[{"page":"249","OA_place":"publisher","publication_status":"published","doi":"10.15479/AT:ISTA:8822","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization."}],"oa_version":"Published Version","citation":{"ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","mla":"Hajny, Jakub. <i>Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>.","chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>.","apa":"Hajny, J. (2020). <i>Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria."},"month":"12","status":"public","related_material":{"record":[{"id":"449","status":"public","relation":"part_of_dissertation"},{"id":"7500","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6260","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7427"},{"relation":"part_of_dissertation","status":"public","id":"191"}]},"oa":1,"file_date_updated":"2021-12-08T23:30:03Z","ddc":["580"],"date_published":"2020-12-01T00:00:00Z","supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"date_updated":"2026-04-08T07:28:35Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","year":"2020","has_accepted_license":"1","type":"dissertation","language":[{"iso":"eng"}],"_id":"8822","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","last_name":"Hajny","full_name":"Hajny, Jakub","first_name":"Jakub"}],"title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","article_processing_charge":"No","date_created":"2020-12-01T12:38:18Z","corr_author":"1","file":[{"embargo_to":"open_access","creator":"jhajny","file_size":91279806,"file_name":"Jakub Hajný IST Austria final_JH.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8919","date_created":"2020-12-04T07:27:52Z","date_updated":"2021-07-16T22:30:03Z","checksum":"210a9675af5e4c78b0b56d920ac82866","relation":"source_file"},{"file_id":"8933","date_created":"2020-12-09T15:04:41Z","access_level":"open_access","file_size":68707697,"file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","content_type":"application/pdf","creator":"jhajny","relation":"main_file","checksum":"1781385b4aa73eba89cc76c6172f71d2","date_updated":"2021-12-08T23:30:03Z","embargo":"2021-12-07"}],"degree_awarded":"PhD"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","year":"2020","day":"30","acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","ddc":["570"],"date_published":"2020-12-30T00:00:00Z","oa":1,"file_date_updated":"2021-12-31T23:30:04Z","date_updated":"2026-04-08T07:28:54Z","supervisor":[{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","first_name":"Daria E"}],"citation":{"ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","apa":"Emtenani, S. (2020). <i>Metabolic regulation of Drosophila macrophage tissue invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>.","mla":"Emtenani, Shamsi. <i>Metabolic Regulation of Drosophila Macrophage Tissue Invasion</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>."},"oa_version":"Published Version","related_material":{"record":[{"id":"8557","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6187","status":"public"}]},"status":"public","month":"12","OA_place":"publisher","publication_status":"published","page":"141","doi":"10.15479/AT:ISTA:8983","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers.","lang":"eng"}],"corr_author":"1","date_created":"2020-12-30T15:41:26Z","degree_awarded":"PhD","file":[{"creator":"semtenan","file_size":10848175,"file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"8984","date_created":"2020-12-30T15:34:01Z","date_updated":"2021-12-31T23:30:04Z","embargo":"2021-12-30","checksum":"ec2797ab7a6f253b35df0572b36d1b43","relation":"main_file"},{"content_type":"application/pdf","file_size":10073648,"access_level":"closed","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","date_created":"2020-12-30T15:37:36Z","file_id":"8985","embargo_to":"open_access","creator":"semtenan","relation":"source_file","date_updated":"2021-12-31T23:30:04Z","checksum":"cc30e6608a9815414024cf548dff3b3a"}],"article_processing_charge":"No","title":"Metabolic regulation of Drosophila macrophage tissue invasion","publisher":"Institute of Science and Technology Austria","department":[{"_id":"DaSi"}],"author":[{"id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","last_name":"Emtenani","full_name":"Emtenani, Shamsi","first_name":"Shamsi"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"_id":"8983","language":[{"iso":"eng"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]}},{"day":"18","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-23T09:36:47Z","corr_author":"1","title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","article_processing_charge":"No","date_updated":"2026-04-15T22:31:06Z","oa":1,"date_published":"2020-09-18T00:00:00Z","acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","publication":"bioRxiv","month":"09","status":"public","main_file_link":[{"url":"https://doi.org/10.1101/2020.09.18.301481","open_access":"1"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10614"},{"relation":"dissertation_contains","status":"public","id":"8983"}]},"author":[{"first_name":"Vera","full_name":"Belyaeva, Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","full_name":"Wachner, Stephanie"},{"first_name":"Igor","full_name":"Gridchyn, Igor","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929"},{"first_name":"Markus","full_name":"Linder, Markus","last_name":"Linder"},{"id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","last_name":"Emtenani","full_name":"Emtenani, Shamsi","first_name":"Shamsi"},{"first_name":"Attila","full_name":"György, Attila","last_name":"György","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","full_name":"Sibilia, Maria","last_name":"Sibilia"},{"first_name":"Daria E","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"citation":{"ieee":"V. Belyaeva <i>et al.</i>, “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” <i>bioRxiv</i>. .","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, <a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>.","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>."},"abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues."}],"doi":"10.1101/2020.09.18.301481","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions"},{"name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration","_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800"}],"type":"preprint","language":[{"iso":"eng"}],"ec_funded":1,"publication_status":"draft","acknowledged_ssus":[{"_id":"LifeSc"}],"_id":"8557"},{"abstract":[{"text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies.","lang":"eng"}],"doi":"10.15479/AT:ISTA:8340","alternative_title":["ISTA Thesis"],"OA_place":"publisher","publication_status":"published","page":"242","status":"public","month":"09","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6848"}]},"oa_version":"None","citation":{"mla":"Kampjut, Domen. <i>Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>.","chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>.","apa":"Kampjut, D. (2020). <i>Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020."},"supervisor":[{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"date_updated":"2026-04-08T07:43:58Z","file_date_updated":"2021-09-11T22:30:04Z","oa":1,"ddc":["572"],"date_published":"2020-09-09T00:00:00Z","acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","day":"09","year":"2020","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-008-4"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"type":"dissertation","language":[{"iso":"eng"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"_id":"8340","author":[{"last_name":"Kampjut","orcid":"0000-0002-6018-3422","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen","full_name":"Kampjut, Domen"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"LeSa"}],"title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","article_processing_charge":"No","file":[{"creator":"dkampjut","embargo_to":"open_access","date_created":"2020-09-08T13:32:06Z","file_id":"8345","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"ThesisFull20200908.docx","file_size":166146359,"checksum":"dd270baf82121eb4472ad19d77bf227c","date_updated":"2021-09-11T22:30:04Z","relation":"source_file"},{"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Thesis_Kampjut.pdf","file_size":13873769,"date_created":"2020-09-14T15:02:20Z","file_id":"8393","creator":"dernst","relation":"main_file","embargo":"2021-09-10","date_updated":"2021-09-11T22:30:04Z","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c"}],"degree_awarded":"PhD","date_created":"2020-09-07T18:42:23Z","corr_author":"1"},{"article_type":"original","external_id":{"isi":["000519008300005"],"pmid":["32152532"]},"article_processing_charge":"No","title":"Gene amplification as a form of population-level gene expression regulation","date_created":"2020-04-08T15:20:53Z","file":[{"checksum":"ef3bbf42023e30b2c24a6278025d2040","date_updated":"2020-10-09T09:56:01Z","relation":"main_file","creator":"dernst","date_created":"2020-10-09T09:56:01Z","file_id":"8640","success":1,"content_type":"application/pdf","file_name":"2020_NatureEcolEvo_Tomanek.pdf","file_size":745242,"access_level":"open_access"}],"language":[{"iso":"eng"}],"type":"journal_article","_id":"7652","intvolume":"         4","publication_identifier":{"issn":["2397-334X"]},"project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"issue":"4","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publisher":"Springer Nature","author":[{"full_name":"Tomanek, Isabella","first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","last_name":"Tomanek"},{"first_name":"Rok","full_name":"Grah, Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560"},{"last_name":"Lagator","first_name":"M.","full_name":"Lagator, M."},{"last_name":"Andersson","full_name":"Andersson, A. M. C.","first_name":"A. M. C."},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C"}],"quality_controlled":"1","ddc":["570"],"date_published":"2020-04-01T00:00:00Z","file_date_updated":"2020-10-09T09:56:01Z","oa":1,"publication":"Nature Ecology & Evolution","acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","isi":1,"volume":4,"date_updated":"2026-04-15T22:31:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","day":"01","has_accepted_license":"1","year":"2020","publication_status":"published","page":"612-625","doi":"10.1038/s41559-020-1132-7","abstract":[{"text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature.","lang":"eng"}],"pmid":1,"citation":{"ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. 2020;4(4):612-625. doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology &#38; Evolution 4 (2020) 612–625.","ieee":"I. Tomanek <i>et al.</i>, “Gene amplification as a form of population-level gene expression regulation,” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>.","chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., &#38; Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology &#38; Evolution. 4(4), 612–625."},"oa_version":"Submitted Version","month":"04","status":"public","related_material":{"record":[{"relation":"research_data","status":"public","id":"7016"},{"id":"7383","status":"public","relation":"research_data"},{"status":"public","id":"8155","relation":"dissertation_contains"},{"status":"public","id":"8653","relation":"used_in_publication"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","description":"News on IST Homepage"}]}},{"author":[{"last_name":"Tomanek","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella","full_name":"Tomanek, Isabella"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"publication_identifier":{"issn":["2663-337X"]},"_id":"8653","type":"dissertation","language":[{"iso":"eng"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_ITomanek_final_201016.docx","file_size":25131884,"access_level":"closed","date_created":"2020-10-16T12:14:21Z","file_id":"8666","embargo_to":"open_access","creator":"itomanek","relation":"source_file","date_updated":"2021-10-20T22:30:03Z","checksum":"c01d9f59794b4b70528f37637c17ad02"},{"checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","date_updated":"2021-10-20T22:30:03Z","embargo":"2021-10-19","relation":"main_file","creator":"itomanek","date_created":"2020-10-16T12:14:21Z","file_id":"8667","content_type":"application/pdf","access_level":"open_access","file_size":15405675,"file_name":"Thesis_ITomanek_final_201016.pdf"}],"degree_awarded":"PhD","corr_author":"1","date_created":"2020-10-13T13:02:33Z","title":"The evolution of gene expression by copy number and point mutations","article_processing_charge":"No","related_material":{"record":[{"relation":"research_data","id":"7652","status":"public"}]},"month":"10","status":"public","oa_version":"Published Version","citation":{"ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8653\">10.15479/AT:ISTA:8653</a>","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","apa":"Tomanek, I. (2020). <i>The evolution of gene expression by copy number and point mutations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8653\">https://doi.org/10.15479/AT:ISTA:8653</a>","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8653\">https://doi.org/10.15479/AT:ISTA:8653</a>.","mla":"Tomanek, Isabella. <i>The Evolution of Gene Expression by Copy Number and Point Mutations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8653\">10.15479/AT:ISTA:8653</a>."},"alternative_title":["ISTA Thesis"],"abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously.  Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments.  ","lang":"eng"}],"doi":"10.15479/AT:ISTA:8653","publication_status":"published","page":"117","OA_place":"publisher","year":"2020","has_accepted_license":"1","day":"13","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"date_updated":"2026-04-08T07:29:19Z","supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"file_date_updated":"2021-10-20T22:30:03Z","oa":1,"date_published":"2020-10-13T00:00:00Z","ddc":["576"]},{"oa_version":"Published Version","citation":{"apa":"Morandell, J. (2020). <i>Illuminating the role of Cul3 in autism spectrum disorder pathogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8620\">https://doi.org/10.15479/AT:ISTA:8620</a>","ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria.","mla":"Morandell, Jasmin. <i>Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8620\">10.15479/AT:ISTA:8620</a>.","chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8620\">https://doi.org/10.15479/AT:ISTA:8620</a>.","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","short":"J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020.","ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8620\">10.15479/AT:ISTA:8620</a>"},"status":"public","month":"10","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7800"},{"id":"8131","status":"public","relation":"part_of_dissertation"}]},"page":"138","publication_status":"published","OA_place":"publisher","abstract":[{"lang":"eng","text":"The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages."}],"doi":"10.15479/AT:ISTA:8620","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"12","year":"2020","has_accepted_license":"1","oa":1,"file_date_updated":"2021-10-16T22:30:04Z","date_published":"2020-10-12T00:00:00Z","ddc":["610"],"acknowledgement":"I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support.","supervisor":[{"first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-14T09:07:16Z","department":[{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Morandell, Jasmin","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell"}],"type":"dissertation","language":[{"iso":"eng"}],"_id":"8620","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and 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pathogenesis","article_processing_charge":"No"},{"file":[{"date_updated":"2020-07-14T12:48:03Z","checksum":"c6799ab5daba80efe8e2ed63c15f8c81","relation":"main_file","creator":"rsix","content_type":"application/pdf","file_name":"2020.01.10.902064v1.full.pdf","file_size":2931370,"access_level":"open_access","date_created":"2020-05-05T14:31:19Z","file_id":"7801"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"corr_author":"1","date_created":"2020-05-05T14:31:33Z","article_processing_charge":"No","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","author":[{"first_name":"Jasmin","full_name":"Morandell, Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lena A","full_name":"Schwarz, Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","full_name":"Basilico, Bernadette","first_name":"Bernadette"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","last_name":"Tasciyan","full_name":"Tasciyan, Saren","first_name":"Saren"},{"last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","full_name":"Nicolas, Armel"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","full_name":"Knaus, Lisa","first_name":"Lisa"},{"first_name":"Zoe","full_name":"Dobler, Zoe","last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia"}],"department":[{"_id":"JoDa"},{"_id":"GaNo"},{"_id":"LifeSc"}],"publisher":"Cold Spring Harbor Laboratory","project":[{"grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"},{"grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"PreCl"}],"_id":"7800","language":[{"iso":"eng"}],"type":"preprint","has_accepted_license":"1","year":"2020","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-15T22:31:19Z","publication":"bioRxiv","date_published":"2020-01-11T00:00:00Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:03Z","oa":1,"related_material":{"record":[{"id":"9429","status":"public","relation":"later_version"},{"status":"public","id":"8620","relation":"dissertation_contains"}]},"month":"01","status":"public","citation":{"ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer, C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv (n.d.).","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.01.10.902064 \">10.1101/2020.01.10.902064 </a>","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv, <a href=\"https://doi.org/10.1101/2020.01.10.902064 \">10.1101/2020.01.10.902064 </a>.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer, C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.01.10.902064 \">https://doi.org/10.1101/2020.01.10.902064 </a>","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.01.10.902064 \">https://doi.org/10.1101/2020.01.10.902064 </a>.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.01.10.902064 \">10.1101/2020.01.10.902064 </a>."},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages."}],"doi":"10.1101/2020.01.10.902064 ","publication_status":"draft"},{"type":"journal_article","language":[{"iso":"eng"}],"ec_funded":1,"intvolume":"        65","_id":"8131","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy","grant_number":"F7807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}],"issue":"12","department":[{"_id":"GaNo"}],"publisher":"Elsevier","quality_controlled":"1","author":[{"first_name":"Bernadette","full_name":"Basilico, Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","full_name":"Morandell, Jasmin","first_name":"Jasmin"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia"}],"external_id":{"isi":["000598918900019"],"pmid":["32659636"]},"article_type":"original","title":"Molecular mechanisms for targeted ASD treatments","article_processing_charge":"Yes (via OA deal)","date_created":"2020-07-19T22:00:58Z","corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"file":[{"file_size":1381545,"access_level":"open_access","file_name":"2020_CurrentOpGenetics_Basilico.pdf","content_type":"application/pdf","file_id":"8146","success":1,"date_created":"2020-07-22T06:47:45Z","creator":"dernst","relation":"main_file","date_updated":"2020-07-22T06:47:45Z"}],"page":"126-137","publication_status":"published","abstract":[{"lang":"eng","text":"The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes."}],"doi":"10.1016/j.gde.2020.06.004","pmid":1,"oa_version":"Published Version","citation":{"ieee":"B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted ASD treatments,” <i>Current Opinion in Genetics and Development</i>, vol. 65, no. 12. Elsevier, pp. 126–137, 2020.","short":"B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development 65 (2020) 126–137.","ama":"Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. <i>Current Opinion in Genetics and Development</i>. 2020;65(12):126-137. doi:<a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">10.1016/j.gde.2020.06.004</a>","ista":"Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.","apa":"Basilico, B., Morandell, J., &#38; Novarino, G. (2020). Molecular mechanisms for targeted ASD treatments. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">https://doi.org/10.1016/j.gde.2020.06.004</a>","chicago":"Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms for Targeted ASD Treatments.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">https://doi.org/10.1016/j.gde.2020.06.004</a>.","mla":"Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.” <i>Current Opinion in Genetics and Development</i>, vol. 65, no. 12, Elsevier, 2020, pp. 126–37, doi:<a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">10.1016/j.gde.2020.06.004</a>."},"status":"public","month":"12","related_material":{"record":[{"id":"8620","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2020-07-22T06:47:45Z","oa":1,"date_published":"2020-12-01T00:00:00Z","ddc":["570"],"isi":1,"publication":"Current Opinion in Genetics and Development","volume":65,"date_updated":"2026-04-15T22:31:19Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","day":"01","year":"2020","has_accepted_license":"1"},{"external_id":{"pmid":["32581372"],"isi":["000532688300008"]},"article_type":"original","title":"Cellular locomotion using environmental topography","article_processing_charge":"No","date_created":"2020-05-24T22:01:01Z","type":"journal_article","language":[{"iso":"eng"}],"intvolume":"       582","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"_id":"7885","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911"},{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"}],"department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1101/793919","open_access":"1"}],"quality_controlled":"1","author":[{"orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","full_name":"Reversat, Anne","first_name":"Anne"},{"last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","first_name":"Florian R","full_name":"Gärtner, Florian R"},{"full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp"},{"first_name":"Saren","full_name":"Tasciyan, Saren","last_name":"Tasciyan","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aguilera Servin, Juan L","first_name":"Juan L","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin"},{"last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert"},{"first_name":"Miroslav","full_name":"Hons, Miroslav","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348"},{"last_name":"Piel","full_name":"Piel, Matthieu","first_name":"Matthieu"},{"last_name":"Callan-Jones","first_name":"Andrew","full_name":"Callan-Jones, Andrew"},{"last_name":"Voituriez","full_name":"Voituriez, Raphael","first_name":"Raphael"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"oa":1,"date_published":"2020-06-25T00:00:00Z","acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","publication":"Nature","isi":1,"volume":582,"date_updated":"2026-04-15T22:31:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","day":"25","year":"2020","page":"582–585","publication_status":"published","OA_place":"repository","doi":"10.1038/s41586-020-2283-z","abstract":[{"text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.","lang":"eng"}],"pmid":1,"OA_type":"green","oa_version":"Preprint","citation":{"ieee":"A. Reversat <i>et al.</i>, “Cellular locomotion using environmental topography,” <i>Nature</i>, vol. 582. Springer Nature, pp. 582–585, 2020.","short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. <i>Nature</i>. 2020;582:582–585. doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>","ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>","chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>.","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>, vol. 582, Springer Nature, 2020, pp. 582–585, doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>."},"month":"06","status":"public","related_material":{"record":[{"status":"public","id":"14697","relation":"dissertation_contains"},{"status":"public","id":"12401","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/"}]}},{"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","article_processing_charge":"No","external_id":{"isi":["000577280200001"],"pmid":["32901014"]},"article_type":"original","file":[{"relation":"main_file","date_updated":"2020-09-18T13:02:37Z","checksum":"88f92544889eb18bb38e25629a422a86","file_size":1002818,"access_level":"open_access","file_name":"2020_NatureComm_Arnold.pdf","content_type":"application/pdf","success":1,"file_id":"8530","date_created":"2020-09-18T13:02:37Z","creator":"dernst"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"corr_author":"1","date_created":"2020-09-18T10:56:20Z","project":[{"call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","call_identifier":"H2020","name":"Quantum readout techniques and technologies"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"publication_identifier":{"issn":["2041-1723"]},"intvolume":"        11","ec_funded":1,"_id":"8529","acknowledged_ssus":[{"_id":"NanoFab"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","article_number":"4460","author":[{"full_name":"Arnold, Georg M","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","last_name":"Arnold"},{"last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","first_name":"Matthias","full_name":"Wulf, Matthias"},{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","full_name":"Barzanjeh, Shabir"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena"},{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R"},{"last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","full_name":"Hease, William J"},{"last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","first_name":"Farid","full_name":"Hassani, Farid"},{"first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"department":[{"_id":"JoFi"}],"publisher":"Springer Nature","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_updated":"2026-04-15T22:31:25Z","volume":11,"isi":1,"acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","publication":"Nature Communications","file_date_updated":"2020-09-18T13:02:37Z","oa":1,"date_published":"2020-09-08T00:00:00Z","ddc":["530"],"year":"2020","has_accepted_license":"1","day":"08","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform."}],"doi":"10.1038/s41467-020-18269-z","publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"13056","status":"public"},{"relation":"dissertation_contains","id":"18871","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41467-020-18912-9","relation":"erratum"},{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release"}]},"month":"09","status":"public","oa_version":"Published Version","citation":{"ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>.","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>."},"pmid":1},{"external_id":{"isi":["000674680100001"]},"article_type":"original","title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","article_processing_charge":"No","date_created":"2021-02-12T10:41:28Z","corr_author":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","checksum":"b70b12ded6d7660d4c9037eb09bfed0c","date_updated":"2021-02-12T11:16:16Z","date_created":"2021-02-12T11:16:16Z","success":1,"file_id":"9115","content_type":"application/pdf","file_name":"2020_PRXQuantum_Hease.pdf","file_size":2146924,"access_level":"open_access","creator":"dernst"}],"type":"journal_article","language":[{"iso":"eng"}],"intvolume":"         1","ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"_id":"9114","publication_identifier":{"issn":["2691-3399"]},"project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"issue":"2","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"quality_controlled":"1","article_number":"020315","author":[{"first_name":"William J","full_name":"Hease, William J","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166"},{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez"},{"last_name":"Sahu","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","full_name":"Sahu, Rishabh"},{"last_name":"Wulf","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Wulf, Matthias"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","last_name":"Arnold","full_name":"Arnold, Georg M","first_name":"Georg M"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."},{"full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"file_date_updated":"2021-02-12T11:16:16Z","oa":1,"date_published":"2020-11-23T00:00:00Z","ddc":["530"],"isi":1,"publication":"PRX Quantum","acknowledgement":"The authors acknowledge the support of T. Menner, A. Arslani, and T. Asenov from the Miba machine shop for machining the microwave cavity, and thank S. Barzanjeh, F. Sedlmeir, and C. Marquardt for fruitful discussions. This work is supported by IST Austria and the European Research Council under Grant No. 758053 (ERC StG QUNNECT). W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411.\r\nG.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71) and the European Union’s Horizon 2020 research and innovation program under Grant No. 899354 (FET Open SuperQuLAN). H.G.L.S. acknowledges support from the Aotearoa/New Zealand’s MBIE Endeavour Smart Ideas Grant No UOOX1805.","volume":1,"date_updated":"2026-04-15T22:31:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","day":"23","year":"2020","has_accepted_license":"1","publication_status":"published","doi":"10.1103/prxquantum.1.020315","abstract":[{"text":"Microwave photonics lends the advantages of fiber optics to electronic sensing and communication systems. In contrast to nonlinear optics, electro-optic devices so far require classical modulation fields whose variance is dominated by electronic or thermal noise rather than quantum fluctuations. Here we demonstrate bidirectional single-sideband conversion of X band microwave to C band telecom light with a microwave mode occupancy as low as 0.025 ± 0.005 and an added output noise of less than or equal to 0.074 photons. This is facilitated by radiative cooling and a triply resonant ultra-low-loss transducer operating at millikelvin temperatures. The high bandwidth of 10.7 MHz and total (internal) photon conversion\r\nefficiency of 0.03% (0.67%) combined with the extremely slow heating rate of 1.1 added output noise photons per second for the highest available pump power of 1.48 mW puts near-unity efficiency pulsed quantum transduction within reach. Together with the non-Gaussian resources of superconducting qubits this might provide the practical foundation to extend the range and scope of current quantum networks in analogy to electrical repeaters in classical fiber optic communication.","lang":"eng"}],"oa_version":"Published Version","citation":{"ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel HGL, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. 1(2), 020315.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H. G. L., &#38; Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.1.020315\">https://doi.org/10.1103/prxquantum.1.020315</a>","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald G.L. Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” <i>PRX Quantum</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/prxquantum.1.020315\">https://doi.org/10.1103/prxquantum.1.020315</a>.","mla":"Hease, William J., et al. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” <i>PRX Quantum</i>, vol. 1, no. 2, 020315, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/prxquantum.1.020315\">10.1103/prxquantum.1.020315</a>.","ieee":"W. J. Hease <i>et al.</i>, “Bidirectional electro-optic wavelength conversion in the quantum ground state,” <i>PRX Quantum</i>, vol. 1, no. 2. American Physical Society, 2020.","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. <i>PRX Quantum</i>. 2020;1(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.1.020315\">10.1103/prxquantum.1.020315</a>","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H.G.L. Schwefel, J.M. Fink, PRX Quantum 1 (2020)."},"month":"11","status":"public","related_material":{"record":[{"status":"public","id":"13071","relation":"research_data"},{"id":"13175","status":"public","relation":"dissertation_contains"},{"status":"public","id":"12900","relation":"dissertation_contains"},{"id":"18871","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release"}]}},{"author":[{"last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Skrivan, Tomas"},{"last_name":"Soderstrom","first_name":"Andreas","full_name":"Soderstrom, Andreas"},{"last_name":"Johansson","full_name":"Johansson, John","first_name":"John"},{"full_name":"Sprenger, Christoph","first_name":"Christoph","last_name":"Sprenger"},{"last_name":"Museth","full_name":"Museth, Ken","first_name":"Ken"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"article_number":"65","quality_controlled":"1","issue":"4","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"language":[{"iso":"eng"}],"type":"journal_article","_id":"8535","acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"intvolume":"        39","file":[{"content_type":"application/pdf","file_size":20223953,"access_level":"open_access","file_name":"2020_ACM_Skrivan.pdf","date_created":"2020-09-21T07:51:44Z","file_id":"8541","success":1,"creator":"dernst","relation":"main_file","date_updated":"2020-09-21T07:51:44Z","checksum":"c3a680893f01cc4a9e961ff0a4cfa12f"}],"date_created":"2020-09-20T22:01:37Z","corr_author":"1","article_processing_charge":"No","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","article_type":"original","external_id":{"isi":["000583700300038"]},"month":"07","status":"public","citation":{"ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &#38; Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>.","mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>."},"oa_version":"Published Version","abstract":[{"text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.","lang":"eng"}],"doi":"10.1145/3386569.3392466","publication_status":"published","day":"08","has_accepted_license":"1","year":"2020","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","volume":39,"date_updated":"2026-04-16T08:26:38Z","date_published":"2020-07-08T00:00:00Z","ddc":["000"],"file_date_updated":"2020-09-21T07:51:44Z","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","publication":"ACM Transactions on Graphics","isi":1},{"status":"public","month":"01","pmid":1,"oa_version":"Published Version","citation":{"ama":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. <i>Journal of neuroscience</i>. 2020;40(1):131-142. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">10.1523/JNEUROSCI.1571-19.2019</a>","short":"L. Piriya Ananda Babu, H.Y. Wang, K. Eguchi, L. Guillaud, T. Takahashi, Journal of Neuroscience 40 (2020) 131–142.","ieee":"L. Piriya Ananda Babu, H. Y. Wang, K. Eguchi, L. Guillaud, and T. Takahashi, “Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission,” <i>Journal of neuroscience</i>, vol. 40, no. 1. Society for Neuroscience, pp. 131–142, 2020.","chicago":"Piriya Ananda Babu, Lashmi, Han Ying Wang, Kohgaku Eguchi, Laurent Guillaud, and Tomoyuki Takahashi. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2020. <a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">https://doi.org/10.1523/JNEUROSCI.1571-19.2019</a>.","mla":"Piriya Ananda Babu, Lashmi, et al. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” <i>Journal of Neuroscience</i>, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 131–42, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">10.1523/JNEUROSCI.1571-19.2019</a>.","ista":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. 2020. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of neuroscience. 40(1), 131–142.","apa":"Piriya Ananda Babu, L., Wang, H. Y., Eguchi, K., Guillaud, L., &#38; Takahashi, T. (2020). Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">https://doi.org/10.1523/JNEUROSCI.1571-19.2019</a>"},"doi":"10.1523/JNEUROSCI.1571-19.2019","abstract":[{"text":"Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission.","lang":"eng"}],"page":"131-142","publication_status":"published","day":"02","year":"2020","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","volume":40,"date_updated":"2026-04-16T08:27:29Z","oa":1,"file_date_updated":"2020-07-14T12:47:56Z","ddc":["570"],"date_published":"2020-01-02T00:00:00Z","publication":"Journal of neuroscience","isi":1,"quality_controlled":"1","author":[{"first_name":"Lashmi","full_name":"Piriya Ananda Babu, Lashmi","last_name":"Piriya Ananda Babu"},{"first_name":"Han Ying","full_name":"Wang, Han Ying","last_name":"Wang"},{"last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku"},{"last_name":"Guillaud","full_name":"Guillaud, Laurent","first_name":"Laurent"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"issue":"1","department":[{"_id":"RySh"}],"publisher":"Society for Neuroscience","publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"type":"journal_article","language":[{"iso":"eng"}],"intvolume":"        40","_id":"7339","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2020-01-20T14:44:10Z","file_id":"7345","content_type":"application/pdf","file_name":"2020_JourNeuroscience_Piriya.pdf","file_size":4460781,"access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"92f5e8a47f454fc131fb94cd7f106e60","date_updated":"2020-07-14T12:47:56Z"}],"date_created":"2020-01-19T23:00:38Z","title":"Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission","article_processing_charge":"No","external_id":{"isi":["000505167600013"],"pmid":["31767677"]},"article_type":"original"},{"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2020","day":"03","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","isi":1,"publication":"Physical Review Letters","date_published":"2020-07-03T00:00:00Z","arxiv":1,"oa":1,"date_updated":"2026-04-16T08:21:58Z","volume":125,"citation":{"ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. 2020;125(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","ieee":"A. S. Chatterley <i>et al.</i>, “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” <i>Physical Review Letters</i>, vol. 125, no. 1. American Physical Society, 2020.","chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>.","mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>.","ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>"},"oa_version":"Preprint","pmid":1,"month":"07","status":"public","publication_status":"published","abstract":[{"text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes.","lang":"eng"}],"doi":"10.1103/PhysRevLett.125.013001","date_created":"2020-07-26T22:01:02Z","article_type":"original","external_id":{"isi":["000544526900006"],"arxiv":["2006.02694"],"pmid":["32678640"]},"article_processing_charge":"No","title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","issue":"1","author":[{"last_name":"Chatterley","full_name":"Chatterley, Adam S.","first_name":"Adam S."},{"full_name":"Christiansen, Lars","first_name":"Lars","last_name":"Christiansen"},{"last_name":"Schouder","first_name":"Constant A.","full_name":"Schouder, Constant A."},{"first_name":"Anders V.","full_name":"Jørgensen, Anders V.","last_name":"Jørgensen"},{"last_name":"Shepperson","full_name":"Shepperson, Benjamin","first_name":"Benjamin"},{"last_name":"Cherepanov","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","full_name":"Cherepanov, Igor"},{"full_name":"Bighin, Giacomo","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","last_name":"Bighin"},{"first_name":"Robert E.","full_name":"Zillich, Robert E.","last_name":"Zillich"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"}],"quality_controlled":"1","article_number":"013001","main_file_link":[{"url":"https://arxiv.org/abs/2006.02694","open_access":"1"}],"_id":"8170","ec_funded":1,"intvolume":"       125","language":[{"iso":"eng"}],"type":"journal_article","project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]}},{"volume":14,"date_updated":"2026-04-16T08:28:50Z","date_published":"2020-03-13T00:00:00Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:01Z","oa":1,"isi":1,"publication":"Frontiers in Computational Neuroscience","day":"13","has_accepted_license":"1","year":"2020","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","abstract":[{"text":"We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement.","lang":"eng"}],"doi":"10.3389/fncom.2020.00020","publication_status":"published","month":"03","status":"public","pmid":1,"citation":{"ieee":"M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” <i>Frontiers in Computational Neuroscience</i>, vol. 14. Frontiers, 2020.","ama":"Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. <i>Frontiers in Computational Neuroscience</i>. 2020;14. doi:<a href=\"https://doi.org/10.3389/fncom.2020.00020\">10.3389/fncom.2020.00020</a>","short":"M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).","ista":"Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.","apa":"Berry, M. J., &#38; Tkačik, G. (2020). Clustering of neural activity: A design principle for population codes. <i>Frontiers in Computational Neuroscience</i>. Frontiers. <a href=\"https://doi.org/10.3389/fncom.2020.00020\">https://doi.org/10.3389/fncom.2020.00020</a>","chicago":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” <i>Frontiers in Computational Neuroscience</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fncom.2020.00020\">https://doi.org/10.3389/fncom.2020.00020</a>.","mla":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” <i>Frontiers in Computational Neuroscience</i>, vol. 14, 20, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fncom.2020.00020\">10.3389/fncom.2020.00020</a>."},"oa_version":"Published Version","article_processing_charge":"No","title":"Clustering of neural activity: A design principle for population codes","article_type":"original","external_id":{"isi":["000525543200001"],"pmid":["32231528"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","date_updated":"2020-07-14T12:48:01Z","checksum":"2b1da23823eae9cedbb42d701945b61e","file_size":4082937,"file_name":"2020_Frontiers_Berry.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"7659","date_created":"2020-04-14T12:20:39Z","creator":"dernst"}],"date_created":"2020-04-12T22:00:40Z","publication_identifier":{"eissn":["1662-5188"]},"language":[{"iso":"eng"}],"type":"journal_article","_id":"7656","intvolume":"        14","author":[{"full_name":"Berry, Michael J.","first_name":"Michael J.","last_name":"Berry"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"article_number":"20","quality_controlled":"1","publisher":"Frontiers","department":[{"_id":"GaTk"}]},{"date_created":"2020-03-22T23:00:46Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"dernst","file_size":507414,"access_level":"open_access","file_name":"2020_FrontiersPlants_Nimeth.pdf","content_type":"application/pdf","file_id":"7607","date_created":"2020-03-23T09:03:40Z","date_updated":"2020-07-14T12:48:01Z","checksum":"57c37209f7b6712ced86c0f11b2be74e","relation":"main_file"}],"article_type":"original","external_id":{"isi":["000518903600001"]},"article_processing_charge":"No","title":"Alternative splicing and DNA damage response in plants","publisher":"Frontiers","department":[{"_id":"FyKo"}],"author":[{"last_name":"Nimeth","full_name":"Nimeth, Barbara Anna","first_name":"Barbara Anna"},{"last_name":"Riegler","orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan","full_name":"Riegler, Stefan"},{"full_name":"Kalyna, Maria","first_name":"Maria","last_name":"Kalyna"}],"article_number":"91","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","_id":"7603","intvolume":"        11","publication_identifier":{"eissn":["1664-462X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","day":"19","has_accepted_license":"1","year":"2020","ddc":["580"],"date_published":"2020-02-19T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:48:01Z","isi":1,"publication":"Frontiers in Plant Science","volume":11,"date_updated":"2026-04-16T08:28:17Z","citation":{"short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","ama":"Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>","ieee":"B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","mla":"Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>, vol. 11, 91, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>.","chicago":"Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>.","apa":"Nimeth, B. A., Riegler, S., &#38; Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91."},"oa_version":"Published Version","status":"public","month":"02","publication_status":"published","abstract":[{"text":"Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.","lang":"eng"}],"doi":"10.3389/fpls.2020.00091"},{"external_id":{"isi":["000510916500025"],"arxiv":["1906.02785"]},"article_type":"original","title":"Limits on amplifiers of natural selection under death-Birth updating","article_processing_charge":"No","date_created":"2019-12-23T13:45:11Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"7441","date_created":"2020-02-03T07:32:42Z","access_level":"open_access","file_name":"2020_PlosCompBio_Tkadlec.pdf","file_size":1817531,"content_type":"application/pdf","creator":"dernst","relation":"main_file","checksum":"ce32ee2d2f53aed832f78bbd47e882df","date_updated":"2020-07-14T12:47:53Z"}],"type":"journal_article","language":[{"iso":"eng"}],"ec_funded":1,"intvolume":"        16","_id":"7212","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","article_number":"e1007494","quality_controlled":"1","author":[{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"file_date_updated":"2020-07-14T12:47:53Z","oa":1,"ddc":["000"],"arxiv":1,"date_published":"2020-01-17T00:00:00Z","isi":1,"publication":"PLoS computational biology","volume":16,"date_updated":"2026-04-16T08:32:38Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","day":"17","year":"2020","has_accepted_license":"1","publication_status":"published","abstract":[{"text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process.","lang":"eng"}],"doi":"10.1371/journal.pcbi.1007494","oa_version":"Published Version","citation":{"ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” <i>PLoS computational biology</i>, vol. 16. Public Library of Science, 2020.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. <i>PLoS computational biology</i>. 2020;16. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">10.1371/journal.pcbi.1007494</a>","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">https://doi.org/10.1371/journal.pcbi.1007494</a>","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” <i>PLoS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">https://doi.org/10.1371/journal.pcbi.1007494</a>.","mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” <i>PLoS Computational Biology</i>, vol. 16, e1007494, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">10.1371/journal.pcbi.1007494</a>."},"status":"public","month":"01","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7196"}]}},{"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2020","has_accepted_license":"1","day":"08","publication":"ACM Transactions on Graphics","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","isi":1,"oa":1,"file_date_updated":"2020-11-23T09:03:19Z","date_published":"2020-07-08T00:00:00Z","ddc":["000"],"date_updated":"2026-04-16T08:29:36Z","volume":39,"oa_version":"Submitted Version","citation":{"ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., &#38; Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>.","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>.","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020)."},"related_material":{"record":[{"status":"public","id":"19630","relation":"dissertation_contains"}]},"status":"public","month":"07","publication_status":"published","abstract":[{"lang":"eng","text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film."}],"doi":"10.1145/3386569.3392405","date_created":"2020-09-13T22:01:18Z","file":[{"relation":"main_file","date_updated":"2020-11-23T09:03:19Z","checksum":"813831ca91319d794d9748c276b24578","content_type":"application/pdf","access_level":"open_access","file_size":14935529,"file_name":"2020_soapfilm_submitted.pdf","date_created":"2020-11-23T09:03:19Z","success":1,"file_id":"8795","creator":"dernst"}],"external_id":{"isi":["000583700300004"]},"article_type":"original","title":"A model for soap film dynamics with evolving thickness","article_processing_charge":"No","department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","issue":"4","quality_controlled":"1","article_number":"31","author":[{"last_name":"Ishida","orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige","full_name":"Ishida, Sadashige"},{"id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak","full_name":"Synak, Peter","first_name":"Peter"},{"first_name":"Fumiya","full_name":"Narita, Fumiya","last_name":"Narita"},{"first_name":"Toshiya","full_name":"Hachisuka, Toshiya","last_name":"Hachisuka"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392405"}],"ec_funded":1,"intvolume":"        39","_id":"8384","acknowledged_ssus":[{"_id":"ScienComp"}],"type":"journal_article","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]}},{"publication_status":"published","abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"doi":"10.1145/3386569.3392412","citation":{"ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392412\">10.1145/3386569.3392412</a>","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392412\">https://doi.org/10.1145/3386569.3392412</a>.","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392412\">10.1145/3386569.3392412</a>.","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2020). Homogenized yarn-level cloth. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392412\">https://doi.org/10.1145/3386569.3392412</a>"},"oa_version":"Submitted Version","status":"public","month":"07","related_material":{"record":[{"id":"12358","status":"public","relation":"dissertation_contains"}]},"ddc":["000"],"date_published":"2020-07-08T00:00:00Z","oa":1,"file_date_updated":"2020-11-23T09:01:22Z","isi":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","publication":"ACM Transactions on Graphics","volume":39,"date_updated":"2026-04-16T08:31:55Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","day":"08","has_accepted_license":"1","year":"2020","language":[{"iso":"eng"}],"type":"journal_article","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"8385","ec_funded":1,"intvolume":"        39","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"issue":"4","department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392412"}],"author":[{"last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Sperl, Georg"},{"last_name":"Narain","full_name":"Narain, Rahul","first_name":"Rahul"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"article_number":"48","quality_controlled":"1","article_type":"original","external_id":{"isi":["000583700300021"]},"article_processing_charge":"No","title":"Homogenized yarn-level cloth","date_created":"2020-09-13T22:01:18Z","corr_author":"1","file":[{"creator":"dernst","date_created":"2020-11-23T09:01:22Z","success":1,"file_id":"8794","content_type":"application/pdf","file_name":"2020_hylc_submitted.pdf","file_size":38922662,"access_level":"open_access","checksum":"cf4c1d361c3196c4bd424520a5588205","date_updated":"2020-11-23T09:01:22Z","relation":"main_file"}]}]