[{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"}],"abstract":[{"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\".","lang":"eng"}],"oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"file_id":"9390","checksum":"80a905c4eef24dab6fb247e81a3d67f5","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-05-14T11:42:23Z","file_name":"Notebook_Valentini.pdf","creator":"mvalenti","date_updated":"2021-05-14T11:42:23Z","file_size":10572981},{"file_name":"Experimental_data.zip","date_created":"2021-05-14T11:56:48Z","creator":"mvalenti","file_size":99076111,"date_updated":"2021-05-14T11:56:48Z","checksum":"1e61a7e63949448a8db0091cdac23570","file_id":"9391","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"}],"year":"2021","has_accepted_license":"1","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2021-05-14T12:07:53Z","contributor":[{"last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","contributor_type":"contact_person"}],"date_published":"2021-01-01T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"8910","status":"public"}]},"doi":"10.15479/AT:ISTA:9389","_id":"9389","status":"public","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","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:40:09Z","citation":{"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","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","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).","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.","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.","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."},"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"file_date_updated":"2021-05-14T11:56:48Z","title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","article_processing_charge":"No","author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","full_name":"Valentini, Marco"}]},{"publisher":"American Physical Society","quality_controlled":"1","oa":1,"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.","date_published":"2021-04-15T00:00:00Z","doi":"10.1103/physrevresearch.3.l022005","date_created":"2021-12-16T18:50:57Z","has_accepted_license":"1","year":"2021","day":"15","publication":"Physical Review Research","project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"article_number":"L022005","author":[{"full_name":"Aggarwal, Kushagra","orcid":"0000-0001-9985-9293","last_name":"Aggarwal","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra"},{"first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357"},{"last_name":"Sammak","full_name":"Sammak, Amir","first_name":"Amir"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"last_name":"Martí-Sánchez","full_name":"Martí-Sánchez, Sara","first_name":"Sara"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"first_name":"Jeroen","full_name":"Danon, Jeroen","last_name":"Danon"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"external_id":{"arxiv":["2012.00322"]},"article_processing_charge":"No","title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","citation":{"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.","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.","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","month":"04","intvolume":" 3","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"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."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"earlier_version","id":"8831","status":"public"},{"relation":"research_data","status":"public","id":"8834"}]},"issue":"2","volume":3,"ec_funded":1,"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"60a1bc9c9b616b1b155044bb8cfc6484","file_id":"10561","file_size":1917512,"date_updated":"2021-12-17T08:12:37Z","creator":"cchlebak","file_name":"2021_PhysRevResearch_Aggarwal.pdf","date_created":"2021-12-17T08:12:37Z"}],"language":[{"iso":"eng"}],"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":["general engineering"],"_id":"10559","department":[{"_id":"GeKa"}],"file_date_updated":"2021-12-17T08:12:37Z","date_updated":"2024-02-21T12:41:26Z","ddc":["620"]},{"project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"20211720","title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","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","full_name":"Macon, Ariana","last_name":"Macon"},{"last_name":"Hontoria","full_name":"Hontoria, Francisco","first_name":"Francisco"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000697643700001"],"pmid":["34547909"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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.","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","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","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","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."},"quality_controlled":"1","publisher":"The Royal Society","oa":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_published":"2021-09-22T00:00:00Z","doi":"10.1098/rspb.2021.1720","date_created":"2021-10-21T07:46:06Z","day":"22","publication":"Proceedings of the Royal Society B: Biological Sciences","has_accepted_license":"1","isi":1,"year":"2021","status":"public","keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"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)"},"_id":"10166","file_date_updated":"2021-10-22T11:48:02Z","department":[{"_id":"BeVi"}],"ddc":["595"],"date_updated":"2024-02-21T12:40:29Z","month":"09","intvolume":" 288","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"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"}],"related_material":{"record":[{"status":"public","id":"9949","relation":"research_data"}],"link":[{"url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1","relation":"supplementary_material"}]},"volume":288,"issue":"1959","ec_funded":1,"file":[{"file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","date_created":"2021-10-22T11:48:02Z","file_size":995806,"date_updated":"2021-10-22T11:48:02Z","creator":"cchlebak","success":1,"checksum":"76e7f253b7040bca2ad76f82bd7c45c0","file_id":"10172","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"publication_status":"published"},{"_id":"9192","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","status":"public","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.","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","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","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)."},"date_updated":"2024-02-21T12:41:09Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arathoon","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"last_name":"Baskett","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-02-24T17:45:13Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","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."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","year":"2021","has_accepted_license":"1","day":"26","file":[{"date_created":"2021-02-24T17:45:13Z","file_name":"Data_Code.zip","date_updated":"2021-02-24T17:45:13Z","file_size":5934452,"creator":"larathoo","checksum":"f85537815809a8a4b7da9d01163f88c0","file_id":"9193","success":1,"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file"}],"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","first_name":"Louise S","contributor_type":"project_member"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","contributor_type":"project_member","last_name":"Field","orcid":"0000-0002-4014-8478"},{"contributor_type":"project_member","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","contributor_type":"project_leader","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:9192","date_published":"2021-02-26T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"11411","status":"public"},{"status":"public","id":"11321","relation":"later_version"},{"status":"public","id":"8254","relation":"earlier_version"}]}},{"status":"public","type":"research_data","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":"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","author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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."},"date_updated":"2024-02-21T12:40:30Z","month":"08","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"None","doi":"10.15479/AT:ISTA:9949","date_published":"2021-08-24T00:00:00Z","related_material":{"record":[{"id":"10166","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-21T13:44:22Z","file":[{"date_updated":"2021-08-21T13:43:59Z","file_size":139188306,"creator":"bvicoso","date_created":"2021-08-21T13:43:59Z","file_name":"Data.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"90461837eed66beac6fa302993cf0ca9","file_id":"9950","success":1}],"day":"24","has_accepted_license":"1","year":"2021"},{"ddc":["570"],"date_updated":"2024-02-21T12:41:41Z","file_date_updated":"2021-02-04T12:30:48Z","department":[{"_id":"GaTk"}],"_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)"},"file":[{"checksum":"e29f2b42651bef8e034781de8781ffac","file_id":"9092","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-02-04T12:30:48Z","file_name":"2021_PlosComBio_Kavcic.pdf","date_updated":"2021-02-04T12:30:48Z","file_size":3690053,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","volume":17,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7673"},{"id":"8930","status":"public","relation":"research_data"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"01","intvolume":" 17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","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.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529."},"title":"Minimal biophysical model of combined antibiotic action","author":[{"orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"}],"article_processing_charge":"Yes","external_id":{"isi":["000608045000010"]},"article_number":"e1008529","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"day":"07","publication":"PLOS Computational Biology","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1371/journal.pcbi.1008529","date_published":"2021-01-07T00:00:00Z","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},{"ec_funded":1,"related_material":{"record":[{"status":"public","id":"8951","relation":"research_data"}]},"volume":10,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"9284","checksum":"3c2f44058c2dd45a5a1027f09d263f8e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"elife-65993-v2.pdf","date_created":"2021-03-23T10:12:58Z","creator":"bkavcic","file_size":1390469,"date_updated":"2021-03-23T10:12:58Z"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"intvolume":" 10","month":"03","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."}],"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2021-03-23T10:12:58Z","ddc":["570"],"date_updated":"2024-02-21T12:41:57Z","keyword":["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)"},"type":"journal_article","article_type":"original","_id":"9283","date_created":"2021-03-23T10:11:46Z","doi":"10.7554/elife.65993","date_published":"2021-03-08T00:00:00Z","publication":"eLife","day":"08","year":"2021","isi":1,"has_accepted_license":"1","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","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).","title":"Local genetic context shapes the function of a gene regulatory network","external_id":{"isi":["000631050900001"]},"article_processing_charge":"Yes","author":[{"last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A"},{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek"},{"last_name":"Caruso Carter","full_name":"Caruso Carter, Caroline","first_name":"Caroline"},{"first_name":"Elisabeth","full_name":"Sonnleitner, Elisabeth","last_name":"Sonnleitner"},{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"full_name":"Paixão, Tiago","last_name":"Paixão","first_name":"Tiago"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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).","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","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","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.","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."},"project":[{"name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","grant_number":"628377","_id":"2517526A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"I03901","name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks","_id":"268BFA92-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e65993"},{"article_number":"272","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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."},"title":"Volume decomposition for two-piece rigid casting","author":[{"last_name":"Alderighi","full_name":"Alderighi, Thomas","first_name":"Thomas"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"},{"first_name":"Nico","full_name":"Pietroni, Nico","last_name":"Pietroni"}],"external_id":{"isi":["000729846700077"]},"article_processing_charge":"No","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).","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"day":"01","publication":"ACM Transactions on Graphics","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-12-01T00:00:00Z","doi":"10.1145/3478513.3480555","date_created":"2021-10-27T07:08:19Z","_id":"10184","status":"public","type":"journal_article","article_type":"original","ddc":["000"],"date_updated":"2024-02-28T12:52:48Z","department":[{"_id":"BeBi"}],"file_date_updated":"2021-10-27T07:08:07Z","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"}],"month":"12","intvolume":" 40","main_file_link":[{"open_access":"1","url":"http://vcg.isti.cnr.it/Publications/2021/AMBCP21"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"384ece7a9ad1026787ba9560b04336d5","file_id":"10185","creator":"bbickel","date_updated":"2021-10-27T07:08:07Z","file_size":107708317,"date_created":"2021-10-27T07:08:07Z","file_name":"rigidmolds-authorversion.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368 "]},"publication_status":"published","volume":40,"issue":"6","ec_funded":1},{"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"}],"month":"06","intvolume":" 17","publication_identifier":{"eissn":["1549-6333"],"issn":["1549-6325"]},"publication_status":"published","file":[{"creator":"pdavies","file_size":587404,"date_updated":"2021-06-10T19:33:56Z","file_name":"MISMM-arxiv.pdf","date_created":"2021-06-10T19:33:56Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"a21c627683890c309a68f6389302c408","file_id":"9542"}],"language":[{"iso":"eng"}],"volume":17,"issue":"2","related_material":{"record":[{"status":"public","id":"7802","relation":"earlier_version"}]},"ec_funded":1,"_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.","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"ACM Transactions on Algorithms","doi":"10.1145/3451992","date_published":"2021-06-01T00:00:00Z","date_created":"2021-06-10T19:31:05Z","article_number":"16","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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","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","short":"A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Artur","full_name":"Czumaj, Artur","last_name":"Czumaj"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","last_name":"Davies"},{"first_name":"Merav","full_name":"Parter, Merav","last_name":"Parter"}],"external_id":{"isi":["000661311300006"],"arxiv":["1912.05390"]},"article_processing_charge":"No","title":"Graph sparsification for derandomizing massively parallel computation with low space"},{"department":[{"_id":"MiLe"}],"date_updated":"2024-02-29T12:34:10Z","keyword":["General Physics and Astronomy"],"status":"public","type":"journal_article","article_type":"original","_id":"10134","ec_funded":1,"volume":127,"issue":"16","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"intvolume":" 127","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/2011.06279","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"title":"Anderson localization of composite particles","external_id":{"isi":["000707495700001"],"arxiv":["2011.06279"]},"article_processing_charge":"No","author":[{"last_name":"Suzuki","orcid":"0000-0003-4982-5970","full_name":"Suzuki, Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","first_name":"Fumika"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"first_name":"Wojciech H.","last_name":"Zurek","full_name":"Zurek, Wojciech H."},{"last_name":"Krems","full_name":"Krems, Roman V.","first_name":"Roman V."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","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.","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","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.","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."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"article_number":"160602","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,"oa":1,"quality_controlled":"1","publisher":"American Physical Society ","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"},{"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."}],"month":"07","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2005.07761","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450380706"]},"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","id":"15074","status":"public"}]},"ec_funded":1,"_id":"9678","status":"public","type":"conference","conference":{"start_date":"2021-07-06","end_date":"2021-07-08","location":" Virtual Event, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures "},"date_updated":"2024-03-05T07:13:12Z","department":[{"_id":"DaAl"}],"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.","quality_controlled":"1","oa":1,"day":"06","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","year":"2021","doi":"10.1145/3409964.3461785","date_published":"2021-07-06T00:00:00Z","date_created":"2021-07-18T22:01:22Z","page":"129-139","project":[{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"840605","name":"Coordination in constrained and natural distributed systems"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"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.","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.","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. 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Virtual Event, United States. https://doi.org/10.1145/3409964.3461785","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."},"title":"Efficient load-balancing through distributed token dropping","author":[{"first_name":"Sebastian","full_name":"Brandt, Sebastian","last_name":"Brandt"},{"first_name":"Barbara","full_name":"Keller, Barbara","last_name":"Keller"},{"last_name":"Rybicki","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"},{"last_name":"Uitto","full_name":"Uitto, Jara","first_name":"Jara"}],"external_id":{"arxiv":["2005.07761"]},"article_processing_charge":"No"},{"project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021).","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” Algorithmica. Springer Nature, 2021.","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."},"title":"Dynamic averaging load balancing on cycles","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2003.09297"],"isi":["000734004600001"]},"author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731"},{"last_name":"Sabour","full_name":"Sabour, Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba"}],"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).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Algorithmica","day":"24","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2020-08-24T06:24:04Z","doi":"10.1007/s00453-021-00905-9","date_published":"2021-12-24T00:00:00Z","_id":"8286","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)"},"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming ","start_date":"2020-07-08","location":"Virtual, Online; Germany","end_date":"2020-07-11"},"type":"journal_article","article_type":"original","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","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"21169b25b0c8e17b21e12af22bff9870","file_id":"10577","success":1,"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"}],"publication_status":"published","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"ec_funded":1,"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.4230/LIPIcs.ICALP.2020.7"}],"record":[{"id":"15077","status":"public","relation":"earlier_version"}]}},{"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"citation":{"chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"The polaron at strong coupling","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","day":"20","page":"180","date_published":"2021-08-20T00:00:00Z","doi":"10.15479/at:ista:9733","date_created":"2021-07-27T15:48:30Z","_id":"9733","type":"dissertation","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)"},"status":"public","supervisor":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"date_updated":"2024-03-06T12:30:44Z","ddc":["515","519","539"],"file_date_updated":"2022-03-10T12:13:57Z","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"08","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"Thesis_FeliciangeliA.pdf","date_created":"2021-08-19T14:03:48Z","file_size":1958710,"date_updated":"2021-09-06T09:28:56Z","creator":"dfelicia","checksum":"e88bb8ca43948abe060eb2d2fa719881","file_id":"9944","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"checksum":"72810843abee83705853505b3f8348aa","file_id":"9945","content_type":"application/octet-stream","access_level":"closed","relation":"source_file","date_created":"2021-08-19T14:06:35Z","file_name":"thesis.7z","date_updated":"2022-03-10T12:13:57Z","file_size":3771669,"creator":"dfelicia"}],"language":[{"iso":"eng"}],"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"},{"relation":"part_of_dissertation","id":"9781","status":"public"},{"status":"public","id":"9791","relation":"part_of_dissertation"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/"},{"quality_controlled":"1","publisher":"Journal of Machine Learning Research","oa":1,"date_published":"2021-04-01T00:00:00Z","date_created":"2021-06-20T22:01:33Z","page":"1−43","day":"01","publication":"Journal of Machine Learning Research","has_accepted_license":"1","year":"2021","title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","author":[{"first_name":"Ali","last_name":"Ramezani-Kebrya","full_name":"Ramezani-Kebrya, Ali"},{"first_name":"Fartash","full_name":"Faghri, Fartash","last_name":"Faghri"},{"last_name":"Markov","full_name":"Markov, Ilya","first_name":"Ilya"},{"last_name":"Aksenov","full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Roy","full_name":"Roy, Daniel M.","first_name":"Daniel M."}],"external_id":{"arxiv":["1908.06077"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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.","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."},"month":"04","intvolume":" 22","scopus_import":"1","main_file_link":[{"url":"https://www.jmlr.org/papers/v22/20-255.html","open_access":"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."}],"issue":"114","volume":22,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"6428aa8bcb67768b6949c99b55d5281d","file_id":"9595","file_size":11237154,"date_updated":"2021-06-23T07:09:41Z","creator":"asandaue","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf","date_created":"2021-06-23T07:09:41Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15324435"],"eissn":["15337928"]},"publication_status":"published","status":"public","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":"9571","department":[{"_id":"DaAl"}],"file_date_updated":"2021-06-23T07:09:41Z","ddc":["000"],"date_updated":"2024-03-06T12:22:07Z"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1097-4199"]},"publication_status":"published","issue":"4","volume":109,"ec_funded":1,"oa_version":"Preprint","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"}],"month":"02","intvolume":" 109","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.06.14.151258","open_access":"1"}],"date_updated":"2024-03-06T12:12:48Z","department":[{"_id":"SiHi"}],"_id":"8544","status":"public","article_type":"original","type":"journal_article","day":"17","publication":"Neuron","year":"2021","doi":"10.1016/j.neuron.2020.11.028","date_published":"2021-02-17T00:00:00Z","date_created":"2020-09-21T11:59:47Z","page":"P629-644.E8","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.","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","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."},"title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","author":[{"full_name":"Takeo, Yukari H.","last_name":"Takeo","first_name":"Yukari H."},{"last_name":"Shuster","full_name":"Shuster, S. Andrew","first_name":"S. Andrew"},{"first_name":"Linnie","last_name":"Jiang","full_name":"Jiang, Linnie"},{"last_name":"Hu","full_name":"Hu, Miley","first_name":"Miley"},{"first_name":"David J.","full_name":"Luginbuhl, David J.","last_name":"Luginbuhl"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras","full_name":"Contreras, Ximena"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark J.","last_name":"Wagner","full_name":"Wagner, Mark J."},{"first_name":"Surya","last_name":"Ganguli","full_name":"Ganguli, Surya"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"}],"article_processing_charge":"No","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}]},{"status":"public","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"type":"preprint","article_number":"2107.03720 ","_id":"9791","title":"The effective mass problem for the Landau-Pekar equations","department":[{"_id":"RoSe"}],"author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli"},{"full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","last_name":"Rademacher","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"}],"external_id":{"arxiv":["2107.03720"]},"article_processing_charge":"No","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. arXiv.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv.","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” arXiv. .","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, 2107.03720.","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, n.d."},"date_updated":"2024-03-06T12:30:45Z","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.03720"}],"oa":1,"oa_version":"Preprint","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..","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"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10755"},{"id":"9733","status":"public","relation":"dissertation_contains"}]},"date_published":"2021-07-08T00:00:00Z","date_created":"2021-08-06T08:49:45Z","ec_funded":1,"day":"08","language":[{"iso":"eng"}],"publication":"arXiv","publication_status":"submitted","year":"2021"},{"citation":{"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.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","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","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","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.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F"},{"full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","last_name":"Sokolowski"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"article_processing_charge":"No","external_id":{"isi":["000637809600006"]},"title":"Statistical analysis and optimality of neural systems","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"isi":1,"year":"2021","day":"07","publication":"Neuron","page":"1227-1241.e5","doi":"10.1016/j.neuron.2021.01.020","date_published":"2021-04-07T00:00:00Z","date_created":"2020-02-28T11:00:12Z","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.","quality_controlled":"1","publisher":"Cell Press","oa":1,"date_updated":"2024-03-06T14:22:51Z","department":[{"_id":"GaTk"}],"_id":"7553","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":109,"related_material":{"record":[{"status":"public","id":"15020","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/","relation":"press_release"}]},"issue":"7","ec_funded":1,"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."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/848374","open_access":"1"}],"month":"04","intvolume":" 109"},{"conference":{"name":"AISTATS: Artificial Intelligence and Statistics","location":"Virtual, San Diego, CA, United States","end_date":"2021-04-15","start_date":"2021-04-13"},"type":"conference","status":"public","_id":"10598","department":[{"_id":"MaMo"}],"date_updated":"2024-03-07T10:36:53Z","main_file_link":[{"url":"https://proceedings.mlr.press/v130/mondelli21a.html","open_access":"1"}],"alternative_title":["Proceedings of Machine Learning Research"],"scopus_import":"1","intvolume":" 130","month":"04","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"}],"oa_version":"Preprint","related_material":{"record":[{"relation":"later_version","status":"public","id":"12480"}]},"volume":130,"publication_status":"published","publication_identifier":{"issn":["2640-3498"]},"language":[{"iso":"eng"}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"external_id":{"arxiv":["2010.03460"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan","first_name":"Ramji"}],"editor":[{"full_name":"Banerjee, Arindam","last_name":"Banerjee","first_name":"Arindam"},{"first_name":"Kenji","full_name":"Fukumizu, Kenji","last_name":"Fukumizu"}],"title":"Approximate message passing with spectral initialization for generalized linear models","citation":{"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.","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.","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.","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.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"ML Research Press","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.","page":"397-405","date_created":"2022-01-03T11:34:22Z","date_published":"2021-04-01T00:00:00Z","year":"2021","publication":"Proceedings of The 24th International Conference on Artificial Intelligence and Statistics","day":"01"},{"quality_controlled":"1","publisher":"Springer Nature","oa":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.","date_published":"2021-02-25T00:00:00Z","doi":"10.1007/s11081-020-09544-5","date_created":"2020-08-03T14:29:57Z","page":"2627-2653","day":"25","publication":"Optimization and Engineering","isi":1,"has_accepted_license":"1","year":"2021","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"title":"New strong convergence method for the sum of two maximal monotone operators","author":[{"orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dong","full_name":"Dong, Qiao-Li","first_name":"Qiao-Li"},{"full_name":"Liu, Lu-Lu","last_name":"Liu","first_name":"Lu-Lu"},{"full_name":"Yao, Jen-Chih","last_name":"Yao","first_name":"Jen-Chih"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000559345400001"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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."},"month":"02","intvolume":" 22","scopus_import":"1","oa_version":"Published Version","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."}],"volume":22,"ec_funded":1,"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}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1389-4420"],"eissn":["1573-2924"]},"publication_status":"published","status":"public","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":"8196","department":[{"_id":"VlKo"}],"file_date_updated":"2020-08-03T15:24:39Z","ddc":["510"],"date_updated":"2024-03-07T14:39:29Z"},{"project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425"},{"name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"The germanium quantum information route","author":[{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"first_name":"Christoph","full_name":"Kloeffel, Christoph","last_name":"Kloeffel"},{"first_name":"Floris A.","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris A."},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"first_name":"Maksym","last_name":"Myronov","full_name":"Myronov, Maksym"},{"first_name":"Jian-Jun","last_name":"Zhang","full_name":"Zhang, Jian-Jun"},{"full_name":"Franceschi, Silvano De","last_name":"Franceschi","first_name":"Silvano De"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"}],"article_processing_charge":"No","external_id":{"arxiv":["2004.08133"],"isi":["000600826100003"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","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."},"quality_controlled":"1","publisher":"Springer Nature","oa":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_published":"2021-10-01T00:00:00Z","doi":"10.1038/s41578-020-00262-z","date_created":"2020-12-02T10:52:51Z","page":"926–943 ","day":"01","publication":"Nature Reviews Materials","isi":1,"year":"2021","status":"public","article_type":"original","type":"journal_article","_id":"8911","department":[{"_id":"GeKa"}],"date_updated":"2024-03-07T14:48:57Z","month":"10","intvolume":" 6","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.08133"}],"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"}],"volume":6,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2058-8437"]},"publication_status":"published"},{"date_updated":"2024-03-07T14:51:11Z","department":[{"_id":"HeEd"}],"_id":"8338","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"ec_funded":1,"volume":66,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 66","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.00856"}],"scopus_import":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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."},"title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","external_id":{"arxiv":["1908.00856"],"isi":["000564488500002"]},"article_processing_charge":"No","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"first_name":"Alexander I.","full_name":"Bobenko, Alexander I.","last_name":"Bobenko"},{"full_name":"Schief, Wolfgang K.","last_name":"Schief","first_name":"Wolfgang K."},{"full_name":"Techter, Jan","last_name":"Techter","first_name":"Jan"}],"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"publication":"Discrete and Computational Geometry","day":"01","year":"2021","isi":1,"date_created":"2020-09-06T22:01:13Z","date_published":"2021-10-01T00:00:00Z","doi":"10.1007/s00454-020-00240-w","page":"938-976","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).","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"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.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Distributed Computing","day":"01","year":"2021","isi":1,"date_created":"2020-06-07T22:00:54Z","date_published":"2021-12-01T00:00:00Z","doi":"10.1007/s00446-020-00380-5","page":"463-487","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.","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","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","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","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1903.05956"],"isi":["000556444600001"]},"author":[{"first_name":"Keren","full_name":"Censor-Hillel, Keren","last_name":"Censor-Hillel"},{"first_name":"Michal","full_name":"Dory, Michal","last_name":"Dory"},{"first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne","last_name":"Korhonen"},{"first_name":"Dean","full_name":"Leitersdorf, Dean","last_name":"Leitersdorf"}],"oa_version":"Published Version","abstract":[{"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. ","lang":"eng"}],"intvolume":" 34","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00446-020-00380-5"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"volume":34,"related_material":{"record":[{"relation":"earlier_version","id":"6933","status":"public"}]},"_id":"7939","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-07T14:43:39Z","department":[{"_id":"DaAl"}]},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686.","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.","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.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000558119300001"]},"author":[{"first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat"},{"first_name":"Ramsay","full_name":"Dyer, Ramsay","last_name":"Dyer"},{"last_name":"Ghosh","full_name":"Ghosh, Arijit","first_name":"Arijit"},{"last_name":"Lieutier","full_name":"Lieutier, Andre","first_name":"Andre"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken"}],"title":"Local conditions for triangulating submanifolds of Euclidean space","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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"Discrete and Computational Geometry","day":"01","page":"666-686","date_created":"2020-08-11T07:11:51Z","doi":"10.1007/s00454-020-00233-9","date_published":"2021-09-01T00:00:00Z","_id":"8248","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","date_updated":"2024-03-07T14:54:59Z","ddc":["510"],"department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00233-9"}],"scopus_import":"1","intvolume":" 66","month":"09","publication_status":"published","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":66},{"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","oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","day":"15","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2020-05-24T22:01:00Z","doi":"10.1002/wdev.383","date_published":"2021-04-15T00:00:00Z","article_number":"e383","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Morphogen control of growth and pattern in the spinal cord","grant_number":"F07802"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","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.","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","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","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).","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."},"title":"Regulation of size and scale in vertebrate spinal cord development","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["32391980"],"isi":["000531419400001"]},"author":[{"last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","date_created":"2020-11-24T13:11:39Z","file_size":2527276,"date_updated":"2020-11-24T13:11:39Z","creator":"dernst","success":1,"file_id":"8800","checksum":"f0a7745d48afa09ea7025e876a0145a8","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["17597692"],"issn":["17597684"]},"ec_funded":1,"related_material":{"record":[{"id":"14323","status":"public","relation":"dissertation_contains"}]},"_id":"7883","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":["570"],"date_updated":"2024-03-07T15:03:00Z","file_date_updated":"2020-11-24T13:11:39Z","department":[{"_id":"AnKi"}]},{"_id":"7905","status":"public","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)"},"ddc":["510"],"date_updated":"2024-03-07T15:01:58Z","file_date_updated":"2020-11-25T09:06:41Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"06","intvolume":" 65","scopus_import":"1","file":[{"date_created":"2020-11-25T09:06:41Z","file_name":"2020_DiscreteCompGeometry_Brown.pdf","creator":"dernst","date_updated":"2020-11-25T09:06:41Z","file_size":1013730,"file_id":"8803","checksum":"487a84ea5841b75f04f66d7ebd71b67e","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"publication_status":"published","volume":65,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.","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."},"title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","author":[{"last_name":"Brown","full_name":"Brown, Adam","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425"},{"first_name":"Bei","last_name":"Wang","full_name":"Wang, Bei"}],"external_id":{"isi":["000536324700001"],"arxiv":["1712.07734"]},"article_processing_charge":"Yes (via OA deal)","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.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"01","publication":"Discrete and Computational Geometry","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1007/s00454-020-00206-y","date_published":"2021-06-01T00:00:00Z","date_created":"2020-05-30T10:26:04Z","page":"1166-1198"},{"date_updated":"2024-03-07T15:07:53Z","ddc":["510"],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-10-05T14:53:40Z","_id":"8601","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","publication_status":"published","publication_identifier":{"issn":["01788051"],"eissn":["14322064"]},"language":[{"iso":"eng"}],"file":[{"checksum":"611ae28d6055e1e298d53a57beb05ef4","file_id":"8612","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-05T14:53:40Z","file_name":"2020_ProbTheory_Cipolloni.pdf","creator":"dernst","date_updated":"2020-10-05T14:53:40Z","file_size":497032}],"ec_funded":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"02","citation":{"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.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021).","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2021.","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","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","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1908.00969"],"isi":["000572724600002"]},"author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"title":"Edge universality for non-Hermitian random matrices","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"year":"2021","has_accepted_license":"1","isi":1,"publication":"Probability Theory and Related Fields","day":"01","date_created":"2020-10-04T22:01:37Z","date_published":"2021-02-01T00:00:00Z","doi":"10.1007/s00440-020-01003-7","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126.","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.","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","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","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."},"title":"New inertial relaxed method for solving split feasibilities","author":[{"last_name":"Shehu","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"last_name":"Gibali","full_name":"Gibali, Aviv","first_name":"Aviv"}],"external_id":{"isi":["000537342300001"]},"article_processing_charge":"Yes (via OA deal)","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).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Optimization Letters","has_accepted_license":"1","isi":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","_id":"7925","status":"public","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)"},"ddc":["510"],"date_updated":"2024-03-07T15:00:43Z","file_date_updated":"2024-03-07T14:58:51Z","department":[{"_id":"VlKo"}],"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","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"63c5f31cd04626152a19f97a2476281b","file_id":"15089","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"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1862-4480"],"issn":["1862-4472"]},"publication_status":"published","volume":15,"ec_funded":1},{"date_updated":"2024-03-25T12:31:39Z","extern":"1","type":"journal_article","article_type":"review","keyword":["General Biochemistry","Genetics and Molecular Biology"],"status":"public","_id":"15151","volume":184,"issue":"14","publication_status":"published","publication_identifier":{"issn":["0092-8674"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2021.05.029","open_access":"1"}],"scopus_import":"1","intvolume":" 184","month":"07","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."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","last_name":"Michael","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia"},{"full_name":"Thomä, Nicolas H.","last_name":"Thomä","first_name":"Nicolas H."}],"title":"Reading the chromatinized genome","citation":{"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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3599-3611","date_created":"2024-03-21T07:54:19Z","doi":"10.1016/j.cell.2021.05.029","date_published":"2021-07-08T00:00:00Z","year":"2021","publication":"Cell","day":"08","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"day":"01","publication":"Nature Protocols","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1038/s41596-021-00526-0","date_published":"2021-06-01T00:00:00Z","date_created":"2021-05-30T22:01:24Z","page":"2947–2967","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,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","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."},"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","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","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"},{"id":"4952F31E-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","last_name":"Suter"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"article_processing_charge":"No","external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"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":{"eissn":["17502799"],"issn":["17542189"]},"publication_status":"published","issue":"6","volume":16,"ec_funded":1,"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","ddc":["570"],"date_updated":"2023-08-10T22:30:51Z","file_date_updated":"2021-12-02T23:30:05Z","department":[{"_id":"PeJo"}],"_id":"9438","status":"public","article_type":"original","type":"journal_article"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."},"title":"Wound healing in the Arabidopsis root meristem","article_processing_charge":"No","author":[{"first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926"}],"project":[{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"13","year":"2021","has_accepted_license":"1","date_created":"2021-09-09T07:37:20Z","date_published":"2021-09-13T00:00:00Z","doi":"10.15479/at:ista:9992","page":"168","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["575"],"date_updated":"2023-09-07T13:38:33Z","supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-09-15T22:30:26Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"_id":"9992","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","language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-09T07:29:48Z","file_name":"Thesis_vupload.docx","date_updated":"2021-09-15T22:30:26Z","file_size":25179004,"creator":"lhoermaye","file_id":"9993","checksum":"c763064adaa720e16066c1a4f9682bbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file"},{"file_id":"9996","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","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}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"id":"6351","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6943","relation":"part_of_dissertation"},{"id":"8002","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"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. "}],"month":"09","alternative_title":["ISTA Thesis"]},{"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/647800"}],"scopus_import":"1","intvolume":" 1","month":"12","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Submitted Version","ec_funded":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/spot-the-difference/","relation":"press_release"}],"record":[{"relation":"software","id":"10110","status":"public"}]},"issue":"12","volume":1,"publication_status":"published","publication_identifier":{"issn":["2662-8457"]},"language":[{"iso":"eng"}],"file":[{"creator":"patrickd","file_size":1699466,"date_updated":"2022-06-18T22:30:03Z","file_name":"Guzmanetal2021.pdf","date_created":"2022-06-02T12:51:07Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-06-17","file_id":"11430","checksum":"9fec5b667909ef52be96d502e4f8c2ae"},{"file_size":3005651,"date_updated":"2022-06-18T22:30:03Z","creator":"patrickd","file_name":"Guzmanetal2021Suppl.pdf","title":"Supplementary Material","date_created":"2022-06-02T12:53:47Z","content_type":"application/pdf","relation":"supplementary_material","access_level":"open_access","embargo":"2022-06-17","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","file_id":"11431"}],"type":"journal_article","article_type":"original","keyword":["general medicine"],"status":"public","_id":"10816","file_date_updated":"2022-06-18T22:30:03Z","department":[{"_id":"PeJo"}],"date_updated":"2023-08-10T22:30:10Z","ddc":["610"],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.).","page":"830-842","date_created":"2022-03-04T08:32:36Z","doi":"10.1038/s43588-021-00157-1","date_published":"2021-12-16T00:00:00Z","year":"2021","has_accepted_license":"1","publication":"Nature Computational Science","day":"16","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"article_processing_charge":"No","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","last_name":"Guzmán"},{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"last_name":"Suter","full_name":"Suter, Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","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.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.","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.","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.","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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.","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.","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"},"date_updated":"2024-03-27T23:30:11Z","ddc":["005"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","last_name":"Guzmán"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","last_name":"Suter","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"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","_id":"10110","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"},"status":"public","has_accepted_license":"1","year":"2021","day":"16","file":[{"file_size":332990101,"date_updated":"2021-10-08T08:46:04Z","creator":"cchlebak","file_name":"patternseparation-main (1).zip","date_created":"2021-10-08T08:46:04Z","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","success":1,"checksum":"f92f8931cad0aa7e411c1715337bf408","file_id":"10114"}],"date_published":"2021-12-16T00:00:00Z","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","status":"public","id":"10816"}]},"doi":"10.15479/AT:ISTA:10110","date_created":"2021-10-08T06:44:22Z","license":"https://opensource.org/licenses/GPL-3.0","abstract":[{"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.","lang":"eng"}],"publisher":"IST Austria","oa":1,"month":"12"},{"author":[{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"},{"last_name":"Savin","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","date_updated":"2024-03-27T23:30:16Z","citation":{"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.).","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","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","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.","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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"},"status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"_id":"10077","date_published":"2021-09-29T00:00:00Z","doi":"10.1101/2021.09.28.460602","related_material":{"record":[{"status":"public","id":"11932","relation":"dissertation_contains"}]},"date_created":"2021-10-04T06:23:34Z","ec_funded":1,"year":"2021","publication_status":"submitted","day":"29","publication":"bioRxiv","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"oa":1,"month":"09","abstract":[{"lang":"eng","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."}],"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."},{"date_updated":"2023-09-05T15:34:44Z","ddc":["540"],"file_date_updated":"2021-09-16T22:30:03Z","department":[{"_id":"StFr"}],"_id":"9250","type":"journal_article","article_type":"original","status":"public","keyword":["General Chemistry","General Chemical Engineering"],"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"publication_status":"published","file":[{"embargo":"2021-09-15","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","file_id":"9276","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","date_created":"2021-03-22T11:46:00Z","file_size":1811448,"date_updated":"2021-09-16T22:30:03Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":13,"issue":"5","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","month":"03","intvolume":" 13","citation":{"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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Petit","full_name":"Petit, Yann K.","first_name":"Yann K."},{"last_name":"Mourad","full_name":"Mourad, Eléonore","first_name":"Eléonore"},{"first_name":"Christian","full_name":"Prehal, Christian","last_name":"Prehal"},{"first_name":"Christian","full_name":"Leypold, Christian","last_name":"Leypold"},{"first_name":"Andreas","last_name":"Windischbacher","full_name":"Windischbacher, Andreas"},{"first_name":"Daniel","last_name":"Mijailovic","full_name":"Mijailovic, Daniel"},{"last_name":"Slugovc","full_name":"Slugovc, Christian","first_name":"Christian"},{"first_name":"Sergey M.","full_name":"Borisov, Sergey M.","last_name":"Borisov"},{"first_name":"Egbert","last_name":"Zojer","full_name":"Zojer, Egbert"},{"first_name":"Sergio","last_name":"Brutti","full_name":"Brutti, Sergio"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger"}],"article_processing_charge":"No","external_id":{"isi":["000629296400001"],"pmid":["33723377"]},"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","isi":1,"has_accepted_license":"1","year":"2021","day":"15","publication":"Nature Chemistry","page":"465-471","doi":"10.1038/s41557-021-00643-z","date_published":"2021-03-15T00:00:00Z","date_created":"2021-03-16T11:12:20Z","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},{"ddc":["570"],"date_updated":"2023-09-07T13:33:27Z","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"file_date_updated":"2022-07-02T22:30:06Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"_id":"9623","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","language":[{"iso":"eng"}],"file":[{"file_id":"9624","checksum":"e039225a47ef32666d59bf35ddd30ecf","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","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_name":"PhDThesis_SCM.pdf","date_created":"2021-07-01T14:46:25Z","creator":"scaballe","file_size":17094958,"date_updated":"2022-07-02T22:30:06Z","embargo":"2022-07-01","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_id":"9625","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-012-1"]},"related_material":{"record":[{"id":"9750","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9006","status":"public"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"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"}],"month":"07","alternative_title":["ISTA Thesis"],"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.","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","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.","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."},"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","article_processing_charge":"No","author":[{"full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"}],"year":"2021","has_accepted_license":"1","date_created":"2021-07-01T14:50:17Z","doi":"10.15479/at:ista:9623","date_published":"2021-07-01T00:00:00Z","page":"111","oa":1,"publisher":"Institute of Science and Technology Austria"},{"title":"Cytoplasm's got moves","article_processing_charge":"No","external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"author":[{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","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.","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","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."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","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.","date_created":"2021-01-17T23:01:10Z","doi":"10.1016/j.devcel.2020.12.002","date_published":"2021-01-25T00:00:00Z","page":"P213-226","publication":"Developmental Cell","day":"25","year":"2021","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"9006","department":[{"_id":"CaHe"}],"date_updated":"2024-03-27T23:30:18Z","intvolume":" 56","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","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"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"9623","status":"public"}]},"issue":"2","volume":56,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]}},{"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","full_name":"Morandell, Jasmin","last_name":"Morandell"},{"last_name":"Schwarz","full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A"},{"full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan"},{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A"},{"first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel","last_name":"Nicolas"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","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"},{"full_name":"Dobler, Zoe","last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","first_name":"Zoe"},{"first_name":"Emanuele","last_name":"Cacci","full_name":"Cacci, Emanuele"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"external_id":{"isi":["000658769900010"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","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."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Neural stem cells in autism and epilepsy","grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"3058","doi":"10.1038/s41467-021-23123-x","date_published":"2021-05-24T00:00:00Z","date_created":"2021-05-28T11:49:46Z","day":"24","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2021","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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).","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2021-05-28T12:39:43Z","ddc":["572"],"date_updated":"2024-03-27T23:30:23Z","status":"public","keyword":["General Biochemistry","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)"},"_id":"9429","volume":12,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7800"},{"relation":"dissertation_contains","id":"12401","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}]},"issue":"1","ec_funded":1,"file":[{"success":1,"file_id":"9430","checksum":"337e0f7959c35ec959984cacdcb472ba","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_NatureCommunications_Morandell.pdf","date_created":"2021-05-28T12:39:43Z","file_size":9358599,"date_updated":"2021-05-28T12:39:43Z","creator":"kschuh"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","month":"05","intvolume":" 12","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"}]},{"_id":"10058","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":"dissertation","keyword":["qubits","quantum computing","holes"],"status":"public","date_updated":"2023-09-08T11:41:08Z","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"ddc":["621","539"],"file_date_updated":"2022-12-20T23:30:07Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2022-12-20T23:30:07Z","file_size":32397600,"creator":"djirovec","date_created":"2021-09-30T14:29:14Z","file_name":"PHD_Thesis_Jirovec_Source.zip","content_type":"application/x-zip-compressed","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","file_id":"10061"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_id":"10087","embargo":"2022-10-06","date_updated":"2022-12-20T23:30:07Z","file_size":26910829,"creator":"djirovec","date_created":"2021-10-05T07:56:49Z","file_name":"PHD_Thesis_pdfa2b_1.pdf"}],"related_material":{"record":[{"status":"public","id":"8831","relation":"part_of_dissertation"},{"id":"10065","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10066","relation":"part_of_dissertation"},{"id":"8909","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5816","status":"public"}]},"project":[{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"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.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","ieee":"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","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"}],"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","day":"05","page":"151","date_created":"2021-09-30T07:53:49Z","date_published":"2021-10-05T00:00:00Z","doi":"10.15479/at:ista:10058"},{"status":"public","type":"journal_article","article_type":"original","_id":"8909","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"date_updated":"2024-03-27T23:30:26Z","month":"08","intvolume":" 20","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.13755"}],"oa_version":"Preprint","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."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"related_material":{"record":[{"relation":"research_data","id":"9323","status":"public"},{"id":"10058","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}]},"issue":"8","volume":20,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"publication_status":"published","project":[{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"title":"A singlet triplet hole spin qubit in planar Ge","author":[{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"last_name":"Hofmann","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"full_name":"Mutter, Philipp M.","last_name":"Mutter","first_name":"Philipp M."},{"full_name":"Tavani, Giulio","last_name":"Tavani","first_name":"Giulio"},{"last_name":"Botifoll","full_name":"Botifoll, Marc","first_name":"Marc"},{"full_name":"Crippa, Alessandro","orcid":"0000-0002-2968-611X","last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","first_name":"Alessandro"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver"},{"last_name":"Martins","orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","first_name":"Frederico"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Borovkov","full_name":"Borovkov, Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","first_name":"Maksim"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"article_processing_charge":"No","external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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.","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."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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_published":"2021-08-01T00:00:00Z","doi":"10.1038/s41563-021-01022-2","date_created":"2020-12-02T10:50:47Z","page":"1106–1112","day":"01","publication":"Nature Materials","isi":1,"year":"2021"},{"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.","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.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Huljev, Karla","last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","year":"2021","has_accepted_license":"1","day":"18","page":"101","date_created":"2021-05-17T12:31:30Z","date_published":"2021-05-18T00:00:00Z","doi":"10.15479/at:ista:9397","oa":1,"publisher":"Institute of Science and Technology Austria","date_updated":"2023-09-07T13:32:32Z","supervisor":[{"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"}],"ddc":["571"],"file_date_updated":"2022-05-21T22:30:04Z","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"_id":"9397","type":"dissertation","status":"public","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-05-17T12:29:12Z","file_name":"KHuljev_Thesis_corrections.docx","creator":"khuljev","date_updated":"2022-05-21T22:30:04Z","file_size":47799741,"file_id":"9398","checksum":"7f98532f5324a0b2f3fa8de2967baa19","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"embargo":"2022-05-20","checksum":"bf512f8a1e572a543778fc4b227c01ba","file_id":"9401","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"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05"},{"type":"preprint","project":[{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","_id":"10066","article_number":"2107.12975","external_id":{"arxiv":["2107.12975"]},"article_processing_charge":"No","author":[{"first_name":"B.","full_name":"Severin, B.","last_name":"Severin"},{"first_name":"D. T.","last_name":"Lennon","full_name":"Lennon, D. T."},{"full_name":"Camenzind, L. C.","last_name":"Camenzind","first_name":"L. C."},{"first_name":"F.","last_name":"Vigneau","full_name":"Vigneau, F."},{"last_name":"Fedele","full_name":"Fedele, F.","first_name":"F."},{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"A.","last_name":"Ballabio","full_name":"Ballabio, A."},{"first_name":"D.","last_name":"Chrastina","full_name":"Chrastina, D."},{"first_name":"G.","full_name":"Isella, G.","last_name":"Isella"},{"last_name":"Kruijf","full_name":"Kruijf, M. de","first_name":"M. de"},{"first_name":"M. J.","full_name":"Carballido, M. J.","last_name":"Carballido"},{"first_name":"S.","full_name":"Svab, S.","last_name":"Svab"},{"full_name":"Kuhlmann, A. V.","last_name":"Kuhlmann","first_name":"A. V."},{"first_name":"F. R.","full_name":"Braakman, F. R.","last_name":"Braakman"},{"first_name":"S.","last_name":"Geyer","full_name":"Geyer, S."},{"last_name":"Froning","full_name":"Froning, F. N. M.","first_name":"F. N. M."},{"full_name":"Moon, H.","last_name":"Moon","first_name":"H."},{"last_name":"Osborne","full_name":"Osborne, M. A.","first_name":"M. A."},{"last_name":"Sejdinovic","full_name":"Sejdinovic, D.","first_name":"D."},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"},{"last_name":"Zumbühl","full_name":"Zumbühl, D. M.","first_name":"D. M."},{"first_name":"G. A. D.","full_name":"Briggs, G. A. D.","last_name":"Briggs"},{"first_name":"N.","last_name":"Ares","full_name":"Ares, N."}],"department":[{"_id":"GeKa"}],"title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","date_updated":"2024-03-27T23:30:26Z","citation":{"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.","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","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","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. .","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12975","open_access":"1"}],"oa":1,"month":"07","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"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.","oa_version":"Preprint","date_created":"2021-10-01T12:40:22Z","related_material":{"record":[{"relation":"dissertation_contains","id":"10058","status":"public"}]},"doi":"10.48550/arXiv.2107.12975","date_published":"2021-07-27T00:00:00Z","year":"2021","publication_status":"submitted","publication":"arXiv","language":[{"iso":"eng"}],"day":"27"},{"citation":{"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.","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.","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","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.","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).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000651761700001"]},"article_processing_charge":"No","author":[{"first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481"},{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676"},{"first_name":"Diego","last_name":"Fernández-Fernández","full_name":"Fernández-Fernández, Diego"},{"full_name":"Fritzius, Thorsten","last_name":"Fritzius","first_name":"Thorsten"},{"full_name":"Kleindienst, David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Önal","full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"last_name":"Gassmann","full_name":"Gassmann, Martin","first_name":"Martin"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"full_name":"Kulik, Akos","last_name":"Kulik","first_name":"Akos"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"}],"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","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","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2021","isi":1,"has_accepted_license":"1","publication":"eLife","day":"29","date_created":"2021-05-30T22:01:23Z","date_published":"2021-04-29T00:00:00Z","doi":"10.7554/ELIFE.68274","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","date_updated":"2024-03-27T23:30:30Z","ddc":["570"],"department":[{"_id":"RySh"},{"_id":"PeJo"}],"file_date_updated":"2021-05-31T09:43:09Z","_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","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6ebcb79999f889766f7cd79ee134ad28","file_id":"9440","creator":"cziletti","file_size":8174719,"date_updated":"2021-05-31T09:43:09Z","file_name":"2021_eLife_Bhandari.pdf","date_created":"2021-05-31T09:43:09Z"}],"ec_funded":1,"related_material":{"link":[{"url":"https://doi.org/10.1101/2020.04.16.045112","relation":"earlier_version"}],"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"volume":10,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"04"},{"type":"dissertation","status":"public","_id":"9562","file_date_updated":"2022-07-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"date_updated":"2023-09-11T12:55:53Z","supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"ddc":["570"],"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9756"},{"relation":"part_of_dissertation","status":"public","id":"9437"},{"status":"public","id":"8532","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"612"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis.pdf","date_created":"2021-06-17T14:03:14Z","creator":"dkleindienst","file_size":77299142,"date_updated":"2022-07-02T22:30:04Z","embargo":"2022-07-01","file_id":"9563","checksum":"659df5518db495f679cb1df9e9bd1d94","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_name":"Thesis_source.zip","date_created":"2021-06-17T14:04:30Z","creator":"dkleindienst","file_size":369804895,"date_updated":"2022-07-02T22:30:04Z","checksum":"3bcf63a2b19e5b6663be051bea332748","file_id":"9564","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip"}],"article_processing_charge":"No","author":[{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","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.","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"124","date_created":"2021-06-17T14:10:47Z","date_published":"2021-06-01T00:00:00Z","doi":"10.15479/at:ista:9562","year":"2021","has_accepted_license":"1","day":"01"},{"language":[{"iso":"eng"}],"file":[{"creator":"akafshda","file_size":5251507,"date_updated":"2021-12-23T23:30:04Z","file_name":"Thesis-pdfa.pdf","date_created":"2020-12-22T20:08:44Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2021-12-22","checksum":"d1b9db3725aed34dadd81274aeb9426c","file_id":"8969"},{"file_name":"source.zip","date_created":"2020-12-22T20:08:50Z","creator":"akafshda","file_size":10636756,"date_updated":"2021-03-04T23:30:04Z","file_id":"8970","checksum":"1661df7b393e6866d2460eba3c905130","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"1386","relation":"part_of_dissertation"},{"status":"public","id":"1437","relation":"part_of_dissertation"},{"status":"public","id":"311","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6056","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6380"},{"relation":"part_of_dissertation","id":"639","status":"public"},{"id":"66","status":"public","relation":"part_of_dissertation"},{"id":"6780","status":"public","relation":"part_of_dissertation"},{"id":"6918","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7810"},{"status":"public","id":"6175","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6378"},{"id":"6490","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7014","status":"public"},{"relation":"part_of_dissertation","id":"8089","status":"public"},{"relation":"part_of_dissertation","id":"8728","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7158"},{"relation":"part_of_dissertation","id":"5977","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6009"},{"relation":"part_of_dissertation","status":"public","id":"6340"},{"relation":"part_of_dissertation","status":"public","id":"949"}]},"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"01","alternative_title":["ISTA Thesis"],"ddc":["005"],"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"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"file_date_updated":"2021-12-23T23:30:04Z","_id":"8934","status":"public","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","day":"01","year":"2021","has_accepted_license":"1","date_created":"2020-12-10T12:17:07Z","doi":"10.15479/AT:ISTA:8934","date_published":"2021-01-01T00:00:00Z","page":"278","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","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","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.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","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","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."},"title":"Parameterized and algebro-geometric advances in static program analysis","article_processing_charge":"No","author":[{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady"}],"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"}]},{"ddc":["570"],"date_updated":"2023-09-07T13:34:38Z","supervisor":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","last_name":"Sixt"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"file_date_updated":"2022-12-20T23:30:05Z","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"_id":"10307","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"creator":"ktomasek","file_size":13266088,"date_updated":"2022-12-20T23:30:05Z","file_name":"ThesisTomasekKathrin.pdf","date_created":"2021-11-18T15:07:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-11-18","checksum":"b39c9e0ef18d0484d537a67551effd02","file_id":"10308"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_id":"10309","file_size":7539509,"date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek","file_name":"ThesisTomasekKathrin.docx","date_created":"2021-11-18T15:07:46Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"10316","status":"public"}]},"oa_version":"Published Version","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"}],"month":"11","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","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.","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","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307."},"title":"Pathogenic Escherichia coli hijack the host immune response","article_processing_charge":"No","author":[{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin"}],"day":"18","year":"2021","has_accepted_license":"1","date_created":"2021-11-18T15:05:06Z","doi":"10.15479/at:ista:10307","date_published":"2021-11-18T00:00:00Z","page":"73","oa":1,"publisher":"Institute of Science and Technology Austria"},{"status":"public","project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911","call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425"}],"type":"preprint","_id":"10316","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"last_name":"Glatzová","full_name":"Glatzová, Ivana","first_name":"Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d"},{"full_name":"Lukesch, Michael S.","last_name":"Lukesch","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"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","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","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","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.","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.","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."},"date_updated":"2024-03-27T23:30:35Z","month":"10","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"oa":1,"oa_version":"Preprint","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.","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"}],"related_material":{"record":[{"relation":"later_version","id":"11843","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10307"}]},"doi":"10.1101/2021.10.18.464770","date_published":"2021-10-18T00:00:00Z","ec_funded":1,"date_created":"2021-11-19T12:24:16Z","day":"18","publication":"bioRxiv","language":[{"iso":"eng"}],"year":"2021","publication_status":"submitted"},{"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","oa":1,"publisher":"Embo Press","quality_controlled":"1","year":"2021","has_accepted_license":"1","isi":1,"publication":"EMBO Journal","day":"01","date_created":"2021-01-17T23:01:12Z","doi":"10.15252/embj.2020106862","date_published":"2021-02-01T00:00:00Z","article_number":"e106862","project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"},{"_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","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"citation":{"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.","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.","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.","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.","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).","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"author":[{"last_name":"Ötvös","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"last_name":"Vega","full_name":"Vega, Andrea","first_name":"Andrea"},{"full_name":"O’Brien, Jose","last_name":"O’Brien","first_name":"Jose"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed"},{"last_name":"Antonielli","full_name":"Antonielli, Livio","first_name":"Livio"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"last_name":"Cuesta","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Artner","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina"},{"last_name":"Bouguyon","full_name":"Bouguyon, Eleonore","first_name":"Eleonore"},{"last_name":"Gojon","full_name":"Gojon, Alain","first_name":"Alain"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez","first_name":"Rodrigo A."},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","acknowledged_ssus":[{"_id":"Bio"}],"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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 40","month":"02","publication_status":"published","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"dc55c900f3b061d6c2790b8813d759a3","file_id":"9110","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_Embo_Otvos.pdf","date_created":"2021-02-11T12:28:29Z","file_size":2358617,"date_updated":"2021-02-11T12:28:29Z","creator":"dernst"}],"issue":"3","volume":40,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","description":"News on IST Homepage"}]},"_id":"9010","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":"2024-03-27T23:30:39Z","ddc":["580"],"file_date_updated":"2021-02-11T12:28:29Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}]},{"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":"9913","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"file_date_updated":"2021-10-05T13:36:42Z","date_updated":"2024-03-27T23:30:39Z","ddc":["580"],"scopus_import":"1","intvolume":" 22","month":"09","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":22,"issue":"9","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}]},"publication_status":"published","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"10090","checksum":"750de03dc3b715c37090126c1548ba13","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_EmboR_Vega.pdf","date_created":"2021-10-05T13:36:42Z","file_size":3144854,"date_updated":"2021-10-05T13:36:42Z","creator":"cchlebak"}],"article_number":"e51813","article_processing_charge":"Yes","external_id":{"isi":["000681754200001"],"pmid":["34357701 "]},"author":[{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"full_name":"Fredes, Isabel","last_name":"Fredes","first_name":"Isabel"},{"first_name":"José","full_name":"O’Brien, José","last_name":"O’Brien"},{"full_name":"Shen, Zhouxin","last_name":"Shen","first_name":"Zhouxin"},{"first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"last_name":"Abualia","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Briggs, Steven P.","last_name":"Briggs","first_name":"Steven P."},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."}],"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","citation":{"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.","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.","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.","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","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","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.","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Wiley","quality_controlled":"1","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).","date_created":"2021-08-15T22:01:30Z","doi":"10.15252/embr.202051813","date_published":"2021-09-06T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"EMBO Reports","day":"06"},{"_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)"},"ddc":["580","581"],"supervisor":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-19T14:42:45Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:06Z","oa_version":"Published Version","abstract":[{"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. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"11","alternative_title":["ISTA Thesis"],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"dea38b98aa4da1cea03dcd0f10862818","file_id":"10331","embargo":"2022-11-23","creator":"rabualia","date_updated":"2022-12-20T23:30:06Z","file_size":28005730,"date_created":"2021-11-22T14:48:21Z","file_name":"AbualiaPhDthesisfinalv3.pdf"},{"file_name":"AbualiaPhDthesisfinalv3.docx","date_created":"2021-11-22T14:48:34Z","creator":"rabualia","file_size":62841883,"date_updated":"2022-12-20T23:30:06Z","file_id":"10332","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"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"},{"relation":"part_of_dissertation","id":"47","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","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.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 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","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303."},"title":"Role of hormones in nitrate regulated growth","author":[{"last_name":"Abualia","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"22","has_accepted_license":"1","year":"2021","date_published":"2021-11-22T00:00:00Z","doi":"10.15479/at:ista:10303","date_created":"2021-11-18T11:20:59Z","page":"139"},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"02","year":"2021","has_accepted_license":"1","date_created":"2021-08-29T12:36:50Z","doi":"10.15479/at:ista:9962","date_published":"2021-09-02T00:00:00Z","page":"182","project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","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.","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.","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.","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"},"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","article_processing_charge":"No","author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"date_created":"2021-08-30T09:17:39Z","file_name":"Thesis_Hansen.docx","creator":"ahansen","date_updated":"2022-09-03T22:30:04Z","file_size":10629190,"checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","file_id":"9971","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-09-02","file_id":"9972","checksum":"204fa40321a1c6289b68c473634c4bf3","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"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"8569","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"960"}]},"_id":"9962","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"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":"dissertation","ddc":["570"],"date_updated":"2023-09-22T09:58:30Z","supervisor":[{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"file_date_updated":"2022-09-03T22:30:04Z"}]