[{"oa_version":"Published Version","has_accepted_license":"1","year":"2021","article_type":"original","publication_identifier":{"eissn":["20452322"]},"scopus_import":"1","external_id":{"pmid":["34330988"],"isi":["000683329100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-11T10:42:58Z","abstract":[{"lang":"eng","text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period."}],"_id":"9905","date_published":"2021-07-30T00:00:00Z","article_number":"15729","file":[{"file_id":"9927","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-16T11:36:49Z","success":1,"creator":"asandaue","file_size":3432001,"file_name":"2021_ScientificReports_Rella.pdf","checksum":"ac86892ed17e6724c7251844da5cef5c","access_level":"open_access","date_updated":"2021-08-16T11:36:49Z"}],"article_processing_charge":"Yes","issue":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":11,"file_date_updated":"2021-08-16T11:36:49Z","oa":1,"publication_status":"published","type":"journal_article","author":[{"last_name":"Rella","full_name":"Rella, Simon","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"full_name":"Kulikova, Yuliya A.","first_name":"Yuliya A.","last_name":"Kulikova"},{"first_name":"Emmanouil T.","full_name":"Dermitzakis, Emmanouil T.","last_name":"Dermitzakis"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"}],"day":"30","title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","citation":{"ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &#38; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>.","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021."},"ec_funded":1,"ddc":["570","610"],"doi":"10.1038/s41598-021-95025-3","language":[{"iso":"eng"}],"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/","description":"News on IST Website"}]},"pmid":1,"acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","date_created":"2021-08-15T22:01:26Z","month":"07","intvolume":"        11","status":"public","publication":"Scientific Reports","department":[{"_id":"FyKo"}],"quality_controlled":"1","isi":1,"publisher":"Springer Nature"},{"_id":"9906","abstract":[{"lang":"eng","text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways."}],"date_published":"2021-08-04T00:00:00Z","file":[{"checksum":"be7f0042607ca60549cb27513c19c6af","date_updated":"2021-08-16T09:29:17Z","access_level":"open_access","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","file_size":2646018,"creator":"asandaue","date_created":"2021-08-16T09:29:17Z","success":1,"content_type":"application/pdf","file_id":"9922","relation":"main_file"}],"article_number":"8385","issue":"16","article_processing_charge":"Yes","volume":22,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2021-08-16T09:29:17Z","oa":1,"publication_status":"published","year":"2021","oa_version":"Published Version","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"date_updated":"2023-08-11T10:34:13Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000689147400001"]},"date_created":"2021-08-15T22:01:27Z","month":"08","intvolume":"        22","status":"public","department":[{"_id":"SiHi"}],"quality_controlled":"1","publication":"International Journal of Molecular Sciences","isi":1,"publisher":"MDPI","author":[{"first_name":"Iveta","full_name":"Yotova, Iveta","last_name":"Yotova"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"},{"orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian"},{"full_name":"Proestling, Katharina","first_name":"Katharina","last_name":"Proestling"},{"last_name":"Haslinger","full_name":"Haslinger, Isabella","first_name":"Isabella"},{"last_name":"Kuessel","first_name":"Lorenz","full_name":"Kuessel, Lorenz"},{"last_name":"Perricos","full_name":"Perricos, Alexandra","first_name":"Alexandra"},{"last_name":"Husslein","full_name":"Husslein, Heinrich","first_name":"Heinrich"},{"full_name":"Wenzl, René","first_name":"René","last_name":"Wenzl"}],"type":"journal_article","day":"04","title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","citation":{"mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16, 8385, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>.","chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>.","ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","ieee":"I. Yotova <i>et al.</i>, “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16. MDPI, 2021.","ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. 2021;22(16). doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>","short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021)."},"doi":"10.3390/ijms22168385","ddc":["570"],"language":[{"iso":"eng"}],"acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources."},{"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.3390/ijms22158350","acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"}],"pmid":1,"day":"01","type":"journal_article","author":[{"first_name":"Naďa","full_name":"Labajová, Naďa","last_name":"Labajová"},{"last_name":"Baranova","full_name":"Baranova, Natalia S.","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124"},{"last_name":"Jurásek","first_name":"Miroslav","full_name":"Jurásek, Miroslav"},{"last_name":"Vácha","full_name":"Vácha, Robert","first_name":"Robert"},{"full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barák","full_name":"Barák, Imrich","first_name":"Imrich"}],"ec_funded":1,"citation":{"mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021.","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021)."},"title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","quality_controlled":"1","department":[{"_id":"MaLo"}],"publication":"International Journal of Molecular Sciences","intvolume":"        22","status":"public","publisher":"MDPI","isi":1,"month":"08","date_created":"2021-08-15T22:01:27Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-11T10:34:44Z","scopus_import":"1","external_id":{"isi":["000681815400001"],"pmid":["34361115"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"article_type":"original","has_accepted_license":"1","year":"2021","oa_version":"Published Version","file_date_updated":"2021-08-16T09:35:56Z","volume":22,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"file":[{"file_size":6132410,"creator":"asandaue","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","checksum":"a4bc06e9a2c803ceff5a91f10b174054","access_level":"open_access","date_updated":"2021-08-16T09:35:56Z","file_id":"9923","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-16T09:35:56Z","success":1}],"article_number":"8350","_id":"9907","abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"date_published":"2021-08-01T00:00:00Z","issue":"15","article_processing_charge":"Yes"},{"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.3390/genes12081136","ec_funded":1,"citation":{"mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>, vol. 12, no. 8, 1136, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>.","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>.","ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136.","ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., &#38; Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021)."},"title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","day":"01","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","first_name":"Marion A L","full_name":"Picard, Marion A L","last_name":"Picard"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz"},{"last_name":"Bertrand","full_name":"Bertrand, Stéphanie","first_name":"Stéphanie"},{"last_name":"Escriva","full_name":"Escriva, Hector","first_name":"Hector"}],"type":"journal_article","publisher":"MDPI","isi":1,"quality_controlled":"1","department":[{"_id":"BeVi"}],"publication":"Genes","status":"public","intvolume":"        12","month":"08","date_created":"2021-08-15T22:01:27Z","date_updated":"2023-08-11T10:42:32Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000690475900001"]},"publication_identifier":{"eissn":["20734425"]},"article_type":"review","year":"2021","oa_version":"Published Version","has_accepted_license":"1","publication_status":"published","oa":1,"file_date_updated":"2021-08-16T09:49:35Z","volume":12,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"8","article_processing_charge":"Yes","file":[{"creator":"asandaue","file_size":2297655,"file_name":"2021_Genes_Picard.pdf","access_level":"open_access","date_updated":"2021-08-16T09:49:35Z","checksum":"744e60e56d290a96da3c91a9779f886f","relation":"main_file","file_id":"9926","content_type":"application/pdf","success":1,"date_created":"2021-08-16T09:49:35Z"}],"article_number":"1136","_id":"9908","date_published":"2021-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems."}]},{"isi":1,"publisher":"MDPI","status":"public","intvolume":"        12","department":[{"_id":"JiFr"}],"quality_controlled":"1","publication":"Genes","date_created":"2021-08-15T22:01:28Z","month":"07","acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","doi":"10.3390/genes12081141","ddc":["580","570"],"language":[{"iso":"eng"}],"title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","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).","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>","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>.","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.","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>."},"type":"journal_article","author":[{"full_name":"Zeng, Yinwei","first_name":"Yinwei","last_name":"Zeng"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge"},{"first_name":"Hoang Khai","full_name":"Trinh, Hoang Khai","last_name":"Trinh"},{"first_name":"Thomas","full_name":"Heugebaert, Thomas","last_name":"Heugebaert"},{"first_name":"Christian V.","full_name":"Stevens, Christian V.","last_name":"Stevens"},{"first_name":"Irene","full_name":"Garcia-Maquilon, Irene","last_name":"Garcia-Maquilon"},{"full_name":"Rodriguez, Pedro L.","first_name":"Pedro L.","last_name":"Rodriguez"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Geelen","full_name":"Geelen, Danny","first_name":"Danny"}],"day":"27","oa":1,"publication_status":"published","volume":12,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2021-08-16T09:02:40Z","issue":"8","article_processing_charge":"Yes","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."}],"_id":"9909","date_published":"2021-07-27T00:00:00Z","article_number":"1141","file":[{"date_created":"2021-08-16T09:02:40Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"9919","checksum":"3d99535618cf9a5b14d264408fa52e97","date_updated":"2021-08-16T09:02:40Z","access_level":"open_access","file_name":"2021_Genes_Zeng.pdf","file_size":1340305,"creator":"asandaue"}],"publication_identifier":{"eissn":["20734425"]},"date_updated":"2023-08-11T10:32:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000690558000001"]},"oa_version":"Published Version","has_accepted_license":"1","year":"2021","article_type":"original"},{"publication_status":"published","oa":1,"file_date_updated":"2021-08-16T09:14:36Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":29,"article_processing_charge":"Yes (in subscription journal)","issue":"7","file":[{"relation":"main_file","file_id":"9921","content_type":"application/pdf","date_created":"2021-08-16T09:14:36Z","success":1,"file_size":1079395,"creator":"asandaue","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","checksum":"a676d76f91b0dbe0504c63e469129c2a","access_level":"open_access","date_updated":"2021-08-16T09:14:36Z"}],"_id":"9910","date_published":"2021-07-01T00:00:00Z","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."}],"scopus_import":"1","external_id":{"pmid":["33664501"],"isi":["000625853200001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-11T10:33:42Z","publication_identifier":{"issn":["10184813"],"eissn":["14765438"]},"article_type":"original","year":"2021","oa_version":"Published Version","has_accepted_license":"1","publisher":"Springer Nature","isi":1,"publication":"European Journal of Human Genetics","quality_controlled":"1","department":[{"_id":"FyKo"}],"intvolume":"        29","status":"public","page":"1082-1091","month":"07","date_created":"2021-08-15T22:01:28Z","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"}],"pmid":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).","language":[{"iso":"eng"}],"doi":"10.1038/s41431-021-00836-7","ddc":["576"],"citation":{"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>.","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.","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.","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>.","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.","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>","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>"},"ec_funded":1,"title":"The limits of normal approximation for adult height","day":"01","author":[{"last_name":"Slavskii","first_name":"Sergei A.","full_name":"Slavskii, Sergei A."},{"first_name":"Ivan A.","full_name":"Kuznetsov, Ivan A.","last_name":"Kuznetsov"},{"first_name":"Tatiana I.","full_name":"Shashkova, Tatiana I.","last_name":"Shashkova"},{"first_name":"Georgii A.","full_name":"Bazykin, Georgii A.","last_name":"Bazykin"},{"first_name":"Tatiana I.","full_name":"Axenovich, Tatiana I.","last_name":"Axenovich"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"first_name":"Yurii S.","full_name":"Aulchenko, Yurii S.","last_name":"Aulchenko"}],"type":"journal_article"},{"article_processing_charge":"Yes","issue":"1","_id":"9911","date_published":"2021-08-11T00:00:00Z","abstract":[{"lang":"eng","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."}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/jmi.13041","open_access":"1"}],"publication_status":"published","volume":284,"oa_version":"Published Version","year":"2021","article_type":"original","publication_identifier":{"issn":["0022-2720"],"eissn":["1365-2818"]},"external_id":{"isi":["000683702700001"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-11T10:30:40Z","page":"56-73","date_created":"2021-08-15T22:01:29Z","month":"08","isi":1,"publisher":"Wiley","intvolume":"       284","status":"public","publication":"Journal of Microscopy","quality_controlled":"1","department":[{"_id":"Bio"}],"title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","citation":{"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>.","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.","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.","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>."},"author":[{"last_name":"Nelson","full_name":"Nelson, Glyn","first_name":"Glyn"},{"first_name":"Ulrike","full_name":"Boehm, Ulrike","last_name":"Boehm"},{"last_name":"Bagley","full_name":"Bagley, Steve","first_name":"Steve"},{"first_name":"Peter","full_name":"Bajcsy, Peter","last_name":"Bajcsy"},{"last_name":"Bischof","full_name":"Bischof, Johanna","first_name":"Johanna"},{"first_name":"Claire M.","full_name":"Brown, Claire M.","last_name":"Brown"},{"last_name":"Dauphin","full_name":"Dauphin, Aurélien","first_name":"Aurélien"},{"last_name":"Dobbie","first_name":"Ian M.","full_name":"Dobbie, Ian M."},{"last_name":"Eriksson","full_name":"Eriksson, John E.","first_name":"John E."},{"last_name":"Faklaris","full_name":"Faklaris, Orestis","first_name":"Orestis"},{"first_name":"Julia","full_name":"Fernandez-Rodriguez, Julia","last_name":"Fernandez-Rodriguez"},{"first_name":"Alexia","full_name":"Ferrand, Alexia","last_name":"Ferrand"},{"full_name":"Gelman, Laurent","first_name":"Laurent","last_name":"Gelman"},{"first_name":"Ali","full_name":"Gheisari, Ali","last_name":"Gheisari"},{"full_name":"Hartmann, Hella","first_name":"Hella","last_name":"Hartmann"},{"full_name":"Kukat, Christian","first_name":"Christian","last_name":"Kukat"},{"full_name":"Laude, Alex","first_name":"Alex","last_name":"Laude"},{"full_name":"Mitkovski, Miso","first_name":"Miso","last_name":"Mitkovski"},{"last_name":"Munck","full_name":"Munck, Sebastian","first_name":"Sebastian"},{"last_name":"North","first_name":"Alison J.","full_name":"North, Alison J."},{"first_name":"Tobias M.","full_name":"Rasse, Tobias M.","last_name":"Rasse"},{"last_name":"Resch-Genger","full_name":"Resch-Genger, Ute","first_name":"Ute"},{"last_name":"Schuetz","full_name":"Schuetz, Lucas C.","first_name":"Lucas C."},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"last_name":"Strambio-De-Castillia","first_name":"Caterina","full_name":"Strambio-De-Castillia, Caterina"},{"full_name":"Swedlow, Jason R.","first_name":"Jason R.","last_name":"Swedlow"},{"full_name":"Alexopoulos, Ioannis","first_name":"Ioannis","last_name":"Alexopoulos"},{"last_name":"Aumayr","full_name":"Aumayr, Karin","first_name":"Karin"},{"last_name":"Avilov","full_name":"Avilov, Sergiy","first_name":"Sergiy"},{"first_name":"Gert Jan","full_name":"Bakker, Gert Jan","last_name":"Bakker"},{"full_name":"Bammann, Rodrigo R.","first_name":"Rodrigo R.","last_name":"Bammann"},{"full_name":"Bassi, Andrea","first_name":"Andrea","last_name":"Bassi"},{"last_name":"Beckert","first_name":"Hannes","full_name":"Beckert, Hannes"},{"last_name":"Beer","full_name":"Beer, Sebastian","first_name":"Sebastian"},{"full_name":"Belyaev, Yury","first_name":"Yury","last_name":"Belyaev"},{"first_name":"Jakob","full_name":"Bierwagen, Jakob","last_name":"Bierwagen"},{"last_name":"Birngruber","full_name":"Birngruber, Konstantin A.","first_name":"Konstantin A."},{"last_name":"Bosch","full_name":"Bosch, Manel","first_name":"Manel"},{"full_name":"Breitlow, Juergen","first_name":"Juergen","last_name":"Breitlow"},{"last_name":"Cameron","first_name":"Lisa A.","full_name":"Cameron, Lisa A."},{"full_name":"Chalfoun, Joe","first_name":"Joe","last_name":"Chalfoun"},{"last_name":"Chambers","first_name":"James J.","full_name":"Chambers, James J."},{"last_name":"Chen","full_name":"Chen, Chieh Li","first_name":"Chieh Li"},{"last_name":"Conde-Sousa","first_name":"Eduardo","full_name":"Conde-Sousa, Eduardo"},{"full_name":"Corbett, Alexander D.","first_name":"Alexander D.","last_name":"Corbett"},{"first_name":"Fabrice P.","full_name":"Cordelieres, Fabrice P.","last_name":"Cordelieres"},{"last_name":"Nery","first_name":"Elaine Del","full_name":"Nery, Elaine Del"},{"full_name":"Dietzel, Ralf","first_name":"Ralf","last_name":"Dietzel"},{"full_name":"Eismann, Frank","first_name":"Frank","last_name":"Eismann"},{"first_name":"Elnaz","full_name":"Fazeli, Elnaz","last_name":"Fazeli"},{"first_name":"Andreas","full_name":"Felscher, Andreas","last_name":"Felscher"},{"first_name":"Hans","full_name":"Fried, Hans","last_name":"Fried"},{"last_name":"Gaudreault","first_name":"Nathalie","full_name":"Gaudreault, Nathalie"},{"first_name":"Wah Ing","full_name":"Goh, Wah Ing","last_name":"Goh"},{"last_name":"Guilbert","first_name":"Thomas","full_name":"Guilbert, Thomas"},{"last_name":"Hadleigh","full_name":"Hadleigh, Roland","first_name":"Roland"},{"last_name":"Hemmerich","full_name":"Hemmerich, Peter","first_name":"Peter"},{"last_name":"Holst","first_name":"Gerhard A.","full_name":"Holst, Gerhard A."},{"last_name":"Itano","first_name":"Michelle S.","full_name":"Itano, Michelle S."},{"last_name":"Jaffe","first_name":"Claudia B.","full_name":"Jaffe, Claudia B."},{"last_name":"Jambor","full_name":"Jambor, Helena K.","first_name":"Helena K."},{"last_name":"Jarvis","first_name":"Stuart C.","full_name":"Jarvis, Stuart C."},{"first_name":"Antje","full_name":"Keppler, Antje","last_name":"Keppler"},{"full_name":"Kirchenbuechler, David","first_name":"David","last_name":"Kirchenbuechler"},{"first_name":"Marcel","full_name":"Kirchner, Marcel","last_name":"Kirchner"},{"last_name":"Kobayashi","first_name":"Norio","full_name":"Kobayashi, Norio"},{"full_name":"Krens, Gabriel","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kunis","first_name":"Susanne","full_name":"Kunis, Susanne"},{"last_name":"Lacoste","full_name":"Lacoste, Judith","first_name":"Judith"},{"full_name":"Marcello, Marco","first_name":"Marco","last_name":"Marcello"},{"first_name":"Gabriel G.","full_name":"Martins, Gabriel G.","last_name":"Martins"},{"first_name":"Daniel J.","full_name":"Metcalf, Daniel J.","last_name":"Metcalf"},{"last_name":"Mitchell","first_name":"Claire A.","full_name":"Mitchell, Claire A."},{"full_name":"Moore, Joshua","first_name":"Joshua","last_name":"Moore"},{"last_name":"Mueller","first_name":"Tobias","full_name":"Mueller, Tobias"},{"last_name":"Nelson","full_name":"Nelson, Michael S.","first_name":"Michael S."},{"last_name":"Ogg","full_name":"Ogg, Stephen","first_name":"Stephen"},{"full_name":"Onami, Shuichi","first_name":"Shuichi","last_name":"Onami"},{"first_name":"Alexandra L.","full_name":"Palmer, Alexandra L.","last_name":"Palmer"},{"full_name":"Paul-Gilloteaux, Perrine","first_name":"Perrine","last_name":"Paul-Gilloteaux"},{"first_name":"Jaime A.","full_name":"Pimentel, Jaime A.","last_name":"Pimentel"},{"last_name":"Plantard","first_name":"Laure","full_name":"Plantard, Laure"},{"first_name":"Santosh","full_name":"Podder, Santosh","last_name":"Podder"},{"last_name":"Rexhepaj","first_name":"Elton","full_name":"Rexhepaj, Elton"},{"first_name":"Arnaud","full_name":"Royon, Arnaud","last_name":"Royon"},{"last_name":"Saari","first_name":"Markku A.","full_name":"Saari, Markku A."},{"first_name":"Damien","full_name":"Schapman, Damien","last_name":"Schapman"},{"last_name":"Schoonderwoert","first_name":"Vincent","full_name":"Schoonderwoert, Vincent"},{"full_name":"Schroth-Diez, Britta","first_name":"Britta","last_name":"Schroth-Diez"},{"last_name":"Schwartz","full_name":"Schwartz, Stanley","first_name":"Stanley"},{"first_name":"Michael","full_name":"Shaw, Michael","last_name":"Shaw"},{"last_name":"Spitaler","first_name":"Martin","full_name":"Spitaler, Martin"},{"full_name":"Stoeckl, Martin T.","first_name":"Martin T.","last_name":"Stoeckl"},{"full_name":"Sudar, Damir","first_name":"Damir","last_name":"Sudar"},{"last_name":"Teillon","first_name":"Jeremie","full_name":"Teillon, Jeremie"},{"first_name":"Stefan","full_name":"Terjung, Stefan","last_name":"Terjung"},{"first_name":"Roland","full_name":"Thuenauer, Roland","last_name":"Thuenauer"},{"first_name":"Christian D.","full_name":"Wilms, Christian D.","last_name":"Wilms"},{"last_name":"Wright","first_name":"Graham D.","full_name":"Wright, Graham D."},{"last_name":"Nitschke","full_name":"Nitschke, Roland","first_name":"Roland"}],"type":"journal_article","day":"11","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.","doi":"10.1111/jmi.13041","language":[{"iso":"eng"}]},{"date_created":"2021-08-15T22:01:29Z","month":"12","page":"4205–4269","intvolume":"        22","status":"public","quality_controlled":"1","department":[{"_id":"LaEr"}],"publication":"Annales Henri Poincaré ","isi":1,"publisher":"Springer Nature","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7327-856X","full_name":"Nemish, Yuriy","first_name":"Yuriy","last_name":"Nemish"}],"type":"journal_article","day":"01","title":"Scattering in quantum dots via noncommutative rational functions","ec_funded":1,"citation":{"short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré  22 (2021) 4205–4269.","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>","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>","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.","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 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>."},"ddc":["510"],"doi":"10.1007/s00023-021-01085-6","language":[{"iso":"eng"}],"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.","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"_id":"9912","date_published":"2021-12-01T00:00:00Z","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"}],"file":[{"date_updated":"2022-05-12T12:50:27Z","access_level":"open_access","checksum":"8d6bac0e2b0a28539608b0538a8e3b38","file_name":"2021_AnnHenriPoincare_Erdoes.pdf","creator":"dernst","file_size":1162454,"success":1,"date_created":"2022-05-12T12:50:27Z","content_type":"application/pdf","relation":"main_file","file_id":"11365"}],"article_processing_charge":"Yes (in subscription journal)","arxiv":1,"volume":22,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-05-12T12:50:27Z","oa":1,"publication_status":"published","oa_version":"Published Version","year":"2021","has_accepted_license":"1","article_type":"original","publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"date_updated":"2023-08-11T10:31:48Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1911.05112"],"isi":["000681531500001"]},"scopus_import":"1"},{"doi":"10.15252/embr.202051813","ddc":["580"],"language":[{"iso":"eng"}],"acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","pmid":1,"related_material":{"record":[{"status":"public","id":"10303","relation":"dissertation_contains"}]},"type":"journal_article","author":[{"last_name":"Vega","first_name":"Andrea","full_name":"Vega, Andrea"},{"first_name":"Isabel","full_name":"Fredes, Isabel","last_name":"Fredes"},{"full_name":"O’Brien, José","first_name":"José","last_name":"O’Brien"},{"first_name":"Zhouxin","full_name":"Shen, Zhouxin","last_name":"Shen"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","first_name":"Krisztina","last_name":"Ötvös"},{"full_name":"Abualia, Rashed","first_name":"Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"last_name":"Briggs","first_name":"Steven P.","full_name":"Briggs, Steven P."},{"first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez"}],"day":"06","title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","citation":{"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.","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.","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>.","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).","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>"},"status":"public","intvolume":"        22","quality_controlled":"1","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"publication":"EMBO Reports","isi":1,"publisher":"Wiley","date_created":"2021-08-15T22:01:30Z","month":"09","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-03-25T23:30:22Z","external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"scopus_import":"1","has_accepted_license":"1","oa_version":"Published Version","year":"2021","article_type":"original","volume":22,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2021-10-05T13:36:42Z","oa":1,"publication_status":"published","_id":"9913","date_published":"2021-09-06T00:00:00Z","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"}],"file":[{"content_type":"application/pdf","file_id":"10090","relation":"main_file","date_created":"2021-10-05T13:36:42Z","success":1,"file_name":"2021_EmboR_Vega.pdf","file_size":3144854,"creator":"cchlebak","checksum":"750de03dc3b715c37090126c1548ba13","date_updated":"2021-10-05T13:36:42Z","access_level":"open_access"}],"article_number":"e51813","issue":"9","article_processing_charge":"Yes"},{"related_material":{"record":[{"id":"9928","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8755","relation":"part_of_dissertation"}]},"ddc":["539"],"doi":"10.15479/at:ista:9920","language":[{"iso":"eng"}],"keyword":["quantum computing","superinductor","quantum metrology"],"title":"Geometric superinductors and their applications in circuit quantum electrodynamics","citation":{"mla":"Peruzzo, Matilda. <i>Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>.","ieee":"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.","chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>.","apa":"Peruzzo, M. (2021). <i>Geometric superinductors and their applications in circuit quantum electrodynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021."},"alternative_title":["ISTA Thesis"],"author":[{"full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","day":"19","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"page":"149","date_created":"2021-08-16T09:44:09Z","supervisor":[{"last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"month":"08","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication_identifier":{"isbn":["978-3-99078-013-8"],"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-09-10T12:23:56Z","year":"2021","oa_version":"Published Version","has_accepted_license":"1","oa":1,"publication_status":"published","file_date_updated":"2021-09-06T08:39:47Z","article_processing_charge":"No","_id":"9920","date_published":"2021-08-19T00:00:00Z","abstract":[{"lang":"eng","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."}],"file":[{"date_created":"2021-08-16T09:33:21Z","content_type":"application/x-zip-compressed","file_id":"9924","relation":"source_file","date_updated":"2021-09-06T08:39:47Z","access_level":"closed","checksum":"3cd1986efde5121d7581f6fcf9090da8","file_name":"GeometricSuperinductorsForCQED.zip","creator":"mperuzzo","file_size":151387283},{"date_created":"2021-08-18T14:20:06Z","content_type":"application/pdf","file_id":"9939","relation":"main_file","date_updated":"2021-09-06T08:39:47Z","access_level":"open_access","checksum":"50928c621cdf0775d7a5906b9dc8602c","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","creator":"mperuzzo","file_size":17596344},{"file_size":17592425,"creator":"mperuzzo","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","checksum":"37f486aa1b622fe44af00d627ec13f6c","description":"Extra copy of the thesis as PDF/A-2b","access_level":"closed","date_updated":"2021-09-06T08:39:47Z","file_id":"9940","relation":"other","content_type":"application/pdf","date_created":"2021-08-18T14:20:09Z"}]},{"author":[{"first_name":"Matilda","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628"},{"last_name":"Hassani","full_name":"Hassani, Farid","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Szep, Gregory","first_name":"Gregory","last_name":"Szep"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea","first_name":"Andrea","last_name":"Trioni"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin"},{"last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"type":"journal_article","day":"24","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","citation":{"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>.","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.","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.","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.","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>","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>"},"ec_funded":1,"doi":"10.1103/PRXQuantum.2.040341","ddc":["530"],"keyword":["quantum physics","mesoscale and nanoscale physics"],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"13057","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"9920"}]},"project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"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.","date_created":"2021-08-17T08:14:18Z","month":"11","page":"040341","status":"public","intvolume":"         2","publication":"PRX Quantum","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"quality_controlled":"1","isi":1,"publisher":"American Physical Society","oa_version":"Published Version","has_accepted_license":"1","year":"2021","article_type":"original","publication_identifier":{"eissn":["2691-3399"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"scopus_import":"1","external_id":{"arxiv":["2106.05882"],"isi":["000723015100001"]},"date_updated":"2023-09-07T13:31:22Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9928","date_published":"2021-11-24T00:00:00Z","abstract":[{"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.","lang":"eng"}],"file":[{"date_created":"2022-01-18T11:29:33Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"10641","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","date_updated":"2022-01-18T11:29:33Z","access_level":"open_access","file_name":"2021_PRXQuantum_Peruzzo.pdf","file_size":4247422,"creator":"cchlebak"}],"article_processing_charge":"No","issue":"4","arxiv":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":2,"file_date_updated":"2022-01-18T11:29:33Z","oa":1,"publication_status":"published"},{"type":"conference","author":[{"last_name":"Czumaj","full_name":"Czumaj, Artur","first_name":"Artur"},{"last_name":"Davies","first_name":"Peter","full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}],"day":"21","conference":{"start_date":"2021-07-26","end_date":"2021-07-30","name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy"},"title":"Component stability in low-space massively parallel computation","ec_funded":1,"citation":{"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.","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>","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>","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.","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.","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>.","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>."},"doi":"10.1145/3465084.3467903","language":[{"iso":"eng"}],"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.","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"date_created":"2021-08-17T18:11:16Z","month":"07","page":"481–491","status":"public","department":[{"_id":"DaAl"}],"quality_controlled":"1","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","isi":1,"publisher":"Association for Computing Machinery","oa_version":"Submitted Version","year":"2021","publication_identifier":{"isbn":["9781450385480"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-17T07:11:32Z","external_id":{"arxiv":["2106.01880"],"isi":["000744439800049"]},"_id":"9933","date_published":"2021-07-21T00:00:00Z","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","arxiv":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.01880"}],"publication_status":"published"},{"publication_status":"published","main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/153753"}],"oa":1,"article_processing_charge":"No","_id":"9935","date_published":"2021-07-21T00:00:00Z","abstract":[{"lang":"eng","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."}],"external_id":{"isi":["000744439800048"]},"date_updated":"2023-08-17T07:11:03Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"oa_version":"Submitted Version","year":"2021","publisher":"Association for Computing Machinery","isi":1,"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","department":[{"_id":"DaAl"}],"quality_controlled":"1","status":"public","page":"469–479","month":"07","date_created":"2021-08-17T18:14:15Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"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.","language":[{"iso":"eng"}],"doi":"10.1145/3465084.3467937","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>","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>","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.","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>.","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.","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>."},"ec_funded":1,"title":"Improved deterministic (Δ+1) coloring in low-space MPC","conference":{"location":"Virtual, Italy","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2021-07-30","start_date":"2021-07-26"},"day":"21","author":[{"last_name":"Czumaj","first_name":"Artur","full_name":"Czumaj, Artur"},{"orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","full_name":"Davies, Peter","first_name":"Peter","last_name":"Davies"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"type":"conference"},{"file_date_updated":"2021-09-03T12:34:28Z","publication_status":"published","oa":1,"file":[{"file_id":"9948","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-20T19:59:44Z","file_size":"320453","creator":"fmuehlbo","file_name":"differentialmonitoring-techreport.pdf","checksum":"0f9aafd59444cb6bdca6925d163ab946","access_level":"open_access","date_updated":"2021-09-03T12:34:28Z"}],"_id":"9946","date_published":"2021-09-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","date_updated":"2023-08-14T07:20:29Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","year":"2021","oa_version":"Published Version","department":[{"_id":"ToHe"}],"status":"public","publisher":"IST Austria","month":"09","date_created":"2021-08-20T20:00:37Z","page":"17","keyword":["run-time verification","software engineering","implicit specification"],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9946","ddc":["005"],"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"related_material":{"record":[{"relation":"other","id":"9281","status":"public"},{"status":"public","relation":"shorter_version","id":"10108"}]},"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.","day":"01","author":[{"orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian","first_name":"Fabian","last_name":"Mühlböck"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"citation":{"short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, 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.","ieee":"F. Mühlböck and T. A. Henzinger, <i>Differential monitoring</i>. IST Austria, 2021.","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>.","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>."},"title":"Differential monitoring"},{"citation":{"chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. <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.","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>.","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>.","short":"B. Vicoso, (2021).","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>"},"title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","day":"24","year":"2021","oa_version":"None","has_accepted_license":"1","type":"research_data","author":[{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"related_material":{"record":[{"id":"10166","relation":"used_in_publication","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:40:30Z","doi":"10.15479/AT:ISTA:9949","article_processing_charge":"No","file":[{"content_type":"application/zip","file_id":"9950","relation":"main_file","date_created":"2021-08-21T13:43:59Z","success":1,"file_name":"Data.zip","creator":"bvicoso","file_size":139188306,"checksum":"90461837eed66beac6fa302993cf0ca9","date_updated":"2021-08-21T13:43:59Z","access_level":"open_access"}],"month":"08","_id":"9949","date_published":"2021-08-24T00:00:00Z","date_created":"2021-08-21T13:44:22Z","publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"BeVi"}],"file_date_updated":"2021-08-21T13:43:59Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"language":[{"iso":"eng"}],"date_updated":"2023-08-11T10:56:04Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000744439800005"]},"scopus_import":"1","doi":"10.1145/3465084.3467915","publication_identifier":{"isbn":["9781450385480"]},"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.","day":"21","oa_version":"None","year":"2021","type":"conference","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"id":"4B865388-F248-11E8-B48F-1D18A9856A87","last_name":"Töpfer","full_name":"Töpfer, Martin","first_name":"Martin"},{"last_name":"Uznański","first_name":"Przemysław","full_name":"Uznański, Przemysław"}],"citation":{"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>","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>.","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.","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.","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>."},"conference":{"location":"Virtual, Italy","name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2021-07-26","end_date":"2021-07-30"},"title":"Comparison dynamics in population protocols","quality_controlled":"1","department":[{"_id":"DaAl"}],"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","status":"public","publication_status":"published","publisher":"Association for Computing Machinery","isi":1,"month":"07","_id":"9951","date_published":"2021-07-21T00:00:00Z","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."}],"date_created":"2021-08-22T22:01:20Z","page":"55-65","article_processing_charge":"No"},{"date_published":"2021-07-01T00:00:00Z","_id":"9952","abstract":[{"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.","lang":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"9954","date_created":"2021-08-23T07:32:20Z","success":1,"file_name":"2021_JournalOfCellScience_Chaigne.pdf","creator":"asandaue","file_size":8651724,"checksum":"f086f9d7cb63b2474c01921cb060c513","date_updated":"2021-08-23T07:32:20Z","access_level":"open_access"}],"article_number":"jcs255018","article_processing_charge":"Yes (in subscription journal)","issue":"14","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":134,"file_date_updated":"2021-08-23T07:32:20Z","oa":1,"publication_status":"published","year":"2021","has_accepted_license":"1","oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["14779137"],"issn":["00219533"]},"scopus_import":"1","external_id":{"isi":["000681395800008"]},"date_updated":"2023-08-11T10:55:36Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-08-22T22:01:20Z","month":"07","intvolume":"       134","status":"public","publication":"Journal of Cell Science","quality_controlled":"1","department":[{"_id":"EdHa"}],"isi":1,"publisher":"The Company of Biologists","author":[{"last_name":"Chaigne","full_name":"Chaigne, Agathe","first_name":"Agathe"},{"last_name":"Smith","first_name":"Matthew B.","full_name":"Smith, Matthew B."},{"first_name":"R. L.","full_name":"Cavestany, R. L.","last_name":"Cavestany"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Chalut","full_name":"Chalut, Kevin J.","first_name":"Kevin J."},{"first_name":"Ewa K.","full_name":"Paluch, Ewa K.","last_name":"Paluch"}],"type":"journal_article","day":"01","title":"Three-dimensional geometry controls division symmetry in stem cell colonies","citation":{"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>.","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.","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.","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>.","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>"},"doi":"10.1242/jcs.255018","ddc":["570"],"language":[{"iso":"eng"}],"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."},{"isi":1,"publisher":"Elsevier","intvolume":"        97","status":"public","quality_controlled":"1","department":[{"_id":"GaNo"}],"publication":"Brain, Behavior, and Immunity","page":"423-439","date_created":"2021-08-22T22:01:21Z","month":"10","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.","pmid":1,"doi":"10.1016/j.bbi.2021.07.022","language":[{"iso":"eng"}],"title":"Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice","citation":{"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>","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>","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.","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>.","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.","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."},"type":"journal_article","author":[{"full_name":"Picard, Katherine","first_name":"Katherine","last_name":"Picard"},{"last_name":"Bisht","full_name":"Bisht, Kanchan","first_name":"Kanchan"},{"last_name":"Poggini","first_name":"Silvia","full_name":"Poggini, Silvia"},{"last_name":"Garofalo","first_name":"Stefano","full_name":"Garofalo, Stefano"},{"last_name":"Golia","full_name":"Golia, Maria Teresa","first_name":"Maria Teresa"},{"first_name":"Bernadette","full_name":"Basilico, Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"last_name":"Abdallah","full_name":"Abdallah, Fatima","first_name":"Fatima"},{"last_name":"Ciano Albanese","full_name":"Ciano Albanese, Naomi","first_name":"Naomi"},{"first_name":"Irmgard","full_name":"Amrein, Irmgard","last_name":"Amrein"},{"last_name":"Vernoux","first_name":"Nathalie","full_name":"Vernoux, Nathalie"},{"full_name":"Sharma, Kaushik","first_name":"Kaushik","last_name":"Sharma"},{"last_name":"Hui","first_name":"Chin Wai","full_name":"Hui, Chin Wai"},{"full_name":"C. Savage, Julie","first_name":"Julie","last_name":"C. Savage"},{"first_name":"Cristina","full_name":"Limatola, Cristina","last_name":"Limatola"},{"full_name":"Ragozzino, Davide","first_name":"Davide","last_name":"Ragozzino"},{"full_name":"Maggi, Laura","first_name":"Laura","last_name":"Maggi"},{"first_name":"Igor","full_name":"Branchi, Igor","last_name":"Branchi"},{"full_name":"Tremblay, Marie Ève","first_name":"Marie Ève","last_name":"Tremblay"}],"day":"01","oa":1,"main_file_link":[{"url":"https://www.zora.uzh.ch/id/eprint/208855/1/ZORA208855.pdf","open_access":"1"}],"publication_status":"published","volume":97,"article_processing_charge":"No","_id":"9953","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."}],"date_published":"2021-10-01T00:00:00Z","publication_identifier":{"issn":["0889-1591"]},"date_updated":"2023-10-03T09:49:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","external_id":{"isi":["000702878400007"],"pmid":["34343616"]},"year":"2021","oa_version":"Submitted Version","article_type":"original"},{"conference":{"location":"Nashville, TN, United States; Virtual","end_date":"2021-06-25","start_date":"2021-06-20","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"title":"Monocular reconstruction of neural face reflectance fields","citation":{"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.","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>","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>","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.","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.","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>.","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>."},"author":[{"last_name":"B R","full_name":"B R, Mallikarjun","first_name":"Mallikarjun"},{"full_name":"Tewari, Ayush","first_name":"Ayush","last_name":"Tewari"},{"last_name":"Oh","first_name":"Tae-Hyun","full_name":"Oh, Tae-Hyun"},{"first_name":"Tim","full_name":"Weyrich, Tim","last_name":"Weyrich"},{"last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"last_name":"Seidel","full_name":"Seidel, Hans-Peter","first_name":"Hans-Peter"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"},{"last_name":"Elgharib","full_name":"Elgharib, Mohamed","first_name":"Mohamed"},{"first_name":"Christian","full_name":"Theobalt, Christian","last_name":"Theobalt"}],"type":"conference","day":"01","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.","ddc":["000"],"doi":"10.1109/CVPR46437.2021.00476","language":[{"iso":"eng"}],"page":"4791-4800","date_created":"2021-08-24T06:03:00Z","month":"09","isi":1,"publisher":"IEEE","status":"public","department":[{"_id":"BeBi"}],"quality_controlled":"1","publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","year":"2021","has_accepted_license":"1","oa_version":"Preprint","publication_identifier":{"issn":["1063-6919"],"isbn":["978-166544509-2"]},"date_updated":"2023-08-11T11:08:35Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"arxiv":["2008.10247"],"isi":["000739917304096"]},"article_processing_charge":"No","arxiv":1,"_id":"9957","date_published":"2021-09-01T00:00:00Z","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"}],"file":[{"file_name":"R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf","creator":"bbickel","file_size":4746649,"date_updated":"2021-08-24T06:02:15Z","access_level":"open_access","checksum":"961db0bde76dd87cf833930080bb9f38","content_type":"application/pdf","relation":"main_file","file_id":"9958","date_created":"2021-08-24T06:02:15Z"}],"oa":1,"publication_status":"published","file_date_updated":"2021-08-24T06:02:15Z"},{"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.","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"doi":"10.1103/PhysRevLett.127.090602","language":[{"iso":"eng"}],"title":"Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving","ec_funded":1,"citation":{"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>","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.","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.","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>."},"type":"journal_article","author":[{"last_name":"Maskara","first_name":"N.","full_name":"Maskara, N."},{"orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios","full_name":"Michailidis, Alexios"},{"last_name":"Ho","first_name":"W. W.","full_name":"Ho, W. W."},{"last_name":"Bluvstein","full_name":"Bluvstein, D.","first_name":"D."},{"last_name":"Choi","first_name":"S.","full_name":"Choi, S."},{"first_name":"M. D.","full_name":"Lukin, M. D.","last_name":"Lukin"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"day":"27","isi":1,"publisher":"American Physical Society","status":"public","intvolume":"       127","department":[{"_id":"MaSe"}],"quality_controlled":"1","publication":"Physical Review Letters","date_created":"2021-08-28T08:08:58Z","month":"08","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"date_updated":"2023-08-11T10:57:51Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2102.13160"],"isi":["000692200100002"]},"oa_version":"Submitted Version","year":"2021","article_type":"letter_note","main_file_link":[{"url":"https://arxiv.org/abs/2102.13160","open_access":"1"}],"oa":1,"publication_status":"published","volume":127,"issue":"9","article_processing_charge":"No","arxiv":1,"_id":"9960","date_published":"2021-08-27T00:00:00Z","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"}],"article_number":"090602"}]