuit elements to ultralow-power magnetic memories.","lang":"eng"}],"pmid":1,"oa_version":"Preprint","volume":588,"issue":"7836","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","keyword":["multidisciplinary"],"_id":"10618","date_updated":"2022-01-13T14:21:04Z","extern":"1"},{"citation":{"ama":"Alexandradinata A, Armitage NP, Baydin A, et al. The future of the correlated electron problem. arXiv.","apa":"Alexandradinata, A., Armitage, N. P., Baydin, A., Bi, W., Cao, Y., Changlani, H. J., … Zong, A. (n.d.). The future of the correlated electron problem. arXiv.","ieee":"A. Alexandradinata et al., “The future of the correlated electron problem,” arXiv. .","short":"A. Alexandradinata, N.P. Armitage, A. Baydin, W. Bi, Y. Cao, H.J. Changlani, E. Chertkov, E.H. da Silva Neto, L. Delacretaz, I. El Baggari, G.M. Ferguson, W.J. Gannon, S.A.A. Ghorashi, B.H. Goodge, O. Goulko, G. Grissonnache, A. Hallas, I.M. Hayes, Y. He, E.W. Huang, A. Kogar, D. Kumah, J.Y. Lee, A. Legros, F. Mahmood, Y. Maximenko, N. Pellatz, H. Polshyn, T. Sarkar, A. Scheie, K.L. Seyler, Z. Shi, B. Skinner, L. Steinke, K. Thirunavukkuarasu, T.V. Trevisan, M. Vogl, P.A. Volkov, Y. Wang, Y. Wang, D. Wei, K. Wei, S. Yang, X. Zhang, Y.-H. Zhang, L. Zhao, A. Zong, ArXiv (n.d.).","mla":"Alexandradinata, A., et al. “The Future of the Correlated Electron Problem.” ArXiv.","ista":"Alexandradinata A, Armitage NP, Baydin A, Bi W, Cao Y, Changlani HJ, Chertkov E, da Silva Neto EH, Delacretaz L, El Baggari I, Ferguson GM, Gannon WJ, Ghorashi SAA, Goodge BH, Goulko O, Grissonnache G, Hallas A, Hayes IM, He Y, Huang EW, Kogar A, Kumah D, Lee JY, Legros A, Mahmood F, Maximenko Y, Pellatz N, Polshyn H, Sarkar T, Scheie A, Seyler KL, Shi Z, Skinner B, Steinke L, Thirunavukkuarasu K, Trevisan TV, Vogl M, Volkov PA, Wang Y, Wang Y, Wei D, Wei K, Yang S, Zhang X, Zhang Y-H, Zhao L, Zong A. The future of the correlated electron problem. arXiv, .","chicago":"Alexandradinata, A, N.P. Armitage, Andrey Baydin, Wenli Bi, Yue Cao, Hitesh J. Changlani, Eli Chertkov, et al. “The Future of the Correlated Electron Problem.” ArXiv, n.d."},"date_updated":"2022-01-24T08:05:51Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","external_id":{"arxiv":["2010.00584"]},"article_processing_charge":"No","author":[{"full_name":"Alexandradinata, A","last_name":"Alexandradinata","first_name":"A"},{"full_name":"Armitage, N.P.","last_name":"Armitage","first_name":"N.P."},{"first_name":"Andrey","last_name":"Baydin","full_name":"Baydin, Andrey"},{"first_name":"Wenli","full_name":"Bi, Wenli","last_name":"Bi"},{"first_name":"Yue","full_name":"Cao, Yue","last_name":"Cao"},{"first_name":"Hitesh J.","last_name":"Changlani","full_name":"Changlani, Hitesh J."},{"first_name":"Eli","full_name":"Chertkov, Eli","last_name":"Chertkov"},{"full_name":"da Silva Neto, Eduardo H.","last_name":"da Silva Neto","first_name":"Eduardo H."},{"last_name":"Delacretaz","full_name":"Delacretaz, Luca","first_name":"Luca"},{"full_name":"El Baggari, Ismail","last_name":"El Baggari","first_name":"Ismail"},{"first_name":"G.M.","full_name":"Ferguson, G.M.","last_name":"Ferguson"},{"first_name":"William J.","last_name":"Gannon","full_name":"Gannon, William J."},{"first_name":"Sayed Ali Akbar","full_name":"Ghorashi, Sayed Ali Akbar","last_name":"Ghorashi"},{"first_name":"Berit H.","full_name":"Goodge, Berit H.","last_name":"Goodge"},{"last_name":"Goulko","full_name":"Goulko, Olga","first_name":"Olga"},{"first_name":"G.","full_name":"Grissonnache, G.","last_name":"Grissonnache"},{"last_name":"Hallas","full_name":"Hallas, Alannah","first_name":"Alannah"},{"first_name":"Ian M.","last_name":"Hayes","full_name":"Hayes, Ian M."},{"last_name":"He","full_name":"He, Yu","first_name":"Yu"},{"first_name":"Edwin W.","last_name":"Huang","full_name":"Huang, Edwin W."},{"first_name":"Anshu","last_name":"Kogar","full_name":"Kogar, Anshu"},{"full_name":"Kumah, Divine","last_name":"Kumah","first_name":"Divine"},{"last_name":"Lee","full_name":"Lee, Jong Yeon","first_name":"Jong Yeon"},{"first_name":"A.","last_name":"Legros","full_name":"Legros, A."},{"first_name":"Fahad","last_name":"Mahmood","full_name":"Mahmood, Fahad"},{"first_name":"Yulia","full_name":"Maximenko, Yulia","last_name":"Maximenko"},{"last_name":"Pellatz","full_name":"Pellatz, Nick","first_name":"Nick"},{"orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy"},{"last_name":"Sarkar","full_name":"Sarkar, Tarapada","first_name":"Tarapada"},{"full_name":"Scheie, Allen","last_name":"Scheie","first_name":"Allen"},{"first_name":"Kyle L.","full_name":"Seyler, Kyle L.","last_name":"Seyler"},{"first_name":"Zhenzhong","last_name":"Shi","full_name":"Shi, Zhenzhong"},{"first_name":"Brian","full_name":"Skinner, Brian","last_name":"Skinner"},{"last_name":"Steinke","full_name":"Steinke, Lucia","first_name":"Lucia"},{"first_name":"K.","full_name":"Thirunavukkuarasu, K.","last_name":"Thirunavukkuarasu"},{"last_name":"Trevisan","full_name":"Trevisan, Thaís Victa","first_name":"Thaís Victa"},{"full_name":"Vogl, Michael","last_name":"Vogl","first_name":"Michael"},{"full_name":"Volkov, Pavel A.","last_name":"Volkov","first_name":"Pavel A."},{"full_name":"Wang, Yao","last_name":"Wang","first_name":"Yao"},{"last_name":"Wang","full_name":"Wang, Yishu","first_name":"Yishu"},{"first_name":"Di","last_name":"Wei","full_name":"Wei, Di"},{"last_name":"Wei","full_name":"Wei, Kaya","first_name":"Kaya"},{"first_name":"Shuolong","last_name":"Yang","full_name":"Yang, Shuolong"},{"first_name":"Xian","full_name":"Zhang, Xian","last_name":"Zhang"},{"full_name":"Zhang, Ya-Hui","last_name":"Zhang","first_name":"Ya-Hui"},{"first_name":"Liuyan","last_name":"Zhao","full_name":"Zhao, Liuyan"},{"full_name":"Zong, Alfred","last_name":"Zong","first_name":"Alfred"}],"title":"The future of the correlated electron problem","_id":"10650","type":"preprint","status":"public","publication_status":"submitted","year":"2020","language":[{"iso":"eng"}],"publication":"arXiv","day":"01","page":"55","date_created":"2022-01-20T10:55:36Z","date_published":"2020-10-01T00:00:00Z","abstract":[{"text":"The understanding of material systems with strong electron-electron interactions is the central problem in modern condensed matter physics. Despite this, the essential physics of many of these materials is still not understood and we have no overall perspective on their properties. Moreover, we have very little ability to make predictions in this class of systems. In this manuscript we share our personal views of what the major open problems are in correlated electron systems and we discuss some possible routes to make progress in this rich and fascinating field. This manuscript is the result of the vigorous discussions and deliberations that took place at Johns Hopkins University during a three-day workshop January 27, 28, and 29, 2020 that brought together six senior scientists and 46 more junior scientists. Our hope, is that the topics we have presented will provide inspiration for others working in this field and motivation for the idea that significant progress can be made on very hard problems if we focus our collective energies.","lang":"eng"}],"acknowledgement":"We thank NSF CMP program for suggestions regarding the topic and general structure of the workshop. This project was supported by the NSF DMR-2002329 and The Gordon and Betty Moore Foundation (GBMF) EPiQS initiative. We would like to sincerely thank A. Kapitulnik, A. J. Leggett, M.B. Maple, T.M. McQueen, M. Norman, P. S. Riseborough, and G. A. Sawatzky for their lectures at the workshop and advice on the writing of this manuscript. We would also like to thank G. Blumberg, C. Broholm, S. Crooker, N. Drichko, and A. Patel for helpful consultation on topics discussed\r\nherein. A number of individuals also had independent support: (AA, EH; GBMF-4305), (IMH; GBMF-9071), (HJC; NHMFL is supported by the NSF DMR-1644779 and the state of Florida), (YH, AZ; Miller Institute for Basic Research in Science), (YC; US DOE-BES DEAC02-06CH11357), (AS; Spallation Neutron Source, a DOE Office of Science User Facility operated by ORNL), (SAAG; ARO-W911NF-18-1-0290, NSF DMR-1455233), (YW; DOE-BES DE-SC0019331, GBMF-4532).","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2010.00584"}],"oa":1,"month":"10"},{"title":"A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits","article_processing_charge":"No","author":[{"first_name":"Ramin","last_name":"Hasani","full_name":"Hasani, Ramin"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","full_name":"Amini, Alexander","last_name":"Amini"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2020. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. Proceedings of the 37th International Conference on Machine Learning. ML: Machine LearningPMLR, PMLR, , 4082–4093.","chicago":"Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu Grosu. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” In Proceedings of the 37th International Conference on Machine Learning, 4082–93. PMLR, 2020.","ama":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In: Proceedings of the 37th International Conference on Machine Learning. PMLR. ; 2020:4082-4093.","apa":"Hasani, R., Lechner, M., Amini, A., Rus, D., & Grosu, R. (2020). A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In Proceedings of the 37th International Conference on Machine Learning (pp. 4082–4093). Virtual.","short":"R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–4093.","ieee":"R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, pp. 4082–4093.","mla":"Hasani, Ramin, et al. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–93."},"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2022-01-25T15:50:34Z","date_published":"2020-01-01T00:00:00Z","page":"4082-4093","publication":"Proceedings of the 37th International Conference on Machine Learning","year":"2020","has_accepted_license":"1","oa":1,"quality_controlled":"1","acknowledgement":"RH and RG are partially supported by Horizon-2020 ECSEL Project grant No. 783163 (iDev40), Productive 4.0, and ATBMBFW CPS-IoT Ecosystem. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award). AA is supported by the National Science Foundation (NSF) Graduate Research Fellowship\r\nProgram. RH and DR are partially supported by The Boeing Company and JP Morgan Chase. This research work is\r\npartially drawn from the PhD dissertation of RH.\r\n","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2022-01-26T11:08:51Z","ddc":["000"],"date_updated":"2022-01-26T11:14:27Z","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"conference":{"start_date":"2020-07-12","end_date":"2020-07-18","location":"Virtual","name":"ML: Machine Learning"},"type":"conference","series_title":"PMLR","_id":"10673","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"c9a4a29161777fc1a89ef451c040e3b1","file_id":"10691","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PMLR_Hasani.pdf","date_created":"2022-01-26T11:08:51Z","creator":"cchlebak","file_size":2329798,"date_updated":"2022-01-26T11:08:51Z"}],"publication_status":"published","publication_identifier":{"issn":["2640-3498"]},"main_file_link":[{"open_access":"1","url":"http://proceedings.mlr.press/v119/hasani20a.html"}],"scopus_import":"1","alternative_title":["PMLR"],"oa_version":"Published Version","abstract":[{"text":"We propose a neural information processing system obtained by re-purposing the function of a biological neural circuit model to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model of biological neural circuits reparameterized for the control of alternative tasks. We first demonstrate that ONCs realize networks with higher maximum flow compared to arbitrary wired networks. We then learn instances of ONCs to control a series of robotic tasks, including the autonomous parking of a real-world rover robot. For reconfiguration of the purpose of the neural circuit, we adopt a search-based optimization algorithm. Ordinary neural circuits perform on par and, in some cases, significantly surpass the performance of contemporary deep learning models. ONC networks are compact, 77% sparser than their counterpart neural controllers, and their neural dynamics are fully interpretable at the cell-level.","lang":"eng"}]},{"abstract":[{"text":"High quality graphene heterostructures host an array of fractional quantum Hall isospin ferromagnets with diverse spin and valley orders. While a variety of phase transitions have been observed, disentangling the isospin phase diagram of these states is hampered by the absence of direct probes of spin and valley order. I will describe nonlocal transport measurements based on launching spin waves from a gate defined lateral heterojunction, performed in ultra-clean Corbino geometry graphene devices. At high magnetic fields, we find that the spin-wave transport signal is detected in all FQH states between ν = 0 and 1; however, between ν = 1 and 2 only odd numerator FQH states show finite nonlocal transport, despite the identical ground state spin polarizations in odd- and even numerator states. The results reveal that the neutral spin-waves are both spin and sublattice polarized making them a sensitive probe of ground state sublattice structure. Armed with this understanding, we use nonlocal transport signal to a magnetic field tuned isospin phase transition, showing that the emergent even denominator state at ν = 1/2 in monolayer graphene is indeed a multicomponent state featuring equal populations on each sublattice.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["Bulletin of the American Physical Society"],"main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR20/Session/B54.7"}],"month":"03","intvolume":" 65","publication_identifier":{"issn":["0003-0503"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":65,"_id":"10693","type":"conference","conference":{"name":"APS: American Physical Society","end_date":"2020-03-06","location":"Denver, CO, United States","start_date":"2020-03-02"},"status":"public","date_updated":"2022-01-27T10:58:38Z","extern":"1","quality_controlled":"1","publisher":"American Physical Society","oa":1,"year":"2020","day":"01","publication":"APS March Meeting 2020","date_published":"2020-03-01T00:00:00Z","date_created":"2022-01-27T10:50:10Z","article_number":"B54. 00007","citation":{"mla":"Zhou, Haoxin, et al. “Sublattice Resolved Spin Wave Transport through Graphene Fractional Quantum Hall States as a Probe of Isospin Order.” APS March Meeting 2020, vol. 65, no. 1, B54. 00007, American Physical Society, 2020.","short":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020.","ieee":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, and A. Young, “Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.","ama":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.","apa":"Zhou, H., Polshyn, H., Tanaguchi, T., Watanabe, K., & Young, A. (2020). Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.","chicago":"Zhou, Haoxin, Hryhoriy Polshyn, Takashi Tanaguchi, Kenji Watanabe, and Andrea Young. “Sublattice Resolved Spin Wave Transport through Graphene Fractional Quantum Hall States as a Probe of Isospin Order.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020.","ista":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. 2020. Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B54. 00007."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Haoxin","full_name":"Zhou, Haoxin","last_name":"Zhou"},{"last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"Takashi","last_name":"Tanaguchi","full_name":"Tanaguchi, Takashi"},{"first_name":"Kenji","full_name":"Watanabe, Kenji","last_name":"Watanabe"},{"full_name":"Young, Andrea","last_name":"Young","first_name":"Andrea"}],"article_processing_charge":"No","title":"Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order"},{"_id":"10698","status":"public","type":"conference","conference":{"name":"APS: American Physical Society","location":"Denver, CO, United States","end_date":"2020-03-06","start_date":"2020-03-02"},"extern":"1","date_updated":"2023-02-21T15:57:52Z","oa_version":"Published Version","abstract":[{"text":"This is the second of three talks describing the observation and characterization of a ferromagnetic moiré heterostructure based on twisted bilayer graphene aligned to hexagonal boron nitride. I will compare the qualitative and quantitative features of this observed quantum anomalous Hall state to traditional systems engineered from thin film (Bi,Sb)2Te3 topological insulators. In particular, we find that the measured electronic energy gap of ~30K is several times higher than the Curie temperature, consistent with a lack of disorder associated with magnetic dopants. In this system, the quantization arises from spontaneous ferromagnetic polarization into a single spin and valley moiré subband, which is topological despite the lack of spin orbit coupling. I will also discuss the observation of current induced switching, which allows the magnetic state of the heterostructure to be controllably reversed with currents as small as a few nanoamperes.","lang":"eng"}],"month":"03","intvolume":" 65","alternative_title":["Bulletin of the American Physical Society"],"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR20/Session/B59.11","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","related_material":{"record":[{"relation":"other","id":"10619","status":"public"}]},"volume":65,"article_number":"B59.00011","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Serlin M, Tschirhart C, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.","apa":"Serlin, M., Tschirhart, C., Polshyn, H., Zhang, Y., Zhu, J., Huber, M. E., … Young, A. (2020). Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.","short":"M. Serlin, C. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, M.E. Huber, L. Balents, K. Watanabe, T. Tanaguchi, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020.","ieee":"M. Serlin et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.","mla":"Serlin, Marec, et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part II: Temperature Dependence and Current Switching.” APS March Meeting 2020, vol. 65, no. 1, B59.00011, American Physical Society, 2020.","ista":"Serlin M, Tschirhart C, Polshyn H, Zhang Y, Zhu J, Huber ME, Balents L, Watanabe K, Tanaguchi T, Young A. 2020. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B59.00011.","chicago":"Serlin, Marec, Charles Tschirhart, Hryhoriy Polshyn, Yuxuan Zhang, Jiacheng Zhu, Martin E. Huber, Leon Balents, Kenji Watanabe, Takashi Tanaguchi, and Andrea Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part II: Temperature Dependence and Current Switching.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020."},"title":"Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching","author":[{"full_name":"Serlin, Marec","last_name":"Serlin","first_name":"Marec"},{"first_name":"Charles","full_name":"Tschirhart, Charles","last_name":"Tschirhart"},{"first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"first_name":"Yuxuan","last_name":"Zhang","full_name":"Zhang, Yuxuan"},{"last_name":"Zhu","full_name":"Zhu, Jiacheng","first_name":"Jiacheng"},{"first_name":"Martin E.","last_name":"Huber","full_name":"Huber, Martin E."},{"first_name":"Leon","last_name":"Balents","full_name":"Balents, Leon"},{"first_name":"Kenji","full_name":"Watanabe, Kenji","last_name":"Watanabe"},{"first_name":"Takashi","last_name":"Tanaguchi","full_name":"Tanaguchi, Takashi"},{"first_name":"Andrea","full_name":"Young, Andrea","last_name":"Young"}],"external_id":{"arxiv":["1907.00261"]},"article_processing_charge":"No","acknowledgement":"I would like to thank the MURI Program, AFOSR, Sloan Foundation, and the ARO for their generous support of this work.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"01","publication":"APS March Meeting 2020","year":"2020","date_published":"2020-03-01T00:00:00Z","date_created":"2022-01-28T10:46:57Z"},{"article_number":"B59.00013","title":"Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry","author":[{"first_name":"Charles","last_name":"Tschirhart","full_name":"Tschirhart, Charles"},{"full_name":"Serlin, Marec","last_name":"Serlin","first_name":"Marec"},{"last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy"},{"full_name":"Zhang, Yuxuan","last_name":"Zhang","first_name":"Yuxuan"},{"last_name":"Zhu","full_name":"Zhu, Jiacheng","first_name":"Jiacheng"},{"first_name":"Leon","full_name":"Balents, Leon","last_name":"Balents"},{"first_name":"Martin E.","full_name":"Huber, Martin E.","last_name":"Huber"},{"full_name":"Watanabe, Kenji","last_name":"Watanabe","first_name":"Kenji"},{"full_name":"Tanaguchi, Takashi","last_name":"Tanaguchi","first_name":"Takashi"},{"first_name":"Andrea","last_name":"Young","full_name":"Young, Andrea"}],"article_processing_charge":"No","external_id":{"arxiv":["1907.00261"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Tschirhart C, Serlin M, Polshyn H, Zhang Y, Zhu J, Balents L, Huber ME, Watanabe K, Tanaguchi T, Young A. 2020. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B59.00013.","chicago":"Tschirhart, Charles, Marec Serlin, Hryhoriy Polshyn, Yuxuan Zhang, Jiacheng Zhu, Leon Balents, Martin E. Huber, Kenji Watanabe, Takashi Tanaguchi, and Andrea Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part III: Scanning Probe Magnetometry.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020.","ieee":"C. Tschirhart et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.","short":"C. Tschirhart, M. Serlin, H. Polshyn, Y. Zhang, J. Zhu, L. Balents, M.E. Huber, K. Watanabe, T. Tanaguchi, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020.","ama":"Tschirhart C, Serlin M, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.","apa":"Tschirhart, C., Serlin, M., Polshyn, H., Zhang, Y., Zhu, J., Balents, L., … Young, A. (2020). Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.","mla":"Tschirhart, Charles, et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part III: Scanning Probe Magnetometry.” APS March Meeting 2020, vol. 65, no. 1, B59.00013, American Physical Society, 2020."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"I would like to thank the MURI program, Sloan foundation, AFOSR, and ARO for their generous support of this work. I would also like to thank the NSF GRFP and the Hertz foundation for their generous support of my graduate studies.","date_published":"2020-03-01T00:00:00Z","date_created":"2022-01-28T10:57:49Z","day":"01","publication":"APS March Meeting 2020","year":"2020","status":"public","type":"conference","conference":{"name":"APS: American Physical Society","location":"Denver, CO, United States","end_date":"2020-03-06","start_date":"2020-03-02"},"_id":"10699","extern":"1","date_updated":"2023-02-21T15:57:52Z","month":"03","intvolume":" 65","alternative_title":["Bulletin of the American Physical Society"],"main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR20/Session/B59.13"}],"oa_version":"Published Version","abstract":[{"text":"This is the third of three talks describing the observation and characterization of a ferromagnetic moiré heterostructure based on twisted bilayer graphene aligned to hexagonal boron nitride. In this segment I will present scanning probe magnetometry data acquired using a nanoSQUID-on-tip microscope, which provides ~150 nm spatial resolution and a field sensitivity of ~10 nT/rtHz. We study the distribution of magnetic domains within the device as a function of density, magnetic field training, and DC current. Our data allow us to constrain the magnitude of the orbital magnetic moment of the electrons in the QAH state. Comparison with simultaneously acquired transport data allows us to precisely correlate single domain dynamics with discrete jumps in the observed anomalous Hall signal.","lang":"eng"}],"volume":65,"related_material":{"record":[{"relation":"other","id":"10619","status":"public"}]},"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-0503"]},"publication_status":"published"},{"main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR20/Session/B59.12"}],"alternative_title":["Bulletin of the American Physical Society"],"intvolume":" 65","month":"03","abstract":[{"text":"We report the observation of a quantized anomalous Hall effect in a moiré heterostructure consisting of twisted bilayer graphene aligned to an encapsulating hBN substrate. The effect occurs at a density of 3 electrons per superlattice unit cell, where we observe magnetic hysteresis and a Hall resistance quantized to within 0.1% of the resistance quantum at temperatures as high as 3K. In this first of 3 talks, I will describe the fabrication procedure for our device as well as basic transport characterization measurements. I will introduce the phenomenology of twisted bilayer graphene and present evidence for hBN alignment as manifested in the hierarchy of symmetry-breaking gaps and anomalous magnetoresistance.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"other","id":"10619","status":"public"}]},"volume":65,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"conference":{"name":"APS: American Physical Society","start_date":"2020-03-02","location":"Denver, CO, United States","end_date":"2020-03-06"},"type":"conference","status":"public","_id":"10697","date_updated":"2023-02-21T15:57:52Z","extern":"1","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"I would like to thank the MURI program, Sloan foundation, AFOSR, and ARO for their generous support of this work.","date_created":"2022-01-28T10:28:35Z","date_published":"2020-03-01T00:00:00Z","year":"2020","publication":"APS March Meeting 2020","day":"01","article_number":"B59.00012","external_id":{"arxiv":["1907.00261"]},"article_processing_charge":"No","author":[{"full_name":"Zhang, Yuxuan","last_name":"Zhang","first_name":"Yuxuan"},{"full_name":"Serlin, Marec","last_name":"Serlin","first_name":"Marec"},{"last_name":"Tschirhart","full_name":"Tschirhart, Charles","first_name":"Charles"},{"first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn"},{"last_name":"Zhu","full_name":"Zhu, Jiacheng","first_name":"Jiacheng"},{"full_name":"Balents, Leon","last_name":"Balents","first_name":"Leon"},{"first_name":"Martin E.","last_name":"Huber","full_name":"Huber, Martin E."},{"last_name":"Taniguchi","full_name":"Taniguchi, Takashi","first_name":"Takashi"},{"last_name":"Watanabe","full_name":"Watanabe, Kenji","first_name":"Kenji"},{"first_name":"Andrea","full_name":"Young, Andrea","last_name":"Young"}],"title":"Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport","citation":{"mla":"Zhang, Yuxuan, et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part I: Device Fabrication and Transport.” APS March Meeting 2020, vol. 65, no. 1, B59.00012, American Physical Society, 2020.","apa":"Zhang, Y., Serlin, M., Tschirhart, C., Polshyn, H., Zhu, J., Balents, L., … Young, A. (2020). Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.","ama":"Zhang Y, Serlin M, Tschirhart C, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.","short":"Y. Zhang, M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, L. Balents, M.E. Huber, T. Taniguchi, K. Watanabe, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020.","ieee":"Y. Zhang et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.","chicago":"Zhang, Yuxuan, Marec Serlin, Charles Tschirhart, Hryhoriy Polshyn, Jiacheng Zhu, Leon Balents, Martin E. Huber, Takashi Taniguchi, Kenji Watanabe, and Andrea Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part I: Device Fabrication and Transport.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020.","ista":"Zhang Y, Serlin M, Tschirhart C, Polshyn H, Zhu J, Balents L, Huber ME, Taniguchi T, Watanabe K, Young A. 2020. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B59.00012."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"_id":"10696","status":"public","conference":{"name":"APS: American Physical Society","start_date":"2020-03-02","end_date":"2020-03-06","location":"Denver, CO, United States"},"type":"conference","extern":"1","date_updated":"2022-02-08T10:22:08Z","oa_version":"Published Version","abstract":[{"text":"We experimentally investigate twisted van der Waals heterostructures of monolayer graphene rotated with respect to a bernal stacked graphene bilayer. We report transport measurements for devices with twist angles between 0.9 and 1.4°. The electric field allows efficient tuning of the width, isolation and the topology of the moiré bands in this system. By comparing magnetoresistance measurements to numerical simulations, we develop an understanding of the band structure. Finally, we observe correlated states at half- and quarter-fillings, which arise when narrow moire sublattice band is isolated by energy gaps from dispersive bands. We investigate the effects of in-plane and out-of-plane magnetic field on these states and discuss the implication for their spin- and valley- polarization.","lang":"eng"}],"intvolume":" 65","month":"03","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR20/Session/B51.5"}],"alternative_title":["Bulletin of the American Physical Society"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0003-0503"]},"issue":"1","volume":65,"article_number":"B51.00005","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Polshyn, Hryhoriy, et al. “Correlated States and Tunable Topological Bands in Twisted Monolayer-Bilayer Graphene Heterostructures.” APS March Meeting 2020, vol. 65, no. 1, B51.00005, American Physical Society, 2020.","apa":"Polshyn, H., Zhu, J., Kumar, M., Taniguchi, T., Watanabe, K., MacDonald, A., & Young, A. (2020). Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.","ama":"Polshyn H, Zhu J, Kumar M, et al. Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.","ieee":"H. Polshyn et al., “Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.","short":"H. Polshyn, J. Zhu, M. Kumar, T. Taniguchi, K. Watanabe, A. MacDonald, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020.","chicago":"Polshyn, Hryhoriy, Jihang Zhu, Manish Kumar, Takashi Taniguchi, Kenji Watanabe, Allan MacDonald, and Andrea Young. “Correlated States and Tunable Topological Bands in Twisted Monolayer-Bilayer Graphene Heterostructures.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020.","ista":"Polshyn H, Zhu J, Kumar M, Taniguchi T, Watanabe K, MacDonald A, Young A. 2020. Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B51.00005."},"title":"Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures","article_processing_charge":"No","author":[{"first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"last_name":"Zhu","full_name":"Zhu, Jihang","first_name":"Jihang"},{"full_name":"Kumar, Manish","last_name":"Kumar","first_name":"Manish"},{"first_name":"Takashi","last_name":"Taniguchi","full_name":"Taniguchi, Takashi"},{"first_name":"Kenji","full_name":"Watanabe, Kenji","last_name":"Watanabe"},{"first_name":"Allan","last_name":"MacDonald","full_name":"MacDonald, Allan"},{"first_name":"Andrea","full_name":"Young, Andrea","last_name":"Young"}],"oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"APS March Meeting 2020","day":"01","year":"2020","date_created":"2022-01-28T10:09:19Z","date_published":"2020-03-01T00:00:00Z"},{"acknowledgement":"We acknowledge discussions with B. Halperin, C. Huang, A. Macdonald and M. Zalatel. Experimental work at UCSB was supported by the Army Research Office under awards nos. MURI W911NF-16-1-0361 and W911NF-16-1-0482. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by MEXT (Japan) and CREST (JPMJCR15F3), JST. A.F.Y. acknowledges the support of the David and Lucile Packard Foundation and and Alfred. P. Sloan Foundation.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"year":"2020","day":"01","publication":"Nature Physics","page":"154-158","date_published":"2020-02-01T00:00:00Z","doi":"10.1038/s41567-019-0729-8","date_created":"2022-01-28T12:04:09Z","citation":{"apa":"Zhou, H., Polshyn, H., Taniguchi, T., Watanabe, K., & Young, A. F. (2020). Skyrmion solids in monolayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0729-8","ama":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. Skyrmion solids in monolayer graphene. Nature Physics. 2020;16(2):154-158. doi:10.1038/s41567-019-0729-8","ieee":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young, “Skyrmion solids in monolayer graphene,” Nature Physics, vol. 16, no. 2. Springer Nature, pp. 154–158, 2020.","short":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, A.F. Young, Nature Physics 16 (2020) 154–158.","mla":"Zhou, Haoxin, et al. “Skyrmion Solids in Monolayer Graphene.” Nature Physics, vol. 16, no. 2, Springer Nature, 2020, pp. 154–58, doi:10.1038/s41567-019-0729-8.","ista":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. 2020. Skyrmion solids in monolayer graphene. Nature Physics. 16(2), 154–158.","chicago":"Zhou, Haoxin, Hryhoriy Polshyn, Takashi Taniguchi, Kenji Watanabe, and Andrea F. Young. “Skyrmion Solids in Monolayer Graphene.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-019-0729-8."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Zhou","full_name":"Zhou, Haoxin","first_name":"Haoxin"},{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"first_name":"Takashi","full_name":"Taniguchi, Takashi","last_name":"Taniguchi"},{"last_name":"Watanabe","full_name":"Watanabe, Kenji","first_name":"Kenji"},{"first_name":"Andrea F.","full_name":"Young, Andrea F.","last_name":"Young"}],"external_id":{"arxiv":["1904.11485"]},"article_processing_charge":"No","title":"Skyrmion solids in monolayer graphene","abstract":[{"text":"Partially filled Landau levels host competing electronic orders. For example, electron solids may prevail close to integer filling of the Landau levels before giving way to fractional quantum Hall liquids at higher carrier density1,2. Here, we report the observation of an electron solid with non-collinear spin texture in monolayer graphene, consistent with solidification of skyrmions3—topological spin textures characterized by quantized electrical charge4,5. We probe the spin texture of the solids using a modified Corbino geometry that allows ferromagnetic magnons to be launched and detected6,7. We find that magnon transport is highly efficient when one Landau level is filled (ν=1), consistent with quantum Hall ferromagnetic spin polarization. However, even minimal doping immediately quenches the magnon signal while leaving the vanishing low-temperature charge conductivity unchanged. Our results can be understood by the formation of a solid of charged skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay. Data near fractional fillings show evidence of several fractional skyrmion solids, suggesting that graphene hosts a highly tunable landscape of coupled spin and charge orders.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.11485"}],"month":"02","intvolume":" 16","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":16,"_id":"10701","article_type":"original","type":"journal_article","status":"public","date_updated":"2022-01-31T07:10:07Z","extern":"1"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","publication":"Advanced Biosystems","day":"01","year":"2020","has_accepted_license":"1","date_created":"2022-04-07T07:43:57Z","doi":"10.1002/adbi.202000044","date_published":"2020-05-01T00:00:00Z","article_number":"2000044","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev, and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” Advanced Biosystems. Wiley, 2020. https://doi.org/10.1002/adbi.202000044.","ista":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 4(5), 2000044.","mla":"Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” Advanced Biosystems, vol. 4, no. 5, 2000044, Wiley, 2020, doi:10.1002/adbi.202000044.","ama":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 2020;4(5). doi:10.1002/adbi.202000044","apa":"Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., & Hetzer, M. (2020). Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. Wiley. https://doi.org/10.1002/adbi.202000044","short":"S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced Biosystems 4 (2020).","ieee":"S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease,” Advanced Biosystems, vol. 4, no. 5. Wiley, 2020."},"title":"Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease","external_id":{"pmid":["32402127"]},"article_processing_charge":"No","author":[{"first_name":"Simone","last_name":"Bersini","full_name":"Bersini, Simone"},{"last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael","first_name":"Rafael"},{"last_name":"Huang","full_name":"Huang, Ling","first_name":"Ling"},{"first_name":"Maxim N.","full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established."}],"intvolume":" 4","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2020_AdvancedBiosystems_Bersini.pdf","date_created":"2022-04-08T07:06:05Z","file_size":2490829,"date_updated":"2022-04-08T07:06:05Z","creator":"dernst","success":1,"file_id":"11134","checksum":"5584d9a1609812dc75c02ce1e35d2ec0","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["2366-7478","2366-7478"]},"volume":4,"issue":"5","_id":"11056","keyword":["General Biochemistry","Genetics and Molecular Biology","Biomedical Engineering","Biomaterials"],"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","ddc":["570"],"extern":"1","date_updated":"2022-07-18T08:30:48Z","file_date_updated":"2022-04-08T07:06:05Z"},{"date_updated":"2022-07-18T08:30:37Z","ddc":["570"],"extern":"1","file_date_updated":"2022-04-08T06:53:10Z","_id":"11055","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","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"11132","checksum":"f8b3821349a194050be02570d8fe7d4b","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_eLife_Bersini.pdf","date_created":"2022-04-08T06:53:10Z","file_size":4399825,"date_updated":"2022-04-08T06:53:10Z","creator":"dernst"}],"volume":9,"abstract":[{"lang":"eng","text":"Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 9","month":"09","citation":{"mla":"Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” ELife, vol. 9, e54383, eLife Sciences Publications, 2020, doi:10.7554/elife.54383.","apa":"Bersini, S., Schulte, R., Huang, L., Tsai, H., & Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.54383","ama":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 2020;9. doi:10.7554/elife.54383","short":"S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).","ieee":"S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” eLife, vol. 9. eLife Sciences Publications, 2020.","chicago":"Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.54383.","ista":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","external_id":{"pmid":["32896271"]},"article_processing_charge":"No","author":[{"full_name":"Bersini, Simone","last_name":"Bersini","first_name":"Simone"},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"first_name":"Ling","last_name":"Huang","full_name":"Huang, Ling"},{"first_name":"Hannah","full_name":"Tsai, Hannah","last_name":"Tsai"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"title":"Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome","article_number":"e54383","year":"2020","has_accepted_license":"1","publication":"eLife","day":"08","date_created":"2022-04-07T07:43:48Z","date_published":"2020-09-08T00:00:00Z","doi":"10.7554/elife.54383","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications"},{"day":"17","publication":"Neuron","year":"2020","date_published":"2020-06-17T00:00:00Z","doi":"10.1016/j.neuron.2020.05.031","date_created":"2022-04-07T07:43:36Z","page":"899-911","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.031.","ista":"Cho UH, Hetzer M. 2020. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. 106(6), 899–911.","mla":"Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” Neuron, vol. 106, no. 6, Elsevier, 2020, pp. 899–911, doi:10.1016/j.neuron.2020.05.031.","apa":"Cho, U. H., & Hetzer, M. (2020). Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.05.031","ama":"Cho UH, Hetzer M. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. 2020;106(6):899-911. doi:10.1016/j.neuron.2020.05.031","short":"U.H. Cho, M. Hetzer, Neuron 106 (2020) 899–911.","ieee":"U. H. Cho and M. Hetzer, “Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging,” Neuron, vol. 106, no. 6. Elsevier, pp. 899–911, 2020."},"title":"Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging","author":[{"full_name":"Cho, Ukrae H.","last_name":"Cho","first_name":"Ukrae H."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"external_id":{"pmid":["32553207"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","issue":"6","volume":106,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging.","lang":"eng"}],"month":"06","intvolume":" 106","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.05.031","open_access":"1"}],"extern":"1","date_updated":"2022-07-18T08:29:35Z","_id":"11054","status":"public","keyword":["General Neuroscience"],"article_type":"review","type":"journal_article"},{"oa":1,"publisher":"Cold Spring Harbor Laboratory Press","quality_controlled":"1","page":"913-930","date_created":"2022-04-07T07:44:09Z","doi":"10.1101/gad.335794.119","date_published":"2020-04-28T00:00:00Z","year":"2020","has_accepted_license":"1","publication":"Genes & Development","day":"28","external_id":{"pmid":["32499403"]},"article_processing_charge":"No","author":[{"first_name":"Hyeseon","last_name":"Kang","full_name":"Kang, Hyeseon"},{"full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev","first_name":"Maxim N."},{"first_name":"Zhichao","last_name":"Xu","full_name":"Xu, Zhichao"},{"first_name":"Sahaana","last_name":"Chandran","full_name":"Chandran, Sahaana"},{"last_name":"Dixon","full_name":"Dixon, Jesse R.","first_name":"Jesse R."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"title":"Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation","citation":{"chicago":"Kang, Hyeseon, Maxim N. Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse R. Dixon, and Martin Hetzer. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” Genes & Development. Cold Spring Harbor Laboratory Press, 2020. https://doi.org/10.1101/gad.335794.119.","ista":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. 2020. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes & Development. 34(13–14), 913–930.","mla":"Kang, Hyeseon, et al. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” Genes & Development, vol. 34, no. 13–14, Cold Spring Harbor Laboratory Press, 2020, pp. 913–30, doi:10.1101/gad.335794.119.","short":"H. Kang, M.N. Shokhirev, Z. Xu, S. Chandran, J.R. Dixon, M. Hetzer, Genes & Development 34 (2020) 913–930.","ieee":"H. Kang, M. N. Shokhirev, Z. Xu, S. Chandran, J. R. Dixon, and M. Hetzer, “Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation,” Genes & Development, vol. 34, no. 13–14. Cold Spring Harbor Laboratory Press, pp. 913–930, 2020.","apa":"Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., & Hetzer, M. (2020). Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes & Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.335794.119","ama":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes & Development. 2020;34(13-14):913-930. doi:10.1101/gad.335794.119"},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","scopus_import":"1","intvolume":" 34","month":"04","abstract":[{"text":"During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":34,"issue":"13-14","publication_status":"published","publication_identifier":{"issn":["0890-9369","1549-5477"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"84e92d40e67936c739628315c238daf9","file_id":"11136","success":1,"creator":"dernst","date_updated":"2022-04-08T07:12:33Z","file_size":4406772,"date_created":"2022-04-08T07:12:33Z","file_name":"2020_GenesDevelopment_Kang.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)"},"article_type":"original","type":"journal_article","keyword":["Developmental Biology","Genetics"],"status":"public","_id":"11057","file_date_updated":"2022-04-08T07:12:33Z","date_updated":"2022-07-18T08:31:08Z","ddc":["570"],"extern":"1"},{"author":[{"first_name":"Simone","last_name":"Bersini","full_name":"Bersini, Simone"},{"full_name":"Lytle, Nikki K","last_name":"Lytle","first_name":"Nikki K"},{"full_name":"Schulte, Roberta","last_name":"Schulte","first_name":"Roberta"},{"first_name":"Ling","full_name":"Huang, Ling","last_name":"Huang"},{"first_name":"Geoffrey M","last_name":"Wahl","full_name":"Wahl, Geoffrey M"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"external_id":{"pmid":["31959624"]},"article_processing_charge":"No","title":"Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling","citation":{"mla":"Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” Life Science Alliance, vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:10.26508/lsa.201900623.","ama":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 2020;3(1). doi:10.26508/lsa.201900623","apa":"Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., & Hetzer, M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. Life Science Alliance. https://doi.org/10.26508/lsa.201900623","short":"S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life Science Alliance 3 (2020).","ieee":"S. Bersini, N. K. Lytle, R. Schulte, L. Huang, G. M. Wahl, and M. Hetzer, “Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling,” Life Science Alliance, vol. 3, no. 1. Life Science Alliance, 2020.","chicago":"Bersini, Simone, Nikki K Lytle, Roberta Schulte, Ling Huang, Geoffrey M Wahl, and Martin Hetzer. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” Life Science Alliance. Life Science Alliance, 2020. https://doi.org/10.26508/lsa.201900623.","ista":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. 2020. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 3(1), e201900623."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_number":"e201900623","date_published":"2020-01-01T00:00:00Z","doi":"10.26508/lsa.201900623","date_created":"2022-04-07T07:44:18Z","has_accepted_license":"1","year":"2020","day":"01","publication":"Life Science Alliance","quality_controlled":"1","publisher":"Life Science Alliance","oa":1,"file_date_updated":"2022-04-08T07:33:01Z","date_updated":"2022-07-18T08:31:20Z","extern":"1","ddc":["570"],"article_type":"original","type":"journal_article","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)"},"status":"public","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"_id":"11058","volume":3,"issue":"1","publication_identifier":{"issn":["2575-1077"]},"publication_status":"published","file":[{"date_created":"2022-04-08T07:33:01Z","file_name":"2020_LifeScienceAlliance_Bersini.pdf","date_updated":"2022-04-08T07:33:01Z","file_size":2653960,"creator":"dernst","checksum":"3bf33e7e93bef7823287807206b69b38","file_id":"11137","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 3","abstract":[{"text":"Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis.","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"volume":638,"publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2003.12083","open_access":"1"}],"scopus_import":"1","intvolume":" 638","month":"06","abstract":[{"text":"Context. The Lyα emitter (LAE) fraction, XLAE, is a potentially powerful probe of the evolution of the intergalactic neutral hydrogen gas fraction. However, uncertainties in the measurement of XLAE are still under debate.\r\nAims. Thanks to deep data obtained with the integral field spectrograph Multi Unit Spectroscopic Explorer (MUSE), we can measure the evolution of the LAE fraction homogeneously over a wide redshift range of z ≈ 3–6 for UV-faint galaxies (down to UV magnitudes of M1500 ≈ −17.75). This is a significantly fainter range than in former studies (M1500 ≤ −18.75) and it allows us to probe the bulk of the population of high-redshift star-forming galaxies.\r\nMethods. We constructed a UV-complete photometric-redshift sample following UV luminosity functions and measured the Lyα emission with MUSE using the latest (second) data release from the MUSE Hubble Ultra Deep Field Survey.\r\nResults. We derived the redshift evolution of XLAE for M1500 ∈ [ − 21.75; −17.75] for the first time with a equivalent width range EW(Lyα) ≥ 65 Å and found low values of XLAE ≲ 30% at z ≲ 6. The best-fit linear relation is XLAE = 0.07+0.06−0.03z − 0.22+0.12−0.24. For M1500 ∈ [ − 20.25; −18.75] and EW(Lyα) ≥ 25 Å, our XLAE values are consistent with those in the literature within 1σ at z ≲ 5, but our median values are systematically lower than reported values over the whole redshift range. In addition, we do not find a significant dependence of XLAE on M1500 for EW(Lyα) ≥ 50 Å at z ≈ 3–4, in contrast with previous work. The differences in XLAE mainly arise from selection biases for Lyman Break Galaxies (LBGs) in the literature: UV-faint LBGs are more easily selected if they have strong Lyα emission, hence XLAE is biased towards higher values when those samples are used.\r\nConclusions. Our results suggest either a lower increase of XLAE towards z ≈ 6 than previously suggested, or even a turnover of XLAE at z ≈ 5.5, which may be the signature of a late or patchy reionization process. We compared our results with predictions from a cosmological galaxy evolution model. We find that a model with a bursty star formation (SF) can reproduce our observed LAE fractions much better than models where SF is a smooth function of time.","lang":"eng"}],"oa_version":"Published Version","date_updated":"2022-07-19T09:35:20Z","extern":"1","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","dark ages / reionization / first stars / early Universe / cosmology: observations / galaxies: evolution / galaxies: high-redshift / intergalactic medium"],"status":"public","_id":"11503","date_created":"2022-07-06T09:50:48Z","doi":"10.1051/0004-6361/201937340","date_published":"2020-06-03T00:00:00Z","year":"2020","publication":"Astronomy & Astrophysics","day":"03","oa":1,"quality_controlled":"1","publisher":"EDP Sciences","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions. We would like to express our gratitude to Stephane De Barros and Pablo Arrabal Haro for kindly providing their data plotted in Figs. 1, 2, and 8. We are grateful to Kazuhiro Shimasaku, Masami Ouchi, Rieko Momose, Daniel Schaerer, Hidenobu Yajima, Taku Okamura, Makoto Ando, and Hinako Goto for giving insightful comments and suggestions. This work is based on observations taken by VLT, which is operated by European Southern Observatory. This research made use of Astropy (http://www.astropy.org), which is a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018), MARZ, MPDAF, and matplotlib (Hunter 2007). H.K. acknowledges support from Japan Society for the Promotion of Science (JSPS) through the JSPS Research Fellowship for Young Scientists and Overseas Challenge Program for Young Researchers. AV acknowledges support from the ERC starting grant 757258-TRIPLE and the SNF Professorship 176808-TRIPLE. This work was supported by the project FOGHAR (Agence Nationale de la Recherche, ANR-13-BS05-0010-02). JB acknowledges support from the ORAGE project from the Agence Nationale de la Recherche under grant ANR-14-CE33-0016-03. JR acknowledges support from the ERC starting grant 336736-CALENDS. T. H. acknowledges supports by the Grant-inAid for Scientic Research 19J01620.","external_id":{"arxiv":["2003.12083"]},"article_processing_charge":"No","author":[{"first_name":"Haruka","full_name":"Kusakabe, Haruka","last_name":"Kusakabe"},{"first_name":"Jérémy","full_name":"Blaizot, Jérémy","last_name":"Blaizot"},{"first_name":"Thibault","full_name":"Garel, Thibault","last_name":"Garel"},{"last_name":"Verhamme","full_name":"Verhamme, Anne","first_name":"Anne"},{"last_name":"Bacon","full_name":"Bacon, Roland","first_name":"Roland"},{"first_name":"Johan","full_name":"Richard, Johan","last_name":"Richard"},{"last_name":"Hashimoto","full_name":"Hashimoto, Takuya","first_name":"Takuya"},{"full_name":"Inami, Hanae","last_name":"Inami","first_name":"Hanae"},{"first_name":"Simon","last_name":"Conseil","full_name":"Conseil, Simon"},{"first_name":"Bruno","full_name":"Guiderdoni, Bruno","last_name":"Guiderdoni"},{"full_name":"Drake, Alyssa B.","last_name":"Drake","first_name":"Alyssa B."},{"last_name":"Christian Herenz","full_name":"Christian Herenz, Edmund","first_name":"Edmund"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"first_name":"Pascal","full_name":"Oesch, Pascal","last_name":"Oesch"},{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Anna Marino, Raffaella","last_name":"Anna Marino","first_name":"Raffaella"},{"first_name":"Kasper","full_name":"Borello Schmidt, Kasper","last_name":"Borello Schmidt"},{"last_name":"Pelló","full_name":"Pelló, Roser","first_name":"Roser"},{"first_name":"Michael","last_name":"Maseda","full_name":"Maseda, Michael"},{"full_name":"Leclercq, Floriane","last_name":"Leclercq","first_name":"Floriane"},{"full_name":"Kerutt, Josephine","last_name":"Kerutt","first_name":"Josephine"},{"first_name":"Guillaume","last_name":"Mahler","full_name":"Mahler, Guillaume"}],"title":"The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6","citation":{"short":"H. Kusakabe, J. Blaizot, T. Garel, A. Verhamme, R. Bacon, J. Richard, T. Hashimoto, H. Inami, S. Conseil, B. Guiderdoni, A.B. Drake, E. Christian Herenz, J. Schaye, P. Oesch, J.J. Matthee, R. Anna Marino, K. Borello Schmidt, R. Pelló, M. Maseda, F. Leclercq, J. Kerutt, G. Mahler, Astronomy & Astrophysics 638 (2020).","ieee":"H. Kusakabe et al., “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6,” Astronomy & Astrophysics, vol. 638. EDP Sciences, 2020.","apa":"Kusakabe, H., Blaizot, J., Garel, T., Verhamme, A., Bacon, R., Richard, J., … Mahler, G. (2020). The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201937340","ama":"Kusakabe H, Blaizot J, Garel T, et al. The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics. 2020;638. doi:10.1051/0004-6361/201937340","mla":"Kusakabe, Haruka, et al. “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα Emitter Fraction from z = 3 to z = 6.” Astronomy & Astrophysics, vol. 638, A12, EDP Sciences, 2020, doi:10.1051/0004-6361/201937340.","ista":"Kusakabe H, Blaizot J, Garel T, Verhamme A, Bacon R, Richard J, Hashimoto T, Inami H, Conseil S, Guiderdoni B, Drake AB, Christian Herenz E, Schaye J, Oesch P, Matthee JJ, Anna Marino R, Borello Schmidt K, Pelló R, Maseda M, Leclercq F, Kerutt J, Mahler G. 2020. The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics. 638, A12.","chicago":"Kusakabe, Haruka, Jérémy Blaizot, Thibault Garel, Anne Verhamme, Roland Bacon, Johan Richard, Takuya Hashimoto, et al. “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα Emitter Fraction from z = 3 to z = 6.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201937340."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A12"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations"],"status":"public","article_type":"original","type":"journal_article","_id":"11504","extern":"1","date_updated":"2022-07-19T09:36:58Z","intvolume":" 635","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/2002.05731","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present spatially resolved maps of six individually-detected Lyman α haloes (LAHs) as well as a first statistical analysis of the Lyman α (Lyα) spectral signature in the circum-galactic medium of high-redshift star-forming galaxies (−17.5 > MUV > −21.5) using the Multi-Unit Spectroscopic Explorer. Our resolved spectroscopic analysis of the LAHs reveals significant intrahalo variations of the Lyα line profile. Using a three-dimensional two-component model for the Lyα emission, we measured the full width at half maximum (FWHM), the peak velocity shift, and the asymmetry of the Lyα line in the core and in the halo of 19 galaxies. We find that the Lyα line shape is statistically different in the halo compared to the core (in terms of width, peak wavelength, and asymmetry) for ≈40% of our galaxies. Similarly to object-by-object based studies and a recent resolved study using lensing, we find a correlation between the peak velocity shift and the width of the Lyα line both at the interstellar and circum-galactic scales. This trend has been predicted by radiative transfer simulations of galactic winds as a result of resonant scattering in outflows. While there is a lack of correlation between the spectral properties and the spatial scale lengths of our LAHs, we find a correlation between the width of the line in the LAH and the halo flux fraction. Interestingly, UV bright galaxies (MUV < −20) show broader, more redshifted, and less asymmetric Lyα lines in their haloes. The most significant correlation found is for the FWHM of the line and the UV continuum slope of the galaxy, suggesting that the redder galaxies have broader Lyα lines. The generally broad and red line shapes found in the halo component suggest that the Lyα haloes are powered either by scattering processes through an outflowing medium, fluorescent emission from outflowing cold clumps of gas, or a mix of both. Considering the large diversity of the Lyα line profiles observed in our sample and the lack of strong correlation, the interpretation of our results is still broadly open and underlines the need for realistic spatially resolved models of the LAHs.","lang":"eng"}],"volume":635,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"article_number":"A82","title":"The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3","external_id":{"arxiv":["2002.05731"]},"article_processing_charge":"No","author":[{"full_name":"Leclercq, Floriane","last_name":"Leclercq","first_name":"Floriane"},{"last_name":"Bacon","full_name":"Bacon, Roland","first_name":"Roland"},{"full_name":"Verhamme, Anne","last_name":"Verhamme","first_name":"Anne"},{"full_name":"Garel, Thibault","last_name":"Garel","first_name":"Thibault"},{"first_name":"Jérémy","last_name":"Blaizot","full_name":"Blaizot, Jérémy"},{"full_name":"Brinchmann, Jarle","last_name":"Brinchmann","first_name":"Jarle"},{"full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo","first_name":"Sebastiano"},{"full_name":"Claeyssens, Adélaïde","last_name":"Claeyssens","first_name":"Adélaïde"},{"full_name":"Conseil, Simon","last_name":"Conseil","first_name":"Simon"},{"last_name":"Contini","full_name":"Contini, Thierry","first_name":"Thierry"},{"first_name":"Takuya","last_name":"Hashimoto","full_name":"Hashimoto, Takuya"},{"first_name":"Edmund Christian","full_name":"Herenz, Edmund Christian","last_name":"Herenz"},{"first_name":"Haruka","last_name":"Kusakabe","full_name":"Kusakabe, Haruka"},{"first_name":"Raffaella Anna","last_name":"Marino","full_name":"Marino, Raffaella Anna"},{"full_name":"Maseda, Michael","last_name":"Maseda","first_name":"Michael"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"first_name":"Peter","last_name":"Mitchell","full_name":"Mitchell, Peter"},{"full_name":"Pezzulli, Gabriele","last_name":"Pezzulli","first_name":"Gabriele"},{"first_name":"Johan","last_name":"Richard","full_name":"Richard, Johan"},{"first_name":"Kasper Borello","last_name":"Schmidt","full_name":"Schmidt, Kasper Borello"},{"first_name":"Lutz","full_name":"Wisotzki, Lutz","last_name":"Wisotzki"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Leclercq, Floriane, et al. “The MUSE Hubble Ultra Deep Field Survey: XIII. Spatially Resolved Spectral Properties of Lyman α Haloes around Star-Forming Galaxies at z > 3.” Astronomy & Astrophysics, vol. 635, A82, EDP Sciences, 2020, doi:10.1051/0004-6361/201937339.","short":"F. Leclercq, R. Bacon, A. Verhamme, T. Garel, J. Blaizot, J. Brinchmann, S. Cantalupo, A. Claeyssens, S. Conseil, T. Contini, T. Hashimoto, E.C. Herenz, H. Kusakabe, R.A. Marino, M. Maseda, J.J. Matthee, P. Mitchell, G. Pezzulli, J. Richard, K.B. Schmidt, L. Wisotzki, Astronomy & Astrophysics 635 (2020).","ieee":"F. Leclercq et al., “The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3,” Astronomy & Astrophysics, vol. 635. EDP Sciences, 2020.","ama":"Leclercq F, Bacon R, Verhamme A, et al. The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3. Astronomy & Astrophysics. 2020;635. doi:10.1051/0004-6361/201937339","apa":"Leclercq, F., Bacon, R., Verhamme, A., Garel, T., Blaizot, J., Brinchmann, J., … Wisotzki, L. (2020). The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201937339","chicago":"Leclercq, Floriane, Roland Bacon, Anne Verhamme, Thibault Garel, Jérémy Blaizot, Jarle Brinchmann, Sebastiano Cantalupo, et al. “The MUSE Hubble Ultra Deep Field Survey: XIII. Spatially Resolved Spectral Properties of Lyman α Haloes around Star-Forming Galaxies at z > 3.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201937339.","ista":"Leclercq F, Bacon R, Verhamme A, Garel T, Blaizot J, Brinchmann J, Cantalupo S, Claeyssens A, Conseil S, Contini T, Hashimoto T, Herenz EC, Kusakabe H, Marino RA, Maseda M, Matthee JJ, Mitchell P, Pezzulli G, Richard J, Schmidt KB, Wisotzki L. 2020. The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3. Astronomy & Astrophysics. 635, A82."},"oa":1,"publisher":"EDP Sciences","quality_controlled":"1","acknowledgement":"F.L., R.B., and S.C. acknowledge support from the ERC advanced grant 339659-MUSICOS. F.L., T.G., H.K., and A.V. acknowledge support from the ERC starting grant ERC-757258-TRIPLE. A.C. and J.R. acknowledge support from the ERC starting grant 336736-CALENDS. J.B. acknowledges support by FCT/MCTES through national funds (PID-DAC) by grant UID/FIS/04434/2019 and through Investigador FCT Contract No.IF/01654/2014/CP1215/CT0003. T.H. was supported by Leading Initiative for Excellent Young Researchers, MEXT, Japan.","date_created":"2022-07-06T09:56:20Z","doi":"10.1051/0004-6361/201937339","date_published":"2020-03-11T00:00:00Z","publication":"Astronomy & Astrophysics","day":"11","year":"2020"},{"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":641,"abstract":[{"text":"We investigated the ultraviolet (UV) spectral properties of faint Lyman-α emitters (LAEs) in the redshift range 2.9 ≤ z ≤ 4.6, and we provide material to prepare future observations of the faint Universe. We used data from the MUSE Hubble Ultra Deep Survey to construct mean rest-frame spectra of continuum-faint (median MUV of −18 and down to MUV of −16), low stellar mass (median value of 108.4 M⊙ and down to 107 M⊙) LAEs at redshift z ≳ 3. We computed various averaged spectra of LAEs, subsampled on the basis of their observational (e.g., Lyα strength, UV magnitude and spectral slope) and physical (e.g., stellar mass and star-formation rate) properties. We searched for UV spectral features other than Lyα, such as higher ionization nebular emission lines and absorption features. We successfully observed the O III]λ1666 and [C III]λ1907+C III]λ1909 collisionally excited emission lines and the He IIλ1640 recombination feature, as well as the resonant C IVλλ1548,1551 doublet either in emission or P-Cygni. We compared the observed spectral properties of the different mean spectra and find the emission lines to vary with the observational and physical properties of the LAEs. In particular, the mean spectra of LAEs with larger Lyα equivalent widths, fainter UV magnitudes, bluer UV spectral slopes, and lower stellar masses show the strongest nebular emission. The line ratios of these lines are similar to those measured in the spectra of local metal-poor galaxies, while their equivalent widths are weaker compared to the handful of extreme values detected in individual spectra of z > 2 galaxies. This suggests that weak UV features are likely ubiquitous in high z, low-mass, and faint LAEs. We publicly released the stacked spectra, as they can serve as empirical templates for the design of future observations, such as those with the James Webb Space Telescope and the Extremely Large Telescope.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2007.01878","open_access":"1"}],"month":"09","intvolume":" 641","date_updated":"2022-07-19T09:35:43Z","extern":"1","_id":"11501","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution / galaxies: high-redshift / ISM: lines and bands / ultraviolet: ISM / ultraviolet: galaxies"],"year":"2020","day":"18","publication":"Astronomy & Astrophysics","doi":"10.1051/0004-6361/202038133","date_published":"2020-09-18T00:00:00Z","date_created":"2022-07-06T09:38:16Z","acknowledgement":"We thank Margherita Talia, Stéphane Charlot, Adele Plat and Alba Vidal-García for helpful discussions. This work is supported by the ERC advanced grant 339659-MUSICOS (R. Bacon). AF acknowledges the support from grant PRIN MIUR 2017 20173ML3WW. MVM and JP would like to thank the Leiden/ESA Astrophysics Program for Summer Students (LEAPS) for funding at the outset of this project. FL, HK, and AV acknowledge support from the ERC starting grant ERC-757258-TRIPLE. TH was supported by Leading Initiative for Excellent Young Researchers, MEXT, Japan. JB acknowledges support by FCT/MCTES through national funds by the grant UID/FIS/04434/2019, UIDB/04434/2020 and UIDP/04434/2020 and through the Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. HI acknowledges support from JSPS KAKENHI Grant Number JP19K23462. We would also like to thank the organizers and participants of the Leiden Lorentz Center workshop: Revolutionary Spectroscopy of Today as a Springboard to Webb. This work made use of several open source python packages: NUMPY (van der Walt et al. 2011), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration 2013) and MPDAF (MUSE Python Data Analysis Framework, Piqueras et al. 2019).","quality_controlled":"1","publisher":"EDP Sciences","oa":1,"citation":{"ista":"Feltre A, Maseda MV, Bacon R, Pradeep J, Leclercq F, Kusakabe H, Wisotzki L, Hashimoto T, Schmidt KB, Blaizot J, Brinchmann J, Boogaard L, Cantalupo S, Carton D, Inami H, Kollatschny W, Marino RA, Matthee JJ, Nanayakkara T, Richard J, Schaye J, Tresse L, Urrutia T, Verhamme A, Weilbacher PM. 2020. The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3. Astronomy & Astrophysics. 641, A118.","chicago":"Feltre, Anna, Michael V. Maseda, Roland Bacon, Jayadev Pradeep, Floriane Leclercq, Haruka Kusakabe, Lutz Wisotzki, et al. “The MUSE Hubble Ultra Deep Field Survey: XV. The Mean Rest-UV Spectra of Lyα Emitters at z > 3.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/202038133.","ieee":"A. Feltre et al., “The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3,” Astronomy & Astrophysics, vol. 641. EDP Sciences, 2020.","short":"A. Feltre, M.V. Maseda, R. Bacon, J. Pradeep, F. Leclercq, H. Kusakabe, L. Wisotzki, T. Hashimoto, K.B. Schmidt, J. Blaizot, J. Brinchmann, L. Boogaard, S. Cantalupo, D. Carton, H. Inami, W. Kollatschny, R.A. Marino, J.J. Matthee, T. Nanayakkara, J. Richard, J. Schaye, L. Tresse, T. Urrutia, A. Verhamme, P.M. Weilbacher, Astronomy & Astrophysics 641 (2020).","apa":"Feltre, A., Maseda, M. V., Bacon, R., Pradeep, J., Leclercq, F., Kusakabe, H., … Weilbacher, P. M. (2020). The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202038133","ama":"Feltre A, Maseda MV, Bacon R, et al. The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3. Astronomy & Astrophysics. 2020;641. doi:10.1051/0004-6361/202038133","mla":"Feltre, Anna, et al. “The MUSE Hubble Ultra Deep Field Survey: XV. The Mean Rest-UV Spectra of Lyα Emitters at z > 3.” Astronomy & Astrophysics, vol. 641, A118, EDP Sciences, 2020, doi:10.1051/0004-6361/202038133."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Feltre","full_name":"Feltre, Anna","first_name":"Anna"},{"full_name":"Maseda, Michael V.","last_name":"Maseda","first_name":"Michael V."},{"full_name":"Bacon, Roland","last_name":"Bacon","first_name":"Roland"},{"first_name":"Jayadev","last_name":"Pradeep","full_name":"Pradeep, Jayadev"},{"full_name":"Leclercq, Floriane","last_name":"Leclercq","first_name":"Floriane"},{"first_name":"Haruka","full_name":"Kusakabe, Haruka","last_name":"Kusakabe"},{"last_name":"Wisotzki","full_name":"Wisotzki, Lutz","first_name":"Lutz"},{"first_name":"Takuya","last_name":"Hashimoto","full_name":"Hashimoto, Takuya"},{"last_name":"Schmidt","full_name":"Schmidt, Kasper B.","first_name":"Kasper B."},{"first_name":"Jeremy","full_name":"Blaizot, Jeremy","last_name":"Blaizot"},{"first_name":"Jarle","full_name":"Brinchmann, Jarle","last_name":"Brinchmann"},{"first_name":"Leindert","full_name":"Boogaard, Leindert","last_name":"Boogaard"},{"first_name":"Sebastiano","full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo"},{"last_name":"Carton","full_name":"Carton, David","first_name":"David"},{"first_name":"Hanae","full_name":"Inami, Hanae","last_name":"Inami"},{"first_name":"Wolfram","full_name":"Kollatschny, Wolfram","last_name":"Kollatschny"},{"full_name":"Marino, Raffaella A.","last_name":"Marino","first_name":"Raffaella A."},{"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":"Nanayakkara","full_name":"Nanayakkara, Themiya","first_name":"Themiya"},{"first_name":"Johan","full_name":"Richard, Johan","last_name":"Richard"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"full_name":"Tresse, Laurence","last_name":"Tresse","first_name":"Laurence"},{"full_name":"Urrutia, Tanya","last_name":"Urrutia","first_name":"Tanya"},{"last_name":"Verhamme","full_name":"Verhamme, Anne","first_name":"Anne"},{"first_name":"Peter M.","last_name":"Weilbacher","full_name":"Weilbacher, Peter M."}],"article_processing_charge":"No","external_id":{"arxiv":["2007.01878"]},"title":"The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3","article_number":"A118"},{"title":"Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2","external_id":{"arxiv":["2002.06207"]},"article_processing_charge":"No","author":[{"first_name":"Behnam","full_name":"Darvish, Behnam","last_name":"Darvish"},{"full_name":"Scoville, Nick Z.","last_name":"Scoville","first_name":"Nick Z."},{"full_name":"Martin, Christopher","last_name":"Martin","first_name":"Christopher"},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"first_name":"Bahram","full_name":"Mobasher, Bahram","last_name":"Mobasher"},{"first_name":"Alessandro","last_name":"Rettura","full_name":"Rettura, Alessandro"},{"last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"first_name":"Peter","full_name":"Capak, Peter","last_name":"Capak"},{"full_name":"Chartab, Nima","last_name":"Chartab","first_name":"Nima"},{"first_name":"Shoubaneh","full_name":"Hemmati, Shoubaneh","last_name":"Hemmati"},{"last_name":"Masters","full_name":"Masters, Daniel","first_name":"Daniel"},{"first_name":"Hooshang","full_name":"Nayyeri, Hooshang","last_name":"Nayyeri"},{"last_name":"O’Sullivan","full_name":"O’Sullivan, Donal","first_name":"Donal"},{"first_name":"Ana","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana"},{"first_name":"Zahra","full_name":"Sattari, Zahra","last_name":"Sattari"},{"last_name":"Shahidi","full_name":"Shahidi, Abtin","first_name":"Abtin"},{"full_name":"Salvato, Mara","last_name":"Salvato","first_name":"Mara"},{"full_name":"Lemaux, Brian C.","last_name":"Lemaux","first_name":"Brian C."},{"last_name":"Fèvre","full_name":"Fèvre, Olivier Le","first_name":"Olivier Le"},{"first_name":"Olga","last_name":"Cucciati","full_name":"Cucciati, Olga"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"B. Darvish, N.Z. Scoville, C. Martin, D. Sobral, B. Mobasher, A. Rettura, J.J. Matthee, P. Capak, N. Chartab, S. Hemmati, D. Masters, H. Nayyeri, D. O’Sullivan, A. Paulino-Afonso, Z. Sattari, A. Shahidi, M. Salvato, B.C. Lemaux, O.L. Fèvre, O. Cucciati, The Astrophysical Journal 892 (2020).","ieee":"B. Darvish et al., “Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2,” The Astrophysical Journal, vol. 892, no. 1. IOP Publishing, 2020.","apa":"Darvish, B., Scoville, N. Z., Martin, C., Sobral, D., Mobasher, B., Rettura, A., … Cucciati, O. (2020). Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab75c3","ama":"Darvish B, Scoville NZ, Martin C, et al. Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. The Astrophysical Journal. 2020;892(1). doi:10.3847/1538-4357/ab75c3","mla":"Darvish, Behnam, et al. “Spectroscopic Confirmation of a Coma Cluster Progenitor at z ∼ 2.2.” The Astrophysical Journal, vol. 892, no. 1, 8, IOP Publishing, 2020, doi:10.3847/1538-4357/ab75c3.","ista":"Darvish B, Scoville NZ, Martin C, Sobral D, Mobasher B, Rettura A, Matthee JJ, Capak P, Chartab N, Hemmati S, Masters D, Nayyeri H, O’Sullivan D, Paulino-Afonso A, Sattari Z, Shahidi A, Salvato M, Lemaux BC, Fèvre OL, Cucciati O. 2020. Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. The Astrophysical Journal. 892(1), 8.","chicago":"Darvish, Behnam, Nick Z. Scoville, Christopher Martin, David Sobral, Bahram Mobasher, Alessandro Rettura, Jorryt J Matthee, et al. “Spectroscopic Confirmation of a Coma Cluster Progenitor at z ∼ 2.2.” The Astrophysical Journal. IOP Publishing, 2020. https://doi.org/10.3847/1538-4357/ab75c3."},"article_number":"8","date_created":"2022-07-06T13:10:51Z","doi":"10.3847/1538-4357/ab75c3","date_published":"2020-03-19T00:00:00Z","publication":"The Astrophysical Journal","day":"19","year":"2020","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","acknowledgement":"We are thankful to the anonymous referee for useful comments and suggestions that improved the quality of this paper. B.D. acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. B.D. is thankful to Andreas Faisst, Laura Danly, and Matthew Burlando for their companionship during the observing run. B.D. is grateful to the COSMOS team for their useful comments during the team meeting in New York City 2019 May 14–17. A.R. research was made possible by Friends of W. M. Keck Observatory who philanthropically support the Keck Science Collaborative (KSC) fund. The observations presented herein were obtained at the W. M. Keck Observatory (program C236, PI Scoville), which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. The authors would like to recognize and acknowledge the very prominent cultural role and reverence that the summit of Maunakea has always had within the indigenous Hawaiian community. We are fortunate to have the opportunity to perform observations from this mountain.","extern":"1","date_updated":"2022-07-19T09:31:35Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","type":"journal_article","article_type":"original","_id":"11513","volume":892,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"intvolume":" 892","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/2002.06207","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We report the spectroscopic confirmation of a new protocluster in the COSMOS field at z ∼ 2.2, COSMOS Cluster 2.2 (CC2.2), originally identified as an overdensity of narrowband selected Hα emitting candidates. With only two masks of Keck/MOSFIRE near-IR spectroscopy in both H (∼1.47–1.81 μm) and K (∼1.92–2.40 μm) bands (∼1.5 hr each), we confirm 35 unique protocluster members with at least two emission lines detected with S/N > 3. Combined with 12 extra members from the zCOSMOS-deep spectroscopic survey (47 in total), we estimate a mean redshift and a line-of-sight velocity dispersion of zmean = 2.23224 ± 0.00101 and σlos = 645 ± 69 km s−1 for this protocluster, respectively. Assuming virialization and spherical symmetry for the system, we estimate a total mass of Mvir ∼ (1–2) ×1014M⊙ for the structure. We evaluate a number density enhancement of δg ∼ 7 for this system and we argue that the structure is likely not fully virialized at z ∼ 2.2. However, in a spherical collapse model, δg is expected to grow to a linear matter enhancement of ∼1.9 by z = 0, exceeding the collapse threshold of 1.69, and leading to a fully collapsed and virialized Coma-type structure with a total mass of Mdyn(z = 0) ∼ 9.2 × 1014M⊙ by now. This observationally efficient confirmation suggests that large narrowband emission-line galaxy surveys, when combined with ancillary photometric data, can be used to effectively trace the large-scale structure and protoclusters at a time when they are mostly dominated by star-forming galaxies.","lang":"eng"}]},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1910.03593","open_access":"1"}],"month":"08","intvolume":" 496","abstract":[{"lang":"eng","text":"Ly α emission lines are typically found to be redshifted with respect to the systemic redshifts of galaxies, likely due to resonant scattering of Ly α photons. Here, we measure the average velocity offset for a sample of 96 z ≈ 3.3 Ly α emitters (LAEs) with a median Ly α flux (luminosity) of ≈10−17 erg cm−2 s−1 (≈1042 erg s−1) and a median star formation rate (SFR) of ≈1.3 M⊙ yr−1 (not corrected for possible dust extinction), detected by the Multi-Unit Spectroscopic Explorer as part of our MUSEQuBES circumgalactic medium (CGM) survey. By postulating that the stacked CGM absorption profiles of these LAEs, probed by eight background quasars, must be centred on the systemic redshift, we measure an average velocity offset, Voffset = 171\\pm 8 km s−1, between the Ly α emission peak and the systemic redshift. The observed Voffset is lower by factors of ≈1.4 and ≈2.6 compared to the velocity offsets measured for narrow-band-selected LAEs and Lyman break galaxies, respectively, which probe galaxies with higher masses and SFRs. Consistent with earlier studies based on direct measurements for individual objects, we find that the Voffset is correlated with the full width at half-maximum of the red peak of the Ly α line, and anticorrelated with the rest-frame equivalent width. Moreover, we find that Voffset is correlated with SFR with a sub-linear scaling relation, Voffset∝SFR0.16±0.03. Adopting the mass scaling for main-sequence galaxies, such a relation suggests that Voffset scales with the circular velocity of the dark matter haloes hosting the LAEs."}],"oa_version":"Preprint","volume":496,"issue":"2","related_material":{"link":[{"url":"https://doi.org/10.1093/mnras/staa2668","relation":"erratum"}]},"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: haloes","galaxies: high-redshift","quasars: absorption lines"],"_id":"11528","date_updated":"2022-08-18T11:00:24Z","extern":"1","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"acknowledgement":"We thank the anonymous referee for useful suggestions. This study is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme(s): 094.A-0131(B), 095.A 0200(A), 096.A0222(A), 097.A-0089(A), and 099.A-0159(A). SM acknowledges support from the Alexander von Humboldt Foundation, Germany. SM thanks Christian Herenz for useful discussion. SC gratefully acknowledges support from Swiss National Science Foundation grant PP00P2 163824. JB acknowledges support by FCT/MCTES through national funds by grant UID/FIS/04434/2019 and through Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. NB and JZ acknowledge support from ANR grant ANR-17-CE31- 0017 (3DGasFlows). AC and JR acknowledge support from the ERC starting grant 336736-CALENDS. MA acknowledges support from European Union’s H2020 Marie Skłodowska-Curie Actions grant 721463 to the SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness (MINECO) under grant number AYA2016-76219-P. MA also acknowledges support from the Fundacion BBVA under its 2017 programme of assistance to ´scientific research groups, for the project ‘Using machine-learning techniques to drag galaxies from the noise in deep imaging’. FL and AV acknowledge support from the ERC starting grant ERC757258-TRIPLE.","page":"1013-1022","doi":"10.1093/mnras/staa1347","date_published":"2020-08-01T00:00:00Z","date_created":"2022-07-07T10:20:11Z","year":"2020","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","author":[{"first_name":"Sowgat","last_name":"Muzahid","full_name":"Muzahid, Sowgat"},{"full_name":"Schaye, Joop","last_name":"Schaye","first_name":"Joop"},{"first_name":"Raffaella Anna","last_name":"Marino","full_name":"Marino, Raffaella Anna"},{"last_name":"Cantalupo","full_name":"Cantalupo, Sebastiano","first_name":"Sebastiano"},{"first_name":"Jarle","full_name":"Brinchmann, Jarle","last_name":"Brinchmann"},{"first_name":"Thierry","last_name":"Contini","full_name":"Contini, Thierry"},{"last_name":"Wendt","full_name":"Wendt, Martin","first_name":"Martin"},{"full_name":"Wisotzki, Lutz","last_name":"Wisotzki","first_name":"Lutz"},{"last_name":"Zabl","full_name":"Zabl, Johannes","first_name":"Johannes"},{"first_name":"Nicolas","full_name":"Bouché, Nicolas","last_name":"Bouché"},{"full_name":"Akhlaghi, Mohammad","last_name":"Akhlaghi","first_name":"Mohammad"},{"full_name":"Chen, Hsiao-Wen","last_name":"Chen","first_name":"Hsiao-Wen"},{"last_name":"Claeyssens","full_name":"Claeyssens, Adélaîde","first_name":"Adélaîde"},{"full_name":"Johnson, Sean","last_name":"Johnson","first_name":"Sean"},{"first_name":"Floriane","last_name":"Leclercq","full_name":"Leclercq, Floriane"},{"last_name":"Maseda","full_name":"Maseda, Michael","first_name":"Michael"},{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Richard, Johan","last_name":"Richard","first_name":"Johan"},{"first_name":"Tanya","full_name":"Urrutia, Tanya","last_name":"Urrutia"},{"first_name":"Anne","last_name":"Verhamme","full_name":"Verhamme, Anne"}],"article_processing_charge":"No","external_id":{"arxiv":["1910.03593"]},"title":"MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles","citation":{"ista":"Muzahid S, Schaye J, Marino RA, Cantalupo S, Brinchmann J, Contini T, Wendt M, Wisotzki L, Zabl J, Bouché N, Akhlaghi M, Chen H-W, Claeyssens A, Johnson S, Leclercq F, Maseda M, Matthee JJ, Richard J, Urrutia T, Verhamme A. 2020. MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. Monthly Notices of the Royal Astronomical Society. 496(2), 1013–1022.","chicago":"Muzahid, Sowgat, Joop Schaye, Raffaella Anna Marino, Sebastiano Cantalupo, Jarle Brinchmann, Thierry Contini, Martin Wendt, et al. “MUSEQuBES: Calibrating the Redshifts of Lyα Emitters Using Stacked Circumgalactic Medium Absorption Profiles.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa1347.","ieee":"S. Muzahid et al., “MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles,” Monthly Notices of the Royal Astronomical Society, vol. 496, no. 2. Oxford University Press, pp. 1013–1022, 2020.","short":"S. Muzahid, J. Schaye, R.A. Marino, S. Cantalupo, J. Brinchmann, T. Contini, M. Wendt, L. Wisotzki, J. Zabl, N. Bouché, M. Akhlaghi, H.-W. Chen, A. Claeyssens, S. Johnson, F. Leclercq, M. Maseda, J.J. Matthee, J. Richard, T. Urrutia, A. Verhamme, Monthly Notices of the Royal Astronomical Society 496 (2020) 1013–1022.","ama":"Muzahid S, Schaye J, Marino RA, et al. MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. Monthly Notices of the Royal Astronomical Society. 2020;496(2):1013-1022. doi:10.1093/mnras/staa1347","apa":"Muzahid, S., Schaye, J., Marino, R. A., Cantalupo, S., Brinchmann, J., Contini, T., … Verhamme, A. (2020). MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa1347","mla":"Muzahid, Sowgat, et al. “MUSEQuBES: Calibrating the Redshifts of Lyα Emitters Using Stacked Circumgalactic Medium Absorption Profiles.” Monthly Notices of the Royal Astronomical Society, vol. 496, no. 2, Oxford University Press, 2020, pp. 1013–22, doi:10.1093/mnras/staa1347."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Matthee JJ, Pezzulli G, Mackenzie R, et al. The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. Monthly Notices of the Royal Astronomical Society. 2020;498(2):3043-3059. doi:10.1093/mnras/staa2550","apa":"Matthee, J. J., Pezzulli, G., Mackenzie, R., Cantalupo, S., Kusakabe, H., Leclercq, F., … Nanayakkara, T. (2020). The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa2550","ieee":"J. J. Matthee et al., “The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6,” Monthly Notices of the Royal Astronomical Society, vol. 498, no. 2. Oxford University Press, pp. 3043–3059, 2020.","short":"J.J. Matthee, G. Pezzulli, R. Mackenzie, S. Cantalupo, H. Kusakabe, F. Leclercq, D. Sobral, J. Richard, L. Wisotzki, S. Lilly, L. Boogaard, R. Marino, M. Maseda, T. Nanayakkara, Monthly Notices of the Royal Astronomical Society 498 (2020) 3043–3059.","mla":"Matthee, Jorryt J., et al. “The Nature of CR7 Revealed with MUSE: A Young Starburst Powering Extended Ly α Emission at z = 6.6.” Monthly Notices of the Royal Astronomical Society, vol. 498, no. 2, Oxford University Press, 2020, pp. 3043–59, doi:10.1093/mnras/staa2550.","ista":"Matthee JJ, Pezzulli G, Mackenzie R, Cantalupo S, Kusakabe H, Leclercq F, Sobral D, Richard J, Wisotzki L, Lilly S, Boogaard L, Marino R, Maseda M, Nanayakkara T. 2020. The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. Monthly Notices of the Royal Astronomical Society. 498(2), 3043–3059.","chicago":"Matthee, Jorryt J, Gabriele Pezzulli, Ruari Mackenzie, Sebastiano Cantalupo, Haruka Kusakabe, Floriane Leclercq, David Sobral, et al. “The Nature of CR7 Revealed with MUSE: A Young Starburst Powering Extended Ly α Emission at z = 6.6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa2550."},"title":"The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6","author":[{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"last_name":"Pezzulli","full_name":"Pezzulli, Gabriele","first_name":"Gabriele"},{"last_name":"Mackenzie","full_name":"Mackenzie, Ruari","first_name":"Ruari"},{"first_name":"Sebastiano","full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo"},{"last_name":"Kusakabe","full_name":"Kusakabe, Haruka","first_name":"Haruka"},{"last_name":"Leclercq","full_name":"Leclercq, Floriane","first_name":"Floriane"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"first_name":"Johan","last_name":"Richard","full_name":"Richard, Johan"},{"first_name":"Lutz","last_name":"Wisotzki","full_name":"Wisotzki, Lutz"},{"full_name":"Lilly, Simon","last_name":"Lilly","first_name":"Simon"},{"first_name":"Leindert","full_name":"Boogaard, Leindert","last_name":"Boogaard"},{"first_name":"Raffaella","full_name":"Marino, Raffaella","last_name":"Marino"},{"first_name":"Michael","full_name":"Maseda, Michael","last_name":"Maseda"},{"full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara","first_name":"Themiya"}],"article_processing_charge":"No","external_id":{"arxiv":["2008.01731"]},"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"day":"01","publication":"Monthly Notices of the Royal Astronomical Society","year":"2020","doi":"10.1093/mnras/staa2550","date_published":"2020-10-01T00:00:00Z","date_created":"2022-07-07T10:36:01Z","page":"3043-3059","_id":"11529","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","dark ages","reionization","first stars","cosmology: observations"],"type":"journal_article","article_type":"original","extern":"1","date_updated":"2022-08-18T11:04:05Z","oa_version":"Preprint","abstract":[{"text":"CR7 is among the most luminous Ly α emitters (LAEs) known at z = 6.6 and consists of at least three UV components that are surrounded by Ly α emission. Previous studies have suggested that it may host an extreme ionizing source. Here, we present deep integral field spectroscopy of CR7 with VLT/Multi Unit Spectroscopic Explorer (MUSE). We measure extended emission with a similar halo scale length as typical LAEs at z ≈ 5. CR7’s Ly α halo is clearly elongated along the direction connecting the multiple components, likely tracing the underlying gas distribution. The Ly α emission originates almost exclusively from the brightest UV component, but we also identify a faint kinematically distinct Ly α emitting region nearby a fainter component. Combined with new near-infrared data, the MUSE data show that the rest-frame Ly α equivalent width (EW) is ≈100 Å. This is a factor 4 higher than the EW measured in low-redshift analogues with carefully matched Ly α profiles (and thus arguably H I column density), but this EW can plausibly be explained by star formation. Alternative scenarios requiring active galactic nucleus (AGN) powering are also disfavoured by the narrower and steeper Ly α spectrum and much smaller IR to UV ratio compared to obscured AGN in other Ly α blobs. CR7’s Ly α emission, while extremely luminous, resembles the emission in more common LAEs at lower redshifts very well and is likely powered by a young metal-poor starburst.","lang":"eng"}],"month":"10","intvolume":" 498","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.01731"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","volume":498,"issue":"2"},{"date_updated":"2022-08-18T11:27:43Z","extern":"1","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: high-redshift","galaxies: star formation"],"status":"public","_id":"11533","issue":"1","volume":493,"publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1910.02959","open_access":"1"}],"scopus_import":"1","intvolume":" 493","month":"03","abstract":[{"text":"We explore deep rest-frame UV to FIR data in the COSMOS field to measure the individual spectral energy distributions (SED) of the ∼4000 SC4K (Sobral et al.) Lyman α (Ly α) emitters (LAEs) at z ∼ 2–6. We find typical stellar masses of 109.3 ± 0.6 M⊙ and star formation rates (SFR) of SFRSED=4.4+10.5−2.4 M⊙ yr−1 and SFRLyα=5.9+6.3−2.6 M⊙ yr−1, combined with very blue UV slopes of β=−2.1+0.5−0.4, but with significant variations within the population. MUV and β are correlated in a similar way to UV-selected sources, but LAEs are consistently bluer. This suggests that LAEs are the youngest and/or most dust-poor subset of the UV-selected population. We also study the Ly α rest-frame equivalent width (EW0) and find 45 ‘extreme’ LAEs with EW0 > 240 Å (3σ), implying a low number density of (7 ± 1) × 10−7 Mpc−3. Overall, we measure little to no evolution of the Ly α EW0 and scale length parameter (w0), which are consistently high (EW0=140+280−70 Å, w0=129+11−11 Å) from z ∼ 6 to z ∼ 2 and below. However, w0 is anticorrelated with MUV and stellar mass. Our results imply that sources selected as LAEs have a high Ly α escape fraction (fesc,Ly α) irrespective of cosmic time, but fesc,Ly α is still higher for UV-fainter and lower mass LAEs. The least massive LAEs (<109.5 M⊙) are typically located above the star formation ‘main sequence’ (MS), but the offset from the MS decreases towards z ∼ 6 and towards 1010 M⊙. Our results imply a lack of evolution in the properties of LAEs across time and reveals the increasing overlap in properties of LAEs and UV-continuum selected galaxies as typical star-forming galaxies at high redshift effectively become LAEs.","lang":"eng"}],"oa_version":"Preprint","article_processing_charge":"No","external_id":{"arxiv":["1910.02959"]},"author":[{"last_name":"Santos","full_name":"Santos, S","first_name":"S"},{"first_name":"D","last_name":"Sobral","full_name":"Sobral, D"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"last_name":"Calhau","full_name":"Calhau, J","first_name":"J"},{"first_name":"E","full_name":"da Cunha, E","last_name":"da Cunha"},{"full_name":"Ribeiro, B","last_name":"Ribeiro","first_name":"B"},{"first_name":"A","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, A"},{"last_name":"Arrabal Haro","full_name":"Arrabal Haro, P","first_name":"P"},{"first_name":"J","full_name":"Butterworth, J","last_name":"Butterworth"}],"title":"The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs","citation":{"ama":"Santos S, Sobral D, Matthee JJ, et al. The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. Monthly Notices of the Royal Astronomical Society. 2020;493(1):141-160. doi:10.1093/mnras/staa093","apa":"Santos, S., Sobral, D., Matthee, J. J., Calhau, J., da Cunha, E., Ribeiro, B., … Butterworth, J. (2020). The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa093","ieee":"S. Santos et al., “The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs,” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 1. Oxford University Press, pp. 141–160, 2020.","short":"S. Santos, D. Sobral, J.J. Matthee, J. Calhau, E. da Cunha, B. Ribeiro, A. Paulino-Afonso, P. Arrabal Haro, J. Butterworth, Monthly Notices of the Royal Astronomical Society 493 (2020) 141–160.","mla":"Santos, S., et al. “The Evolution of Rest-Frame UV Properties, Ly α EWs, and the SFR–Stellar Mass Relation at z ∼ 2–6 for SC4K LAEs.” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 1, Oxford University Press, 2020, pp. 141–60, doi:10.1093/mnras/staa093.","ista":"Santos S, Sobral D, Matthee JJ, Calhau J, da Cunha E, Ribeiro B, Paulino-Afonso A, Arrabal Haro P, Butterworth J. 2020. The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. Monthly Notices of the Royal Astronomical Society. 493(1), 141–160.","chicago":"Santos, S, D Sobral, Jorryt J Matthee, J Calhau, E da Cunha, B Ribeiro, A Paulino-Afonso, P Arrabal Haro, and J Butterworth. “The Evolution of Rest-Frame UV Properties, Ly α EWs, and the SFR–Stellar Mass Relation at z ∼ 2–6 for SC4K LAEs.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa093."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"141-160","date_created":"2022-07-07T12:05:23Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1093/mnras/staa093","year":"2020","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"We thank the anonymous referee for the valuable feedback that significantly improved the quality and clarity of this paper. SS and JC acknowledge studentships from Lancaster University. APA acknowledges support from Fundação para a Ciência e a Tecnologia through the project PTDC/FISAST/31546/2017. The authors would like to thank Ali Khostovan, Sara Perez Sanchez, Alex Bennett and Tom Rose for contributions and discussions in the early stages of this work. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by CALET and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Finally, the authors acknowledge the unique value of the publicly available analysis software TOPCAT (Taylor 2005) and publicly available programming language Python, including the numpy, pyfits, matplotlib, scipy and astropy (Astropy Collaboration et al. 2013) packages. This work is based on the public SC4K sample of LAEs (Sobral et al. 2018a) and we release the full catalogue with all the photometry and properties derived in this paper, in electronic format, along with the relevant tables."},{"extern":"1","date_updated":"2022-08-18T11:29:53Z","_id":"11534","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","dark ages","reionization","first stars","cosmology: observations"],"status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"volume":492,"issue":"2","oa_version":"Preprint","abstract":[{"text":"The observed properties of the Lyman-α (Ly α) emission line are a powerful probe of neutral gas in and around galaxies. We present spatially resolved Ly α spectroscopy with VLT/MUSE targeting VR7, a UV-luminous galaxy at z = 6.532 with moderate Ly α equivalent width (EW0 ≈ 38 Å). These data are combined with deep resolved [CII]158μm spectroscopy obtained with ALMA and UV imaging from HST and we also detect UV continuum with MUSE. Ly α emission is clearly detected with S/N ≈ 40 and FWHM of 374 km s−1. Ly α and [C II] are similarly extended beyond the UV, with effective radius reff = 2.1 ± 0.2 kpc for a single exponential model or reff,Lyα,halo=3.45+1.08−0.87 kpc when measured jointly with the UV continuum. The Ly α profile is broader and redshifted with respect to the [C II] line (by 213 km s−1), but there are spatial variations that are qualitatively similar in both lines and coincide with resolved UV components. This suggests that the emission originates from two components with plausibly different H I column densities. We place VR7 in the context of other galaxies at similar and lower redshift. The Ly α halo scale length is similar at different redshifts and velocity shifts with respect to the systemic are typically smaller. Overall, we find little indications of a more neutral vicinity at higher redshift. This means that the local (∼10 kpc) neutral gas conditions that determine the observed Ly α properties in VR7 resemble the conditions in post-reionization galaxies.","lang":"eng"}],"intvolume":" 492","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1909.06376","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Matthee, Jorryt J, David Sobral, Max Gronke, Gabriele Pezzulli, Sebastiano Cantalupo, Huub Röttgering, Behnam Darvish, and Sérgio Santos. “Resolved Lyman-α Properties of a Luminous Lyman-Break Galaxy in a Large Ionized Bubble at z = 6.53 .” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/stz3554.","ista":"Matthee JJ, Sobral D, Gronke M, Pezzulli G, Cantalupo S, Röttgering H, Darvish B, Santos S. 2020. Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . Monthly Notices of the Royal Astronomical Society. 492(2), 1778–1790.","mla":"Matthee, Jorryt J., et al. “Resolved Lyman-α Properties of a Luminous Lyman-Break Galaxy in a Large Ionized Bubble at z = 6.53 .” Monthly Notices of the Royal Astronomical Society, vol. 492, no. 2, Oxford University Press, 2020, pp. 1778–90, doi:10.1093/mnras/stz3554.","apa":"Matthee, J. J., Sobral, D., Gronke, M., Pezzulli, G., Cantalupo, S., Röttgering, H., … Santos, S. (2020). Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz3554","ama":"Matthee JJ, Sobral D, Gronke M, et al. Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . Monthly Notices of the Royal Astronomical Society. 2020;492(2):1778-1790. doi:10.1093/mnras/stz3554","short":"J.J. Matthee, D. Sobral, M. Gronke, G. Pezzulli, S. Cantalupo, H. Röttgering, B. Darvish, S. Santos, Monthly Notices of the Royal Astronomical Society 492 (2020) 1778–1790.","ieee":"J. J. Matthee et al., “Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 ,” Monthly Notices of the Royal Astronomical Society, vol. 492, no. 2. Oxford University Press, pp. 1778–1790, 2020."},"title":"Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 ","external_id":{"arxiv":["1909.06376"]},"article_processing_charge":"No","author":[{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"first_name":"Max","last_name":"Gronke","full_name":"Gronke, Max"},{"first_name":"Gabriele","last_name":"Pezzulli","full_name":"Pezzulli, Gabriele"},{"last_name":"Cantalupo","full_name":"Cantalupo, Sebastiano","first_name":"Sebastiano"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"},{"first_name":"Behnam","full_name":"Darvish, Behnam","last_name":"Darvish"},{"last_name":"Santos","full_name":"Santos, Sérgio","first_name":"Sérgio"}],"publication":"Monthly Notices of the Royal Astronomical Society","day":"01","year":"2020","date_created":"2022-07-07T12:21:36Z","doi":"10.1093/mnras/stz3554","date_published":"2020-02-01T00:00:00Z","page":"1778-1790","acknowledgement":"We thank the referee for their suggestions and constructive comments that helped to improve the presentation of our results. Based on observations obtained with the Very Large Telescope, program 99.A-0462. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program #14699. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2017.1.01451.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan) and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. MG acknowledges support from NASA grant NNX17AK58G. GP and SC gratefully acknowledge support from Swiss National Science Foundation grant PP00P2 163824. BD acknowledges financial support from the National Science Foundation, grant number 1716907. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, SCIPY (Jones et al. 2001; Hunter 2007; van der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration 2013) packages, the astronomical imaging tools SEXTRACTOR, SWARP, and SCAMP (Bertin & Arnouts 1996; Bertin 2006, 2010) and the TOPCAT analysis tool (Taylor 2013).","oa":1,"publisher":"Oxford University Press","quality_controlled":"1"},{"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"acknowledgement":"We would like to thank the anonymous referee for a thoughtful report and suggestions that have improved this manuscript. We are also grateful to everyone involved in the Spitzer Space Telescope mission and everyone at the Spitzer Science Center: we are truly fortunate to have been able to use data from this facility. J. B. acknowledges support by FCT/MCTES through national funds by this grant UID/FIS/04434/2019 and through the Investigador FCT contract no. IF/01654/2014/CP1215/CT0003. S. C. gratefully acknowledges support from Swiss National Science Foundation grant PP00P2 163824. We would also like to thank Mauro Stefanon for his assistance with de-blending the IRAC photometry, Pieter van Dokkum for a number of useful suggestions, and Daniel Schaerer for information regarding the stellar population models. This study is based on observations made with ESO telescopes at the La Silla Paranal Observatory under programs IDs 094.A-2089(B), 095.A0010(A), 096.A-0045(A), and 096.A-0045(B).","doi":"10.1093/mnras/staa622","date_published":"2020-04-01T00:00:00Z","date_created":"2022-07-07T10:46:41Z","page":"5120-5130","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","year":"2020","title":"Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters","author":[{"first_name":"Michael V","last_name":"Maseda","full_name":"Maseda, Michael V"},{"first_name":"Roland","last_name":"Bacon","full_name":"Bacon, Roland"},{"full_name":"Lam, Daniel","last_name":"Lam","first_name":"Daniel"},{"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":"Brinchmann, Jarle","last_name":"Brinchmann","first_name":"Jarle"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"last_name":"Labbe","full_name":"Labbe, Ivo","first_name":"Ivo"},{"first_name":"Kasper B","full_name":"Schmidt, Kasper B","last_name":"Schmidt"},{"last_name":"Boogaard","full_name":"Boogaard, Leindert","first_name":"Leindert"},{"full_name":"Bouwens, Rychard","last_name":"Bouwens","first_name":"Rychard"},{"last_name":"Cantalupo","full_name":"Cantalupo, Sebastiano","first_name":"Sebastiano"},{"first_name":"Marijn","last_name":"Franx","full_name":"Franx, Marijn"},{"first_name":"Takuya","full_name":"Hashimoto, Takuya","last_name":"Hashimoto"},{"full_name":"Inami, Hanae","last_name":"Inami","first_name":"Hanae"},{"last_name":"Kusakabe","full_name":"Kusakabe, Haruka","first_name":"Haruka"},{"first_name":"Guillaume","last_name":"Mahler","full_name":"Mahler, Guillaume"},{"first_name":"Themiya","full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara"},{"last_name":"Richard","full_name":"Richard, Johan","first_name":"Johan"},{"full_name":"Wisotzki, Lutz","last_name":"Wisotzki","first_name":"Lutz"}],"article_processing_charge":"No","external_id":{"arxiv":["2002.11117"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Maseda MV, Bacon R, Lam D, Matthee JJ, Brinchmann J, Schaye J, Labbe I, Schmidt KB, Boogaard L, Bouwens R, Cantalupo S, Franx M, Hashimoto T, Inami H, Kusakabe H, Mahler G, Nanayakkara T, Richard J, Wisotzki L. 2020. Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. Monthly Notices of the Royal Astronomical Society. 493(4), 5120–5130.","chicago":"Maseda, Michael V, Roland Bacon, Daniel Lam, Jorryt J Matthee, Jarle Brinchmann, Joop Schaye, Ivo Labbe, et al. “Elevated Ionizing Photon Production Efficiency in Faint High-Equivalent-Width Lyman-α Emitters.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa622.","ama":"Maseda MV, Bacon R, Lam D, et al. Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. Monthly Notices of the Royal Astronomical Society. 2020;493(4):5120-5130. doi:10.1093/mnras/staa622","apa":"Maseda, M. V., Bacon, R., Lam, D., Matthee, J. J., Brinchmann, J., Schaye, J., … Wisotzki, L. (2020). Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa622","short":"M.V. Maseda, R. Bacon, D. Lam, J.J. Matthee, J. Brinchmann, J. Schaye, I. Labbe, K.B. Schmidt, L. Boogaard, R. Bouwens, S. Cantalupo, M. Franx, T. Hashimoto, H. Inami, H. Kusakabe, G. Mahler, T. Nanayakkara, J. Richard, L. Wisotzki, Monthly Notices of the Royal Astronomical Society 493 (2020) 5120–5130.","ieee":"M. V. Maseda et al., “Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters,” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 4. Oxford University Press, pp. 5120–5130, 2020.","mla":"Maseda, Michael V., et al. “Elevated Ionizing Photon Production Efficiency in Faint High-Equivalent-Width Lyman-α Emitters.” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 4, Oxford University Press, 2020, pp. 5120–30, doi:10.1093/mnras/staa622."},"month":"04","intvolume":" 493","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1093/mnras/staa622","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"While low-luminosity galaxies dominate number counts at all redshifts, their contribution to cosmic reionization is poorly understood due to a lack of knowledge of their physical properties. We isolate a sample of 35 z ≈ 4–5 continuum-faint Lyman-α emitters from deep VLT/MUSE spectroscopy and directly measure their H α emission using stacked Spitzer/IRAC Ch. 1 photometry. Based on Hubble Space Telescope imaging, we determine that the average UV continuum magnitude is fainter than −16 (≈ 0.01 L⋆), implying a median Lyman-α equivalent width of 259 Å. By combining the H α measurement with the UV magnitude, we determine the ionizing photon production efficiency, ξion, a first for such faint galaxies. The measurement of log10 (ξion [Hz erg−1]) = 26.28 (+0.28−0.40) is in excess of literature measurements of both continuum- and emission line-selected samples, implying a more efficient production of ionizing photons in these lower luminosity, Lyman-α-selected systems. We conclude that this elevated efficiency can be explained by stellar populations with metallicities between 4 × 10−4 and 0.008, with light-weighted ages less than 3 Myr."}],"volume":493,"issue":"4","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","Galaxies: evolution","Galaxies: high-redshift","Galaxies: ISM"],"article_type":"original","type":"journal_article","_id":"11531","extern":"1","date_updated":"2022-08-18T11:23:27Z"},{"publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}],"volume":495,"issue":"2","abstract":[{"text":"A prediction of the classic active galactic nucleus (AGN) unification model is the presence of ionization cones with different orientations depending on the AGN type. Confirmations of this model exist for present times, but it is less clear in the early Universe. Here, we use the morphology of giant Ly α nebulae around AGNs at redshift z ∼ 3 to probe AGN emission and therefore the validity of the AGN unification model at this redshift. We compare the spatial morphology of 19 nebulae previously found around type I AGNs with a new sample of four Ly α nebulae detected around type II AGNs. Using two independent techniques, we find that nebulae around type II AGNs are more asymmetric than around type I, at least at radial distances r > 30 physical kpc (pkpc) from the ionizing source. We conclude that the type I and type II AGNs in our sample show evidence of different surrounding ionizing geometries. This suggests that the classical AGN unification model is also valid for high-redshift sources. Finally, we discuss how the lack of asymmetry in the inner parts (r ≲ 30 pkpc) and the associated high values of the He II to Ly α ratios in these regions could indicate additional sources of (hard) ionizing radiation originating within or in proximity of the AGN host galaxies. This work demonstrates that the morphologies of giant Ly α nebulae can be used to understand and study the geometry of high-redshift AGNs on circumnuclear scales and it lays the foundation for future studies using much larger statistical samples.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.01732"}],"scopus_import":"1","intvolume":" 495","month":"06","date_updated":"2022-08-18T11:17:47Z","extern":"1","_id":"11530","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: high-redshift","intergalactic medium","quasars: emission lines","quasars: general"],"status":"public","year":"2020","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","page":"1874-1887","date_created":"2022-07-07T10:40:17Z","doi":"10.1093/mnras/staa1269","date_published":"2020-06-01T00:00:00Z","acknowledgement":"SC and GP gratefully acknowledge support from Swiss National Science Foundation grant PP00P2 163824. MK acknowledges support by DLR500R1904.","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","citation":{"mla":"den Brok, J. S., et al. “Probing the AGN Unification Model at Redshift z ∼ 3 with MUSE Observations of Giant Lyα Nebulae.” Monthly Notices of the Royal Astronomical Society, vol. 495, no. 2, Oxford University Press, 2020, pp. 1874–87, doi:10.1093/mnras/staa1269.","apa":"den Brok, J. S., Cantalupo, S., Mackenzie, R., Marino, R. A., Pezzulli, G., Matthee, J. J., … Kollatschny, W. (2020). Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa1269","ama":"den Brok JS, Cantalupo S, Mackenzie R, et al. Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. Monthly Notices of the Royal Astronomical Society. 2020;495(2):1874-1887. doi:10.1093/mnras/staa1269","short":"J.S. den Brok, S. Cantalupo, R. Mackenzie, R.A. Marino, G. Pezzulli, J.J. Matthee, S.D. Johnson, M. Krumpe, T. Urrutia, W. Kollatschny, Monthly Notices of the Royal Astronomical Society 495 (2020) 1874–1887.","ieee":"J. S. den Brok et al., “Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae,” Monthly Notices of the Royal Astronomical Society, vol. 495, no. 2. Oxford University Press, pp. 1874–1887, 2020.","chicago":"den Brok, J S, S Cantalupo, R Mackenzie, R A Marino, G Pezzulli, Jorryt J Matthee, S D Johnson, M Krumpe, T Urrutia, and W Kollatschny. “Probing the AGN Unification Model at Redshift z ∼ 3 with MUSE Observations of Giant Lyα Nebulae.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa1269.","ista":"den Brok JS, Cantalupo S, Mackenzie R, Marino RA, Pezzulli G, Matthee JJ, Johnson SD, Krumpe M, Urrutia T, Kollatschny W. 2020. Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. Monthly Notices of the Royal Astronomical Society. 495(2), 1874–1887."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2005.01732"]},"article_processing_charge":"No","author":[{"full_name":"den Brok, J S","last_name":"den Brok","first_name":"J S"},{"first_name":"S","full_name":"Cantalupo, S","last_name":"Cantalupo"},{"last_name":"Mackenzie","full_name":"Mackenzie, R","first_name":"R"},{"first_name":"R A","last_name":"Marino","full_name":"Marino, R A"},{"full_name":"Pezzulli, G","last_name":"Pezzulli","first_name":"G"},{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Johnson, S D","last_name":"Johnson","first_name":"S D"},{"full_name":"Krumpe, M","last_name":"Krumpe","first_name":"M"},{"first_name":"T","last_name":"Urrutia","full_name":"Urrutia, T"},{"first_name":"W","last_name":"Kollatschny","full_name":"Kollatschny, W"}],"title":"Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae"},{"oa_version":"Preprint","abstract":[{"text":"Despite recent progress in understanding Ly α emitters (LAEs), relatively little is known regarding their typical black hole activity across cosmic time. Here, we study the X-ray and radio properties of ∼4000 LAEs at 2.2 < z < 6 from the SC4K survey in the COSMOS field. We detect 254 (6.8per cent±0.4per cent) LAEs individually in the X-rays (S/N > 3) with an average luminosity of 1044.31±0.01ergs−1 and average black hole accretion rate (BHAR) of 0.72±0.01 M⊙ yr−1, consistent with moderate to high accreting active galactic neuclei (AGNs). We detect 120 sources in deep radio data (radio AGN fraction of 3.2per cent±0.3per cent). The global AGN fraction (8.6per cent±0.4per cent) rises with Ly α luminosity and declines with increasing redshift. For X-ray-detected LAEs, Ly α luminosities correlate with the BHARs, suggesting that Ly α luminosity becomes a BHAR indicator. Most LAEs (93.1per cent±0.6per cent) at 2 < z < 6 have no detectable X-ray emission (BHARs < 0.017 M⊙ yr−1). The median star formation rate (SFR) of star-forming LAEs from Ly α and radio luminosities is 7.6+6.6−2.8 M⊙ yr−1. The black hole to galaxy growth ratio (BHAR/SFR) for LAEs is <0.0022, consistent with typical star-forming galaxies and the local BHAR/SFR relation. We conclude that LAEs at 2 < z < 6 include two different populations: an AGN population, where Ly α luminosity traces BHAR, and another with low SFRs which remain undetected in even the deepest X-ray stacks but is detected in the radio stacks.","lang":"eng"}],"intvolume":" 493","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.11672"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"volume":493,"issue":"3","_id":"11539","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: evolution","galaxies: high-redshift","quasars: supermassive black holes","galaxies: star formation","cosmology: observations","X-rays: galaxies"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2022-08-18T11:25:31Z","acknowledgement":"JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Camila Correa for help analysing snipshot merger trees. We thank the anonymous referee for constructive comments. We also thank Jarle Brinchmann, Rob Crain, Antonios Katsianis, Paola Popesso, and David Sobral for discussions and suggestions. We also thank the participants of the Lorentz Center workshop ‘A Decade of the Star-Forming Main Sequence’ held on 2017 September 4–8, for discussions and ideas. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, and SCIPY (Hunter 2007) packages and the TOPCAT analysis tool (Taylor 2013).","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","year":"2020","date_created":"2022-07-08T07:34:10Z","doi":"10.1093/mnras/staa476","date_published":"2020-04-01T00:00:00Z","page":"3341-3362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Calhau et al., “The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population,” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 3. Oxford University Press, pp. 3341–3362, 2020.","short":"J. Calhau, D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, A. Stroe, B. Simmons, C. Barlow-Hall, B. Adams, Monthly Notices of the Royal Astronomical Society 493 (2020) 3341–3362.","ama":"Calhau J, Sobral D, Santos S, et al. The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. Monthly Notices of the Royal Astronomical Society. 2020;493(3):3341-3362. doi:10.1093/mnras/staa476","apa":"Calhau, J., Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Stroe, A., … Adams, B. (2020). The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa476","mla":"Calhau, João, et al. “The X-Ray and Radio Activity of Typical and Luminous Ly α Emitters from z ∼ 2 to z ∼ 6: Evidence for a Diverse, Evolving Population.” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 3, Oxford University Press, 2020, pp. 3341–62, doi:10.1093/mnras/staa476.","ista":"Calhau J, Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Stroe A, Simmons B, Barlow-Hall C, Adams B. 2020. The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. Monthly Notices of the Royal Astronomical Society. 493(3), 3341–3362.","chicago":"Calhau, João, David Sobral, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Andra Stroe, Brooke Simmons, Cassandra Barlow-Hall, and Benjamin Adams. “The X-Ray and Radio Activity of Typical and Luminous Ly α Emitters from z ∼ 2 to z ∼ 6: Evidence for a Diverse, Evolving Population.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa476."},"title":"The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population","external_id":{"arxiv":["1909.11672"]},"article_processing_charge":"No","author":[{"last_name":"Calhau","full_name":"Calhau, João","first_name":"João"},{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"first_name":"Sérgio","full_name":"Santos, Sérgio","last_name":"Santos"},{"last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana","first_name":"Ana"},{"first_name":"Andra","full_name":"Stroe, Andra","last_name":"Stroe"},{"first_name":"Brooke","last_name":"Simmons","full_name":"Simmons, Brooke"},{"last_name":"Barlow-Hall","full_name":"Barlow-Hall, Cassandra","first_name":"Cassandra"},{"first_name":"Benjamin","last_name":"Adams","full_name":"Adams, Benjamin"}]}]