[{"author":[{"full_name":"Arathoon, Louise S","first_name":"Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon"}],"publication_identifier":{"issn":["2663 - 337X"]},"month":"12","file":[{"creator":"larathoo","file_size":34101468,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"520bdb61e95e66070e02824947d2c5fa","file_name":"Phd_Thesis_LA.pdf","file_id":"14684","success":1,"date_updated":"2023-12-13T15:37:55Z","date_created":"2023-12-13T15:37:55Z"},{"creator":"larathoo","content_type":"application/zip","relation":"source_file","access_level":"closed","file_size":31052872,"checksum":"d8e59afd0817c98fba2564a264508e5c","file_name":"Phd_Thesis_LA.zip","file_id":"14685","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-13T15:42:23Z"},{"creator":"larathoo","file_size":10713896,"relation":"supplementary_material","content_type":"application/zip","access_level":"closed","checksum":"9a778c949932286f4519e1f1fca2820d","file_id":"14681","file_name":"Supplementary_Materials.zip","date_created":"2023-12-11T19:24:59Z","date_updated":"2023-12-14T08:58:18Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"12","oa_version":"Published Version","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","date_updated":"2023-12-22T11:04:45Z","oa":1,"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_status":"published","ddc":["570"],"abstract":[{"lang":"eng","text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism."}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"date_published":"2023-12-12T00:00:00Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"page":"96","year":"2023","date_created":"2023-12-11T19:30:37Z","citation":{"mla":"Arathoon, Louise S. <i>Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>","apa":"Arathoon, L. S. (2023). <i>Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>"},"related_material":{"record":[{"status":"public","id":"11411","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","ec_funded":1,"_id":"14651","file_date_updated":"2023-12-14T08:58:18Z","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.15479/at:ista:14651"},{"author":[{"first_name":"Yi-Lu","full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","last_name":"Chen"},{"id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","last_name":"Ly","first_name":"Mickaël","full_name":"Ly, Mickaël"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publication_identifier":{"isbn":["9798400702686"]},"month":"08","conference":{"start_date":"2023-08-04","name":"SCA: Symposium on Computer Animation","end_date":"2023-08-06","location":"Los Angeles, CA, United States"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"01","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"status":"public","date_published":"2023-08-01T00:00:00Z","type":"conference_abstract","publisher":"Association for Computing Machinery","quality_controlled":"1","department":[{"_id":"ChWo"}],"article_processing_charge":"No","year":"2023","acknowledgement":"We thank the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing, and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","date_updated":"2024-02-28T12:51:40Z","date_created":"2024-01-08T13:00:24Z","citation":{"apa":"Chen, Y.-L., Ly, M., &#38; Wojtan, C. (2023). Unified treatment of contact, friction and shock-propagation in rigid body animation. In <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3606037.3606836\">https://doi.org/10.1145/3606037.3606836</a>","ista":"Chen Y-L, Ly M, Wojtan C. 2023. Unified treatment of contact, friction and shock-propagation in rigid body animation. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: Symposium on Computer Animation, 5.","mla":"Chen, Yi-Lu, et al. “Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation.” <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>, 5, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3606037.3606836\">10.1145/3606037.3606836</a>.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation.” In <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3606037.3606836\">https://doi.org/10.1145/3606037.3606836</a>.","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Association for Computing Machinery, 2023.","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Unified treatment of contact, friction and shock-propagation in rigid body animation,” in <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>, Los Angeles, CA, United States, 2023.","ama":"Chen Y-L, Ly M, Wojtan C. Unified treatment of contact, friction and shock-propagation in rigid body animation. In: <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>. Association for Computing Machinery; 2023. doi:<a href=\"https://doi.org/10.1145/3606037.3606836\">10.1145/3606037.3606836</a>"},"title":"Unified treatment of contact, friction and shock-propagation in rigid body animation","article_number":"5","language":[{"iso":"eng"}],"_id":"14748","acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","doi":"10.1145/3606037.3606836"},{"_id":"12244","article_type":"original","file_date_updated":"2023-01-30T08:06:56Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"doi":"10.1038/s41593-022-01167-6","year":"2022","acknowledgement":"We thank the scientific service units at ISTA, in particular M. Schunn’s team at the preclinical facility, and especially our colony manager S. Haslinger, for excellent support. We are also grateful to the ISTA Imaging & Optics Facility, and in particular C. Sommer for helping with the data file conversions. We thank R. Erhart from the ISTA Scientific Computing Unit for improving the script performance. We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert group for constant feedback on the project and on the manuscript. This research was supported by the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","keyword":["General Neuroscience"],"citation":{"apa":"Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero, M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>","chicago":"Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>.","mla":"Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>.","ista":"Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 25(10), 1379–1393.","ama":"Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. 2022;25(10):1379-1393. doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>","ieee":"G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022.","short":"G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero, J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature Neuroscience 25 (2022) 1379–1393."},"date_created":"2023-01-16T09:53:07Z","related_material":{"record":[{"id":"12378","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/"}]},"ec_funded":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"}],"date_published":"2022-10-01T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","volume":25,"department":[{"_id":"SaSi"}],"page":"1379-1393","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology."}],"external_id":{"isi":["000862214700001"],"pmid":["36180790"]},"language":[{"iso":"eng"}],"publication":"Nature Neuroscience","article_processing_charge":"No","issue":"10","oa":1,"date_updated":"2024-03-25T23:30:10Z","title":"A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes","isi":1,"intvolume":"        25","has_accepted_license":"1","scopus_import":"1","type":"journal_article","status":"public","pmid":1,"author":[{"last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","first_name":"Gloria","full_name":"Colombo, Gloria"},{"orcid":"0000-0003-0002-1867","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J","first_name":"Ryan J"},{"first_name":"Lida","full_name":"Kanari, Lida","last_name":"Kanari"},{"full_name":"Venturino, Alessandro","first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403"},{"first_name":"Rouven","full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","orcid":"0000-0001-5297-733X"},{"last_name":"Scolamiero","full_name":"Scolamiero, Martina","first_name":"Martina"},{"last_name":"Agerberg","first_name":"Jens","full_name":"Agerberg, Jens"},{"last_name":"Mathys","full_name":"Mathys, Hansruedi","first_name":"Hansruedi"},{"first_name":"Li-Huei","full_name":"Tsai, Li-Huei","last_name":"Tsai"},{"full_name":"Chachólski, Wojciech","first_name":"Wojciech","last_name":"Chachólski"},{"last_name":"Hess","first_name":"Kathryn","full_name":"Hess, Kathryn"},{"first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877"}],"month":"10","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"file":[{"creator":"dernst","access_level":"open_access","file_size":23789835,"content_type":"application/pdf","relation":"main_file","success":1,"checksum":"28431146873096f52e0107b534f178c9","file_id":"12437","file_name":"2022_NatureNeuroscience_Colombo.pdf","date_created":"2023-01-30T08:06:56Z","date_updated":"2023-01-30T08:06:56Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"01"},{"article_number":"iyac123","related_material":{"record":[{"status":"public","id":"11653","relation":"research_data"}]},"ec_funded":1,"keyword":["Genetics"],"citation":{"ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>"},"date_created":"2023-01-16T09:56:10Z","year":"2022","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","doi":"10.1093/genetics/iyac123","acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","_id":"12248","file_date_updated":"2023-01-30T08:59:58Z","abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"external_id":{"isi":["000850270300001"],"pmid":["35977389"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","volume":222,"quality_controlled":"1","department":[{"_id":"BeVi"}],"date_published":"2022-10-01T00:00:00Z","publisher":"Oxford University Press","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"},{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"has_accepted_license":"1","scopus_import":"1","intvolume":"       222","isi":1,"title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","article_processing_charge":"No","issue":"2","date_updated":"2024-03-25T23:30:26Z","oa":1,"publication":"Genetics","language":[{"iso":"eng"}],"file":[{"checksum":"f79ff5383e882ea3f95f3da47a78029d","file_id":"12440","file_name":"2022_Genetics_Elkrewi.pdf","success":1,"date_updated":"2023-01-30T08:59:58Z","date_created":"2023-01-30T08:59:58Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":1347136}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","oa_version":"Published Version","month":"10","publication_identifier":{"issn":["1943-2631"]},"author":[{"full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"full_name":"Khauratovich, Uladzislava","first_name":"Uladzislava","last_name":"Khauratovich","id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A"},{"first_name":"Vincent K","full_name":"Bett, Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"first_name":"Ariana","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Sax, Luca","first_name":"Luca","last_name":"Sax","id":"701c5602-97d8-11ed-96b5-b52773c70189"},{"orcid":"0000-0001-8871-4961","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"full_name":"Hontoria, Francisco","first_name":"Francisco","last_name":"Hontoria"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"type":"journal_article","status":"public","pmid":1},{"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra"}],"date_published":"2022-11-11T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"page":"142","publication_status":"published","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"file_date_updated":"2023-04-12T22:30:03Z","_id":"12378","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"doi":"10.15479/at:ista:12378","year":"2022","citation":{"short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>.","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>"},"date_created":"2023-01-25T14:27:43Z","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"12244","status":"public"}]},"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","author":[{"full_name":"Colombo, Gloria","first_name":"Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902"}],"publication_identifier":{"issn":["2663-337X"]},"month":"11","oa_version":"Published Version","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":23890382,"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"cchlebak","embargo_to":"open_access","date_created":"2023-01-25T14:31:32Z","date_updated":"2023-04-12T22:30:03Z","file_id":"12379","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","file_name":"Gloria_Colombo_Thesis.docx"},{"file_id":"12380","checksum":"8af4319c18b516e8758e9a6cb02b103b","file_name":"Gloria_Colombo_Thesis.pdf","embargo":"2023-04-11","date_updated":"2023-04-12T22:30:03Z","date_created":"2023-01-25T14:31:36Z","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":13802421}],"language":[{"iso":"eng"}],"oa":1,"date_updated":"2023-08-04T09:40:37Z","article_processing_charge":"No","title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","has_accepted_license":"1"},{"external_id":{"arxiv":["2106.11732"]},"abstract":[{"text":"Fairness-aware learning aims at constructing classifiers that not only make accurate predictions, but also do not discriminate against specific groups. It is a fast-growing area of\r\nmachine learning with far-reaching societal impact. However, existing fair learning methods\r\nare vulnerable to accidental or malicious artifacts in the training data, which can cause\r\nthem to unknowingly produce unfair classifiers. In this work we address the problem of\r\nfair learning from unreliable training data in the robust multisource setting, where the\r\navailable training data comes from multiple sources, a fraction of which might not be representative of the true data distribution. We introduce FLEA, a filtering-based algorithm\r\nthat identifies and suppresses those data sources that would have a negative impact on\r\nfairness or accuracy if they were used for training. As such, FLEA is not a replacement of\r\nprior fairness-aware learning methods but rather an augmentation that makes any of them\r\nrobust against unreliable training data. We show the effectiveness of our approach by a\r\ndiverse range of experiments on multiple datasets. Additionally, we prove formally that\r\n–given enough data– FLEA protects the learner against corruptions as long as the fraction of\r\naffected data sources is less than half. Our source code and documentation are available at\r\nhttps://github.com/ISTAustria-CVML/FLEA.","lang":"eng"}],"ddc":["000"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","department":[{"_id":"ChLa"}],"quality_controlled":"1","publisher":"ML Research Press","date_published":"2022-12-22T00:00:00Z","project":[{"name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":" W1260-N35"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/ISTAustria-CVML/FLEA","description":"source code"}]},"citation":{"apa":"Iofinova, E. B., Konstantinov, N. H., &#38; Lampert, C. (2022). FLEA: Provably robust fair multisource learning from unreliable training data. <i>Transactions on Machine Learning Research</i>. ML Research Press.","short":"E.B. Iofinova, N.H. Konstantinov, C. Lampert, Transactions on Machine Learning Research (2022).","ieee":"E. B. Iofinova, N. H. Konstantinov, and C. Lampert, “FLEA: Provably robust fair multisource learning from unreliable training data,” <i>Transactions on Machine Learning Research</i>. ML Research Press, 2022.","ama":"Iofinova EB, Konstantinov NH, Lampert C. FLEA: Provably robust fair multisource learning from unreliable training data. <i>Transactions on Machine Learning Research</i>. 2022.","ista":"Iofinova EB, Konstantinov NH, Lampert C. 2022. FLEA: Provably robust fair multisource learning from unreliable training data. Transactions on Machine Learning Research.","mla":"Iofinova, Eugenia B., et al. “FLEA: Provably Robust Fair Multisource Learning from Unreliable Training Data.” <i>Transactions on Machine Learning Research</i>, ML Research Press, 2022.","chicago":"Iofinova, Eugenia B, Nikola H Konstantinov, and Christoph Lampert. “FLEA: Provably Robust Fair Multisource Learning from Unreliable Training Data.” <i>Transactions on Machine Learning Research</i>. ML Research Press, 2022."},"date_created":"2023-02-02T20:29:57Z","acknowledgement":"The authors would like to thank Bernd Prach, Elias Frantar, Alexandra Peste, Mahdi Nikdan, and Peter Súkeník for their helpful feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). This publication was made possible by an ETH AI Center postdoctoral fellowship granted to Nikola Konstantinov. Eugenia Iofinova was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. ","year":"2022","acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2023-02-23T10:30:04Z","_id":"12495","article_type":"original","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://openreview.net/forum?id=XsPopigZXV"}],"day":"22","file":[{"creator":"dernst","relation":"main_file","access_level":"open_access","file_size":1948063,"content_type":"application/pdf","success":1,"file_name":"2022_TMLR_Iofinova.pdf","checksum":"97c8a8470759cab597abb973ca137a3b","file_id":"12673","date_created":"2023-02-23T10:30:04Z","date_updated":"2023-02-23T10:30:04Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","publication_identifier":{"issn":["2835-8856"]},"author":[{"full_name":"Iofinova, Eugenia B","first_name":"Eugenia B","orcid":"0000-0002-7778-3221","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova"},{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H","full_name":"Konstantinov, Nikola H"},{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"}],"arxiv":1,"type":"journal_article","status":"public","has_accepted_license":"1","title":"FLEA: Provably robust fair multisource learning from unreliable training data","date_updated":"2023-02-23T10:30:54Z","oa":1,"article_processing_charge":"No","publication":"Transactions on Machine Learning Research","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication":"Ecology Letters","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","oa":1,"date_updated":"2023-08-14T11:45:29Z","article_processing_charge":"Yes (via OA deal)","issue":"1","intvolume":"        25","has_accepted_license":"1","scopus_import":"1","isi":1,"pmid":1,"status":"public","type":"journal_article","author":[{"full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","first_name":"Christopher","full_name":"Pull, Christopher"},{"first_name":"Filip","full_name":"Naiser, Filip","last_name":"Naiser"},{"first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger"},{"last_name":"Matas","first_name":"Jiri","full_name":"Matas, Jiri"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"day":"01","oa_version":"Published Version","file":[{"file_size":700087,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"cchlebak","date_updated":"2022-02-03T13:37:11Z","date_created":"2022-02-03T13:37:11Z","file_id":"10721","file_name":"2021_EcologyLetters_CasillasPerez.pdf","checksum":"0bd4210400e9876609b7c538ab4f9a3c","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"month":"01","acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2022-02-03T13:37:11Z","_id":"10284","article_type":"original","doi":"10.1111/ele.13907","date_created":"2021-11-14T23:01:25Z","citation":{"apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &#38; Cremer, S. (2022). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>","mla":"Casillas Perez, Barbara E., et al. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>, vol. 25, no. 1, Wiley, 2022, pp. 89–100, doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>.","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2022. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Ecology Letters. 25(1), 89–100.","chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>.","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. 2022;25(1):89-100. doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies,” <i>Ecology Letters</i>, vol. 25, no. 1. Wiley, pp. 89–100, 2022.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, Ecology Letters 25 (2022) 89–100."},"acknowledgement":"The authors are grateful to G. Tkačik and V. Mireles for advice on data analyses and to A. Schloegl for help using the IST Austria HPC cluster for data processing. The authors thank J. Eilenberg for providing the fungal strain and A.V. Grasse for support with the molecular analysis. The authors also thank the Social Immunity group at IST Austria, in particular B. Milutinović, for discussions throughout and comments on the manuscript.","year":"2022","ec_funded":1,"related_material":{"record":[{"id":"13061","relation":"research_data","status":"public"}]},"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"}],"page":"89-100","department":[{"_id":"SyCr"}],"quality_controlled":"1","volume":25,"publisher":"Wiley","date_published":"2022-01-01T00:00:00Z","publication_status":"published","external_id":{"pmid":["34725912"],"isi":["000713396100001"]},"abstract":[{"text":"Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing ‘superorganisms’––incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.","lang":"eng"}],"ddc":["573"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"language":[{"iso":"eng"}],"publication":"eLife","article_processing_charge":"No","oa":1,"date_updated":"2023-08-02T14:42:55Z","title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","isi":1,"has_accepted_license":"1","scopus_import":"1","intvolume":"        11","type":"journal_article","status":"public","pmid":1,"author":[{"first_name":"Giulio","full_name":"Valperga, Giulio","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E","last_name":"Valperga"},{"first_name":"Mario","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","orcid":"0000-0001-8347-0443"}],"month":"02","publication_identifier":{"eissn":["2050084X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":4095591,"checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","file_id":"10830","file_name":"2022_eLife_Valperga.pdf","success":1,"date_updated":"2022-03-07T07:39:25Z","date_created":"2022-03-07T07:39:25Z"}],"oa_version":"Published Version","day":"24","article_type":"original","_id":"10826","file_date_updated":"2022-03-07T07:39:25Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"doi":"10.7554/eLife.68040","year":"2022","acknowledgement":"We would like to thank Gemma Chandratillake and Merav Cohen for identifying mutants and José David Moñino Sánchez for his help on neurosecretion assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida) for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp, GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets (KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank the CRUK Cambridge Research Institute Genomics Core for next generation sequencing and the Flow Cytometry Facility at LMB for FACS. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing (SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome Investigator Award (209504/Z/17/Z to MdB).","date_created":"2022-03-06T23:01:52Z","citation":{"apa":"Valperga, G., &#38; de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>","short":"G. Valperga, M. de Bono, ELife 11 (2022).","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040.","chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>.","mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>, vol. 11, e68040, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>."},"article_number":"e68040","project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"}],"date_published":"2022-02-24T00:00:00Z","publisher":"eLife Sciences Publications","quality_controlled":"1","volume":11,"department":[{"_id":"MaDe"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"lang":"eng","text":"Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome."}],"external_id":{"pmid":["35201977"],"isi":["000763432300001"]}},{"language":[{"iso":"eng"}],"title":"Genetic basis of flower colour as a model for adaptive evolution","date_updated":"2023-06-23T06:26:41Z","oa":1,"article_processing_charge":"No","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","author":[{"first_name":"Lenka","full_name":"Matejovicova, Lenka","last_name":"Matejovicova","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87"}],"day":"06","oa_version":"Published Version","file":[{"date_updated":"2022-04-07T08:11:34Z","date_created":"2022-04-07T08:11:34Z","file_id":"11129","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","file_name":"LenkaPhD_Official_PDFA.pdf","relation":"main_file","file_size":11906472,"content_type":"application/pdf","access_level":"open_access","creator":"cchlebak"},{"file_size":23036766,"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","creator":"cchlebak","date_updated":"2022-04-07T08:11:51Z","date_created":"2022-04-07T08:11:51Z","file_name":"LenkaPhD Official_source.zip","file_id":"11130","checksum":"99d67040432fd07a225643a212ee8588"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"04","publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"file_date_updated":"2022-04-07T08:11:51Z","_id":"11128","doi":"10.15479/at:ista:11128","citation":{"mla":"Matejovicova, Lenka. <i>Genetic Basis of Flower Colour as a Model for Adaptive Evolution</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>.","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>.","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","apa":"Matejovicova, L. (2022). <i>Genetic basis of flower colour as a model for adaptive evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>"},"date_created":"2022-04-07T08:19:54Z","year":"2022","degree_awarded":"PhD","page":"112","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","date_published":"2022-04-06T00:00:00Z","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline."}],"ddc":["576","582"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"status":"public","type":"journal_article","pmid":1,"author":[{"full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hagen, Wim J.H.","first_name":"Wim J.H.","last_name":"Hagen"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."},{"last_name":"Yu","first_name":"Lingbo","full_name":"Yu, Lingbo"},{"last_name":"Kotecha","full_name":"Kotecha, Abhay","first_name":"Abhay"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"month":"06","publication_identifier":{"issn":["1047-8477"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":7080863,"success":1,"checksum":"0b1eb53447aae8e95ae4c12d193b0b00","file_id":"11722","file_name":"2022_JourStructuralBiology_Obr.pdf","date_created":"2022-08-02T11:07:58Z","date_updated":"2022-08-02T11:07:58Z"}],"oa_version":"Published Version","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Structural Biology","issue":"2","article_processing_charge":"Yes (via OA deal)","oa":1,"date_updated":"2023-08-03T06:25:23Z","title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","isi":1,"intvolume":"       214","has_accepted_license":"1","scopus_import":"1","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"date_published":"2022-06-01T00:00:00Z","publisher":"Elsevier","volume":214,"quality_controlled":"1","department":[{"_id":"FlSc"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"_id":"11155","article_type":"original","file_date_updated":"2022-08-02T11:07:58Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"doi":"10.1016/j.jsb.2022.107852","year":"2022","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","keyword":["Structural Biology"],"citation":{"apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>.","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>.","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022)."},"date_created":"2022-04-15T07:10:26Z","article_number":"107852"},{"doi":"10.1093/genetics/iyac083","acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2022-05-26T12:48:21Z","article_type":"original","_id":"11411","article_number":"iyac083","related_material":{"record":[{"status":"public","id":"14651","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"11321"},{"relation":"research_data","id":"9192","status":"public"}]},"date_created":"2022-05-26T13:44:50Z","citation":{"mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>"},"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","year":"2022","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"volume":221,"quality_controlled":"1","publisher":"Oxford University Press","date_published":"2022-07-01T00:00:00Z","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"external_id":{"pmid":["35639938"],"isi":["000803735800001"]},"abstract":[{"lang":"eng","text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity."}],"ddc":["576"],"publication_status":"published","publication":"Genetics","language":[{"iso":"eng"}],"scopus_import":"1","has_accepted_license":"1","intvolume":"       221","isi":1,"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","date_updated":"2024-02-21T12:38:33Z","oa":1,"issue":"3","article_processing_charge":"No","pmid":1,"type":"journal_article","status":"public","day":"01","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","relation":"main_file","file_size":885374,"access_level":"open_access","creator":"larathoo","date_created":"2022-05-26T12:48:15Z","date_updated":"2022-05-26T12:48:15Z","success":1,"file_name":"Manuscript.pdf","checksum":"cc2d56deb608bd53c5cc02f03a875107","file_id":"11412"},{"date_created":"2022-05-26T12:48:21Z","date_updated":"2022-05-26T12:48:21Z","success":1,"checksum":"693742595b6c7ed809423be01460d083","file_name":"SupplementalMaterial.pdf","file_id":"11413","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":1401704,"creator":"larathoo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1943-2631"]},"month":"07","author":[{"first_name":"Parvathy","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"},{"first_name":"Louise S","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon"},{"orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","full_name":"Baskett, Carina","first_name":"Carina"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda","full_name":"Pickup, Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}]},{"doi":"10.1111/cgf.14478","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"11432","article_type":"original","ec_funded":1,"date_created":"2022-06-05T22:01:49Z","citation":{"short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353.","ama":"Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. 2022;41(2):343-353. doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>","ieee":"C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 343–353, 2022.","ista":"Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. Computer Graphics Forum. 41(2), 343–353.","mla":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 343–53, doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>.","chicago":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>.","apa":"Schreck, C., &#38; Wojtan, C. (2022). Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>"},"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria and MFX Team at INRIA 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.","year":"2022","page":"343-353","department":[{"_id":"ChWo"}],"volume":41,"quality_controlled":"1","publisher":"Wiley","date_published":"2022-05-01T00:00:00Z","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"external_id":{"isi":["000802723900027"]},"abstract":[{"text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics.","lang":"eng"}],"publication_status":"published","publication":"Computer Graphics Forum","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"        41","isi":1,"title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","oa":1,"date_updated":"2023-08-02T06:44:05Z","article_processing_charge":"No","issue":"2","status":"public","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03641349/"}],"day":"01","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"month":"05","author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","full_name":"Schreck, Camille","first_name":"Camille"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}]},{"publication_status":"published","abstract":[{"text":"Thermalizing and localized many-body quantum systems present two distinct dynamical phases of matter. Recently the fate of a localized system coupled to a thermalizing system viewed as a quantum bath received significant theoretical and experimental attention. In this work, we study a mobile impurity, representing a small quantum bath, that interacts locally with an Anderson insulator with a finite density of localized particles. Using static Hartree approximation to obtain an effective disorder strength, we formulate an analytic criterion for the perturbative stability of the localization. Next, we use an approximate dynamical Hartree method and the quasi-exact time-evolved block decimation (TEBD) algorithm to study the dynamics of the system. We find that the dynamical Hartree approach which completely ignores entanglement between the impurity and localized particles predicts the delocalization of the system. In contrast, the full numerical simulation of the unitary dynamics with TEBD suggests the stability of localization on numerically accessible timescales. Finally, using an extension of the density matrix renormalization group algorithm to excited states (DMRG-X), we approximate the highly excited eigenstates of the system. We find that the impurity remains localized in the eigenstates and entanglement is enhanced in a finite region around the position of the impurity, confirming the dynamical predictions. Dynamics and the DMRG-X results provide compelling evidence for the stability of localization.","lang":"eng"}],"external_id":{"isi":["000823050000001"],"arxiv":["2111.08603"]},"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"volume":105,"quality_controlled":"1","department":[{"_id":"MaSe"}],"date_published":"2022-06-27T00:00:00Z","publisher":"American Physical Society","citation":{"mla":"Brighi, Pietro, et al. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, 224208, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>.","chicago":"Brighi, Pietro, Alexios Michailidis, Kristina Kirova, Dmitry A. Abanin, and Maksym Serbyn. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>.","ista":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. 2022. Localization of a mobile impurity interacting with an Anderson insulator. Physical Review B. 105(22), 224208.","ama":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>","ieee":"P. Brighi, A. Michailidis, K. Kirova, D. A. Abanin, and M. Serbyn, “Localization of a mobile impurity interacting with an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","short":"P. Brighi, A. Michailidis, K. Kirova, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","apa":"Brighi, P., Michailidis, A., Kirova, K., Abanin, D. A., &#38; Serbyn, M. (2022). Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>"},"date_created":"2022-06-29T20:19:51Z","year":"2022","acknowledgement":"We thank M. Ljubotina for insightful discussions. P. B., A. M. and M. S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D. A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","article_number":"224208","related_material":{"record":[{"id":"12732","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"11469","article_type":"original","doi":"10.1103/physrevb.105.224208","arxiv":1,"author":[{"full_name":"Brighi, Pietro","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","orcid":"0000-0002-7969-2729"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","orcid":"0000-0002-8443-1064","first_name":"Alexios","full_name":"Michailidis, Alexios"},{"full_name":"Kirova, Kristina","first_name":"Kristina","last_name":"Kirova","id":"4aeda2ae-f847-11ec-98e0-c4a66fe174d4"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","day":"27","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.08603 Focus to learn more"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"06","type":"journal_article","status":"public","title":"Localization of a mobile impurity interacting with an Anderson insulator","issue":"22","article_processing_charge":"No","oa":1,"date_updated":"2023-09-05T12:12:52Z","intvolume":"       105","isi":1,"language":[{"iso":"eng"}],"publication":"Physical Review B"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.07332"}],"day":"27","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"06","arxiv":1,"author":[{"last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","first_name":"Pietro"},{"last_name":"Michailidis","first_name":"Alexios A.","full_name":"Michailidis, Alexios A."},{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym"}],"status":"public","type":"journal_article","intvolume":"       105","isi":1,"title":"Propagation of many-body localization in an Anderson insulator","issue":"22","article_processing_charge":"No","date_updated":"2023-08-03T07:23:52Z","oa":1,"publication":"Physical Review B","language":[{"iso":"eng"}],"abstract":[{"text":"Many-body localization (MBL) is an example of a dynamical phase of matter that avoids thermalization. While the MBL phase is robust to weak local perturbations, the fate of an MBL system coupled to a thermalizing quantum system that represents a “heat bath” is an open question that is actively investigated theoretically and experimentally. In this work, we consider the stability of an Anderson insulator with a finite density of particles interacting with a single mobile impurity—a small quantum bath. We give perturbative arguments that support the stability of localization in the strong interaction regime. Large-scale tensor network simulations of dynamics are employed to corroborate the presence of the localized phase and give quantitative predictions in the thermodynamic limit. We develop a phenomenological description of the dynamics in the strong interaction regime, and we demonstrate that the impurity effectively turns the Anderson insulator into an MBL phase, giving rise to nontrivial entanglement dynamics well captured by our phenomenology.","lang":"eng"}],"external_id":{"isi":["000823050000012"],"arxiv":["2109.07332"]},"publication_status":"published","quality_controlled":"1","volume":105,"department":[{"_id":"MaSe"}],"date_published":"2022-06-27T00:00:00Z","publisher":"American Physical Society","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"related_material":{"record":[{"status":"public","id":"12732","relation":"dissertation_contains"}]},"article_number":"L220203","ec_funded":1,"date_created":"2022-06-29T20:20:47Z","citation":{"short":"P. Brighi, A.A. Michailidis, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","ama":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>","ieee":"P. Brighi, A. A. Michailidis, D. A. Abanin, and M. Serbyn, “Propagation of many-body localization in an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","mla":"Brighi, Pietro, et al. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, L220203, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>.","ista":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. 2022. Propagation of many-body localization in an Anderson insulator. Physical Review B. 105(22), L220203.","chicago":"Brighi, Pietro, Alexios A. Michailidis, Dmitry A. Abanin, and Maksym Serbyn. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>.","apa":"Brighi, P., Michailidis, A. A., Abanin, D. A., &#38; Serbyn, M. (2022). Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>"},"year":"2022","acknowledgement":"We acknowledge useful discussions with M. Ljubotina. P. B., A. M., and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","doi":"10.1103/physrevb.105.l220203","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"11470","article_type":"original"},{"language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","title":"Estimation of yarn-level simulation models for production fabrics","date_updated":"2023-08-03T12:38:30Z","oa":1,"article_processing_charge":"No","issue":"4","scopus_import":"1","intvolume":"        41","isi":1,"type":"journal_article","status":"public","author":[{"first_name":"Georg","full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl"},{"last_name":"Sánchez-Banderas","first_name":"Rosa M.","full_name":"Sánchez-Banderas, Rosa M."},{"last_name":"Li","first_name":"Manwen","full_name":"Li, Manwen"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546"},{"last_name":"Otaduy","full_name":"Otaduy, Miguel A.","first_name":"Miguel A."}],"oa_version":"Published Version","day":"22","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3528223.3530167"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"month":"07","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"11736","article_type":"original","doi":"10.1145/3528223.3530167","date_created":"2022-08-07T22:01:58Z","citation":{"short":"G. Sperl, R.M. Sánchez-Banderas, M. Li, C. Wojtan, M.A. Otaduy, ACM Transactions on Graphics 41 (2022).","ama":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>","ieee":"G. Sperl, R. M. Sánchez-Banderas, M. Li, C. Wojtan, and M. A. Otaduy, “Estimation of yarn-level simulation models for production fabrics,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ista":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. 2022. Estimation of yarn-level simulation models for production fabrics. ACM Transactions on Graphics. 41(4), 65.","mla":"Sperl, Georg, et al. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 65, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>.","chicago":"Sperl, Georg, Rosa M. Sánchez-Banderas, Manwen Li, Chris Wojtan, and Miguel A. Otaduy. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>.","apa":"Sperl, G., Sánchez-Banderas, R. M., Li, M., Wojtan, C., &#38; Otaduy, M. A. (2022). Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>"},"acknowledgement":"We wish to thank the anonymous reviewers for their helpful comments. To develop this project, we were helped by many people both at Under Armour (Clay Dean, Randall Harward, Kyle Blakely, Craig Simile, Michael Seiz, Brooke Malone, Brittainy McFarland, Emilie Phan, Lindsey Kern, Courtney Oswald, Haley Barkley, Bob Chin, Adam Bayer, Connie Kwok, Marielle Newman, Nick Pence, Allison Hicks, Allison White, Candace Rubenstein, Jeremy Stangland, Fred Fagergren, Michael Mazzoleni, Nathaniel Berry, Manuel Frank) and SEDDI (Gabriel Cirio, Alejandro Rodríguez, Sofía Dominguez, Alicia Nicas, Elena Garcés, Daniel Rodríguez, David Pascual, Manuel Godoy, Sergio Suja, Sergio Ruiz, Roberto Condori, Alberto Martín, Graham Sullivan). We also thank the members of the Visual Computing Group at IST Austria and the Multimodal Simulation Lab at URJC for their feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing, and it was funded in part by the European Research Council (ERC Consolidator Grant 772738 TouchDesign).","year":"2022","article_number":"65","related_material":{"link":[{"description":"News on the ISTA website","url":"https://ista.ac.at/en/news/digital-yarn-real-socks/","relation":"press_release"}],"record":[{"id":"12358","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"ChWo"}],"quality_controlled":"1","volume":41,"publisher":"Association for Computing Machinery","date_published":"2022-07-22T00:00:00Z","publication_status":"published","external_id":{"isi":["000830989200114"]},"abstract":[{"lang":"eng","text":"This paper introduces a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compiled a database from physical tests of several different knitted fabrics used in the textile industry. These data span different types of complex knit patterns, yarn compositions, and fabric finishes, and the results demonstrate diverse physical properties like stiffness, nonlinearity, and anisotropy.\r\n\r\nWe then develop a system for approximating these mechanical responses with yarn-level cloth simulation. To do so, we introduce an efficient pipeline for converting between fabric-level data and yarn-level simulation, including a novel swatch-level approximation for speeding up computation, and some small-but-necessary extensions to yarn-level models used in computer graphics. The dataset used for this paper can be found at http://mslab.es/projects/YarnLevelFabrics."}]},{"author":[{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl","first_name":"Felix","full_name":"Pertl, Felix"},{"last_name":"Sobarzo Ponce","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A","full_name":"Sobarzo Ponce, Juan Carlos A"},{"last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7180-6050","first_name":"Lubuna B","full_name":"Shafeek, Lubuna B"},{"last_name":"Cramer","full_name":"Cramer, Tobias","first_name":"Tobias"},{"last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","first_name":"Scott R"}],"arxiv":1,"oa_version":"Preprint","day":"29","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2209.01889","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","publication_identifier":{"eissn":["2475-9953"]},"status":"public","type":"journal_article","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","date_updated":"2023-08-03T14:11:29Z","oa":1,"article_processing_charge":"No","issue":"12","intvolume":"         6","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"publication":"Physical Review Materials","publication_status":"published","external_id":{"arxiv":["2209.01889"],"isi":["000908384800001"]},"abstract":[{"lang":"eng","text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale."}],"project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}],"department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"quality_controlled":"1","volume":6,"publisher":"American Physical Society","date_published":"2022-12-29T00:00:00Z","date_created":"2023-01-08T23:00:53Z","citation":{"apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>.","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>.","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022.","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>"},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","year":"2022","ec_funded":1,"article_number":"125605","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"_id":"12109","article_type":"original","doi":"10.1103/PhysRevMaterials.6.125605"},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":1425655,"creator":"lsazanov","date_updated":"2023-05-30T17:05:31Z","date_created":"2023-05-30T17:05:31Z","file_id":"13104","checksum":"d42a93e24f59e883ef0b5429832391d0","file_name":"EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf","success":1},{"file_size":9842513,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"lsazanov","date_updated":"2023-05-30T17:07:05Z","date_created":"2023-05-30T17:07:05Z","file_id":"13105","checksum":"5422bc0a73b3daadafa262c7ea6deae3","file_name":"EcCxI_manuscript_rev3_SI_All_opt_upd.pdf","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","day":"22","month":"09","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","first_name":"Vladyslav"},{"full_name":"Petrova, Olga","first_name":"Olga","last_name":"Petrova","id":"5D8C9660-5D49-11EA-8188-567B3DDC885E"},{"first_name":"Domen","full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut"},{"last_name":"Wojciechowska-Bason","first_name":"Anna","full_name":"Wojciechowska-Bason, Anna"},{"last_name":"Breese","first_name":"Zara","full_name":"Breese, Zara"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"journal_article","pmid":1,"scopus_import":"1","has_accepted_license":"1","intvolume":"       609","isi":1,"title":"A universal coupling mechanism of respiratory complex I","article_processing_charge":"No","issue":"7928","date_updated":"2023-08-04T08:54:52Z","oa":1,"publication":"Nature","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes."}],"external_id":{"pmid":["36104567"],"isi":["000854788200001"]},"ddc":["572"],"publication_status":"published","quality_controlled":"1","volume":609,"department":[{"_id":"LeSa"}],"page":"808-814","date_published":"2022-09-22T00:00:00Z","publisher":"Springer Nature","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020"}],"related_material":{"record":[{"id":"12781","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41586-022-05457-8","relation":"erratum"},{"url":"https://ista.ac.at/en/news/proton-dominos-kick-off-life/","description":"News on ISTA website","relation":"press_release"}]},"ec_funded":1,"keyword":["Multidisciplinary"],"citation":{"chicago":"Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason, Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>.","mla":"Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14, doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>.","ista":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928), 808–814.","short":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A. Sazanov, Nature 609 (2022) 808–814.","ieee":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” <i>Nature</i>, vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.","ama":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. A universal coupling mechanism of respiratory complex I. <i>Nature</i>. 2022;609(7928):808-814. doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>","apa":"Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z., &#38; Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex I. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>"},"date_created":"2023-01-12T12:04:33Z","year":"2022","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance with collecting cryo-EM data and A. Charnagalov for the assistance with protein purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also supported by the Medical Research Council (UK).","doi":"10.1038/s41586-022-05199-7","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"_id":"12138","article_type":"original","file_date_updated":"2023-05-30T17:07:05Z"},{"type":"journal_article","status":"public","file":[{"creator":"dernst","content_type":"application/pdf","file_size":705195,"access_level":"open_access","relation":"main_file","success":1,"file_name":"2022_AJHG_Ojavee.pdf","checksum":"4cd7f12bfe21a8237bb095eedfa26361","file_id":"12353","date_created":"2023-01-24T09:23:01Z","date_updated":"2023-01-24T09:23:01Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"03","month":"11","publication_identifier":{"issn":["0002-9297"]},"author":[{"full_name":"Ojavee, Sven E.","first_name":"Sven E.","last_name":"Ojavee"},{"first_name":"Zoltan","full_name":"Kutalik, Zoltan","last_name":"Kutalik"},{"first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"}],"publication":"The American Journal of Human Genetics","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"       109","has_accepted_license":"1","isi":1,"title":"Liability-scale heritability estimation for biobank studies of low-prevalence disease","article_processing_charge":"Yes (via OA deal)","issue":"11","oa":1,"date_updated":"2023-08-04T08:56:46Z","volume":109,"quality_controlled":"1","page":"2009-2017","department":[{"_id":"MaRo"}],"date_published":"2022-11-03T00:00:00Z","publisher":"Elsevier","project":[{"name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181"}],"abstract":[{"text":"Theory for liability-scale models of the underlying genetic basis of complex disease provides an important way to interpret, compare, and understand results generated from biological studies. In particular, through estimation of the liability-scale heritability (LSH), liability models facilitate an understanding and comparison of the relative importance of genetic and environmental risk factors that shape different clinically important disease outcomes. Increasingly, large-scale biobank studies that link genetic information to electronic health records, containing hundreds of disease diagnosis indicators that mostly occur infrequently within the sample, are becoming available. Here, we propose an extension of the existing liability-scale model theory suitable for estimating LSH in biobank studies of low-prevalence disease. In a simulation study, we find that our derived expression yields lower mean square error (MSE) and is less sensitive to prevalence misspecification as compared to previous transformations for diseases with  =< 2% population prevalence and LSH of =< 0.45, especially if the biobank sample prevalence is less than that of the wider population. Applying our expression to 13 diagnostic outcomes of  =< 3% prevalence in the UK Biobank study revealed important differences in LSH obtained from the different theoretical expressions that impact the conclusions made when comparing LSH across disease outcomes. This demonstrates the importance of careful consideration for estimation and prediction of low-prevalence disease outcomes and facilitates improved inference of the underlying genetic basis of  =< 2% population prevalence diseases, especially where biobank sample ascertainment results in a healthier sample population.","lang":"eng"}],"external_id":{"isi":["000898683500006"]},"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)"},"ddc":["570"],"publication_status":"published","doi":"10.1016/j.ajhg.2022.09.011","acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","_id":"12142","file_date_updated":"2023-01-24T09:23:01Z","keyword":["Genetics (clinical)","Genetics"],"date_created":"2023-01-12T12:05:28Z","citation":{"apa":"Ojavee, S. E., Kutalik, Z., &#38; Robinson, M. R. (2022). Liability-scale heritability estimation for biobank studies of low-prevalence disease. <i>The American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2022.09.011\">https://doi.org/10.1016/j.ajhg.2022.09.011</a>","short":"S.E. Ojavee, Z. Kutalik, M.R. Robinson, The American Journal of Human Genetics 109 (2022) 2009–2017.","ama":"Ojavee SE, Kutalik Z, Robinson MR. Liability-scale heritability estimation for biobank studies of low-prevalence disease. <i>The American Journal of Human Genetics</i>. 2022;109(11):2009-2017. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2022.09.011\">10.1016/j.ajhg.2022.09.011</a>","ieee":"S. E. Ojavee, Z. Kutalik, and M. R. Robinson, “Liability-scale heritability estimation for biobank studies of low-prevalence disease,” <i>The American Journal of Human Genetics</i>, vol. 109, no. 11. Elsevier, pp. 2009–2017, 2022.","chicago":"Ojavee, Sven E., Zoltan Kutalik, and Matthew Richard Robinson. “Liability-Scale Heritability Estimation for Biobank Studies of Low-Prevalence Disease.” <i>The American Journal of Human Genetics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.ajhg.2022.09.011\">https://doi.org/10.1016/j.ajhg.2022.09.011</a>.","mla":"Ojavee, Sven E., et al. “Liability-Scale Heritability Estimation for Biobank Studies of Low-Prevalence Disease.” <i>The American Journal of Human Genetics</i>, vol. 109, no. 11, Elsevier, 2022, pp. 2009–17, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2022.09.011\">10.1016/j.ajhg.2022.09.011</a>.","ista":"Ojavee SE, Kutalik Z, Robinson MR. 2022. Liability-scale heritability estimation for biobank studies of low-prevalence disease. The American Journal of Human Genetics. 109(11), 2009–2017."},"year":"2022","acknowledgement":"This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181), core funding from the Institute of Science and Technology Austria, and core funding from the Department of Computational Biology of the University of Lausanne. Z.K. was funded by the Swiss National Science Foundation (310030-189147). This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp). We would like to thank the participants of the UK Biobank."},{"language":[{"iso":"eng"}],"publication":"Genetics","date_updated":"2023-08-07T13:47:01Z","oa":1,"issue":"2","article_processing_charge":"No","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","isi":1,"intvolume":"       217","status":"public","type":"journal_article","author":[{"first_name":"Christelle","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani"}],"publication_identifier":{"issn":["1943-2631"]},"month":"02","main_file_link":[{"url":"https://doi.org/10.1093/genetics/iyaa025","open_access":"1"}],"day":"01","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9168","article_type":"original","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/genetics/iyaa025","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","year":"2021","date_created":"2021-02-18T14:41:30Z","citation":{"apa":"Fraisse, C., &#38; Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” <i>Genetics</i>, vol. 217, no. 2. Genetics Society of America, 2021.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. 2021;217(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>. Genetics Society of America, 2021. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>.","mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>.","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025."},"article_number":"iyaa025","project":[{"grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"publisher":"Genetics Society of America","date_published":"2021-02-01T00:00:00Z","department":[{"_id":"NiBa"}],"volume":217,"quality_controlled":"1","publication_status":"published","external_id":{"isi":["000637218100005"]},"abstract":[{"lang":"eng","text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems."}]},{"year":"2021","acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","citation":{"short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV,” <i>Nature</i>, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021.","ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. 2021;598(7880):364-367. doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>","chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. Nature. 598(7880), 364–367.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>"},"date_created":"2021-10-17T22:01:17Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/"}]},"ec_funded":1,"_id":"10146","article_type":"original","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"doi":"10.1038/s41586-021-03927-z","publication_status":"published","abstract":[{"lang":"eng","text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain."}],"external_id":{"pmid":["34616041"],"isi":["000704581600001"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"date_published":"2021-10-14T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","volume":598,"department":[{"_id":"LeSa"}],"page":"364-367","issue":"7880","article_processing_charge":"No","date_updated":"2023-08-14T08:01:21Z","title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV","isi":1,"intvolume":"       598","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Nature","author":[{"full_name":"Vercellino, Irene","first_name":"Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","day":"14","type":"journal_article","status":"public","pmid":1}]