[{"quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes","doi":"10.3390/genes12081141","date_updated":"2023-08-11T10:32:21Z","date_published":"2021-07-27T00:00:00Z","author":[{"first_name":"Yinwei","last_name":"Zeng","full_name":"Zeng, Yinwei"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"full_name":"Trinh, Hoang Khai","last_name":"Trinh","first_name":"Hoang Khai"},{"full_name":"Heugebaert, Thomas","last_name":"Heugebaert","first_name":"Thomas"},{"full_name":"Stevens, Christian V.","last_name":"Stevens","first_name":"Christian V."},{"full_name":"Garcia-Maquilon, Irene","last_name":"Garcia-Maquilon","first_name":"Irene"},{"full_name":"Rodriguez, Pedro L.","last_name":"Rodriguez","first_name":"Pedro L."},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"1141","file_date_updated":"2021-08-16T09:02:40Z","month":"07","isi":1,"language":[{"iso":"eng"}],"ddc":["580","570"],"day":"27","file":[{"file_name":"2021_Genes_Zeng.pdf","checksum":"3d99535618cf9a5b14d264408fa52e97","file_size":1340305,"date_updated":"2021-08-16T09:02:40Z","file_id":"9919","success":1,"date_created":"2021-08-16T09:02:40Z","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","relation":"main_file"}],"publication_status":"published","intvolume":"        12","abstract":[{"lang":"eng","text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition."}],"date_created":"2021-08-15T22:01:28Z","oa_version":"Published Version","publisher":"MDPI","publication":"Genes","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","department":[{"_id":"JiFr"}],"publication_identifier":{"eissn":["20734425"]},"citation":{"short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>."},"issue":"8","external_id":{"isi":["000690558000001"]},"article_type":"original","acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","oa":1,"status":"public","has_accepted_license":"1","year":"2021","_id":"9909","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":12},{"scopus_import":"1","quality_controlled":"1","date_published":"2021-07-01T00:00:00Z","author":[{"last_name":"Slavskii","first_name":"Sergei A.","full_name":"Slavskii, Sergei A."},{"last_name":"Kuznetsov","first_name":"Ivan A.","full_name":"Kuznetsov, Ivan A."},{"full_name":"Shashkova, Tatiana I.","first_name":"Tatiana I.","last_name":"Shashkova"},{"first_name":"Georgii A.","last_name":"Bazykin","full_name":"Bazykin, Georgii A."},{"full_name":"Axenovich, Tatiana I.","last_name":"Axenovich","first_name":"Tatiana I."},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"full_name":"Aulchenko, Yurii S.","last_name":"Aulchenko","first_name":"Yurii S."}],"doi":"10.1038/s41431-021-00836-7","date_updated":"2023-08-11T10:33:42Z","article_processing_charge":"Yes (in subscription journal)","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-08-16T09:14:36Z","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"07","isi":1,"pmid":1,"day":"01","ddc":["576"],"intvolume":"        29","publication_status":"published","file":[{"success":1,"date_created":"2021-08-16T09:14:36Z","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","relation":"main_file","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","checksum":"a676d76f91b0dbe0504c63e469129c2a","file_size":1079395,"file_id":"9921","date_updated":"2021-08-16T09:14:36Z"}],"abstract":[{"lang":"eng","text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait."}],"oa_version":"Published Version","ec_funded":1,"date_created":"2021-08-15T22:01:28Z","department":[{"_id":"FyKo"}],"title":"The limits of normal approximation for adult height","publication":"European Journal of Human Genetics","publisher":"Springer Nature","citation":{"ieee":"S. A. Slavskii <i>et al.</i>, “The limits of normal approximation for adult height,” <i>European Journal of Human Genetics</i>, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021.","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &#38; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. 2021;29(7):1082-1091. doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>","mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>.","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091."},"publication_identifier":{"issn":["10184813"],"eissn":["14765438"]},"status":"public","oa":1,"acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","external_id":{"pmid":["33664501"],"isi":["000625853200001"]},"article_type":"original","issue":"7","_id":"9910","has_accepted_license":"1","year":"2021","page":"1082-1091","volume":29,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_processing_charge":"Yes","date_updated":"2023-08-11T10:30:40Z","doi":"10.1111/jmi.13041","date_published":"2021-08-11T00:00:00Z","author":[{"last_name":"Nelson","first_name":"Glyn","full_name":"Nelson, Glyn"},{"full_name":"Boehm, Ulrike","first_name":"Ulrike","last_name":"Boehm"},{"first_name":"Steve","last_name":"Bagley","full_name":"Bagley, Steve"},{"first_name":"Peter","last_name":"Bajcsy","full_name":"Bajcsy, Peter"},{"first_name":"Johanna","last_name":"Bischof","full_name":"Bischof, Johanna"},{"full_name":"Brown, Claire M.","last_name":"Brown","first_name":"Claire M."},{"full_name":"Dauphin, Aurélien","last_name":"Dauphin","first_name":"Aurélien"},{"full_name":"Dobbie, Ian M.","first_name":"Ian M.","last_name":"Dobbie"},{"full_name":"Eriksson, John E.","last_name":"Eriksson","first_name":"John E."},{"first_name":"Orestis","last_name":"Faklaris","full_name":"Faklaris, Orestis"},{"full_name":"Fernandez-Rodriguez, Julia","first_name":"Julia","last_name":"Fernandez-Rodriguez"},{"first_name":"Alexia","last_name":"Ferrand","full_name":"Ferrand, Alexia"},{"last_name":"Gelman","first_name":"Laurent","full_name":"Gelman, Laurent"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"last_name":"Hartmann","first_name":"Hella","full_name":"Hartmann, Hella"},{"full_name":"Kukat, Christian","first_name":"Christian","last_name":"Kukat"},{"first_name":"Alex","last_name":"Laude","full_name":"Laude, Alex"},{"full_name":"Mitkovski, Miso","last_name":"Mitkovski","first_name":"Miso"},{"last_name":"Munck","first_name":"Sebastian","full_name":"Munck, Sebastian"},{"first_name":"Alison J.","last_name":"North","full_name":"North, Alison J."},{"last_name":"Rasse","first_name":"Tobias M.","full_name":"Rasse, Tobias M."},{"full_name":"Resch-Genger, Ute","last_name":"Resch-Genger","first_name":"Ute"},{"last_name":"Schuetz","first_name":"Lucas C.","full_name":"Schuetz, Lucas C."},{"first_name":"Arne","last_name":"Seitz","full_name":"Seitz, Arne"},{"full_name":"Strambio-De-Castillia, Caterina","last_name":"Strambio-De-Castillia","first_name":"Caterina"},{"first_name":"Jason R.","last_name":"Swedlow","full_name":"Swedlow, Jason R."},{"full_name":"Alexopoulos, Ioannis","first_name":"Ioannis","last_name":"Alexopoulos"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"Karin"},{"full_name":"Avilov, Sergiy","first_name":"Sergiy","last_name":"Avilov"},{"full_name":"Bakker, Gert Jan","last_name":"Bakker","first_name":"Gert Jan"},{"full_name":"Bammann, Rodrigo R.","first_name":"Rodrigo R.","last_name":"Bammann"},{"full_name":"Bassi, Andrea","last_name":"Bassi","first_name":"Andrea"},{"full_name":"Beckert, Hannes","last_name":"Beckert","first_name":"Hannes"},{"full_name":"Beer, Sebastian","last_name":"Beer","first_name":"Sebastian"},{"full_name":"Belyaev, Yury","first_name":"Yury","last_name":"Belyaev"},{"full_name":"Bierwagen, Jakob","last_name":"Bierwagen","first_name":"Jakob"},{"full_name":"Birngruber, Konstantin A.","first_name":"Konstantin A.","last_name":"Birngruber"},{"first_name":"Manel","last_name":"Bosch","full_name":"Bosch, Manel"},{"full_name":"Breitlow, Juergen","last_name":"Breitlow","first_name":"Juergen"},{"full_name":"Cameron, Lisa A.","last_name":"Cameron","first_name":"Lisa A."},{"first_name":"Joe","last_name":"Chalfoun","full_name":"Chalfoun, Joe"},{"full_name":"Chambers, James J.","last_name":"Chambers","first_name":"James J."},{"first_name":"Chieh Li","last_name":"Chen","full_name":"Chen, Chieh Li"},{"full_name":"Conde-Sousa, Eduardo","last_name":"Conde-Sousa","first_name":"Eduardo"},{"first_name":"Alexander D.","last_name":"Corbett","full_name":"Corbett, Alexander D."},{"full_name":"Cordelieres, Fabrice P.","last_name":"Cordelieres","first_name":"Fabrice P."},{"last_name":"Nery","first_name":"Elaine Del","full_name":"Nery, Elaine Del"},{"full_name":"Dietzel, Ralf","last_name":"Dietzel","first_name":"Ralf"},{"full_name":"Eismann, Frank","last_name":"Eismann","first_name":"Frank"},{"last_name":"Fazeli","first_name":"Elnaz","full_name":"Fazeli, Elnaz"},{"full_name":"Felscher, Andreas","first_name":"Andreas","last_name":"Felscher"},{"first_name":"Hans","last_name":"Fried","full_name":"Fried, Hans"},{"full_name":"Gaudreault, Nathalie","last_name":"Gaudreault","first_name":"Nathalie"},{"full_name":"Goh, Wah Ing","first_name":"Wah Ing","last_name":"Goh"},{"full_name":"Guilbert, Thomas","first_name":"Thomas","last_name":"Guilbert"},{"full_name":"Hadleigh, Roland","first_name":"Roland","last_name":"Hadleigh"},{"first_name":"Peter","last_name":"Hemmerich","full_name":"Hemmerich, Peter"},{"full_name":"Holst, Gerhard A.","first_name":"Gerhard A.","last_name":"Holst"},{"first_name":"Michelle S.","last_name":"Itano","full_name":"Itano, Michelle S."},{"first_name":"Claudia B.","last_name":"Jaffe","full_name":"Jaffe, Claudia B."},{"first_name":"Helena K.","last_name":"Jambor","full_name":"Jambor, Helena K."},{"last_name":"Jarvis","first_name":"Stuart C.","full_name":"Jarvis, Stuart C."},{"full_name":"Keppler, Antje","last_name":"Keppler","first_name":"Antje"},{"last_name":"Kirchenbuechler","first_name":"David","full_name":"Kirchenbuechler, David"},{"full_name":"Kirchner, Marcel","last_name":"Kirchner","first_name":"Marcel"},{"last_name":"Kobayashi","first_name":"Norio","full_name":"Kobayashi, Norio"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996"},{"full_name":"Kunis, Susanne","first_name":"Susanne","last_name":"Kunis"},{"full_name":"Lacoste, Judith","last_name":"Lacoste","first_name":"Judith"},{"first_name":"Marco","last_name":"Marcello","full_name":"Marcello, Marco"},{"last_name":"Martins","first_name":"Gabriel G.","full_name":"Martins, Gabriel G."},{"last_name":"Metcalf","first_name":"Daniel J.","full_name":"Metcalf, Daniel J."},{"full_name":"Mitchell, Claire A.","first_name":"Claire A.","last_name":"Mitchell"},{"full_name":"Moore, Joshua","last_name":"Moore","first_name":"Joshua"},{"full_name":"Mueller, Tobias","first_name":"Tobias","last_name":"Mueller"},{"last_name":"Nelson","first_name":"Michael S.","full_name":"Nelson, Michael S."},{"first_name":"Stephen","last_name":"Ogg","full_name":"Ogg, Stephen"},{"full_name":"Onami, Shuichi","last_name":"Onami","first_name":"Shuichi"},{"last_name":"Palmer","first_name":"Alexandra L.","full_name":"Palmer, Alexandra L."},{"first_name":"Perrine","last_name":"Paul-Gilloteaux","full_name":"Paul-Gilloteaux, Perrine"},{"full_name":"Pimentel, Jaime A.","first_name":"Jaime A.","last_name":"Pimentel"},{"first_name":"Laure","last_name":"Plantard","full_name":"Plantard, Laure"},{"last_name":"Podder","first_name":"Santosh","full_name":"Podder, Santosh"},{"full_name":"Rexhepaj, Elton","first_name":"Elton","last_name":"Rexhepaj"},{"last_name":"Royon","first_name":"Arnaud","full_name":"Royon, Arnaud"},{"last_name":"Saari","first_name":"Markku A.","full_name":"Saari, Markku A."},{"full_name":"Schapman, Damien","last_name":"Schapman","first_name":"Damien"},{"full_name":"Schoonderwoert, Vincent","last_name":"Schoonderwoert","first_name":"Vincent"},{"full_name":"Schroth-Diez, Britta","first_name":"Britta","last_name":"Schroth-Diez"},{"full_name":"Schwartz, Stanley","first_name":"Stanley","last_name":"Schwartz"},{"full_name":"Shaw, Michael","first_name":"Michael","last_name":"Shaw"},{"last_name":"Spitaler","first_name":"Martin","full_name":"Spitaler, Martin"},{"full_name":"Stoeckl, Martin T.","last_name":"Stoeckl","first_name":"Martin T."},{"first_name":"Damir","last_name":"Sudar","full_name":"Sudar, Damir"},{"full_name":"Teillon, Jeremie","first_name":"Jeremie","last_name":"Teillon"},{"last_name":"Terjung","first_name":"Stefan","full_name":"Terjung, Stefan"},{"first_name":"Roland","last_name":"Thuenauer","full_name":"Thuenauer, Roland"},{"last_name":"Wilms","first_name":"Christian D.","full_name":"Wilms, Christian D."},{"first_name":"Graham D.","last_name":"Wright","full_name":"Wright, Graham D."},{"first_name":"Roland","last_name":"Nitschke","full_name":"Nitschke, Roland"}],"quality_controlled":"1","scopus_import":"1","publication_status":"published","intvolume":"       284","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"day":"11","isi":1,"month":"08","language":[{"iso":"eng"}],"publisher":"Wiley","publication":"Journal of Microscopy","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","department":[{"_id":"Bio"}],"date_created":"2021-08-15T22:01:29Z","oa_version":"Published Version","abstract":[{"text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":284,"page":"56-73","year":"2021","_id":"9911","issue":"1","article_type":"original","external_id":{"isi":["000683702700001"]},"oa":1,"status":"public","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","publication_identifier":{"issn":["0022-2720"],"eissn":["1365-2818"]},"citation":{"mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. 2021;284(1):56-73. doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. Wiley. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>.","ieee":"G. Nelson <i>et al.</i>, “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” <i>Journal of Microscopy</i>, vol. 284, no. 1. Wiley, pp. 56–73, 2021."}},{"intvolume":"        22","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2022-05-12T12:50:27Z","file_id":"11365","date_updated":"2022-05-12T12:50:27Z","file_size":1162454,"file_name":"2021_AnnHenriPoincare_Erdoes.pdf","checksum":"8d6bac0e2b0a28539608b0538a8e3b38"}],"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"language":[{"iso":"eng"}],"isi":1,"month":"12","day":"01","ddc":["510"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-05-12T12:50:27Z","scopus_import":"1","quality_controlled":"1","author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"first_name":"Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","full_name":"Nemish, Yuriy","last_name":"Nemish","orcid":"0000-0002-7327-856X","first_name":"Yuriy"}],"date_published":"2021-12-01T00:00:00Z","doi":"10.1007/s00023-021-01085-6","date_updated":"2023-08-11T10:31:48Z","article_processing_charge":"Yes (in subscription journal)","_id":"9912","has_accepted_license":"1","year":"2021","page":"4205–4269","volume":22,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. 2021;22:4205–4269. doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré  22 (2021) 4205–4269.","mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>, vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>.","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>.","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” <i>Annales Henri Poincaré </i>, vol. 22. Springer Nature, pp. 4205–4269, 2021.","apa":"Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>"},"publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","oa":1,"status":"public","external_id":{"arxiv":["1911.05112"],"isi":["000681531500001"]},"article_type":"original","oa_version":"Published Version","date_created":"2021-08-15T22:01:29Z","ec_funded":1,"title":"Scattering in quantum dots via noncommutative rational functions","department":[{"_id":"LaEr"}],"publication":"Annales Henri Poincaré ","publisher":"Springer Nature","abstract":[{"text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries.","lang":"eng"}],"arxiv":1},{"intvolume":"        22","file":[{"file_id":"10090","date_updated":"2021-10-05T13:36:42Z","file_size":3144854,"checksum":"750de03dc3b715c37090126c1548ba13","file_name":"2021_EmboR_Vega.pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","date_created":"2021-10-05T13:36:42Z","success":1}],"publication_status":"published","month":"09","isi":1,"language":[{"iso":"eng"}],"pmid":1,"ddc":["580"],"day":"06","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-10-05T13:36:42Z","article_number":"e51813","scopus_import":"1","quality_controlled":"1","date_published":"2021-09-06T00:00:00Z","author":[{"first_name":"Andrea","last_name":"Vega","full_name":"Vega, Andrea"},{"last_name":"Fredes","first_name":"Isabel","full_name":"Fredes, Isabel"},{"full_name":"O’Brien, José","first_name":"José","last_name":"O’Brien"},{"full_name":"Shen, Zhouxin","last_name":"Shen","first_name":"Zhouxin"},{"last_name":"Ötvös","orcid":"0000-0002-5503-4983","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina"},{"full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia","orcid":"0000-0002-9357-9415"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Briggs, Steven P.","last_name":"Briggs","first_name":"Steven P."},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."}],"article_processing_charge":"Yes","doi":"10.15252/embr.202051813","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}]},"date_updated":"2024-03-25T23:30:22Z","_id":"9913","year":"2021","has_accepted_license":"1","volume":22,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","citation":{"chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>.","ieee":"A. Vega <i>et al.</i>, “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” <i>EMBO Reports</i>, vol. 22, no. 9. Wiley, 2021.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. Wiley. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. 2021;22(9). doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>, vol. 22, no. 9, e51813, Wiley, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021)."},"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"status":"public","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","oa":1,"issue":"9","article_type":"original","external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"date_created":"2021-08-15T22:01:30Z","oa_version":"Published Version","publication":"EMBO Reports","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","publisher":"Wiley","abstract":[{"text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.","lang":"eng"}]},{"date_created":"2021-08-16T09:44:09Z","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"title":"Geometric superinductors and their applications in circuit quantum electrodynamics","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.","lang":"eng"}],"supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"_id":"9920","year":"2021","has_accepted_license":"1","page":"149","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","citation":{"short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","mla":"Peruzzo, Matilda. <i>Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics</i>. 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Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021."},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-013-8"]},"oa":1,"status":"public","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"file_date_updated":"2021-09-06T08:39:47Z","degree_awarded":"PhD","keyword":["quantum computing","superinductor","quantum metrology"],"date_published":"2021-08-19T00:00:00Z","author":[{"orcid":"0000-0002-3415-4628","last_name":"Peruzzo","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda"}],"article_processing_charge":"No","related_material":{"record":[{"id":"9928","relation":"part_of_dissertation","status":"public"},{"id":"8755","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:9920","date_updated":"2024-09-10T12:23:56Z","alternative_title":["ISTA Thesis"],"file":[{"file_name":"GeometricSuperinductorsForCQED.zip","checksum":"3cd1986efde5121d7581f6fcf9090da8","file_size":151387283,"date_updated":"2021-09-06T08:39:47Z","file_id":"9924","date_created":"2021-08-16T09:33:21Z","content_type":"application/x-zip-compressed","access_level":"closed","creator":"mperuzzo","relation":"source_file"},{"file_id":"9939","date_updated":"2021-09-06T08:39:47Z","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","checksum":"50928c621cdf0775d7a5906b9dc8602c","file_size":17596344,"creator":"mperuzzo","access_level":"open_access","relation":"main_file","date_created":"2021-08-18T14:20:06Z","content_type":"application/pdf"},{"creator":"mperuzzo","access_level":"closed","relation":"other","description":"Extra copy of the thesis as PDF/A-2b","date_created":"2021-08-18T14:20:09Z","content_type":"application/pdf","file_id":"9940","date_updated":"2021-09-06T08:39:47Z","checksum":"37f486aa1b622fe44af00d627ec13f6c","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","file_size":17592425}],"publication_status":"published","month":"08","language":[{"iso":"eng"}],"ddc":["539"],"day":"19"},{"file_date_updated":"2022-01-18T11:29:33Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"author":[{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo","first_name":"Matilda"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani"},{"full_name":"Szep, Gregory","first_name":"Gregory","last_name":"Szep"},{"last_name":"Trioni","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea"},{"last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-11-24T00:00:00Z","article_processing_charge":"No","date_updated":"2023-09-07T13:31:22Z","doi":"10.1103/PRXQuantum.2.040341","related_material":{"record":[{"status":"public","relation":"research_data","id":"13057"},{"id":"9920","relation":"dissertation_contains","status":"public"}]},"keyword":["quantum physics","mesoscale and nanoscale physics"],"scopus_import":"1","quality_controlled":"1","intvolume":"         2","file":[{"file_id":"10641","date_updated":"2022-01-18T11:29:33Z","file_size":4247422,"file_name":"2021_PRXQuantum_Peruzzo.pdf","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","relation":"main_file","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2022-01-18T11:29:33Z"}],"publication_status":"published","ddc":["530"],"day":"24","isi":1,"month":"11","project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"language":[{"iso":"eng"}],"publication":"PRX Quantum","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"publisher":"American Physical Society","date_created":"2021-08-17T08:14:18Z","ec_funded":1,"oa_version":"Published Version","arxiv":1,"abstract":[{"lang":"eng","text":"There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits."}],"volume":2,"page":"040341","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"9928","year":"2021","has_accepted_license":"1","oa":1,"status":"public","acknowledgement":"We thank W. Hughes for analytic and numerical modeling during the early stages of this work, J. Koch for discussions and support with the scqubits package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros for equipment support, as well as the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise, and E. Flurin for discussions. This work was supported by a NOMIS Foundation research grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria. M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","issue":"4","article_type":"original","external_id":{"isi":["000723015100001"],"arxiv":["2106.05882"]},"citation":{"ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. 2021;2(4):040341. doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2(4), 040341.","mla":"Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>, vol. 2, no. 4, American Physical Society, 2021, p. 040341, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","ieee":"M. Peruzzo <i>et al.</i>, “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” <i>PRX Quantum</i>, vol. 2, no. 4. American Physical Society, p. 040341, 2021.","chicago":"Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>.","apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., &#38; Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>"},"publication_identifier":{"eissn":["2691-3399"]}},{"publication_identifier":{"isbn":["9781450385480"]},"citation":{"ama":"Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel computation. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:481–491. doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>","mla":"Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel Computation.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 481–491, doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491.","ista":"Czumaj A, Davies P, Parter M. 2021. Component stability in low-space massively parallel computation. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 481–491.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively parallel computation,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 481–491.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in Low-Space Massively Parallel Computation.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 481–491. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>.","apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Component stability in low-space massively parallel computation. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 481–491). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>"},"external_id":{"isi":["000744439800049"],"arxiv":["2106.01880"]},"oa":1,"acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411.","status":"public","year":"2021","_id":"9933","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","page":"481–491","abstract":[{"lang":"eng","text":"In this paper, we study the power and limitations of component-stable algorithms in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari, Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space MPC algorithms, which are, informally, defined as algorithms for which the outputs reported by the nodes in different connected components are required to be independent. This very natural notion was introduced to capture most (if not all) of the known efficient MPC algorithms to date, and it was the first general class of MPC algorithms for which one can show non-trivial conditional lower bounds. In this paper we enhance the framework of component-stable algorithms and investigate its effect on the complexity of randomized and deterministic low-space MPC. Our key contributions include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and Uitto. This requires a very delicate amendment of the notion of component stability, which allows us to fill in gaps in the earlier arguments. 2) We also extend the framework to obtain conditional lower bounds for deterministic algorithms and fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate a collection of natural graph problems for which non-component-stable algorithms break the conditional lower bound obtained for component-stable algorithms. This implies that, for both deterministic and randomized algorithms, component-stable algorithms are conditionally weaker than the non-component-stable ones.\r\n\r\nAltogether our results imply that component-stability might limit the computational power of the low-space MPC model, paving the way for improved upper bounds that escape the conditional lower bound setting of Ghaffari, Kuhn, and Uitto."}],"arxiv":1,"ec_funded":1,"date_created":"2021-08-17T18:11:16Z","oa_version":"Submitted Version","publisher":"Association for Computing Machinery","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","title":"Component stability in low-space massively parallel computation","department":[{"_id":"DaAl"}],"isi":1,"month":"07","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"day":"21","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.01880"}],"quality_controlled":"1","article_processing_charge":"No","date_updated":"2023-08-17T07:11:32Z","doi":"10.1145/3465084.3467903","author":[{"full_name":"Czumaj, Artur","last_name":"Czumaj","first_name":"Artur"},{"full_name":"Davies, Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","last_name":"Davies","orcid":"0000-0002-5646-9524"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"date_published":"2021-07-21T00:00:00Z","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2021-07-30","location":"Virtual, Italy","start_date":"2021-07-26"}},{"_id":"9935","year":"2021","page":"469–479","type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Improved deterministic (Δ+1) coloring in low-space MPC. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 469–479). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>","ieee":"A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring in low-space MPC,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 469–479.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 469–479. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>.","mla":"Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 469–479, doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479.","ista":"Czumaj A, Davies P, Parter M. 2021. Improved deterministic (Δ+1) coloring in low-space MPC. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 469–479.","ama":"Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space MPC. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:469–479. doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>"},"publication_identifier":{"isbn":["978-1-4503-8548-0"]},"acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411.","status":"public","oa":1,"external_id":{"isi":["000744439800048"]},"oa_version":"Submitted Version","date_created":"2021-08-17T18:14:15Z","ec_funded":1,"title":"Improved deterministic (Δ+1) coloring in low-space MPC","department":[{"_id":"DaAl"}],"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","publisher":"Association for Computing Machinery","abstract":[{"text":"We present a deterministic O(log log log n)-round low-space Massively Parallel Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex graphs. In this model, every machine has sublinear local space of size n^φ for any arbitrary constant φ \\in (0,1). Our algorithm works under the relaxed setting where each machine is allowed to perform exponential local computations, while respecting the n^φ space and bandwidth limitations.\r\n\r\nOur key technical contribution is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized round complexity for the problem in the local model. Our derandomization employs a combination of tools, notably pseudorandom generators (PRG) and bounded-independence hash functions.\r\n\r\nThe achieved round complexity of O(logloglog n) rounds matches the bound of log(T_local ), which currently serves an upper bound barrier for all known randomized algorithms for locally-checkable problems in this model. Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the (Δ+1)-coloring problem have been known before.","lang":"eng"}],"main_file_link":[{"url":"http://wrap.warwick.ac.uk/153753","open_access":"1"}],"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"isi":1,"month":"07","day":"21","conference":{"location":"Virtual, Italy","start_date":"2021-07-26","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2021-07-30"},"quality_controlled":"1","author":[{"full_name":"Czumaj, Artur","last_name":"Czumaj","first_name":"Artur"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","last_name":"Davies","first_name":"Peter"},{"full_name":"Parter, Merav","last_name":"Parter","first_name":"Merav"}],"date_published":"2021-07-21T00:00:00Z","doi":"10.1145/3465084.3467937","date_updated":"2023-08-17T07:11:03Z","article_processing_charge":"No"},{"publisher":"IST Austria","department":[{"_id":"ToHe"}],"title":"Differential monitoring","oa_version":"Published Version","date_created":"2021-08-20T20:00:37Z","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"type":"technical_report","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"17","has_accepted_license":"1","year":"2021","_id":"9946","status":"public","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","oa":1,"publication_identifier":{"issn":["2664-1690"]},"citation":{"chicago":"Mühlböck, Fabian, and Thomas A Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>.","ieee":"F. Mühlböck and T. A. Henzinger, <i>Differential monitoring</i>. IST Austria, 2021.","apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). <i>Differential monitoring</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>","ama":"Mühlböck F, Henzinger TA. <i>Differential Monitoring</i>. IST Austria; 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>."},"file_date_updated":"2021-09-03T12:34:28Z","related_material":{"record":[{"status":"public","relation":"other","id":"9281"},{"id":"10108","status":"public","relation":"shorter_version"}]},"date_updated":"2023-08-14T07:20:29Z","doi":"10.15479/AT:ISTA:9946","alternative_title":["IST Austria Technical Report"],"article_processing_charge":"No","author":[{"last_name":"Mühlböck","orcid":"0000-0003-1548-0177","first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"date_published":"2021-09-01T00:00:00Z","keyword":["run-time verification","software engineering","implicit specification"],"publication_status":"published","file":[{"file_size":"320453","file_name":"differentialmonitoring-techreport.pdf","checksum":"0f9aafd59444cb6bdca6925d163ab946","date_updated":"2021-09-03T12:34:28Z","file_id":"9948","content_type":"application/pdf","date_created":"2021-08-20T19:59:44Z","relation":"main_file","creator":"fmuehlbo","access_level":"open_access"}],"day":"01","ddc":["005"],"language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"month":"09"},{"date_created":"2021-08-21T13:44:22Z","oa_version":"None","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","file_date_updated":"2021-08-21T13:43:59Z","department":[{"_id":"BeVi"}],"article_processing_charge":"No","related_material":{"record":[{"id":"10166","relation":"used_in_publication","status":"public"}]},"date_updated":"2024-02-21T12:40:30Z","doi":"10.15479/AT:ISTA:9949","date_published":"2021-08-24T00:00:00Z","author":[{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"year":"2021","has_accepted_license":"1","file":[{"date_created":"2021-08-21T13:43:59Z","success":1,"content_type":"application/zip","creator":"bvicoso","access_level":"open_access","relation":"main_file","checksum":"90461837eed66beac6fa302993cf0ca9","file_name":"Data.zip","file_size":139188306,"file_id":"9950","date_updated":"2021-08-21T13:43:59Z"}],"_id":"9949","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","month":"08","citation":{"ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","short":"B. Vicoso, (2021).","mla":"Vicoso, Beatriz. <i>Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>."},"day":"24","status":"public","oa":1},{"publisher":"Association for Computing Machinery","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","title":"Comparison dynamics in population protocols","department":[{"_id":"DaAl"}],"conference":{"start_date":"2021-07-26","location":"Virtual, Italy","end_date":"2021-07-30","name":"PODC: Symposium on Principles of Distributed Computing"},"date_created":"2021-08-22T22:01:20Z","oa_version":"None","article_processing_charge":"No","date_updated":"2023-08-11T10:56:04Z","doi":"10.1145/3465084.3467915","date_published":"2021-07-21T00:00:00Z","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Töpfer","first_name":"Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87","full_name":"Töpfer, Martin"},{"last_name":"Uznański","first_name":"Przemysław","full_name":"Uznański, Przemysław"}],"quality_controlled":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.\r\n\r\nIn this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the \"correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","page":"55-65","year":"2021","publication_status":"published","_id":"9951","external_id":{"isi":["000744439800005"]},"day":"21","acknowledgement":"We would like to thank Rati Gelashvili for very useful discussions, and the PODC anonymous reviewers for their careful reading of our paper, and for their useful remarks. This work is partially supported by the Polish National Science Center (NCN) grant UMO2017/25/B/ST6/02010.","status":"public","isi":1,"month":"07","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450385480"]},"citation":{"ama":"Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:55-65. doi:<a href=\"https://doi.org/10.1145/3465084.3467915\">10.1145/3465084.3467915</a>","short":"D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65.","mla":"Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 55–65, doi:<a href=\"https://doi.org/10.1145/3465084.3467915\">10.1145/3465084.3467915</a>.","ista":"Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.","ieee":"D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population protocols,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 55–65.","chicago":"Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison Dynamics in Population Protocols.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 55–65. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467915\">https://doi.org/10.1145/3465084.3467915</a>.","apa":"Alistarh, D.-A., Töpfer, M., &#38; Uznański, P. (2021). Comparison dynamics in population protocols. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 55–65). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467915\">https://doi.org/10.1145/3465084.3467915</a>"}},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"jcs255018","file_date_updated":"2021-08-23T07:32:20Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","date_updated":"2023-08-11T10:55:36Z","doi":"10.1242/jcs.255018","author":[{"full_name":"Chaigne, Agathe","last_name":"Chaigne","first_name":"Agathe"},{"full_name":"Smith, Matthew B.","last_name":"Smith","first_name":"Matthew B."},{"full_name":"Cavestany, R. L.","last_name":"Cavestany","first_name":"R. L."},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Chalut","first_name":"Kevin J.","full_name":"Chalut, Kevin J."},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."}],"date_published":"2021-07-01T00:00:00Z","file":[{"creator":"asandaue","access_level":"open_access","relation":"main_file","success":1,"date_created":"2021-08-23T07:32:20Z","content_type":"application/pdf","date_updated":"2021-08-23T07:32:20Z","file_id":"9954","file_name":"2021_JournalOfCellScience_Chaigne.pdf","checksum":"f086f9d7cb63b2474c01921cb060c513","file_size":8651724}],"publication_status":"published","intvolume":"       134","isi":1,"month":"07","language":[{"iso":"eng"}],"ddc":["570"],"day":"01","date_created":"2021-08-22T22:01:20Z","oa_version":"Published Version","publisher":"The Company of Biologists","publication":"Journal of Cell Science","department":[{"_id":"EdHa"}],"title":"Three-dimensional geometry controls division symmetry in stem cell colonies","abstract":[{"lang":"eng","text":"Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry."}],"year":"2021","has_accepted_license":"1","_id":"9952","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":134,"publication_identifier":{"issn":["00219533"],"eissn":["14779137"]},"citation":{"mla":"Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” <i>Journal of Cell Science</i>, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:<a href=\"https://doi.org/10.1242/jcs.255018\">10.1242/jcs.255018</a>.","ista":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018.","short":"A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021).","ama":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. <i>Journal of Cell Science</i>. 2021;134(14). doi:<a href=\"https://doi.org/10.1242/jcs.255018\">10.1242/jcs.255018</a>","apa":"Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., &#38; Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.255018\">https://doi.org/10.1242/jcs.255018</a>","ieee":"A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” <i>Journal of Cell Science</i>, vol. 134, no. 14. The Company of Biologists, 2021.","chicago":"Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” <i>Journal of Cell Science</i>. The Company of Biologists, 2021. <a href=\"https://doi.org/10.1242/jcs.255018\">https://doi.org/10.1242/jcs.255018</a>."},"issue":"14","external_id":{"isi":["000681395800008"]},"article_type":"original","status":"public","acknowledgement":"We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support.","oa":1},{"_id":"9953","year":"2021","volume":97,"page":"423-439","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"chicago":"Picard, Katherine, Kanchan Bisht, Silvia Poggini, Stefano Garofalo, Maria Teresa Golia, Bernadette Basilico, Fatima Abdallah, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” <i>Brain, Behavior, and Immunity</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">https://doi.org/10.1016/j.bbi.2021.07.022</a>.","ieee":"K. Picard <i>et al.</i>, “Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice,” <i>Brain, Behavior, and Immunity</i>, vol. 97. Elsevier, pp. 423–439, 2021.","apa":"Picard, K., Bisht, K., Poggini, S., Garofalo, S., Golia, M. T., Basilico, B., … Tremblay, M. È. (2021). Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. <i>Brain, Behavior, and Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">https://doi.org/10.1016/j.bbi.2021.07.022</a>","ama":"Picard K, Bisht K, Poggini S, et al. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. <i>Brain, Behavior, and Immunity</i>. 2021;97:423-439. doi:<a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">10.1016/j.bbi.2021.07.022</a>","short":"K. Picard, K. Bisht, S. Poggini, S. Garofalo, M.T. Golia, B. Basilico, F. Abdallah, N. Ciano Albanese, I. Amrein, N. Vernoux, K. Sharma, C.W. Hui, J. C. Savage, C. Limatola, D. Ragozzino, L. Maggi, I. Branchi, M.È. Tremblay, Brain, Behavior, and Immunity 97 (2021) 423–439.","ista":"Picard K, Bisht K, Poggini S, Garofalo S, Golia MT, Basilico B, Abdallah F, Ciano Albanese N, Amrein I, Vernoux N, Sharma K, Hui CW, C. Savage J, Limatola C, Ragozzino D, Maggi L, Branchi I, Tremblay MÈ. 2021. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 97, 423–439.","mla":"Picard, Katherine, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” <i>Brain, Behavior, and Immunity</i>, vol. 97, Elsevier, 2021, pp. 423–39, doi:<a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">10.1016/j.bbi.2021.07.022</a>."},"publication_identifier":{"issn":["0889-1591"]},"status":"public","acknowledgement":"We acknowledge that Université Laval stands on the traditional and unceded land of the Huron-Wendat peoples; and that the University of Victoria exists on the territory of the Lekwungen peoples and that the Songhees, Esquimalt and WSÁNEÆ peoples have relationships to this land. We thank Emmanuel Planel for the access to the epifluorescence microscope and Julie-Christine Lévesque at the Bioimaging Platform of CRCHU de Québec-Université Laval for technical assistance. We also thank the Centre for Advanced Materials and Related Technology for the access to the confocal microscope with Airyscan. K.P. was supported by a doctoral scholarship from Fonds de Recherche du Québec – Santé (FRQS), an excellence award from Fondation du CHU de Québec, as well as from Centre Thématique de Recherche en Neurosciences and from Fondation Famille-Choquette. K.B. was supported by excellence scholarships from Université Laval and Fondation du CHU de Québec. S.G. is supported by FIRC-AIRC fellowship for Italy 22329/2018 and by Pilot ARISLA NKINALS 2019. C.W.H. and J.C.S. were supported by postdoctoral fellowships from FRQS. This study was funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant (RGPIN-2014-05308) awarded to M.E.T., by ERANET neuron 2017 MicroSynDep to M.E.T. and I.B., and by the Italian Ministry of Health, grant RF-2018-12367249 to I.B, by PRIN 2017, AIRC 2019 and Ministero della Salute RF2018 to C.L. M.E.T. is a Tier II Canada Research Chair in Neurobiology of Aging and Cognition.","oa":1,"article_type":"original","external_id":{"isi":["000702878400007"],"pmid":["34343616"]},"date_created":"2021-08-22T22:01:21Z","oa_version":"Submitted Version","publication":"Brain, Behavior, and Immunity","title":"Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice","department":[{"_id":"GaNo"}],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress."}],"intvolume":"        97","main_file_link":[{"open_access":"1","url":"https://www.zora.uzh.ch/id/eprint/208855/1/ZORA208855.pdf"}],"publication_status":"published","month":"10","isi":1,"language":[{"iso":"eng"}],"pmid":1,"day":"01","scopus_import":"1","quality_controlled":"1","date_published":"2021-10-01T00:00:00Z","author":[{"full_name":"Picard, Katherine","first_name":"Katherine","last_name":"Picard"},{"full_name":"Bisht, Kanchan","first_name":"Kanchan","last_name":"Bisht"},{"first_name":"Silvia","last_name":"Poggini","full_name":"Poggini, Silvia"},{"full_name":"Garofalo, Stefano","first_name":"Stefano","last_name":"Garofalo"},{"last_name":"Golia","first_name":"Maria Teresa","full_name":"Golia, Maria Teresa"},{"first_name":"Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"full_name":"Abdallah, Fatima","first_name":"Fatima","last_name":"Abdallah"},{"full_name":"Ciano Albanese, Naomi","last_name":"Ciano Albanese","first_name":"Naomi"},{"full_name":"Amrein, Irmgard","last_name":"Amrein","first_name":"Irmgard"},{"full_name":"Vernoux, Nathalie","first_name":"Nathalie","last_name":"Vernoux"},{"full_name":"Sharma, Kaushik","last_name":"Sharma","first_name":"Kaushik"},{"first_name":"Chin Wai","last_name":"Hui","full_name":"Hui, Chin Wai"},{"last_name":"C. Savage","first_name":"Julie","full_name":"C. Savage, Julie"},{"first_name":"Cristina","last_name":"Limatola","full_name":"Limatola, Cristina"},{"full_name":"Ragozzino, Davide","last_name":"Ragozzino","first_name":"Davide"},{"last_name":"Maggi","first_name":"Laura","full_name":"Maggi, Laura"},{"last_name":"Branchi","first_name":"Igor","full_name":"Branchi, Igor"},{"last_name":"Tremblay","first_name":"Marie Ève","full_name":"Tremblay, Marie Ève"}],"article_processing_charge":"No","date_updated":"2023-10-03T09:49:18Z","doi":"10.1016/j.bbi.2021.07.022"},{"type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"4791-4800","has_accepted_license":"1","year":"2021","_id":"9957","external_id":{"isi":["000739917304096"],"arxiv":["2008.10247"]},"oa":1,"acknowledgement":"We thank Tarun Yenamandra and Duarte David for helping us with the comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784). We also acknowledge support from InterDigital.","status":"public","publication_identifier":{"isbn":["978-166544509-2"],"issn":["1063-6919"]},"citation":{"apa":"B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., … Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields. In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i> (pp. 4791–4800). Nashville, TN, United States; Virtual: IEEE. <a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">https://doi.org/10.1109/CVPR46437.2021.00476</a>","chicago":"B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel, Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.” In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, 4791–4800. IEEE, 2021. <a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">https://doi.org/10.1109/CVPR46437.2021.00476</a>.","ieee":"M. B R <i>et al.</i>, “Monocular reconstruction of neural face reflectance fields,” in <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, Nashville, TN, United States; Virtual, 2021, pp. 4791–4800.","mla":"B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance Fields.” <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2021, pp. 4791–800, doi:<a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">10.1109/CVPR46437.2021.00476</a>.","ista":"B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance fields. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 4791–4800.","short":"M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800.","ama":"B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance fields. In: <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2021:4791-4800. doi:<a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">10.1109/CVPR46437.2021.00476</a>"},"publisher":"IEEE","title":"Monocular reconstruction of neural face reflectance fields","department":[{"_id":"BeBi"}],"publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","oa_version":"Preprint","date_created":"2021-08-24T06:03:00Z","arxiv":1,"abstract":[{"text":"The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects.","lang":"eng"}],"publication_status":"published","file":[{"date_updated":"2021-08-24T06:02:15Z","file_id":"9958","file_size":4746649,"file_name":"R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf","checksum":"961db0bde76dd87cf833930080bb9f38","relation":"main_file","access_level":"open_access","creator":"bbickel","content_type":"application/pdf","date_created":"2021-08-24T06:02:15Z"}],"day":"01","ddc":["000"],"language":[{"iso":"eng"}],"month":"09","isi":1,"file_date_updated":"2021-08-24T06:02:15Z","conference":{"start_date":"2021-06-20","location":"Nashville, TN, United States; Virtual","end_date":"2021-06-25","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"doi":"10.1109/CVPR46437.2021.00476","date_updated":"2023-08-11T11:08:35Z","article_processing_charge":"No","date_published":"2021-09-01T00:00:00Z","author":[{"full_name":"B R, Mallikarjun","last_name":"B R","first_name":"Mallikarjun"},{"full_name":"Tewari, Ayush","last_name":"Tewari","first_name":"Ayush"},{"full_name":"Oh, Tae-Hyun","first_name":"Tae-Hyun","last_name":"Oh"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"last_name":"Seidel","first_name":"Hans-Peter","full_name":"Seidel, Hans-Peter"},{"last_name":"Pfister","first_name":"Hanspeter","full_name":"Pfister, Hanspeter"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"first_name":"Mohamed","last_name":"Elgharib","full_name":"Elgharib, Mohamed"},{"full_name":"Theobalt, Christian","first_name":"Christian","last_name":"Theobalt"}],"quality_controlled":"1","scopus_import":"1"},{"citation":{"apa":"Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M. D., &#38; Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.127.090602\">https://doi.org/10.1103/PhysRevLett.127.090602</a>","chicago":"Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M. D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.127.090602\">https://doi.org/10.1103/PhysRevLett.127.090602</a>.","ieee":"N. Maskara <i>et al.</i>, “Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving,” <i>Physical Review Letters</i>, vol. 127, no. 9. American Physical Society, 2021.","mla":"Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” <i>Physical Review Letters</i>, vol. 127, no. 9, 090602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.127.090602\">10.1103/PhysRevLett.127.090602</a>.","ista":"Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M. 2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 127(9), 090602.","short":"N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M. Serbyn, Physical Review Letters 127 (2021).","ama":"Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. <i>Physical Review Letters</i>. 2021;127(9). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.127.090602\">10.1103/PhysRevLett.127.090602</a>"},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"status":"public","oa":1,"acknowledgement":"We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini, Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.); the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories and Gauge-Gravity Correspondence – Grant No. DE-SC0021013.","issue":"9","external_id":{"isi":["000692200100002"],"arxiv":["2102.13160"]},"article_type":"letter_note","_id":"9960","year":"2021","volume":127,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","abstract":[{"text":"The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars.","lang":"eng"}],"arxiv":1,"ec_funded":1,"date_created":"2021-08-28T08:08:58Z","oa_version":"Submitted Version","publication":"Physical Review Letters","department":[{"_id":"MaSe"}],"title":"Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving","publisher":"American Physical Society","month":"08","isi":1,"language":[{"iso":"eng"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"day":"27","main_file_link":[{"url":"https://arxiv.org/abs/2102.13160","open_access":"1"}],"intvolume":"       127","publication_status":"published","quality_controlled":"1","date_published":"2021-08-27T00:00:00Z","author":[{"last_name":"Maskara","first_name":"N.","full_name":"Maskara, N."},{"last_name":"Michailidis","orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"first_name":"W. W.","last_name":"Ho","full_name":"Ho, W. W."},{"full_name":"Bluvstein, D.","first_name":"D.","last_name":"Bluvstein"},{"full_name":"Choi, S.","first_name":"S.","last_name":"Choi"},{"first_name":"M. D.","last_name":"Lukin","full_name":"Lukin, M. D."},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"article_processing_charge":"No","doi":"10.1103/PhysRevLett.127.090602","date_updated":"2023-08-11T10:57:51Z","article_number":"090602"},{"issue":"8","article_type":"letter_note","external_id":{"isi":["000689734500009"],"arxiv":["2012.15676"]},"status":"public","acknowledgement":"We thank S. Garratt for useful comments on the manuscript. This work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A., Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1 and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations were performed on the Baobab cluster of the University\r\nof Geneva.","oa":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"citation":{"ama":"Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body localization transition in Floquet systems. <i>Physical Review B</i>. 2021;104(8). doi:<a href=\"https://doi.org/10.1103/PhysRevB.104.L081112\">10.1103/PhysRevB.104.L081112</a>","mla":"Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” <i>Physical Review B</i>, vol. 104, no. 8, L081112, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevB.104.L081112\">10.1103/PhysRevB.104.L081112</a>.","ista":"Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 104(8), L081112.","short":"M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021).","chicago":"Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevB.104.L081112\">https://doi.org/10.1103/PhysRevB.104.L081112</a>.","ieee":"M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across the many-body localization transition in Floquet systems,” <i>Physical Review B</i>, vol. 104, no. 8. American Physical Society, 2021.","apa":"Sonner, M., Serbyn, M., Papić, Z., &#38; Abanin, D. A. (2021). Thouless energy across the many-body localization transition in Floquet systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.104.L081112\">https://doi.org/10.1103/PhysRevB.104.L081112</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":104,"year":"2021","_id":"9961","arxiv":1,"abstract":[{"text":"The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems.","lang":"eng"}],"publisher":"American Physical Society","publication":"Physical Review B","department":[{"_id":"MaSe"}],"title":"Thouless energy across the many-body localization transition in Floquet systems","date_created":"2021-08-28T16:44:55Z","ec_funded":1,"oa_version":"Submitted Version","day":"15","isi":1,"month":"08","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"publication_status":"published","intvolume":"       104","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.15676"}],"article_processing_charge":"No","date_updated":"2023-08-11T10:57:09Z","doi":"10.1103/PhysRevB.104.L081112","author":[{"full_name":"Sonner, Michael","last_name":"Sonner","first_name":"Michael"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."}],"date_published":"2021-08-15T00:00:00Z","quality_controlled":"1","article_number":"L081112"},{"oa":1,"status":"public","citation":{"ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","mla":"Hansen, Andi H. <i>Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>","apa":"Hansen, A. H. (2021). <i>Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>."},"publication_identifier":{"issn":["2663-337X"]},"page":"182","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","_id":"9962","supervisor":[{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","year":"2021","abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","date_created":"2021-08-29T12:36:50Z","oa_version":"Published Version","ddc":["570"],"day":"02","month":"09","language":[{"iso":"eng"}],"project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"}],"file":[{"date_created":"2021-08-30T09:17:39Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ahansen","access_level":"closed","relation":"source_file","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","file_name":"Thesis_Hansen.docx","file_size":10629190,"file_id":"9971","date_updated":"2022-09-03T22:30:04Z"},{"relation":"main_file","access_level":"open_access","creator":"ahansen","content_type":"application/pdf","date_created":"2021-08-30T09:29:44Z","embargo":"2022-09-02","file_id":"9972","date_updated":"2022-09-03T22:30:04Z","file_size":13457469,"file_name":"Thesis_Hansen_PDFA-1a.pdf","checksum":"204fa40321a1c6289b68c473634c4bf3"}],"publication_status":"published","date_published":"2021-09-02T00:00:00Z","author":[{"last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-22T09:58:30Z","doi":"10.15479/at:ista:9962","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8569"},{"relation":"part_of_dissertation","status":"public","id":"960"}]},"degree_awarded":"PhD","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"file_date_updated":"2022-09-03T22:30:04Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"scopus_import":"1","quality_controlled":"1","date_published":"2021-06-21T00:00:00Z","author":[{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Salem, Iosif","first_name":"Iosif","last_name":"Salem"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"},{"last_name":"Yeo","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14506"}]},"doi":"10.23919/IFIPNetworking52078.2021.9472205","date_updated":"2023-11-30T10:54:50Z","article_processing_charge":"No","conference":{"start_date":"2021-06-21","location":"Espoo and Helsinki, Finland","end_date":"2021-06-24","name":"2021 IFIP Networking Conference (IFIP Networking)"},"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"month":"06","isi":1,"day":"21","main_file_link":[{"url":"https://arxiv.org/abs/2104.04293","open_access":"1"}],"publication_status":"published","abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths.","lang":"eng"}],"arxiv":1,"oa_version":"Submitted Version","ec_funded":1,"date_created":"2021-08-29T22:01:16Z","title":"LightPIR: Privacy-preserving route discovery for payment channel networks","department":[{"_id":"KrPi"}],"publisher":"IEEE","citation":{"apa":"Pietrzak, K. Z., Salem, I., Schmid, S., &#38; Yeo, M. X. (2021). LightPIR: Privacy-preserving route discovery for payment channel networks. Presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland: IEEE. <a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">https://doi.org/10.23919/IFIPNetworking52078.2021.9472205</a>","chicago":"Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo. “LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE, 2021. <a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">https://doi.org/10.23919/IFIPNetworking52078.2021.9472205</a>.","ieee":"K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving route discovery for payment channel networks,” presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.","mla":"Pietrzak, Krzysztof Z., et al. <i>LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks</i>. IEEE, 2021, doi:<a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">10.23919/IFIPNetworking52078.2021.9472205</a>.","ista":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving route discovery for payment channel networks. 2021 IFIP Networking Conference (IFIP Networking).","short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.","ama":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route discovery for payment channel networks. In: IEEE; 2021. doi:<a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">10.23919/IFIPNetworking52078.2021.9472205</a>"},"publication_identifier":{"eissn":["1861-2288"],"eisbn":["978-3-9031-7639-3"],"isbn":["978-1-6654-4501-6"]},"oa":1,"status":"public","external_id":{"arxiv":["2104.04293"],"isi":["000853016800008"]},"_id":"9969","year":"2021","type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publisher":"Springer Nature","publication":"Communications in Mathematical Physics","title":"Complete gradient estimates of quantum Markov semigroups","department":[{"_id":"JaMa"}],"ec_funded":1,"date_created":"2021-08-30T10:07:44Z","oa_version":"Published Version","arxiv":1,"abstract":[{"lang":"eng","text":"In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":387,"page":"761–791","year":"2021","has_accepted_license":"1","_id":"9973","article_type":"original","external_id":{"isi":["000691214200001"],"arxiv":["2007.13506"]},"oa":1,"acknowledgement":"Both authors would like to thank Jan Maas for fruitful discussions and helpful comments.","status":"public","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"citation":{"ista":"Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 387, 761–791.","short":"M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791.","mla":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>, vol. 387, Springer Nature, 2021, pp. 761–791, doi:<a href=\"https://doi.org/10.1007/s00220-021-04199-4\">10.1007/s00220-021-04199-4</a>.","ama":"Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. 2021;387:761–791. doi:<a href=\"https://doi.org/10.1007/s00220-021-04199-4\">10.1007/s00220-021-04199-4</a>","apa":"Wirth, M., &#38; Zhang, H. (2021). Complete gradient estimates of quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-021-04199-4\">https://doi.org/10.1007/s00220-021-04199-4</a>","ieee":"M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,” <i>Communications in Mathematical Physics</i>, vol. 387. Springer Nature, pp. 761–791, 2021.","chicago":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00220-021-04199-4\">https://doi.org/10.1007/s00220-021-04199-4</a>."},"file_date_updated":"2021-09-08T09:46:34Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00220-021-04199-4","date_updated":"2023-08-11T11:09:07Z","author":[{"full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","orcid":"0000-0002-0519-4241","last_name":"Wirth"},{"first_name":"Haonan","last_name":"Zhang","full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"date_published":"2021-08-30T00:00:00Z","quality_controlled":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"scopus_import":"1","file":[{"date_created":"2021-09-08T07:34:24Z","content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","relation":"main_file","file_name":"2021_CommunMathPhys_Wirth.pdf","checksum":"8a602f916b1c2b0dc1159708b7cb204b","file_size":505971,"date_updated":"2021-09-08T09:46:34Z","file_id":"9990"}],"publication_status":"published","intvolume":"       387","ddc":["621"],"day":"30","isi":1,"month":"08","language":[{"iso":"eng"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}]}]