[{"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946.","ama":"Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","ieee":"F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p."},"title":"Differential monitoring","article_processing_charge":"No","author":[{"last_name":"Mühlböck","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","oa":1,"publisher":"IST Austria","day":"01","year":"2021","has_accepted_license":"1","date_created":"2021-08-20T20:00:37Z","date_published":"2021-09-01T00:00:00Z","doi":"10.15479/AT:ISTA:9946","page":"17","_id":"9946","keyword":["run-time verification","software engineering","implicit specification"],"status":"public","type":"technical_report","ddc":["005"],"date_updated":"2023-08-14T07:20:29Z","department":[{"_id":"ToHe"}],"file_date_updated":"2021-09-03T12:34:28Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"month":"09","alternative_title":["IST Austria Technical Report"],"language":[{"iso":"eng"}],"file":[{"file_name":"differentialmonitoring-techreport.pdf","date_created":"2021-08-20T19:59:44Z","creator":"fmuehlbo","file_size":"320453","date_updated":"2021-09-03T12:34:28Z","file_id":"9948","checksum":"0f9aafd59444cb6bdca6925d163ab946","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"related_material":{"record":[{"relation":"other","id":"9281","status":"public"},{"id":"10108","status":"public","relation":"shorter_version"}]}},{"publication_identifier":{"eissn":["1996-1944"]},"publication_status":"published","file":[{"file_size":4404141,"date_updated":"2021-10-14T11:56:39Z","creator":"cchlebak","file_name":"2021_Materials_Chang.pdf","date_created":"2021-10-14T11:56:39Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"4929dfc673a3ae77c010b6174279cc1d","file_id":"10140"}],"language":[{"iso":"eng"}],"volume":14,"issue":"18","abstract":[{"text":"Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 14","date_updated":"2023-08-14T08:00:01Z","ddc":["540"],"file_date_updated":"2021-10-14T11:56:39Z","department":[{"_id":"MaIb"}],"_id":"10073","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","isi":1,"year":"2021","day":"19","publication":"Materials","doi":"10.3390/ma14185416","date_published":"2021-09-19T00:00:00Z","date_created":"2021-10-03T22:01:23Z","acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","publisher":"MDPI","quality_controlled":"1","oa":1,"citation":{"chicago":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14185416.","ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","mla":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416, MDPI, 2021, doi:10.3390/ma14185416.","apa":"Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416","ieee":"C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021.","short":"C. Chang, M. Ibáñez, Materials 14 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"external_id":{"pmid":["34576640"],"isi":["000700689400001"]},"article_processing_charge":"Yes","title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","article_number":"5416","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}]},{"file":[{"creator":"dernst","file_size":1008594,"date_updated":"2022-05-06T09:47:18Z","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","date_created":"2022-05-06T09:47:18Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"11352","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"publication_status":"published","month":"06","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"BeVi"}],"file_date_updated":"2022-05-06T09:47:18Z","ddc":["610"],"date_updated":"2023-08-14T08:03:06Z","status":"public","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10167","doi":"10.1093/molbev/msab178","date_published":"2021-06-19T00:00:00Z","date_created":"2021-10-21T07:49:12Z","day":"19","publication":"Molecular Biology and Evolution","isi":1,"has_accepted_license":"1","year":"2021","publisher":"Oxford University Press ","quality_controlled":"1","oa":1,"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","author":[{"orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Moldovan","orcid":"0000-0002-8876-6494","full_name":"Moldovan, Mikhail A.","first_name":"Mikhail A.","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0"},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L","last_name":"Picard"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. Oxford University Press . https://doi.org/10.1093/molbev/msab178","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” Molecular Biology and Evolution. Oxford University Press , 2021."},"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}]},{"external_id":{"isi":["000709050300001"]},"article_processing_charge":"No","author":[{"first_name":"Lisa-Marie","full_name":"Appel, Lisa-Marie","last_name":"Appel"},{"first_name":"Vedran","full_name":"Franke, Vedran","last_name":"Franke"},{"first_name":"Melania","full_name":"Bruno, Melania","last_name":"Bruno"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"first_name":"Aiste","last_name":"Kasiliauskaite","full_name":"Kasiliauskaite, Aiste"},{"last_name":"Kaufmann","full_name":"Kaufmann, Tanja","first_name":"Tanja"},{"last_name":"Schoeberl","full_name":"Schoeberl, Ursula E.","first_name":"Ursula E."},{"first_name":"Martin G.","full_name":"Puchinger, Martin G.","last_name":"Puchinger"},{"last_name":"Kostrhon","full_name":"Kostrhon, Sebastian","first_name":"Sebastian"},{"first_name":"Carmen","last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen"},{"full_name":"Sebesta, Marek","last_name":"Sebesta","first_name":"Marek"},{"last_name":"Beltzung","full_name":"Beltzung, Etienne","first_name":"Etienne"},{"first_name":"Karl","last_name":"Mechtler","full_name":"Mechtler, Karl"},{"last_name":"Lin","full_name":"Lin, Gen","first_name":"Gen"},{"last_name":"Vlasova","full_name":"Vlasova, Anna","first_name":"Anna"},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"},{"first_name":"Rushad","full_name":"Pavri, Rushad","last_name":"Pavri"},{"first_name":"Alexander","full_name":"Stark, Alexander","last_name":"Stark"},{"first_name":"Altuna","last_name":"Akalin","full_name":"Akalin, Altuna"},{"first_name":"Richard","last_name":"Stefl","full_name":"Stefl, Richard"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"},{"last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina"},{"full_name":"Slade, Dea","last_name":"Slade","first_name":"Dea"}],"title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","citation":{"ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26360-2","apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26360-2","ieee":"L.-M. Appel et al., “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"6078","date_created":"2021-10-20T14:40:32Z","doi":"10.1038/s41467-021-26360-2","date_published":"2021-10-19T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"19","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","file_date_updated":"2021-10-21T13:51:49Z","department":[{"_id":"CaBe"}],"date_updated":"2023-08-14T08:02:31Z","ddc":["610"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"status":"public","_id":"10163","issue":"1","related_material":{"link":[{"description":"Preprint ","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","relation":"earlier_version"}]},"volume":12,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"d99fcd51aebde19c21314e3de0148007","file_id":"10169","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_NatComm_Appel.pdf","date_created":"2021-10-21T13:51:49Z","file_size":5111706,"date_updated":"2021-10-21T13:51:49Z","creator":"cchlebak"}],"intvolume":" 12","month":"10","abstract":[{"text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.","lang":"eng"}],"oa_version":"Published Version"},{"issue":"2","volume":40,"ec_funded":1,"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10120","checksum":"33271724215f54a75c39d2ed40f2c502","success":1,"date_updated":"2021-10-11T12:06:50Z","file_size":26026501,"creator":"bbickel","date_created":"2021-10-11T12:06:50Z","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 40","abstract":[{"text":"With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"BeBi"}],"file_date_updated":"2021-10-11T12:06:50Z","date_updated":"2023-08-14T08:01:50Z","ddc":["004"],"article_type":"original","type":"journal_article","status":"public","_id":"9547","page":"205-219","date_published":"2021-05-01T00:00:00Z","doi":"10.1111/cgf.142626","date_created":"2021-06-13T22:01:32Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Computer Graphics Forum","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We thank Sebastian Cucerca for processing and capturing the phys-cal printouts. This work was supported by the Charles University grant SVV-260588 and Czech Science Foundation grant 19-07626S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","author":[{"first_name":"Tobias","full_name":"Rittig, Tobias","last_name":"Rittig"},{"full_name":"Sumin, Denis","last_name":"Sumin","first_name":"Denis"},{"first_name":"Vahid","full_name":"Babaei, Vahid","last_name":"Babaei"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"last_name":"Voloboy","full_name":"Voloboy, Alexey","first_name":"Alexey"},{"last_name":"Wilkie","full_name":"Wilkie, Alexander","first_name":"Alexander"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"},{"first_name":"Jaroslav","full_name":"Křivánek, Jaroslav","last_name":"Křivánek"}],"article_processing_charge":"No","external_id":{"isi":["000657959600017"]},"title":"Neural acceleration of scattering-aware color 3D printing","citation":{"apa":"Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek, J. (2021). Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.142626","ama":"Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 2021;40(2):205-219. doi:10.1111/cgf.142626","short":"T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel, K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219.","ieee":"T. Rittig et al., “Neural acceleration of scattering-aware color 3D printing,” Computer Graphics Forum, vol. 40, no. 2. Wiley, pp. 205–219, 2021.","mla":"Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:10.1111/cgf.142626.","ista":"Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 40(2), 205–219.","chicago":"Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy, Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.142626."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Distributed 3D Object Design","grant_number":"642841"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}]},{"scopus_import":"1","month":"10","intvolume":" 7","abstract":[{"text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials.","lang":"eng"}],"oa_version":"Published Version","issue":"41","volume":7,"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"eissn":["23752548"]},"publication_status":"published","file":[{"file_id":"10189","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-27T14:16:06Z","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","creator":"cziletti","date_updated":"2021-10-27T14:16:06Z","file_size":2441163}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"10177","file_date_updated":"2021-10-27T14:16:06Z","department":[{"_id":"NanoFab"}],"date_updated":"2023-08-14T08:04:42Z","ddc":["530"],"publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","doi":"10.1126/sciadv.abj0127","date_published":"2021-10-08T00:00:00Z","date_created":"2021-10-24T22:01:33Z","has_accepted_license":"1","isi":1,"year":"2021","day":"08","publication":"Science Advances","article_number":"abj0127","author":[{"first_name":"Javier","full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez"},{"first_name":"Jiahua","full_name":"Duan, Jiahua","last_name":"Duan"},{"first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez"},{"full_name":"Álvarez-Pérez, Gonzalo","last_name":"Álvarez-Pérez","first_name":"Gonzalo"},{"first_name":"Kirill V.","full_name":"Voronin, Kirill V.","last_name":"Voronin"},{"first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez"},{"first_name":"Weiliang","full_name":"Ma, Weiliang","last_name":"Ma"},{"first_name":"Qiaoliang","full_name":"Bao, Qiaoliang","last_name":"Bao"},{"last_name":"Volkov","full_name":"Volkov, Valentyn S.","first_name":"Valentyn S."},{"first_name":"Rainer","last_name":"Hillenbrand","full_name":"Hillenbrand, Rainer"},{"last_name":"Nikitin","full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y."},{"last_name":"Alonso-González","full_name":"Alonso-González, Pablo","first_name":"Pablo"}],"external_id":{"isi":["000704912700024"],"arxiv":["2103.10852"]},"article_processing_charge":"Yes","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","citation":{"ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abj0127.","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","ieee":"J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” Science Advances, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abj0127","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abj0127."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"volume":598,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","relation":"press_release","description":"News on IST Webpage"}]},"issue":"7880","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","month":"10","intvolume":" 598","scopus_import":"1","oa_version":"None","pmid":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain."}],"department":[{"_id":"LeSa"}],"date_updated":"2023-08-14T08:01:21Z","status":"public","article_type":"original","type":"journal_article","_id":"10146","date_published":"2021-10-14T00:00:00Z","doi":"10.1038/s41586-021-03927-z","date_created":"2021-10-17T22:01:17Z","page":"364-367","day":"14","publication":"Nature","isi":1,"year":"2021","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV","author":[{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","last_name":"Vercellino"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["34616041"],"isi":["000704581600001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021.","short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z","apa":"Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03927-z","mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z."},"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"date_updated":"2023-08-14T08:04:12Z","department":[{"_id":"MiLe"}],"_id":"10176","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00222488"]},"issue":"10","volume":62,"oa_version":"Preprint","abstract":[{"text":"We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ𝑟-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact.","lang":"eng"}],"intvolume":" 62","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1802.09978","open_access":"1"}],"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:10.1063/5.0037826.","apa":"Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0037826","ama":"Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","ieee":"I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP Publishing, 2021.","chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0037826.","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302."},"title":"Topological field theory on r-spin surfaces and the Arf-invariant","article_processing_charge":"No","external_id":{"isi":["000755638500010"],"arxiv":["1802.09978"]},"author":[{"first_name":"Ingo","full_name":"Runkel, Ingo","last_name":"Runkel"},{"first_name":"Lorant","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","last_name":"Szegedy","full_name":"Szegedy, Lorant","orcid":"0000-0003-2834-5054"}],"article_number":"102302","publication":"Journal of Mathematical Physics","day":"01","year":"2021","isi":1,"date_created":"2021-10-24T22:01:32Z","date_published":"2021-10-01T00:00:00Z","doi":"10.1063/5.0037826","acknowledgement":"We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.”","oa":1,"publisher":"AIP Publishing","quality_controlled":"1"},{"date_published":"2021-10-18T00:00:00Z","doi":"10.15252/embj.2021108714","date_created":"2021-10-24T22:01:34Z","has_accepted_license":"1","isi":1,"year":"2021","day":"18","publication":"EMBO Journal","quality_controlled":"1","publisher":"Embo Press","oa":1,"acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","author":[{"last_name":"Bajaj","full_name":"Bajaj, Sunanjay","first_name":"Sunanjay"},{"first_name":"Joshua A.","full_name":"Bagley, Joshua A.","last_name":"Bagley"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"first_name":"Abel","last_name":"Vertesy","full_name":"Vertesy, Abel"},{"first_name":"Sakurako","last_name":"Nagumo Wong","full_name":"Nagumo Wong, Sakurako"},{"first_name":"Veronica","last_name":"Krenn","full_name":"Krenn, Veronica"},{"first_name":"Julie","last_name":"Lévi-Strauss","full_name":"Lévi-Strauss, Julie"},{"first_name":"Juergen A.","full_name":"Knoblich, Juergen A.","last_name":"Knoblich"}],"external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"article_processing_charge":"Yes (in subscription journal)","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","citation":{"ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714.","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714.","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 2021;40(23). doi:10.15252/embj.2021108714","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021.","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no. 23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e108714","issue":"23","volume":40,"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"publication_status":"published","file":[{"file_name":"2021_EMBO_Bajaj.pdf","date_created":"2021-12-13T14:54:14Z","file_size":7819881,"date_updated":"2021-12-13T14:54:14Z","creator":"alisjak","success":1,"checksum":"78d2d02e775322297e774f72810a41a4","file_id":"10541","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 40","abstract":[{"text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"Bio"}],"file_date_updated":"2021-12-13T14:54:14Z","date_updated":"2023-08-14T08:05:23Z","ddc":["610"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10179"},{"acknowledgement":"L.S., P.G.Z., and A.I.T. thank the financial support of the European Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1. L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108. P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C., S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P., A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1. S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid (SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"18","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1038/s41467-021-26262-3","date_published":"2021-10-18T00:00:00Z","date_created":"2021-10-31T23:01:30Z","article_number":"6063","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063.","chicago":"Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash, Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza, and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3.","ama":"Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3","apa":"Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi, E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3","short":"L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi, A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12 (2021).","ieee":"L. Sortino et al., “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” Nature Communications, vol. 12. Springer Nature, 2021.","mla":"Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3."},"title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","author":[{"last_name":"Sortino","full_name":"Sortino, Luca","first_name":"Luca"},{"first_name":"Panaiot G.","last_name":"Zotev","full_name":"Zotev, Panaiot G."},{"full_name":"Phillips, Catherine L.","last_name":"Phillips","first_name":"Catherine L."},{"first_name":"Alistair J.","last_name":"Brash","full_name":"Brash, Alistair J."},{"full_name":"Cambiasso, Javier","last_name":"Cambiasso","first_name":"Javier"},{"first_name":"Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","full_name":"Marensi, Elena","orcid":"0000-0001-7173-4923"},{"first_name":"A. Mark","last_name":"Fox","full_name":"Fox, A. Mark"},{"full_name":"Maier, Stefan A.","last_name":"Maier","first_name":"Stefan A."},{"full_name":"Sapienza, Riccardo","last_name":"Sapienza","first_name":"Riccardo"},{"first_name":"Alexander I.","full_name":"Tartakovskii, Alexander I.","last_name":"Tartakovskii"}],"external_id":{"arxiv":["2103.16986"],"isi":["000708601800015"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"Single photon emitters in atomically-thin semiconductors can be deterministically positioned using strain induced by underlying nano-structures. Here, we couple monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas providing both optical enhancement and monolayer deformation. For single photon emitters formed on such nano-antennas, we find very low (femto-Joule) saturation pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed on low-refractive-index SiO2 pillars. We show that the key to these observations is the increase on average by a factor of 5 of the quantum efficiency of the emitters coupled to the nano-antennas. This further allows us to gain new insights into their photoluminescence dynamics, revealing the roles of the dark exciton reservoir and Auger processes. We also find that the coherence time of such emitters is limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas as a platform for high-efficiency quantum light generation in monolayer semiconductors.","lang":"eng"}],"month":"10","intvolume":" 12","scopus_import":"1","file":[{"creator":"cchlebak","file_size":1434201,"date_updated":"2021-11-03T11:31:24Z","file_name":"2021_NatComm_Sortino.pdf","date_created":"2021-11-03T11:31:24Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"8580d128389860f732028c521cd5949e","file_id":"10212"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","volume":12,"_id":"10203","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2023-08-14T08:12:12Z","file_date_updated":"2021-11-03T11:31:24Z","department":[{"_id":"BjHo"}]},{"year":"2021","isi":1,"has_accepted_license":"1","publication":"New Journal of Physics","day":"29","date_created":"2021-10-24T22:01:34Z","doi":"10.1088/1367-2630/ac23f1","date_published":"2021-09-29T00:00:00Z","acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","citation":{"mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1.","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” New Journal of Physics, vol. 23, no. 9. IOP Publishing, 2021.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 2021;23(9). doi:10.1088/1367-2630/ac23f1","apa":"Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1.","ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2102.05397"],"isi":["000702042400001"]},"article_processing_charge":"Yes","author":[{"full_name":"Sahu, Preeti","last_name":"Sahu","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti"},{"full_name":"Schwarz, J. M.","last_name":"Schwarz","first_name":"J. M."},{"first_name":"M. Lisa","full_name":"Manning, M. Lisa","last_name":"Manning"}],"title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","article_number":"093043","publication_status":"published","publication_identifier":{"eissn":["13672630"]},"language":[{"iso":"eng"}],"file":[{"file_size":2215016,"date_updated":"2021-10-28T12:06:01Z","creator":"cziletti","file_name":"2021_NewJPhys_Sahu.pdf","date_created":"2021-10-28T12:06:01Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10193","checksum":"ace603e8f0962b3ba55f23fa34f57764"}],"volume":23,"issue":"9","abstract":[{"lang":"eng","text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 23","month":"09","date_updated":"2023-08-14T08:10:31Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2021-10-28T12:06:01Z","_id":"10178","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.10691"}],"scopus_import":"1","month":"10","abstract":[{"lang":"eng","text":"In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space."}],"oa_version":"Published Version","publication_status":"published","publication_identifier":{"eissn":["1877-0541"],"issn":["0927-6947"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"10181","department":[{"_id":"UlWa"}],"date_updated":"2023-08-14T08:11:38Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","date_created":"2021-10-24T22:01:35Z","doi":"10.1007/s11228-021-00612-1","date_published":"2021-10-09T00:00:00Z","year":"2021","isi":1,"publication":"Set-Valued and Variational Analysis","day":"09","external_id":{"isi":["000705774800001"],"arxiv":["2012.10691"]},"article_processing_charge":"No","author":[{"first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","full_name":"Ivanov, Grigory"},{"first_name":"Mariana S.","last_name":"Lopushanski","full_name":"Lopushanski, Mariana S."}],"title":"Rectifiable curves in proximally smooth sets","citation":{"mla":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis, Springer Nature, 2021, doi:10.1007/s11228-021-00612-1.","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1","apa":"Ivanov, G., & Lopushanski, M. S. (2021). Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1","ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” Set-Valued and Variational Analysis. Springer Nature, 2021.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).","chicago":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2021. https://doi.org/10.1007/s11228-021-00612-1.","ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"10202","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-14T10:32:48Z","file_date_updated":"2021-11-09T13:59:26Z","department":[{"_id":"CaHe"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.","lang":"eng"}],"month":"10","intvolume":" 12","scopus_import":"1","file":[{"success":1,"checksum":"c40a69ae94435ecd3a30c9874a11ef2b","file_id":"10262","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_NatureComm_Pradhan.pdf","date_created":"2021-11-09T13:59:26Z","creator":"cziletti","file_size":7144437,"date_updated":"2021-11-09T13:59:26Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","issue":"1","volume":12,"related_material":{"link":[{"url":"https://doi.org/10.1101/2020.11.23.394171 ","relation":"earlier_version","description":"Preprint"}]},"article_number":"6094","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7.","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26234-7","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26234-7","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021).","ieee":"S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7.","ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094."},"title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","author":[{"full_name":"Pradhan, Saurabh J.","last_name":"Pradhan","first_name":"Saurabh J."},{"first_name":"Puli Chandramouli","full_name":"Reddy, Puli Chandramouli","last_name":"Reddy"},{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny"},{"last_name":"Sharma","full_name":"Sharma, Ankita","first_name":"Ankita"},{"last_name":"Sako","full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Oak","full_name":"Oak, Meghana S.","first_name":"Meghana S."},{"full_name":"Shah, Rini","last_name":"Shah","first_name":"Rini"},{"first_name":"Mrinmoy","full_name":"Pal, Mrinmoy","last_name":"Pal"},{"last_name":"Deshpande","full_name":"Deshpande, Ojas","first_name":"Ojas"},{"first_name":"Greg","full_name":"Dsilva, Greg","last_name":"Dsilva"},{"last_name":"Tang","full_name":"Tang, Yin","first_name":"Yin"},{"first_name":"Rakesh","last_name":"Mishra","full_name":"Mishra, Rakesh"},{"full_name":"Deshpande, Girish","last_name":"Deshpande","first_name":"Girish"},{"last_name":"Giraldez","full_name":"Giraldez, Antonio J.","first_name":"Antonio J."},{"first_name":"Mahendra","last_name":"Sonawane","full_name":"Sonawane, Mahendra"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Galande","full_name":"Galande, Sanjeev","first_name":"Sanjeev"}],"article_processing_charge":"Yes","external_id":{"pmid":["34667153"],"isi":["000709050300016"]},"acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"19","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1038/s41467-021-26234-7","date_published":"2021-10-19T00:00:00Z","date_created":"2021-10-31T23:01:29Z"},{"article_number":"760017","project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"citation":{"apa":"Qi, Q., Angermayr, S. A., & Bollenbach, M. T. (2021). Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.760017","ama":"Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.760017","short":"Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).","ieee":"Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.","mla":"Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology, vol. 12, 760017, Frontiers, 2021, doi:10.3389/fmicb.2021.760017.","ista":"Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 12, 760017.","chicago":"Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.760017."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["34745067"],"isi":["000715997300001"]},"article_processing_charge":"No","author":[{"full_name":"Qi, Qin","orcid":"0000-0002-6148-2416","last_name":"Qi","id":"3B22D412-F248-11E8-B48F-1D18A9856A87","first_name":"Qin"},{"first_name":"S. Andreas","last_name":"Angermayr","full_name":"Angermayr, S. Andreas"},{"first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","acknowledgement":"High-throughput sequencing data were generated by the Vienna BioCenter Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and Nadine Kraupner for their constructive feedback. The authors would also like to thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando for technical support.","oa":1,"quality_controlled":"1","publisher":"Frontiers","year":"2021","isi":1,"has_accepted_license":"1","publication":"Frontiers in Microbiology","day":"20","date_created":"2021-11-11T10:39:37Z","date_published":"2021-10-20T00:00:00Z","doi":"10.3389/fmicb.2021.760017","_id":"10271","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["microbiology"],"status":"public","date_updated":"2023-08-14T11:43:23Z","ddc":["610"],"file_date_updated":"2021-11-11T10:54:40Z","abstract":[{"lang":"eng","text":"Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 12","month":"10","publication_status":"published","publication_identifier":{"eissn":["1664-302X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10272","checksum":"d41321748e9588dd3cf03e9a7222127f","file_size":2397203,"date_updated":"2021-11-11T10:54:40Z","creator":"cchlebak","file_name":"2021_FrontiersMicrob_Qi.pdf","date_created":"2021-11-11T10:54:40Z"}],"ec_funded":1,"volume":12},{"volume":388,"issue":"2","publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10715","checksum":"a2c7b6f5d23b5453cd70d1261272283b","file_size":841426,"date_updated":"2022-02-02T10:19:55Z","creator":"cchlebak","file_name":"2021_CommunMathPhys_Cipolloni.pdf","date_created":"2022-02-02T10:19:55Z"}],"scopus_import":"1","intvolume":" 388","month":"10","abstract":[{"lang":"eng","text":"We prove that any deterministic matrix is approximately the identity in the eigenbasis of a large random Wigner matrix with very high probability and with an optimal error inversely proportional to the square root of the dimension. Our theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch (Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity (QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278, 2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020)."}],"oa_version":"Published Version","department":[{"_id":"LaEr"}],"file_date_updated":"2022-02-02T10:19:55Z","date_updated":"2023-08-14T10:29:49Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10221","page":"1005–1048","date_created":"2021-11-07T23:01:25Z","date_published":"2021-10-29T00:00:00Z","doi":"10.1007/s00220-021-04239-z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Communications in Mathematical Physics","day":"29","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","external_id":{"isi":["000712232700001"],"arxiv":["2012.13215"]},"article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"title":"Eigenstate thermalization hypothesis for Wigner matrices","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.","mla":"Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis for Wigner matrices,” Communications in Mathematical Physics, vol. 388, no. 2. Springer Nature, pp. 1005–1048, 2021.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048.","ama":"Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048. doi:10.1007/s00220-021-04239-z","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04239-z"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}]},{"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"isi":["000710850600001"],"arxiv":["2101.12566"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","citation":{"ista":"Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906.","apa":"Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906, doi:10.1007/s00205-021-01715-7."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","page":"1835–1906","date_created":"2021-11-07T23:01:26Z","doi":"10.1007/s00205-021-01715-7","date_published":"2021-10-25T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"Archive for Rational Mechanics and Analysis","day":"25","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10224","department":[{"_id":"RoSe"}],"file_date_updated":"2021-12-14T08:35:42Z","date_updated":"2023-08-14T10:32:19Z","ddc":["530"],"scopus_import":"1","intvolume":" 242","month":"10","abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"3","related_material":{"record":[{"id":"9787","status":"public","relation":"earlier_version"}]},"volume":242,"publication_status":"published","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10544","checksum":"672e9c21b20f1a50854b7c821edbb92f","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-12-14T08:35:42Z","file_name":"2021_Springer_Feliciangeli.pdf","date_updated":"2021-12-14T08:35:42Z","file_size":990529,"creator":"alisjak"}]},{"file_date_updated":"2022-05-16T07:02:27Z","department":[{"_id":"GaNo"}],"date_updated":"2023-08-14T11:46:12Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10281","ec_funded":1,"volume":12,"issue":"11","publication_status":"published","publication_identifier":{"eissn":["2073-4425"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"256cb832a9c3051c7dc741f6423b8cbd","file_id":"11380","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_Genes_Vasic.pdf","date_created":"2022-05-16T07:02:27Z","creator":"dernst","file_size":1335308,"date_updated":"2022-05-16T07:02:27Z"}],"scopus_import":"1","alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"intvolume":" 12","month":"10","abstract":[{"lang":"eng","text":"Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems"}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"isi":["000834044200002"]},"author":[{"first_name":"Verica","last_name":"Vasic","full_name":"Vasic, Verica"},{"first_name":"Mattson S.O.","full_name":"Jones, Mattson S.O.","last_name":"Jones"},{"id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E","first_name":"Denise","last_name":"Haslinger","full_name":"Haslinger, Denise"},{"first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus"},{"full_name":"Schmeisser, Michael J.","last_name":"Schmeisser","first_name":"Michael J."},{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Andreas G.","last_name":"Chiocchetti","full_name":"Chiocchetti, Andreas G."}],"title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","citation":{"chicago":"Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12111746.","ista":"Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.","mla":"Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes, vol. 12, no. 11, 1746, MDPI, 2021, doi:10.3390/genes12111746.","ieee":"V. Vasic et al., “Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment,” Genes, vol. 12, no. 11. MDPI, 2021.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021).","apa":"Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino, G., & Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. MDPI. https://doi.org/10.3390/genes12111746","ama":"Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 2021;12(11). doi:10.3390/genes12111746"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"article_number":"1746","date_created":"2021-11-14T23:01:24Z","date_published":"2021-10-30T00:00:00Z","doi":"10.3390/genes12111746","year":"2021","isi":1,"has_accepted_license":"1","publication":"Genes","day":"30","oa":1,"quality_controlled":"1","publisher":"MDPI","acknowledgement":"This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811); Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was also supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24) both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes for her support in preparing this manuscript."},{"type":"journal_article","article_type":"original","status":"public","_id":"10282","department":[{"_id":"JiFr"}],"date_updated":"2023-08-14T11:46:43Z","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2","open_access":"1"}],"month":"11","intvolume":" 233","abstract":[{"text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.","lang":"eng"}],"pmid":1,"oa_version":"Preprint","volume":233,"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Ivan","last_name":"Kashkan","full_name":"Kashkan, Ivan"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika"},{"first_name":"Katarzyna","full_name":"Retzer, Katarzyna","last_name":"Retzer"},{"first_name":"Jana","full_name":"Humpolíčková, Jana","last_name":"Humpolíčková"},{"full_name":"Jayasree, Aswathy","last_name":"Jayasree","first_name":"Aswathy"},{"last_name":"Filepová","full_name":"Filepová, Roberta","first_name":"Roberta"},{"last_name":"Vondráková","full_name":"Vondráková, Zuzana","first_name":"Zuzana"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"first_name":"Debbie","full_name":"Rombaut, Debbie","last_name":"Rombaut"},{"first_name":"Thomas B.","last_name":"Jacobs","full_name":"Jacobs, Thomas B."},{"full_name":"Frilander, Mikko J.","last_name":"Frilander","first_name":"Mikko J."},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"full_name":"Růžička, Kamil","last_name":"Růžička","first_name":"Kamil"}],"article_processing_charge":"No","external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","citation":{"ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792","ieee":"I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233. Wiley, pp. 329–343, 2021.","short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792.","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233, 329–343.","chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","page":"329-343","doi":"10.1111/nph.17792","date_published":"2021-11-05T00:00:00Z","date_created":"2021-11-14T23:01:24Z","isi":1,"year":"2021","day":"05","publication":"New Phytologist"},{"abstract":[{"lang":"eng","text":"We study conditions under which a finite simplicial complex K can be mapped to ℝd without higher-multiplicity intersections. An almost r-embedding is a map f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on previous constructions of counterexamples (for d ≥ 3r) based on a series of papers by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite 2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection number of the f-images of any r pairwise disjoint simplices of K is zero. This result can be restated in terms of a cohomological obstruction and extends an analogous codimension 3 criterion by the second and fourth authors. As another application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for r = 2 is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"month":"10","intvolume":" 245","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"8183","status":"public","relation":"earlier_version"},{"id":"9308","status":"public","relation":"earlier_version"}]},"volume":245,"_id":"10220","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-14T11:43:55Z","department":[{"_id":"UlWa"}],"acknowledgement":"Research supported by the Swiss National Science Foundation (Project SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169), by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful comments and discussions.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"year":"2021","day":"30","publication":"Israel Journal of Mathematics","page":"501–534 ","date_published":"2021-10-30T00:00:00Z","doi":"10.1007/s11856-021-2216-z","date_created":"2021-11-07T23:01:24Z","project":[{"grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z.","ista":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature, 2021, pp. 501–534, doi:10.1007/s11856-021-2216-z.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-021-2216-z","ama":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534. doi:10.1007/s11856-021-2216-z","ieee":"S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” Israel Journal of Mathematics, vol. 245. Springer Nature, pp. 501–534, 2021.","short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"first_name":"Arkadiy B.","full_name":"Skopenkov, Arkadiy B.","last_name":"Skopenkov"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"external_id":{"isi":["000712942100013"],"arxiv":["1511.03501"]},"article_processing_charge":"No","title":"Eliminating higher-multiplicity intersections. III. Codimension 2"},{"month":"10","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7pvmcvdtj"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism."}],"date_published":"2021-10-29T00:00:00Z","doi":"10.5061/DRYAD.7PVMCVDTJ","related_material":{"record":[{"id":"10284","status":"public","relation":"used_in_publication"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:14:35Z","ec_funded":1,"day":"29","year":"2021","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"status":"public","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"13061","department":[{"_id":"SyCr"}],"title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","author":[{"last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pull","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Naiser","full_name":"Naiser, Filip","first_name":"Filip"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","first_name":"Elisabeth"},{"first_name":"Jiri","last_name":"Matas","full_name":"Matas, Jiri"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. https://doi.org/10.5061/DRYAD.7PVMCVDTJ.","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ.","mla":"Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies. Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ.","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies.” Dryad, 2021.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021).","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., & Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ"},"date_updated":"2023-08-14T11:45:28Z"},{"_id":"10301","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-08-14T11:50:50Z","file_date_updated":"2021-11-18T07:02:02Z","department":[{"_id":"GaNo"}],"oa_version":"Published Version","abstract":[{"text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.","lang":"eng"}],"intvolume":" 10","month":"11","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10302","checksum":"59318e9e41507cec83c2f4070e6ad540","file_size":2477302,"date_updated":"2021-11-18T07:02:02Z","creator":"lgarciar","file_name":"elife-71575-v1.pdf","date_created":"2021-11-18T07:02:02Z"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"volume":10,"article_number":"e71575","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","ieee":"M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575","chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575."},"title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","article_processing_charge":"No","external_id":{"isi":["000720945900001"]},"author":[{"first_name":"María J","full_name":"Conde-Dusman, María J","last_name":"Conde-Dusman"},{"full_name":"Dey, Partha N","last_name":"Dey","first_name":"Partha N"},{"first_name":"Óscar","full_name":"Elía-Zudaire, Óscar","last_name":"Elía-Zudaire"},{"first_name":"Luis E","id":"33D1B084-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda"},{"first_name":"Carmen","full_name":"García-Lira, Carmen","last_name":"García-Lira"},{"full_name":"Grand, Teddy","last_name":"Grand","first_name":"Teddy"},{"first_name":"Victor","full_name":"Briz, Victor","last_name":"Briz"},{"full_name":"Velasco, Eric R","last_name":"Velasco","first_name":"Eric R"},{"first_name":"Raül","full_name":"Andero Galí, Raül","last_name":"Andero Galí"},{"first_name":"Sergio","last_name":"Niñerola","full_name":"Niñerola, Sergio"},{"full_name":"Barco, Angel","last_name":"Barco","first_name":"Angel"},{"first_name":"Pierre","full_name":"Paoletti, Pierre","last_name":"Paoletti"},{"first_name":"John F","last_name":"Wesseling","full_name":"Wesseling, John F"},{"first_name":"Fabrizio","full_name":"Gardoni, Fabrizio","last_name":"Gardoni"},{"last_name":"Tavalin","full_name":"Tavalin, Steven J","first_name":"Steven J"},{"last_name":"Perez-Otaño","full_name":"Perez-Otaño, Isabel","first_name":"Isabel"}],"acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","publication":"eLife","day":"17","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-11-18T06:59:45Z","date_published":"2021-11-17T00:00:00Z","doi":"10.7554/elife.71575"},{"publication":"EMBO Reports","day":"04","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-11-14T23:01:24Z","doi":"10.15252/embr.202153824","date_published":"2021-11-04T00:00:00Z","acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","oa":1,"publisher":"EMBO Press","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021).","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824.","ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824."},"title":"Towards best practices in research: Role of academic core facilities","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000714350000001"]},"author":[{"first_name":"Leonardo","full_name":"Restivo, Leonardo","last_name":"Restivo"},{"last_name":"Gerlach","full_name":"Gerlach, Björn","first_name":"Björn"},{"full_name":"Tsoory, Michael","last_name":"Tsoory","first_name":"Michael"},{"full_name":"Bikovski, Lior","last_name":"Bikovski","first_name":"Lior"},{"full_name":"Badurek, Sylvia","last_name":"Badurek","first_name":"Sylvia"},{"last_name":"Pitzer","full_name":"Pitzer, Claudia","first_name":"Claudia"},{"first_name":"Isabelle C.","last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C."},{"first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont"},{"first_name":"Jonathan","full_name":"Ward, Jonathan","last_name":"Ward"},{"orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael","last_name":"Schunn","first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lucas P.J.J.","last_name":"Noldus","full_name":"Noldus, Lucas P.J.J."},{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"}],"article_number":"e53824","language":[{"iso":"eng"}],"file":[{"file_size":488583,"date_updated":"2022-05-16T07:07:41Z","creator":"dernst","file_name":"2021_EmboReports_Restivo.pdf","date_created":"2022-05-16T07:07:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"74743baa6ef431ef60c3de3bc4da045a","file_id":"11381"}],"publication_status":"published","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":22,"oa_version":"Published Version","abstract":[{"text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.","lang":"eng"}],"intvolume":" 22","month":"11","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-14T11:47:35Z","department":[{"_id":"PreCl"}],"file_date_updated":"2022-05-16T07:07:41Z","_id":"10283","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article"},{"isi":1,"has_accepted_license":"1","year":"2021","day":"08","publication":"Communications Biology","doi":"10.1038/s42003-021-01808-9","date_published":"2021-03-08T00:00:00Z","date_created":"2021-11-19T11:37:29Z","acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","quality_controlled":"1","publisher":"Springer ","oa":1,"citation":{"ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.","ieee":"M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun","orcid":"0000-0002-3219-2022"},{"last_name":"Frank","full_name":"Frank, Anna","first_name":"Anna"},{"first_name":"Hideaki","last_name":"Tanaka","full_name":"Tanaka, Hideaki"},{"first_name":"Akihiro","last_name":"Kawamoto","full_name":"Kawamoto, Akihiro"},{"last_name":"El-Mohsnawy","full_name":"El-Mohsnawy, Eithar","first_name":"Eithar"},{"first_name":"Takayuki","full_name":"Kato, Takayuki","last_name":"Kato"},{"full_name":"Namba, Keiichi","last_name":"Namba","first_name":"Keiichi"},{"last_name":"Gerle","full_name":"Gerle, Christoph","first_name":"Christoph"},{"first_name":"Marc M.","full_name":"Nowaczyk, Marc M.","last_name":"Nowaczyk"},{"first_name":"Genji","last_name":"Kurisu","full_name":"Kurisu, Genji"}],"article_processing_charge":"No","external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","article_number":"304","publication_identifier":{"issn":["2399-3642"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10318","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"date_updated":"2021-11-19T15:09:18Z","file_size":6030261,"creator":"cchlebak","date_created":"2021-11-19T15:09:18Z","file_name":"2021_CommBio_Çoruh.pdf"}],"language":[{"iso":"eng"}],"issue":"1","volume":4,"abstract":[{"lang":"eng","text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 4","date_updated":"2023-08-14T11:51:19Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2021-11-19T15:09:18Z","_id":"10310","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"]},{"volume":10,"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"11372","checksum":"fad13c509b53bb7a2bef9c946a7ca60a","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-13T09:00:29Z","file_name":"2021_eLife_Marconi.pdf","date_updated":"2022-05-13T09:00:29Z","file_size":14137503,"creator":"dernst"}],"scopus_import":"1","intvolume":" 10","month":"11","abstract":[{"text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"EvBe"}],"file_date_updated":"2022-05-13T09:00:29Z","date_updated":"2023-08-14T11:49:23Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"10270","date_created":"2021-11-11T10:05:18Z","doi":"10.7554/elife.72132","date_published":"2021-11-01T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"eLife","day":"01","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","article_processing_charge":"Yes","external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"author":[{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","orcid":"0000-0003-4675-6893","full_name":"Gallemi, Marçal","last_name":"Gallemi"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof","last_name":"Wabnik","full_name":"Wabnik, Krzysztof"}],"title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","citation":{"mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences Publications, 2021, doi:10.7554/elife.72132.","ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132","apa":"Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” eLife, vol. 10. eLife Sciences Publications, 2021.","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132.","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"72132"},{"volume":118,"issue":"45","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"scopus_import":"1","intvolume":" 118","month":"11","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"department":[{"_id":"BjHo"}],"date_updated":"2023-08-14T11:50:10Z","type":"journal_article","article_type":"original","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"status":"public","_id":"10299","date_created":"2021-11-17T13:24:24Z","doi":"10.1073/pnas.2102350118","date_published":"2021-11-03T00:00:00Z","year":"2021","isi":1,"publication":"Proceedings of the National Academy of Sciences","day":"03","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","external_id":{"arxiv":["2103.00023"],"isi":["000720926900019"],"pmid":[" 34732570"]},"article_processing_charge":"No","author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H","last_name":"Choueiri","full_name":"Choueiri, George H"},{"last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M"},{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","last_name":"Varshney","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"first_name":"Sarath","last_name":"Sankar","full_name":"Sankar, Sarath"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"title":"Experimental observation of the origin and structure of elastoinertial turbulence","citation":{"mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021.","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FWF","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids"}],"article_number":"e2102350118"},{"status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10280","file_date_updated":"2021-11-15T13:25:52Z","department":[{"_id":"JePa"}],"ddc":["530"],"date_updated":"2023-08-14T11:48:37Z","month":"11","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials.","lang":"eng"}],"volume":12,"issue":"1","file":[{"file_name":"2021_NatComm_Aubret.pdf","date_created":"2021-11-15T13:25:52Z","file_size":6282703,"date_updated":"2021-11-15T13:25:52Z","creator":"cchlebak","success":1,"file_id":"10292","checksum":"1c392b12b9b7b615d422d9fabe19cdb9","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","article_number":"6398","title":"Metamachines of pluripotent colloids","author":[{"first_name":"Antoine","full_name":"Aubret, Antoine","last_name":"Aubret"},{"first_name":"Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","last_name":"Martinet"},{"last_name":"Palacci","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"}],"external_id":{"isi":["000714754400010"],"pmid":["34737315"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6","apa":"Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6","mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6.","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26699-6."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112.","date_published":"2021-11-04T00:00:00Z","doi":"10.1038/s41467-021-26699-6","date_created":"2021-11-14T23:01:23Z","day":"04","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2021"},{"date_published":"2021-11-01T00:00:00Z","doi":"10.1371/journal.pbio.3001431","date_created":"2021-11-21T23:01:28Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"PLoS Biology","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"acknowledgement":"We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities.","author":[{"full_name":"Chauve, Laetitia","last_name":"Chauve","first_name":"Laetitia"},{"last_name":"Hodge","full_name":"Hodge, Francesca","first_name":"Francesca"},{"first_name":"Sharlene","full_name":"Murdoch, Sharlene","last_name":"Murdoch"},{"first_name":"Fatemah","full_name":"Masoudzadeh, Fatemah","last_name":"Masoudzadeh"},{"last_name":"Mann","full_name":"Mann, Harry Jack","first_name":"Harry Jack"},{"last_name":"Lopez-Clavijo","full_name":"Lopez-Clavijo, Andrea","first_name":"Andrea"},{"first_name":"Hanneke","last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke"},{"first_name":"Greg","last_name":"West","full_name":"West, Greg"},{"first_name":"Bebiana C.","last_name":"Sousa","full_name":"Sousa, Bebiana C."},{"full_name":"Segonds-Pichon, Anne","last_name":"Segonds-Pichon","first_name":"Anne"},{"first_name":"Cheryl","last_name":"Li","full_name":"Li, Cheryl"},{"first_name":"Steven","last_name":"Wingett","full_name":"Wingett, Steven"},{"last_name":"Kienberger","full_name":"Kienberger, Hermine","first_name":"Hermine"},{"first_name":"Karin","last_name":"Kleigrewe","full_name":"Kleigrewe, Karin"},{"last_name":"De Bono","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"},{"first_name":"Michael","last_name":"Wakelam","full_name":"Wakelam, Michael"},{"first_name":"Olivia","full_name":"Casanueva, Olivia","last_name":"Casanueva"}],"external_id":{"pmid":["34723964"],"isi":["000715818400001"]},"article_processing_charge":"No","title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","citation":{"mla":"Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:10.1371/journal.pbio.3001431.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021).","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pbio.3001431.","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 19(11), e3001431."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e3001431","issue":"11","related_material":{"record":[{"relation":"research_data","id":"13069","status":"public"}]},"volume":19,"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10330","checksum":"0c61b667f814fd9435b3ac42036fc36d","file_size":4069215,"date_updated":"2021-11-22T09:34:03Z","creator":"cchlebak","file_name":"2021_PLoSBio_Chauve.pdf","date_created":"2021-11-22T09:34:03Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"11","intvolume":" 19","abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"oa_version":"Published Version","pmid":1,"file_date_updated":"2021-11-22T09:34:03Z","department":[{"_id":"MaDe"}],"date_updated":"2023-08-14T11:53:27Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10322"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15.","ieee":"A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis, pp. 1–15, 2021.","ama":"Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459","apa":"Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2021.1980459","mla":"Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459.","ista":"Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15.","chicago":"Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics. Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459."},"title":"The beauty of random polytopes inscribed in the 2-sphere","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"}],"external_id":{"arxiv":["2007.07783"],"isi":["000710893500001"]},"article_processing_charge":"Yes (via OA deal)","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00342"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Discretization in Geometry and Dynamics","grant_number":"I4887"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"day":"25","publication":"Experimental Mathematics","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1080/10586458.2021.1980459","date_published":"2021-10-25T00:00:00Z","date_created":"2021-11-07T23:01:25Z","page":"1-15","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions.","publisher":"Taylor and Francis","quality_controlled":"1","oa":1,"ddc":["510"],"date_updated":"2023-08-14T11:57:07Z","file_date_updated":"2023-08-14T11:55:10Z","department":[{"_id":"HeEd"}],"_id":"10222","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"2023_ExperimentalMath_Akopyan.pdf","date_created":"2023-08-14T11:55:10Z","file_size":1966019,"date_updated":"2023-08-14T11:55:10Z","creator":"dernst","success":1,"checksum":"3514382e3a1eb87fa6c61ad622874415","file_id":"14053","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1058-6458"],"eissn":["1944-950X"]},"publication_status":"published","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density."}],"month":"10","scopus_import":"1"},{"article_number":"762005","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005.","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021.","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).","ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005","apa":"Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005","chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005.","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005."},"title":"How do chaperones bind (partly) unfolded client proteins?","external_id":{"isi":["000717241700001"],"pmid":["34760928"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Sučec, Iva","last_name":"Sučec","first_name":"Iva"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"acknowledgement":"We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).","oa":1,"quality_controlled":"1","publisher":"Frontiers","publication":"Frontiers in Molecular Biosciences","day":"25","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-11-21T23:01:29Z","doi":"10.3389/fmolb.2021.762005","date_published":"2021-10-25T00:00:00Z","_id":"10323","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["547"],"date_updated":"2023-08-14T11:55:04Z","department":[{"_id":"PaSc"}],"file_date_updated":"2021-11-23T15:06:58Z","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.","lang":"eng"}],"intvolume":" 8","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10333","checksum":"a5c9dbf80dc2c5aaa737f456c941d964","success":1,"date_updated":"2021-11-23T15:06:58Z","file_size":4700798,"creator":"cchlebak","date_created":"2021-11-23T15:06:58Z","file_name":"2021_FrontiersMolBioSc_Sučec.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2296-889X"]},"volume":8},{"date_updated":"2023-08-14T11:54:02Z","department":[{"_id":"JiFr"}],"_id":"10326","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"eissn":["2055-0278"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":7,"abstract":[{"text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"11","intvolume":" 7","citation":{"ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y.","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y","ieee":"E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Enjun","full_name":"Xu, Enjun","last_name":"Xu"},{"first_name":"Liang","full_name":"Chai, Liang","last_name":"Chai"},{"first_name":"Shiqi","full_name":"Zhang, Shiqi","last_name":"Zhang"},{"full_name":"Yu, Ruixue","last_name":"Yu","first_name":"Ruixue"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"last_name":"Xu","full_name":"Xu, Chongyi","first_name":"Chongyi"},{"first_name":"Yuxin","last_name":"Hu","full_name":"Hu, Yuxin"}],"article_processing_charge":"No","external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"title":"Catabolism of strigolactones by a carboxylesterase","isi":1,"year":"2021","day":"11","publication":"Nature Plants","page":"1495–1504 ","date_published":"2021-11-11T00:00:00Z","doi":"10.1038/s41477-021-01011-y","date_created":"2021-11-21T23:01:30Z","acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","publisher":"Springer Nature","quality_controlled":"1"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5547464"}],"oa":1,"publisher":"Zenodo","day":"25","year":"2021","date_created":"2023-05-23T16:40:56Z","related_material":{"record":[{"status":"public","id":"10322","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.5519410","date_published":"2021-12-25T00:00:00Z","_id":"13069","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-08-14T11:53:26Z","citation":{"mla":"Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410."},"department":[{"_id":"MaDe"}],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","article_processing_charge":"No","author":[{"last_name":"Chauve","full_name":"Chauve, Laetitia","first_name":"Laetitia"},{"first_name":"Francesca","last_name":"Hodge","full_name":"Hodge, Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"last_name":"Masoudzadeh","full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah"},{"first_name":"Harry-Jack","full_name":"Mann, Harry-Jack","last_name":"Mann"},{"last_name":"Lopez-Clavijo","full_name":"Lopez-Clavijo, Andrea","first_name":"Andrea"},{"first_name":"Hanneke","last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke"},{"first_name":"Greg","full_name":"West, Greg","last_name":"West"},{"last_name":"Sousa","full_name":"Sousa, Bebiana C.","first_name":"Bebiana C."},{"first_name":"Anne","full_name":"Segonds-Pichon, Anne","last_name":"Segonds-Pichon"},{"first_name":"Cheryl","last_name":"Li","full_name":"Li, Cheryl"},{"full_name":"Wingett, Steven","last_name":"Wingett","first_name":"Steven"},{"first_name":"Hermine","full_name":"Kienberger, Hermine","last_name":"Kienberger"},{"last_name":"Kleigrewe","full_name":"Kleigrewe, Karin","first_name":"Karin"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono"},{"first_name":"Michael","last_name":"Wakelam","full_name":"Wakelam, Michael"},{"full_name":"Casanueva, Olivia","last_name":"Casanueva","first_name":"Olivia"}]},{"publication":"25th International Conference on Financial Cryptography and Data Security","day":"23","year":"2021","isi":1,"date_created":"2021-11-21T23:01:29Z","doi":"10.1007/978-3-662-64331-0_1","date_published":"2021-10-23T00:00:00Z","page":"3-36","acknowledgement":"We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 3–36.","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.","ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.","chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In 25th International Conference on Financial Cryptography and Data Security, 12675:3–36. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_1."},"title":"SoK: Communication across distributed ledgers","external_id":{"isi":["000712016200001"]},"article_processing_charge":"No","author":[{"first_name":"Alexei","last_name":"Zamyatin","full_name":"Zamyatin, Alexei"},{"last_name":"Al-Bassam","full_name":"Al-Bassam, Mustafa","first_name":"Mustafa"},{"first_name":"Dionysis","last_name":"Zindros","full_name":"Zindros, Dionysis"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Moreno-Sanchez, Pedro","last_name":"Moreno-Sanchez","first_name":"Pedro"},{"last_name":"Kiayias","full_name":"Kiayias, Aggelos","first_name":"Aggelos"},{"first_name":"William J.","last_name":"Knottenbelt","full_name":"Knottenbelt, William J."}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["978-3-662-64331-0"],"isbn":["9-783-6626-4330-3"],"eissn":["1611-3349"],"issn":["0302-9743"]},"volume":"12675 ","oa_version":"Preprint","abstract":[{"text":"Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains.","lang":"eng"}],"month":"10","main_file_link":[{"url":"https://eprint.iacr.org/2019/1128","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"date_updated":"2023-08-14T12:59:26Z","department":[{"_id":"ElKo"}],"_id":"10325","status":"public","conference":{"name":"FC: Financial Cryptography","start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05"},"type":"conference"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","date_published":"2021-10-23T00:00:00Z","doi":"10.1007/978-3-662-64331-0_11","date_created":"2021-11-21T23:01:29Z","page":"209-230","day":"23","publication":"25th International Conference on Financial Cryptography and Data Security","isi":1,"year":"2021","title":"Brick: Asynchronous incentive-compatible payment channels","author":[{"full_name":"Avarikioti, Zeta","last_name":"Avarikioti","first_name":"Zeta"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Roger","last_name":"Wattenhofer","full_name":"Wattenhofer, Roger"},{"last_name":"Zindros","full_name":"Zindros, Dionysis","first_name":"Dionysis"}],"external_id":{"isi":["000712016200011"],"arxiv":["1905.11360"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11","ama":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230. doi:10.1007/978-3-662-64331-0_11","ieee":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 209–230.","short":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230.","mla":"Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.","ista":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.","chicago":"Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th International Conference on Financial Cryptography and Data Security, 12675:209–30. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11."},"month":"10","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1905.11360","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.","lang":"eng"}],"volume":"12675 ","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9-783-6626-4330-3"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"]},"publication_status":"published","status":"public","type":"conference","conference":{"start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05","name":"FC: Financial Cryptography"},"_id":"10324","department":[{"_id":"ElKo"}],"date_updated":"2023-08-14T12:59:58Z"},{"type":"journal_article","article_type":"original","status":"public","_id":"10363","department":[{"_id":"CaGu"}],"date_updated":"2023-08-14T13:01:38Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/protein/gzab025"}],"scopus_import":"1","intvolume":" 34","month":"11","abstract":[{"lang":"eng","text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia."}],"oa_version":"Published Version","pmid":1,"volume":34,"publication_status":"published","publication_identifier":{"issn":["1741-0126"],"eissn":["1741-0134"]},"language":[{"iso":"eng"}],"article_number":"gzab025","external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"article_processing_charge":"No","author":[{"full_name":"Lee, Jungmin","last_name":"Lee","first_name":"Jungmin"},{"first_name":"Andyna","last_name":"Vernet","full_name":"Vernet, Andyna"},{"first_name":"Nathalie","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","full_name":"Gruber, Nathalie","last_name":"Gruber"},{"full_name":"Kready, Kasia M.","last_name":"Kready","first_name":"Kasia M."},{"last_name":"Burrill","full_name":"Burrill, Devin R.","first_name":"Devin R."},{"full_name":"Way, Jeffrey C.","last_name":"Way","first_name":"Jeffrey C."},{"full_name":"Silver, Pamela A.","last_name":"Silver","first_name":"Pamela A."}],"title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","citation":{"chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection. Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025.","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025.","mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34, gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025.","apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., & Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzab025","ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 2021;34. doi:10.1093/protein/gzab025","ieee":"J. Lee et al., “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34. Oxford University Press, 2021.","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","date_created":"2021-11-28T23:01:28Z","doi":"10.1093/protein/gzab025","date_published":"2021-11-01T00:00:00Z","year":"2021","isi":1,"publication":"Protein Engineering, Design and Selection","day":"01"},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Cells and Development","day":"17","year":"2021","isi":1,"date_created":"2021-11-28T23:01:30Z","date_published":"2021-11-17T00:00:00Z","doi":"10.1016/j.cdev.2021.203758","article_number":"203758","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758."},"title":"Special rebranding issue: “Quantitative cell and developmental biology”","article_processing_charge":"No","external_id":{"isi":["000974771600028"],"pmid":["34800748"]},"author":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Lennon","full_name":"Lennon, Ana Maria","first_name":"Ana Maria"},{"first_name":"Roberto","full_name":"Mayor, Roberto","last_name":"Mayor"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"}],"pmid":1,"oa_version":"Published Version","intvolume":" 168","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cdev.2021.203758"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2667-2901"]},"volume":168,"issue":"12","_id":"10366","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2023-08-14T13:02:40Z","department":[{"_id":"CaHe"}]},{"ddc":["573"],"date_updated":"2023-08-14T13:18:46Z","file_date_updated":"2021-12-10T08:54:09Z","department":[{"_id":"EdHa"}],"_id":"10402","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"63c56ec75314a71e63e7dd2920b3c5b5","file_id":"10529","success":1,"date_updated":"2021-12-10T08:54:09Z","file_size":2303405,"creator":"cchlebak","date_created":"2021-12-10T08:54:09Z","file_name":"2021_NatComm_Ucar.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"13058","status":"public"}]},"volume":12,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales.","lang":"eng"}],"intvolume":" 12","month":"11","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5.","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5","ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021)."},"title":"Theory of branching morphogenesis by local interactions and global guidance","article_processing_charge":"No","external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar"},{"full_name":"Kamenev, Dmitrii","last_name":"Kamenev","first_name":"Dmitrii"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"last_name":"Fachet","full_name":"Fachet, Dominik C","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","first_name":"Dominik C"},{"first_name":"Francois","last_name":"Lallemend","full_name":"Lallemend, Francois"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"},{"first_name":"Saida","last_name":"Hadjab","full_name":"Hadjab, Saida"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"article_number":"6830","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Nature Communications","day":"24","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-12-05T23:01:40Z","doi":"10.1038/s41467-021-27135-5","date_published":"2021-11-24T00:00:00Z","acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"department":[{"_id":"KrPi"}],"date_updated":"2023-08-14T13:07:46Z","status":"public","conference":{"name":"TCC: Theory of Cryptography Conference","start_date":"2021-11-08","end_date":"2021-11-11","location":"Raleigh, NC, United States"},"type":"conference","_id":"10407","ec_funded":1,"volume":13043,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"]},"intvolume":" 13043","month":"11","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1224"}],"scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound."}],"title":"Trojan-resilience without cryptography","external_id":{"isi":["000728364000014"]},"article_processing_charge":"No","author":[{"first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","full_name":"Chakraborty, Suvradip","last_name":"Chakraborty"},{"last_name":"Dziembowski","full_name":"Dziembowski, Stefan","first_name":"Stefan"},{"first_name":"Małgorzata","last_name":"Gałązka","full_name":"Gałązka, Małgorzata"},{"first_name":"Tomasz","full_name":"Lizurej, Tomasz","last_name":"Lizurej"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo","full_name":"Yeo, Michelle X"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14.","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14","ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","mla":"Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14."},"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2021-12-05T23:01:42Z","doi":"10.1007/978-3-030-90453-1_14","date_published":"2021-11-04T00:00:00Z","page":"397-428","day":"04","year":"2021","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"citation":{"ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.","chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954.","apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954","ieee":"C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000715789500001"]},"article_processing_charge":"No","author":[{"last_name":"Biane","full_name":"Biane, Celia","first_name":"Celia"},{"full_name":"Rückerl, Florian","last_name":"Rückerl","first_name":"Florian"},{"full_name":"Abrahamsson, Therese","last_name":"Abrahamsson","first_name":"Therese"},{"first_name":"Cécile","full_name":"Saint-Cloment, Cécile","last_name":"Saint-Cloment"},{"last_name":"Mariani","full_name":"Mariani, Jean","first_name":"Jean"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Digregorio, David A.","last_name":"Digregorio","first_name":"David A."},{"full_name":"Sherrard, Rachel M.","last_name":"Sherrard","first_name":"Rachel M."},{"last_name":"Cathala","full_name":"Cathala, Laurence","first_name":"Laurence"}],"title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","article_number":"e65954","year":"2021","has_accepted_license":"1","isi":1,"publication":"eLife","day":"03","date_created":"2021-12-05T23:01:40Z","date_published":"2021-11-03T00:00:00Z","doi":"10.7554/eLife.65954","acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_updated":"2023-08-14T13:12:07Z","ddc":["570"],"file_date_updated":"2021-12-10T08:31:41Z","department":[{"_id":"RySh"}],"_id":"10403","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"c7c33c3319428d56e332e22349c50ed3","file_id":"10528","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_eLife_Biane.pdf","date_created":"2021-12-10T08:31:41Z","file_size":13131322,"date_updated":"2021-12-10T08:31:41Z","creator":"cchlebak"}],"volume":10,"abstract":[{"lang":"eng","text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"11"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10401","file_date_updated":"2021-12-06T14:53:41Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2023-08-14T13:04:34Z","intvolume":" 4","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect.","lang":"eng"}],"ec_funded":1,"volume":4,"issue":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10420","checksum":"9097319952cb9a3d96e7fd3aa9813a03","success":1,"date_updated":"2021-12-06T14:53:41Z","file_size":1068984,"creator":"alisjak","date_created":"2021-12-06T14:53:41Z","file_name":"2021_NatComm_Barfknecht.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["23993650"]},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"252","title":"Generation of spin currents by a temperature gradient in a two-terminal device","external_id":{"isi":["10.1038/s42005-021-00753-7"],"arxiv":["2101.02020"]},"article_processing_charge":"No","author":[{"first_name":"Rafael E.","last_name":"Barfknecht","full_name":"Barfknecht, Rafael E."},{"first_name":"Angela","last_name":"Foerster","full_name":"Foerster, Angela"},{"first_name":"Nikolaj T.","full_name":"Zinner, Nikolaj T.","last_name":"Zinner"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7.","ista":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252.","mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7","apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7","ieee":"R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021.","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021)."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z).","date_created":"2021-12-05T23:01:39Z","doi":"10.1038/s42005-021-00753-7","date_published":"2021-11-26T00:00:00Z","publication":"Communications Physics","day":"26","year":"2021","has_accepted_license":"1"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","page":"253-264","date_created":"2021-12-05T23:01:40Z","date_published":"2021-11-27T00:00:00Z","doi":"10.1111/cgf.14418","year":"2021","isi":1,"publication":"Computer Graphics Forum","day":"27","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"article_processing_charge":"No","external_id":{"arxiv":["2110.07667"],"isi":["000722952000024"]},"author":[{"full_name":"Sietzen, Stefan","last_name":"Sietzen","first_name":"Stefan"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner"},{"first_name":"Judy","full_name":"Borowski, Judy","last_name":"Borowski"},{"first_name":"Ramin","full_name":"Hasani, Ramin","last_name":"Hasani"},{"first_name":"Manuela","full_name":"Waldner, Manuela","last_name":"Waldner"}],"title":"Interactive analysis of CNN robustness","citation":{"ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418.","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.07667"}],"scopus_import":"1","intvolume":" 40","month":"11","abstract":[{"text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models.","lang":"eng"}],"oa_version":"Preprint","issue":"7","volume":40,"publication_status":"published","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"10404","department":[{"_id":"ToHe"}],"date_updated":"2023-08-14T13:11:42Z"},{"quality_controlled":"1","publisher":"Annual Reviews","acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","page":"209-233","doi":"10.1146/annurev-genet-071819-103748","date_published":"2021-08-30T00:00:00Z","date_created":"2021-12-05T23:01:41Z","isi":1,"year":"2021","day":"30","publication":"Annual Review of Genetics","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","first_name":"Nikhil","last_name":"Mishra","full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"article_processing_charge":"No","title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","citation":{"mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748.","apa":"Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"08","intvolume":" 55","abstract":[{"lang":"eng","text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future."}],"pmid":1,"oa_version":"None","volume":55,"ec_funded":1,"publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"_id":"10406","department":[{"_id":"CaHe"}],"date_updated":"2023-08-14T13:05:13Z"},{"abstract":[{"lang":"eng","text":"The zip file includes source data used in the main text of the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5257161"}],"oa":1,"month":"08","year":"2021","day":"25","doi":"10.5281/ZENODO.5257160","related_material":{"record":[{"id":"10402","status":"public","relation":"used_in_publication"}]},"date_published":"2021-08-25T00:00:00Z","date_created":"2023-05-23T13:46:34Z","_id":"13058","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","citation":{"short":"M.C. Ucar, (2021).","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160","apa":"Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160","mla":"Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160.","ista":"Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160.","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160."},"date_updated":"2023-08-14T13:18:46Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar"}],"article_processing_charge":"No","department":[{"_id":"EdHa"}],"title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\""},{"oa_version":"Preprint","abstract":[{"text":"Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds log(N) keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting 2log(N) ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks.","lang":"eng"}],"intvolume":" 13044","month":"11","main_file_link":[{"url":"https://eprint.iacr.org/2021/1158","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["978-3-030-90456-2"],"eissn":["1611-3349"],"isbn":["9-783-0309-0455-5"],"issn":["0302-9743"]},"ec_funded":1,"volume":13044,"_id":"10408","status":"public","conference":{"name":"TCC: Theory of Cryptography","location":"Raleigh, NC, United States","end_date":"2021-11-11","start_date":"2021-11-08"},"type":"conference","date_updated":"2023-08-14T13:19:39Z","department":[{"_id":"KrPi"}],"acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"19th International Conference","day":"04","year":"2021","isi":1,"date_created":"2021-12-05T23:01:42Z","doi":"10.1007/978-3-030-90456-2_8","date_published":"2021-11-04T00:00:00Z","page":"222-253","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In 19th International Conference, 13044:222–53. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90456-2_8.","ista":"Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.","mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” 19th International Conference, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:10.1007/978-3-030-90456-2_8.","ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: 19th International Conference. Vol 13044. Springer Nature; 2021:222-253. doi:10.1007/978-3-030-90456-2_8","apa":"Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In 19th International Conference (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90456-2_8","ieee":"J. F. Alwen et al., “Grafting key trees: Efficient key management for overlapping groups,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.","short":"J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253."},"title":"Grafting key trees: Efficient key management for overlapping groups","external_id":{"isi":["000728363700008"]},"article_processing_charge":"No","author":[{"first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","full_name":"Alwen, Joel F"},{"full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606","last_name":"Auerbach","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt"},{"full_name":"Baig, Mirza Ahad","last_name":"Baig","first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel"},{"full_name":"Klein, Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo","last_name":"Pascual Perez","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","first_name":"Guillermo"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"last_name":"Walter","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:10.1103/physrevlett.127.247001.","ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021.","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001","apa":"Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.247001","chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.247001.","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001."},"title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","external_id":{"arxiv":["2109.00011"],"isi":["000923819400004"]},"article_processing_charge":"No","author":[{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"last_name":"Holder","full_name":"Holder, Tobias","first_name":"Tobias"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"}],"article_number":"247001","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication":"Physical Review Letters","day":"09","year":"2021","isi":1,"date_created":"2021-12-10T07:51:33Z","doi":"10.1103/physrevlett.127.247001","date_published":"2021-12-09T00:00:00Z","acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2023-08-14T13:19:13Z","department":[{"_id":"MaSe"}],"_id":"10527","keyword":["general physics and astronomy"],"status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"ec_funded":1,"volume":127,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/","relation":"press_release","description":"News on IST Webpage"}]},"issue":"24","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase."}],"intvolume":" 127","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.00011"}],"scopus_import":"1"},{"date_created":"2021-12-12T23:01:27Z","doi":"10.1039/d1tc02753k","date_published":"2021-12-07T00:00:00Z","page":"16217-16225","publication":"Journal of Materials Chemistry C","day":"07","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Royal Society of Chemistry","acknowledgement":"J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983).","title":"Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties","external_id":{"isi":["000688135700001"]},"article_processing_charge":"No","author":[{"first_name":"Jingjin","full_name":"Dong, Jingjin","last_name":"Dong"},{"first_name":"Selim","full_name":"Sami, Selim","last_name":"Sami"},{"first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"first_name":"Riccardo","last_name":"Alessandri","full_name":"Alessandri, Riccardo"},{"full_name":"Jahani, Fatimeh","last_name":"Jahani","first_name":"Fatimeh"},{"full_name":"Qiu, Li","last_name":"Qiu","first_name":"Li"},{"last_name":"Marrink","full_name":"Marrink, Siewert J.","first_name":"Siewert J."},{"last_name":"Havenith","full_name":"Havenith, Remco W.A.","first_name":"Remco W.A."},{"first_name":"Jan C.","full_name":"Hummelen, Jan C.","last_name":"Hummelen"},{"last_name":"Loi","full_name":"Loi, Maria A.","first_name":"Maria A."},{"full_name":"Portale, Giuseppe","last_name":"Portale","first_name":"Giuseppe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k.","ista":"Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.","mla":"Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:10.1039/d1tc02753k.","apa":"Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k","ama":"Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k","short":"J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225.","ieee":"J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021."},"volume":9,"issue":"45","language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2021-12-13T09:24:42Z","file_size":4979390,"date_created":"2021-12-13T09:24:42Z","file_name":"2021_JMaterChemC_Dong.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6b73c214ce54a6894a5854b4364413d7","file_id":"10538","success":1}],"publication_status":"published","publication_identifier":{"issn":["2050-7534"],"eissn":["2050-7526"]},"intvolume":" 9","month":"12","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications."}],"department":[{"_id":"MaIb"}],"file_date_updated":"2021-12-13T09:24:42Z","ddc":["540"],"date_updated":"2023-08-17T06:18:44Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"10534"},{"abstract":[{"lang":"eng","text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"12","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"22ed4c55fb550f6da02ae55c359be651","file_id":"11384","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-05-16T10:42:22Z","file_name":"2021_eLife_Choi.pdf","creator":"dernst","date_updated":"2022-05-16T10:42:22Z","file_size":2715200}],"ec_funded":1,"volume":10,"_id":"10533","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["genetics and molecular biology"],"status":"public","date_updated":"2023-08-17T06:21:08Z","ddc":["570"],"department":[{"_id":"DaZi"}],"file_date_updated":"2022-05-16T10:42:22Z","acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","year":"2021","has_accepted_license":"1","isi":1,"publication":"eLife","day":"01","date_created":"2021-12-10T13:12:08Z","date_published":"2021-12-01T00:00:00Z","doi":"10.7554/elife.72676","article_number":"e72676","project":[{"grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin","_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020"}],"citation":{"ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72676","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676, eLife Sciences Publications, 2021, doi:10.7554/elife.72676."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["34850679"],"isi":["000754832000001"]},"author":[{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"last_name":"Lyons","full_name":"Lyons, David B","first_name":"David B"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin"},{"scopus_import":"1","month":"11","intvolume":" 11","abstract":[{"text":"TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":11,"publication_identifier":{"eissn":["2234-943X"]},"publication_status":"published","file":[{"date_created":"2021-12-13T13:32:37Z","file_name":"2021_Frontiers_Stefanescu.pdf","date_updated":"2021-12-13T13:32:37Z","file_size":9245199,"creator":"alisjak","file_id":"10539","checksum":"56cbac80e6891ce750511a30161b7792","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10536","department":[{"_id":"DaSi"}],"file_date_updated":"2021-12-13T13:32:37Z","date_updated":"2023-08-17T06:20:32Z","ddc":["610"],"quality_controlled":"1","publisher":"Frontiers","oa":1,"acknowledgement":"The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich.","date_published":"2021-11-18T00:00:00Z","doi":"10.3389/fonc.2021.765151","date_created":"2021-12-12T23:01:27Z","isi":1,"has_accepted_license":"1","year":"2021","day":"18","publication":"Frontiers in Oncology","article_number":"765151","author":[{"first_name":"Cristina","last_name":"Stefanescu","full_name":"Stefanescu, Cristina"},{"last_name":"Van Gogh","full_name":"Van Gogh, Merel","first_name":"Merel"},{"last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko"},{"first_name":"Mathias","last_name":"Heikenwalder","full_name":"Heikenwalder, Mathias"},{"first_name":"Lubor","last_name":"Borsig","full_name":"Borsig, Lubor"}],"external_id":{"isi":["000726603400001"],"pmid":["34868988"]},"article_processing_charge":"No","title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","citation":{"mla":"Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology, vol. 11, 765151, Frontiers, 2021, doi:10.3389/fonc.2021.765151.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","ieee":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” Frontiers in Oncology, vol. 11. Frontiers, 2021.","ama":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 2021;11. doi:10.3389/fonc.2021.765151","apa":"Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., & Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2021.765151","chicago":"Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology. Frontiers, 2021. https://doi.org/10.3389/fonc.2021.765151.","ista":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01136-y.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré.","mla":"Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré, Springer Nature, 2021, doi:10.1007/s00023-021-01136-y.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 2021. doi:10.1007/s00023-021-01136-y","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2021). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. Springer Nature. https://doi.org/10.1007/s00023-021-01136-y","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” Annales Henri Poincaré. Springer Nature, 2021.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré (2021)."},"title":"Bosonization of fermionic many-body dynamics","author":[{"first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091","last_name":"Benedikter"},{"full_name":"Nam, Phan Thành","last_name":"Nam","first_name":"Phan Thành"},{"first_name":"Marcello","last_name":"Porta","full_name":"Porta, Marcello"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"article_processing_charge":"No","external_id":{"isi":["000725405700001"],"arxiv":["2103.08224"]},"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"02","publication":"Annales Henri Poincaré","isi":1,"year":"2021","doi":"10.1007/s00023-021-01136-y","date_published":"2021-12-02T00:00:00Z","date_created":"2021-12-12T23:01:28Z","acknowledgement":"NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-08-17T06:19:14Z","department":[{"_id":"RoSe"}],"_id":"10537","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1424-0637"]},"publication_status":"published","ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations."}],"month":"12","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2103.08224","open_access":"1"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441.","page":"343-452","date_created":"2021-12-16T12:12:33Z","doi":"10.1007/s00205-021-01686-9","date_published":"2021-06-30T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Archive for Rational Mechanics and Analysis","day":"30","external_id":{"arxiv":["1908.02273"],"isi":["000668431200001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"first_name":"Stefan","last_name":"Neukamm","full_name":"Neukamm, Stefan"}],"title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","citation":{"ama":"Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 2021;242(1):343-452. doi:10.1007/s00205-021-01686-9","apa":"Fischer, J. L., & Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01686-9","ieee":"J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” Archive for Rational Mechanics and Analysis, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021.","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","mla":"Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:10.1007/s00205-021-01686-9.","ista":"Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452.","chicago":"Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01686-9."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 242","month":"06","abstract":[{"text":"We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \\mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \\varepsilon >0, we establish homogenization error estimates of the order \\varepsilon in case d\\geqq 3, and of the order \\varepsilon |\\log \\varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \\varepsilon ^\\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\\alpha } regularity theory is available.","lang":"eng"}],"oa_version":"Published Version","issue":"1","volume":242,"publication_status":"published","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"language":[{"iso":"eng"}],"file":[{"checksum":"cc830b739aed83ca2e32c4e0ce266a4c","file_id":"10558","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-12-16T14:58:08Z","file_name":"2021_ArchRatMechAnalysis_Fischer.pdf","date_updated":"2021-12-16T14:58:08Z","file_size":1640121,"creator":"cchlebak"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"status":"public","_id":"10549","file_date_updated":"2021-12-16T14:58:08Z","department":[{"_id":"JuFi"}],"date_updated":"2023-08-17T06:23:21Z","ddc":["530"]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517.","ieee":"C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 486–517.","apa":"Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In 19th International Conference (Vol. 13043, pp. 486–517). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_17","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: 19th International Conference. Vol 13043. Springer Nature; 2021:486-517. doi:10.1007/978-3-030-90453-1_17","mla":"Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 486–517, doi:10.1007/978-3-030-90453-1_17.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 486–517.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In 19th International Conference, 13043:486–517. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_17."},"title":"On treewidth, separators and Yao’s garbling","article_processing_charge":"No","external_id":{"isi":["000728364000017"]},"author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein","full_name":"Klein, Karen"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"19th International Conference","day":"04","year":"2021","isi":1,"date_created":"2021-12-05T23:01:43Z","doi":"10.1007/978-3-030-90453-1_17","date_published":"2021-11-04T00:00:00Z","page":"486-517","acknowledgement":"We are grateful to Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. We would also like to thank Crypto 2021 and TCC 2021 reviewers for their detailed review and suggestions, which helped improve presentation considerably.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_updated":"2023-08-17T06:21:38Z","department":[{"_id":"KrPi"}],"_id":"10409","status":"public","conference":{"name":"TCC: Theory of Cryptography","end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"]},"ec_funded":1,"volume":"13043 ","related_material":{"record":[{"relation":"earlier_version","id":"10044","status":"public"}]},"oa_version":"Preprint","abstract":[{"text":"We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size S and treewidth w with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity. with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.","lang":"eng"}],"month":"11","main_file_link":[{"url":"https://eprint.iacr.org/2021/926","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"]},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y. Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo, and C. Laumann. We acknowledge support from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899.","date_published":"2021-12-14T00:00:00Z","doi":"10.1103/physreva.104.062423","date_created":"2021-12-14T20:46:07Z","day":"14","publication":"Physical Review A","isi":1,"year":"2021","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"article_number":"062423","title":"Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT)","author":[{"last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"article_processing_charge":"No","external_id":{"arxiv":["2106.06344"],"isi":["000753659200004"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 104(6), 062423.","chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/physreva.104.062423.","ieee":"R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT),” Physical Review A, vol. 104, no. 6. American Physical Society, 2021.","short":"R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).","apa":"Medina Ramos, R. A., & Serbyn, M. (2021). Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.104.062423","ama":"Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 2021;104(6). doi:10.1103/physreva.104.062423","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:10.1103/physreva.104.062423."},"month":"12","intvolume":" 104","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.06344"}],"oa_version":"Preprint","abstract":[{"text":"Classical models with complex energy landscapes represent a perspective avenue for the near-term application of quantum simulators. Until now, many theoretical works studied the performance of quantum algorithms for models with a unique ground state. However, when the classical problem is in a so-called clustering phase, the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT model defined on simple hypergraphs. The degeneracy of classical ground state manifold translates into the emergence of an extensive number of Z2 symmetries, which remain intact even in the presence of a quantum transverse magnetic field. We establish a general duality approach that restricts the quantum problem to a given sector of conserved Z2 charges and use it to study how the outcome of the quantum adiabatic algorithm depends on the hypergraph geometry. We show that the tree hypergraph which corresponds to a classically solvable instance of the 3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters a second-order phase transition with a gap vanishing as a power-law in the problem size. The duality developed in this work provides a practical tool for studies of quantum models with classically degenerate energy manifold and reveals potential connections between glasses and gauge theories.","lang":"eng"}],"issue":"6","volume":104,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"10545","department":[{"_id":"MaSe"}],"date_updated":"2023-08-17T06:22:49Z"},{"acknowledgement":"Oded Naor is grateful to the Technion Hiroshi Fujiwara Cyber-Security Research Center for providing a research grant. Part of Oded’s work was done while at Novi Research. This work was funded by the Novi team at Facebook. We also wish to thank the Novi Research team for valuable feedback, and in particular George Danezis, Alberto Sonnino, and Dahlia Malkhi.\r\n","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","day":"21","year":"2021","isi":1,"date_created":"2021-12-16T13:21:13Z","doi":"10.1145/3465084.3467905","date_published":"2021-07-21T00:00:00Z","page":"165-175","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Keidar, Idit, et al. “All You Need Is DAG.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–75, doi:10.1145/3465084.3467905.","ieee":"I. Keidar, E. Kokoris Kogias, O. Naor, and A. Spiegelman, “All You Need is DAG,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 165–175.","short":"I. Keidar, E. Kokoris Kogias, O. Naor, A. Spiegelman, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–175.","apa":"Keidar, I., Kokoris Kogias, E., Naor, O., & Spiegelman, A. (2021). All You Need is DAG. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 165–175). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467905","ama":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. All You Need is DAG. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:165-175. doi:10.1145/3465084.3467905","chicago":"Keidar, Idit, Eleftherios Kokoris Kogias, Oded Naor, and Alexander Spiegelman. “All You Need Is DAG.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 165–75. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467905.","ista":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. 2021. All You Need is DAG. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 165–175."},"title":"All You Need is DAG","external_id":{"isi":["000744439800016"],"arxiv":["2102.08325"]},"article_processing_charge":"No","author":[{"first_name":"Idit","full_name":"Keidar, Idit","last_name":"Keidar"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Naor","full_name":"Naor, Oded","first_name":"Oded"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all values proposed by correct processes eventually get delivered. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication."}],"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08325"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"_id":"10554","status":"public","conference":{"end_date":"2021-07-30","location":"Virtual, Italy","start_date":"2021-07-26","name":"PODC: Principles of Distributed Computing"},"type":"conference","date_updated":"2023-08-17T06:24:44Z","department":[{"_id":"ElKo"}]},{"citation":{"apa":"Goehlich, H., Sartoris, L., Wagner, K.-S., Wendling, C. C., & Roth, O. (2021). Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. Frontiers Media. https://doi.org/10.3389/fevo.2021.626442","ama":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 2021;9. doi:10.3389/fevo.2021.626442","ieee":"H. Goehlich, L. Sartoris, K.-S. Wagner, C. C. Wendling, and O. Roth, “Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels,” Frontiers in Ecology and Evolution, vol. 9. Frontiers Media, 2021.","short":"H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers in Ecology and Evolution 9 (2021).","mla":"Goehlich, Henry, et al. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution, vol. 9, 626442, Frontiers Media, 2021, doi:10.3389/fevo.2021.626442.","ista":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. 2021. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 9, 626442.","chicago":"Goehlich, Henry, Linda Sartoris, Kim-Sara Wagner, Carolin C. Wendling, and Olivia Roth. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution. Frontiers Media, 2021. https://doi.org/10.3389/fevo.2021.626442."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Henry","last_name":"Goehlich","full_name":"Goehlich, Henry"},{"id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","first_name":"Linda","full_name":"Sartoris, Linda","last_name":"Sartoris"},{"full_name":"Wagner, Kim-Sara","last_name":"Wagner","first_name":"Kim-Sara"},{"first_name":"Carolin C.","last_name":"Wendling","full_name":"Wendling, Carolin C."},{"full_name":"Roth, Olivia","last_name":"Roth","first_name":"Olivia"}],"article_processing_charge":"No","external_id":{"isi":["000637736300001"]},"title":"Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels","article_number":"626442","has_accepted_license":"1","isi":1,"year":"2021","day":"25","publication":"Frontiers in Ecology and Evolution","doi":"10.3389/fevo.2021.626442","date_published":"2021-03-25T00:00:00Z","date_created":"2021-12-20T07:53:19Z","acknowledgement":"We are grateful for the help of Kristina Dauven, Andreas Ebner, Janina Röckner, and Paulina Urban for fish collection in the field and fish maintenance. Furthermore, we thank Fabian Wendt for setting up the aquaria system and Tatjana Liese, Paulina Urban, Jakob Gismann, and Thorsten Reusch for support with DNA extraction and analysis of pipefish population structure. The authors acknowledge support of Isabel Tanger, Agnes Piecyk, Jonas Müller, Grace Walls, Sebastian Albrecht, Julia Böge, and Julia Stefanschitz for their support in preparing cDNA and running of Fluidigm chips. A special thank goes to Diana Gill for general lab support, ordering materials and just being the good spirit of our molecular lab, to Till Bayer for bioinformatics support and to Melanie Heckwolf for fruitful discussion and feedback on the manuscript. HG is very grateful for inspirational office space with ocean view provided by Lisa Hentschel and family. This manuscript has been released as a pre-print at BIORXIV.","publisher":"Frontiers Media","quality_controlled":"1","oa":1,"date_updated":"2023-08-17T06:27:22Z","ddc":["597"],"department":[{"_id":"SyCr"}],"file_date_updated":"2021-12-20T10:44:20Z","_id":"10568","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["ecology","evolution","behavior and systematics","trans-generational plasticity","genetic adaptation","local adaptation","phenotypic plasticity","Baltic Sea","climate change","salinity","syngnathids"],"publication_identifier":{"issn":["2296-701X"]},"publication_status":"published","file":[{"success":1,"checksum":"8d6e2b767bb0240a9b5a3a3555be51fd","file_id":"10572","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_Frontiers_Goehlich.pdf","date_created":"2021-12-20T10:44:20Z","creator":"alisjak","file_size":3175085,"date_updated":"2021-12-20T10:44:20Z"}],"language":[{"iso":"eng"}],"volume":9,"abstract":[{"text":"Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 9"},{"doi":"10.3390/cryst11121509","date_published":"2021-12-03T00:00:00Z","date_created":"2022-01-02T23:01:34Z","has_accepted_license":"1","isi":1,"year":"2021","day":"03","publication":"Crystals","quality_controlled":"1","publisher":"MDPI","oa":1,"acknowledgement":"The authors extend their appreciation to King Saud University for funding this work through Researchers Supporting Project number (RSP-2021/387), King Saud University, Riyadh, Saudi Arabia.","author":[{"last_name":"Lu","full_name":"Lu, Yuzheng","first_name":"Yuzheng"},{"first_name":"Naila","last_name":"Arshad","full_name":"Arshad, Naila"},{"first_name":"Muhammad Sultan","last_name":"Irshad","full_name":"Irshad, Muhammad Sultan"},{"first_name":"Iftikhar","full_name":"Ahmed, Iftikhar","last_name":"Ahmed"},{"first_name":"Shafiq","full_name":"Ahmad, Shafiq","last_name":"Ahmad"},{"first_name":"Lina Abdullah","last_name":"Alshahrani","full_name":"Alshahrani, Lina Abdullah"},{"first_name":"Muhammad","full_name":"Yousaf, Muhammad","last_name":"Yousaf"},{"full_name":"Sayed, Abdelaty Edrees","last_name":"Sayed","first_name":"Abdelaty Edrees"},{"orcid":"0000-0002-2111-4846","full_name":"Nauman, Muhammad","last_name":"Nauman","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad"}],"external_id":{"isi":["000736602200001"]},"article_processing_charge":"No","title":"Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination","citation":{"mla":"Lu, Yuzheng, et al. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” Crystals, vol. 11, no. 12, 1509, MDPI, 2021, doi:10.3390/cryst11121509.","ama":"Lu Y, Arshad N, Irshad MS, et al. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. 2021;11(12). doi:10.3390/cryst11121509","apa":"Lu, Y., Arshad, N., Irshad, M. S., Ahmed, I., Ahmad, S., Alshahrani, L. A., … Nauman, M. (2021). Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. MDPI. https://doi.org/10.3390/cryst11121509","ieee":"Y. Lu et al., “Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination,” Crystals, vol. 11, no. 12. MDPI, 2021.","short":"Y. Lu, N. Arshad, M.S. Irshad, I. Ahmed, S. Ahmad, L.A. Alshahrani, M. Yousaf, A.E. Sayed, M. Nauman, Crystals 11 (2021).","chicago":"Lu, Yuzheng, Naila Arshad, Muhammad Sultan Irshad, Iftikhar Ahmed, Shafiq Ahmad, Lina Abdullah Alshahrani, Muhammad Yousaf, Abdelaty Edrees Sayed, and Muhammad Nauman. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” Crystals. MDPI, 2021. https://doi.org/10.3390/cryst11121509.","ista":"Lu Y, Arshad N, Irshad MS, Ahmed I, Ahmad S, Alshahrani LA, Yousaf M, Sayed AE, Nauman M. 2021. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. 11(12), 1509."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1509","issue":"12","volume":11,"publication_identifier":{"eissn":["2073-4352"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10591","checksum":"668e9d777608ce0a3bc2e305133bd06b","success":1,"creator":"alisjak","date_updated":"2022-01-03T09:46:53Z","file_size":4569639,"date_created":"2022-01-03T09:46:53Z","file_name":"2021_Crystals_Yuzheng.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["Hybrid and Composite Crystalline Materials"],"month":"12","intvolume":" 11","abstract":[{"lang":"eng","text":"A facile approach for developing an interfacial solar evaporator by heat localization of solar-thermal energy conversion at water-air liquid composed by in-situ polymerization of Fe2O3 nanoparticles (Fe2O3@PPy) deposited over a facial sponge is proposed. The demonstrated system consists of a floating solar receiver having a vertically cross-linked microchannel for wicking up saline water. The in situ polymerized Fe2O3@PPy interfacial layer promotes diffuse reflection and its rough black surface allows Omni-directional solar absorption (94%) and facilitates efficient thermal localization at the water/air interface and offers a defect-rich surface to promote heat localization (41.9 °C) and excellent thermal management due to cellulosic content. The self-floating composite foam reveals continuous vapors generation at a rate of 1.52 kg m−2 h−1 under one 1 kW m−2 and profound evaporating efficiency (95%) without heat losses that dissipates in its surroundings. Indeed, long-term evaporation experiments reveal the negligible disparity in continuous evaporation rate (33.84 kg m−2/8.3 h) receiving two sun solar intensity, and ensures the stability of the device under intense seawater conditions synchronized with excellent salt rejection potential. More importantly, Raman spectroscopy investigation validates the orange dye rejection via Fe2O3@PPy solar evaporator. The combined advantages of high efficiency, self-floating capability, multimedia rejection, low cost, and this configuration are promising for producing large-scale solar steam generating systems appropriate for commercial clean water yield due to their scalable fabrication."}],"oa_version":"Published Version","file_date_updated":"2022-01-03T09:46:53Z","department":[{"_id":"KiMo"}],"date_updated":"2023-08-17T06:31:20Z","ddc":["620"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10586"},{"date_updated":"2023-08-17T06:26:15Z","ddc":["573"],"file_date_updated":"2021-12-20T10:14:14Z","department":[{"_id":"SyCr"}],"_id":"10569","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1477-9145"],"issn":["0022-0949"]},"publication_status":"published","file":[{"date_created":"2021-12-20T10:14:14Z","file_name":"2021_JExpBio_Szabo.pdf","date_updated":"2021-12-20T10:14:14Z","file_size":607096,"creator":"cchlebak","file_id":"10571","checksum":"75d13a5ec8e3b90e3bc02bd8a9c17eef","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"24","volume":224,"abstract":[{"text":"For animals to survive until reproduction, it is crucial that juveniles successfully detect potential predators and respond with appropriate behavior. The recognition of cues originating from predators can be innate or learned. Cues of various modalities might be used alone or in multi-modal combinations to detect and distinguish predators but studies investigating multi-modal integration in predator avoidance are scarce. Here, we used wild, naive tadpoles of the Neotropical poison frog Allobates femoralis ( Boulenger, 1884) to test their reaction to cues with two modalities from two different sympatrically occurring potential predators: heterospecific predatory Dendrobates tinctorius tadpoles and dragonfly larvae. We presented A. femoralis tadpoles with olfactory or visual cues, or a combination of the two, and compared their reaction to a water control in a between-individual design. In our trials, A. femoralis tadpoles reacted to multi-modal stimuli (a combination of visual and chemical information) originating from dragonfly larvae with avoidance but showed no reaction to uni-modal cues or cues from heterospecific tadpoles. In addition, visual cues from conspecifics increased swimming activity while cues from predators had no effect on tadpole activity. Our results show that A. femoralis tadpoles can innately recognize some predators and probably need both visual and chemical information to effectively avoid them. This is the first study looking at anti-predator behavior in poison frog tadpoles. We discuss how parental care might influence the expression of predator avoidance responses in tadpoles.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","month":"12","intvolume":" 224","citation":{"ista":"Szabo B, Mangione R, Rath M, Pašukonis A, Reber S, Oh J, Ringler M, Ringler E. 2021. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. 224(24), jeb243647.","chicago":"Szabo, B, R Mangione, M Rath, A Pašukonis, SA Reber, Jinook Oh, M Ringler, and E Ringler. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” Journal of Experimental Biology. The Company of Biologists, 2021. https://doi.org/10.1242/jeb.243647.","ama":"Szabo B, Mangione R, Rath M, et al. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. 2021;224(24). doi:10.1242/jeb.243647","apa":"Szabo, B., Mangione, R., Rath, M., Pašukonis, A., Reber, S., Oh, J., … Ringler, E. (2021). Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.243647","short":"B. Szabo, R. Mangione, M. Rath, A. Pašukonis, S. Reber, J. Oh, M. Ringler, E. Ringler, Journal of Experimental Biology 224 (2021).","ieee":"B. Szabo et al., “Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles,” Journal of Experimental Biology, vol. 224, no. 24. The Company of Biologists, 2021.","mla":"Szabo, B., et al. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” Journal of Experimental Biology, vol. 224, no. 24, jeb243647, The Company of Biologists, 2021, doi:10.1242/jeb.243647."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Szabo","full_name":"Szabo, B","first_name":"B"},{"full_name":"Mangione, R","last_name":"Mangione","first_name":"R"},{"first_name":"M","last_name":"Rath","full_name":"Rath, M"},{"first_name":"A","last_name":"Pašukonis","full_name":"Pašukonis, A"},{"last_name":"Reber","full_name":"Reber, SA","first_name":"SA"},{"last_name":"Oh","orcid":"0000-0001-7425-2372","full_name":"Oh, Jinook","first_name":"Jinook","id":"403169A4-080F-11EA-9993-BF3F3DDC885E"},{"first_name":"M","last_name":"Ringler","full_name":"Ringler, M"},{"last_name":"Ringler","full_name":"Ringler, E","first_name":"E"}],"article_processing_charge":"No","external_id":{"isi":["000738259300013"],"pmid":["34845497"]},"title":"Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles","article_number":"jeb243647","isi":1,"has_accepted_license":"1","year":"2021","day":"16","publication":"Journal of Experimental Biology","date_published":"2021-12-16T00:00:00Z","doi":"10.1242/jeb.243647","date_created":"2021-12-20T07:54:22Z","acknowledgement":"We are grateful to Véronique Helfer, Walter Hödl, Lisa Schretzmeyer and Julia Wotke, who assisted with fieldwork in French Guiana. This work was supported by the Austrian Science Fund (FWF) [P24788, T699 and P31518 to E.R.; P33728 to M.R.; J3827 to Thomas Bugnyar, Tecumseh Fitch and Ludwig Huber]; and by the Austrian Bundesministerium für Wissenschaft, Forschung und Wirtschaft [IS761001 to J.O. (Tecumseh Fitch, Thomas Bugnyar and Ludwig Huber)]. A.P. was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 835530. S.A.R. was supported by the HT faculty, Lund University. We thank the CNRS Nouragues Ecological Research Station, which benefited from the ‘Investissement d'Avenir’ grants managed by the Agence Nationale de la Recherche (AnaEE France ANR-11-INBS-0001; Labex CEBA ANR-10-LABX-25-01). Open access funding provided by University of Vienna. Deposited in PMC for immediate release.","publisher":"The Company of Biologists","quality_controlled":"1","oa":1},{"acknowledgement":"The research of A. Abbatiello is supported by Einstein Foundation, Berlin. A. Abbatiello is also member of the Italian National Group for the Mathematical Physics (GNFM) of INdAM. M. Bulíček acknowledges the support of the project No. 20-11027X financed by Czech Science Foundation (GACR). M. Bulíček is member of the Jindřich Nečas Center for Mathematical Modelling. E. Maringová acknowledges support from Charles University Research program UNCE/SCI/023, the grant SVV-2020-260583 by the Ministry of Education, Youth and Sports, Czech Republic and from the Austrian Science Fund (FWF), grants P30000, W1245, and F65.","oa":1,"quality_controlled":"1","publisher":"World Scientific Publishing","publication":"Mathematical Models and Methods in Applied Sciences","day":"13","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-12-26T23:01:27Z","date_published":"2021-10-13T00:00:00Z","doi":"10.1142/S0218202521500470","page":"2165-2212","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"A. Abbatiello, M. Bulíček, and E. Maringová, “On the dynamic slip boundary condition for Navier-Stokes-like problems,” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 11. World Scientific Publishing, pp. 2165–2212, 2021.","short":"A. Abbatiello, M. Bulíček, E. Maringová, Mathematical Models and Methods in Applied Sciences 31 (2021) 2165–2212.","ama":"Abbatiello A, Bulíček M, Maringová E. On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. 2021;31(11):2165-2212. doi:10.1142/S0218202521500470","apa":"Abbatiello, A., Bulíček, M., & Maringová, E. (2021). On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. World Scientific Publishing. https://doi.org/10.1142/S0218202521500470","mla":"Abbatiello, Anna, et al. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 11, World Scientific Publishing, 2021, pp. 2165–212, doi:10.1142/S0218202521500470.","ista":"Abbatiello A, Bulíček M, Maringová E. 2021. On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. 31(11), 2165–2212.","chicago":"Abbatiello, Anna, Miroslav Bulíček, and Erika Maringová. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” Mathematical Models and Methods in Applied Sciences. World Scientific Publishing, 2021. https://doi.org/10.1142/S0218202521500470."},"title":"On the dynamic slip boundary condition for Navier-Stokes-like problems","external_id":{"isi":["000722309400001"],"arxiv":["2009.09057"]},"article_processing_charge":"No","author":[{"last_name":"Abbatiello","full_name":"Abbatiello, Anna","first_name":"Anna"},{"last_name":"Bulíček","full_name":"Bulíček, Miroslav","first_name":"Miroslav"},{"first_name":"Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","last_name":"Maringová","full_name":"Maringová, Erika"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The choice of the boundary conditions in mechanical problems has to reflect the interaction of the considered material with the surface. Still the assumption of the no-slip condition is preferred in order to avoid boundary terms in the analysis and slipping effects are usually overlooked. Besides the “static slip models”, there are phenomena that are not accurately described by them, e.g. at the moment when the slip changes rapidly, the wall shear stress and the slip can exhibit a sudden overshoot and subsequent relaxation. When these effects become significant, the so-called dynamic slip phenomenon occurs. We develop a mathematical analysis of Navier–Stokes-like problems with a dynamic slip boundary condition, which requires a proper generalization of the Gelfand triplet and the corresponding function space setting."}],"intvolume":" 31","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"8c0a9396335f0b70e1f5cbfe450a987a","file_id":"11385","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-05-16T10:55:45Z","file_name":"2021_MathModelsMethods_Abbatiello.pdf","creator":"dernst","date_updated":"2022-05-16T10:55:45Z","file_size":795483}],"publication_status":"published","publication_identifier":{"issn":["0218-2025"],"eissn":["1793-6314"]},"issue":"11","volume":31,"_id":"10575","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-08-17T06:29:01Z","file_date_updated":"2022-05-16T10:55:45Z","department":[{"_id":"JuFi"}]},{"author":[{"full_name":"Chen, Bin","last_name":"Chen","first_name":"Bin"},{"first_name":"Chao","full_name":"Wang, Chao","last_name":"Wang"},{"full_name":"Piovarci, Michael","orcid":"0000-0002-5062-4474","last_name":"Piovarci","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael"},{"first_name":"Hans Peter","full_name":"Seidel, Hans Peter","last_name":"Seidel"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"first_name":"Karol","full_name":"Myszkowski, Karol","last_name":"Myszkowski"},{"full_name":"Serrano, Ana","last_name":"Serrano","first_name":"Ana"}],"article_processing_charge":"Yes","external_id":{"isi":["000673536600003"]},"title":"The effect of geometry and illumination on appearance perception of different material categories","citation":{"ista":"Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K, Serrano A. 2021. The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. 37(12), 2975–2987.","chicago":"Chen, Bin, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, and Ana Serrano. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” Visual Computer. Springer Nature, 2021. https://doi.org/10.1007/s00371-021-02227-x.","apa":"Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., Myszkowski, K., & Serrano, A. (2021). The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. Springer Nature. https://doi.org/10.1007/s00371-021-02227-x","ama":"Chen B, Wang C, Piovarci M, et al. The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. 2021;37(12):2975-2987. doi:10.1007/s00371-021-02227-x","short":"B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, Visual Computer 37 (2021) 2975–2987.","ieee":"B. Chen et al., “The effect of geometry and illumination on appearance perception of different material categories,” Visual Computer, vol. 37, no. 12. Springer Nature, pp. 2975–2987, 2021.","mla":"Chen, Bin, et al. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” Visual Computer, vol. 37, no. 12, Springer Nature, 2021, pp. 2975–87, doi:10.1007/s00371-021-02227-x."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"2975-2987","doi":"10.1007/s00371-021-02227-x","date_published":"2021-12-01T00:00:00Z","date_created":"2021-12-26T23:01:26Z","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Visual Computer","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie, grant agreement N∘ 765911 (RealVision) and from the European Research Council (ERC), grant agreement N∘ 804226 (PERDY). Open Access funding enabled and organized by Projekt DEAL.","department":[{"_id":"BeBi"}],"file_date_updated":"2021-12-27T13:51:08Z","date_updated":"2023-08-17T06:29:34Z","ddc":["000"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10574","volume":37,"issue":"12","publication_identifier":{"eissn":["1432-2315"],"issn":["0178-2789"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10578","checksum":"244cfcac0479ca6e3444c098ab2860a1","file_size":5741094,"date_updated":"2021-12-27T13:51:08Z","creator":"cchlebak","file_name":"2021_VisComput_Chen.pdf","date_created":"2021-12-27T13:51:08Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 37","abstract":[{"text":"The understanding of material appearance perception is a complex problem due to interactions between material reflectance, surface geometry, and illumination. Recently, Serrano et al. collected the largest dataset to date with subjective ratings of material appearance attributes, including glossiness, metallicness, sharpness and contrast of reflections. In this work, we make use of their dataset to investigate for the first time the impact of the interactions between illumination, geometry, and eight different material categories in perceived appearance attributes. After an initial analysis, we select for further analysis the four material categories that cover the largest range for all perceptual attributes: fabric, plastic, ceramic, and metal. Using a cumulative link mixed model (CLMM) for robust regression, we discover interactions between these material categories and four representative illuminations and object geometries. We believe that our findings contribute to expanding the knowledge on material appearance perception and can be useful for many applications, such as scene design, where any particular material in a given shape can be aligned with dominant classes of illumination, so that a desired strength of appearance attributes can be achieved.","lang":"eng"}],"oa_version":"Published Version"},{"department":[{"_id":"EdHa"}],"date_updated":"2023-08-17T06:28:25Z","status":"public","article_type":"original","type":"journal_article","_id":"10573","volume":184,"issue":"26","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"intvolume":" 184","month":"12","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of actomyosin and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering."}],"title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","external_id":{"isi":["000735387500002"]},"article_processing_charge":"No","author":[{"last_name":"Munjal","full_name":"Munjal, Akankshi","first_name":"Akankshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Tsai, Tony Y.C.","last_name":"Tsai","first_name":"Tony Y.C."},{"first_name":"Timothy J.","full_name":"Mitchison, Timothy J.","last_name":"Mitchison"},{"last_name":"Megason","full_name":"Megason, Sean G.","first_name":"Sean G."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.cell.2021.11.025.","ista":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 184(26), 6313–6325.e18.","mla":"Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell, vol. 184, no. 26, Elsevier ; Cell Press, 2021, p. 6313–6325.e18, doi:10.1016/j.cell.2021.11.025.","ieee":"A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” Cell, vol. 184, no. 26. Elsevier ; Cell Press, p. 6313–6325.e18, 2021.","short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18.","apa":"Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., & Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. Elsevier ; Cell Press. https://doi.org/10.1016/j.cell.2021.11.025","ama":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 2021;184(26):6313-6325.e18. doi:10.1016/j.cell.2021.11.025"},"date_created":"2021-12-26T23:01:26Z","date_published":"2021-12-22T00:00:00Z","doi":"10.1016/j.cell.2021.11.025","page":"6313-6325.e18","publication":"Cell","day":"22","year":"2021","isi":1,"oa":1,"publisher":"Elsevier ; Cell Press","quality_controlled":"1","acknowledgement":"We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and members of the Megason lab for useful comments on the manuscript and general feedback. We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on the right in the graphical abstract were created using BioRender. This work was supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by Human Frontiers Science Program LTF and NIH K99HD098918."},{"date_published":"2021-02-03T00:00:00Z","doi":"10.23638/LMCS-17(1:10)2021","date_created":"2022-01-25T16:32:13Z","page":"10:1-10:23","day":"03","publication":"Logical Methods in Computer Science","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"International Federation for Computational Logic","oa":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship).\r\n","title":"Determinacy in discrete-bidding infinite-duration games","author":[{"last_name":"Aghajohari","full_name":"Aghajohari, Milad","first_name":"Milad"},{"last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"article_processing_charge":"No","external_id":{"isi":["000658724600010"],"arxiv":["1905.03588"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Aghajohari, Milad, et al. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science, vol. 17, no. 1, International Federation for Computational Logic, 2021, p. 10:1-10:23, doi:10.23638/LMCS-17(1:10)2021.","ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” Logical Methods in Computer Science, vol. 17, no. 1. International Federation for Computational Logic, p. 10:1-10:23, 2021.","short":"M. Aghajohari, G. Avni, T.A. Henzinger, Logical Methods in Computer Science 17 (2021) 10:1-10:23.","apa":"Aghajohari, M., Avni, G., & Henzinger, T. A. (2021). Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. International Federation for Computational Logic. https://doi.org/10.23638/LMCS-17(1:10)2021","ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 2021;17(1):10:1-10:23. doi:10.23638/LMCS-17(1:10)2021","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science. International Federation for Computational Logic, 2021. https://doi.org/10.23638/LMCS-17(1:10)2021.","ista":"Aghajohari M, Avni G, Henzinger TA. 2021. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 17(1), 10:1-10:23."},"project":[{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"},{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"volume":17,"issue":"1","file":[{"file_id":"10690","checksum":"b35586a50ed1ca8f44767de116d18d81","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-01-26T08:04:50Z","file_name":"2021_LMCS_AGHAJOHAR.pdf","date_updated":"2022-01-26T08:04:50Z","file_size":819878,"creator":"alisjak"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1860-5974"]},"publication_status":"published","month":"02","intvolume":" 17","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets.","lang":"eng"}],"file_date_updated":"2022-01-26T08:04:50Z","department":[{"_id":"ToHe"}],"ddc":["510"],"date_updated":"2023-08-17T06:56:42Z","status":"public","keyword":["computer science","computer science and game theory","logic in computer science"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10674"},{"_id":"10609","status":"public","conference":{"start_date":"2021-12-06","end_date":"2021-12-10","location":"Virtual, Singapore","name":"ASIACRYPT: International Conference on Cryptology in Asia"},"type":"conference","date_updated":"2023-08-17T06:34:41Z","department":[{"_id":"KrPi"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study Multi-party computation (MPC) in the setting of subversion, where the adversary tampers with the machines of honest parties. Our goal is to construct actively secure MPC protocols where parties are corrupted adaptively by an adversary (as in the standard adaptive security setting), and in addition, honest parties’ machines are compromised.\r\nThe idea of reverse firewalls (RF) was introduced at EUROCRYPT’15 by Mironov and Stephens-Davidowitz as an approach to protecting protocols against corruption of honest parties’ devices. Intuitively, an RF for a party P is an external entity that sits between P and the outside world and whose scope is to sanitize P ’s incoming and outgoing messages in the face of subversion of their computer. Mironov and Stephens-Davidowitz constructed a protocol for passively-secure two-party computation. At CRYPTO’20, Chakraborty, Dziembowski and Nielsen constructed a protocol for secure computation with firewalls that improved on this result, both by extending it to multi-party computation protocol, and considering active security in the presence of static corruptions. In this paper, we initiate the study of RF for MPC in the adaptive setting. We put forward a definition for adaptively secure MPC in the reverse firewall setting, explore relationships among the security notions, and then construct reverse firewalls for MPC in this stronger setting of adaptive security. We also resolve the open question of Chakraborty, Dziembowski and Nielsen by removing the need for a trusted setup in constructing RF for MPC. Towards this end, we construct reverse firewalls for adaptively secure augmented coin tossing and adaptively secure zero-knowledge protocols and obtain a constant round adaptively secure MPC protocol in the reverse firewall setting without setup. Along the way, we propose a new multi-party adaptively secure coin tossing protocol in the plain model, that is of independent interest."}],"intvolume":" 13091","month":"12","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1262"}],"alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-030-92074-6"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-92075-3"]},"ec_funded":1,"volume":13091,"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Chakraborty, Suvradip, et al. “Reverse Firewalls for Adaptively Secure MPC without Setup.” 27th International Conference on the Theory and Application of Cryptology and Information Security, vol. 13091, Springer Nature, 2021, pp. 335–64, doi:10.1007/978-3-030-92075-3_12.","apa":"Chakraborty, S., Ganesh, C., Pancholi, M., & Sarkar, P. (2021). Reverse firewalls for adaptively secure MPC without setup. In 27th International Conference on the Theory and Application of Cryptology and Information Security (Vol. 13091, pp. 335–364). Virtual, Singapore: Springer Nature. https://doi.org/10.1007/978-3-030-92075-3_12","ama":"Chakraborty S, Ganesh C, Pancholi M, Sarkar P. Reverse firewalls for adaptively secure MPC without setup. In: 27th International Conference on the Theory and Application of Cryptology and Information Security. Vol 13091. Springer Nature; 2021:335-364. doi:10.1007/978-3-030-92075-3_12","short":"S. Chakraborty, C. Ganesh, M. Pancholi, P. Sarkar, in:, 27th International Conference on the Theory and Application of Cryptology and Information Security, Springer Nature, 2021, pp. 335–364.","ieee":"S. Chakraborty, C. Ganesh, M. Pancholi, and P. Sarkar, “Reverse firewalls for adaptively secure MPC without setup,” in 27th International Conference on the Theory and Application of Cryptology and Information Security, Virtual, Singapore, 2021, vol. 13091, pp. 335–364.","chicago":"Chakraborty, Suvradip, Chaya Ganesh, Mahak Pancholi, and Pratik Sarkar. “Reverse Firewalls for Adaptively Secure MPC without Setup.” In 27th International Conference on the Theory and Application of Cryptology and Information Security, 13091:335–64. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-92075-3_12.","ista":"Chakraborty S, Ganesh C, Pancholi M, Sarkar P. 2021. Reverse firewalls for adaptively secure MPC without setup. 27th International Conference on the Theory and Application of Cryptology and Information Security. ASIACRYPT: International Conference on Cryptology in Asia, LNCS, vol. 13091, 335–364."},"title":"Reverse firewalls for adaptively secure MPC without setup","article_processing_charge":"No","external_id":{"isi":["000927876200012"]},"author":[{"full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"first_name":"Chaya","last_name":"Ganesh","full_name":"Ganesh, Chaya"},{"last_name":"Pancholi","full_name":"Pancholi, Mahak","first_name":"Mahak"},{"full_name":"Sarkar, Pratik","last_name":"Sarkar","first_name":"Pratik"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"27th International Conference on the Theory and Application of Cryptology and Information Security","day":"01","year":"2021","isi":1,"date_created":"2022-01-09T23:01:27Z","date_published":"2021-12-01T00:00:00Z","doi":"10.1007/978-3-030-92075-3_12","page":"335-364"},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Cell division orientation is thought to result from a competition between cell geometry and polarity domains controlling the position of the mitotic spindle during mitosis. Depending on the level of cell shape anisotropy or the strength of the polarity domain, one dominates the other and determines the orientation of the spindle. Whether and how such competition is also at work to determine unequal cell division (UCD), producing daughter cells of different size, remains unclear. Here, we show that cell geometry and polarity domains cooperate, rather than compete, in positioning the cleavage plane during UCDs in early ascidian embryos. We found that the UCDs and their orientation at the ascidian third cleavage rely on the spindle tilting in an anisotropic cell shape, and cortical polarity domains exerting different effects on spindle astral microtubules. By systematically varying mitotic cell shape, we could modulate the effect of attractive and repulsive polarity domains and consequently generate predicted daughter cell size asymmetries and position. We therefore propose that the spindle position during UCD is set by the combined activities of cell geometry and polarity domains, where cell geometry modulates the effect of cortical polarity domain(s)."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"12","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10611","checksum":"759c7a873d554c48a6639e6350746ca6","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-01-10T09:40:37Z","file_name":"2021_eLife_Godard.pdf","creator":"alisjak","date_updated":"2022-01-10T09:40:37Z","file_size":7769934}],"volume":10,"_id":"10606","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-17T06:32:44Z","ddc":["570"],"file_date_updated":"2022-01-10T09:40:37Z","department":[{"_id":"CaHe"}],"acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a collaborative grant from the French Government funding agency Agence National de la Recherche to McDougall (ANR 'MorCell': ANR-17-CE 13-0028) and the Austrian Science Fund to Heisenberg (FWF: I 3601-B27).","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"eLife","day":"21","date_created":"2022-01-09T23:01:26Z","date_published":"2021-12-21T00:00:00Z","doi":"10.7554/eLife.75639","article_number":"e75639","project":[{"_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601"}],"citation":{"mla":"Godard, Benoit G., et al. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife, vol. 10, e75639, eLife Sciences Publications, 2021, doi:10.7554/eLife.75639.","short":"B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021).","ieee":"B. G. Godard, R. Dumollard, C.-P. J. Heisenberg, and A. Mcdougall, “Combined effect of cell geometry and polarity domains determines the orientation of unequal division,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 2021;10. doi:10.7554/eLife.75639","apa":"Godard, B. G., Dumollard, R., Heisenberg, C.-P. J., & Mcdougall, A. (2021). Combined effect of cell geometry and polarity domains determines the orientation of unequal division. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.75639","chicago":"Godard, Benoit G, Remi Dumollard, Carl-Philipp J Heisenberg, and Alex Mcdougall. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.75639.","ista":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. 2021. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 10, e75639."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000733610100001"]},"article_processing_charge":"No","author":[{"last_name":"Godard","full_name":"Godard, Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G"},{"first_name":"Remi","last_name":"Dumollard","full_name":"Dumollard, Remi"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"},{"full_name":"Mcdougall, Alex","last_name":"Mcdougall","first_name":"Alex"}],"title":"Combined effect of cell geometry and polarity domains determines the orientation of unequal division"},{"acknowledgement":"This study was supported by grants of the Austrian Science Fund (FWF) F4414 and W1206-08. Electron microscopy was performed at the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron Microscopy Facility.","quality_controlled":"1","publisher":"Elsevier","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Parkinsonism & Related Disorders","page":"59-65","doi":"10.1016/j.parkreldis.2021.09.007","date_published":"2021-10-01T00:00:00Z","date_created":"2022-01-09T23:01:26Z","citation":{"mla":"Venezia, Serena, et al. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders, vol. 91, Elsevier, 2021, pp. 59–65, doi:10.1016/j.parkreldis.2021.09.007.","apa":"Venezia, S., Kaufmann, W., Wenning, G. K., & Stefanova, N. (2021). Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. Elsevier. https://doi.org/10.1016/j.parkreldis.2021.09.007","ama":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 2021;91:59-65. doi:10.1016/j.parkreldis.2021.09.007","short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism & Related Disorders 91 (2021) 59–65.","ieee":"S. Venezia, W. Kaufmann, G. K. Wenning, and N. Stefanova, “Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease,” Parkinsonism & Related Disorders, vol. 91. Elsevier, pp. 59–65, 2021.","chicago":"Venezia, Serena, Walter Kaufmann, Gregor K. Wenning, and Nadia Stefanova. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders. Elsevier, 2021. https://doi.org/10.1016/j.parkreldis.2021.09.007.","ista":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. 2021. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 91, 59–65."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Venezia, Serena","last_name":"Venezia","first_name":"Serena"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Gregor K.","last_name":"Wenning","full_name":"Wenning, Gregor K."},{"full_name":"Stefanova, Nadia","last_name":"Stefanova","first_name":"Nadia"}],"article_processing_charge":"No","external_id":{"isi":["000701142900012"],"pmid":["34530328"]},"title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","abstract":[{"lang":"eng","text":"The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 91","publication_identifier":{"issn":["1353-8020"],"eissn":["1873-5126"]},"publication_status":"published","file":[{"creator":"alisjak","date_updated":"2022-01-10T13:41:40Z","file_size":6848513,"date_created":"2022-01-10T13:41:40Z","file_name":"2021_Parkinsonism_Venezia.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"360681585acb51e80d17c6b213c56b55","file_id":"10612","success":1}],"language":[{"iso":"eng"}],"volume":91,"_id":"10607","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-17T06:36:01Z","ddc":["610"],"file_date_updated":"2022-01-10T13:41:40Z","department":[{"_id":"EM-Fac"}]},{"article_number":"123042","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ieee":"A. Ghazaryan, E. M. Nica, O. Erten, and P. Ghaemi, “Shadow surface states in topological Kondo insulators,” New Journal of Physics, vol. 23, no. 12. IOP Publishing, 2021.","short":"A. Ghazaryan, E.M. Nica, O. Erten, P. Ghaemi, New Journal of Physics 23 (2021).","apa":"Ghazaryan, A., Nica, E. M., Erten, O., & Ghaemi, P. (2021). Shadow surface states in topological Kondo insulators. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac4124","ama":"Ghazaryan A, Nica EM, Erten O, Ghaemi P. Shadow surface states in topological Kondo insulators. New Journal of Physics. 2021;23(12). doi:10.1088/1367-2630/ac4124","mla":"Ghazaryan, Areg, et al. “Shadow Surface States in Topological Kondo Insulators.” New Journal of Physics, vol. 23, no. 12, 123042, IOP Publishing, 2021, doi:10.1088/1367-2630/ac4124.","ista":"Ghazaryan A, Nica EM, Erten O, Ghaemi P. 2021. Shadow surface states in topological Kondo insulators. New Journal of Physics. 23(12), 123042.","chicago":"Ghazaryan, Areg, Emilian M. Nica, Onur Erten, and Pouyan Ghaemi. “Shadow Surface States in Topological Kondo Insulators.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac4124."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"first_name":"Emilian M.","full_name":"Nica, Emilian M.","last_name":"Nica"},{"full_name":"Erten, Onur","last_name":"Erten","first_name":"Onur"},{"first_name":"Pouyan","full_name":"Ghaemi, Pouyan","last_name":"Ghaemi"}],"article_processing_charge":"No","external_id":{"arxiv":["2012.11625"],"isi":["000734063700001"]},"title":"Shadow surface states in topological Kondo insulators","acknowledgement":"PG acknowledges support from National Science Foundation Awards No. DMR-1824265 for this work. AG acknowledges support from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. EMN is supported by ASU startup grant. OE is in part supported by NSF-DMR-1904716.","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"23","publication":"New Journal of Physics","date_published":"2021-12-23T00:00:00Z","doi":"10.1088/1367-2630/ac4124","date_created":"2022-01-16T23:01:28Z","_id":"10628","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-17T06:54:54Z","ddc":["530"],"file_date_updated":"2022-01-17T10:01:58Z","department":[{"_id":"MiLe"}],"abstract":[{"text":"The surface states of 3D topological insulators in general have negligible quantum oscillations (QOs) when the chemical potential is tuned to the Dirac points. In contrast, we find that topological Kondo insulators (TKIs) can support surface states with an arbitrarily large Fermi surface (FS) when the chemical potential is pinned to the Dirac point. We illustrate that these FSs give rise to finite-frequency QOs, which can become comparable to the extremal area of the unhybridized bulk bands. We show that this occurs when the crystal symmetry is lowered from cubic to tetragonal in a minimal two-orbital model. We label such surface modes as 'shadow surface states'. Moreover, we show that the sufficient next-nearest neighbor out-of-plane hybridization leading to shadow surface states can be self-consistently stabilized for tetragonal TKIs. Consequently, shadow surface states provide an important example of high-frequency QOs beyond the context of cubic TKIs.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 23","publication_identifier":{"issn":["1367-2630"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10632","checksum":"0c3cb6816242fa8afd1cc87a5fe77821","success":1,"creator":"cchlebak","date_updated":"2022-01-17T10:01:58Z","file_size":2533102,"date_created":"2022-01-17T10:01:58Z","file_name":"2021_NewJourPhys_Ghazaryan.pdf"}],"language":[{"iso":"eng"}],"issue":"12","volume":23,"ec_funded":1},{"oa_version":"Preprint","abstract":[{"text":"We combine experimental and theoretical approaches to explore excited rotational states of molecules embedded in helium nanodroplets using CS2 and I2 as examples. Laser-induced nonadiabatic molecular alignment is employed to measure spectral lines for rotational states extending beyond those initially populated at the 0.37 K droplet temperature. We construct a simple quantum-mechanical model, based on a linear rotor coupled to a single-mode bosonic bath, to determine the rotational energy structure in its entirety. The calculated and measured spectral lines are in good agreement. We show that the effect of the surrounding superfluid on molecular rotation can be rationalized by a single quantity, the angular momentum, transferred from the molecule to the droplet.","lang":"eng"}],"month":"12","intvolume":" 104","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://128.84.4.18/abs/2107.00468"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"publication_status":"published","issue":"6","volume":104,"ec_funded":1,"_id":"10631","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-17T06:52:17Z","department":[{"_id":"MiLe"}],"acknowledgement":"I.C. acknowledges the support by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385. G.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.S acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl) and from The Villum Foundation through a Villum Investigator grant no. 25886.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"30","publication":"Physical Review A","isi":1,"year":"2021","doi":"10.1103/PhysRevA.104.L061303","date_published":"2021-12-30T00:00:00Z","date_created":"2022-01-16T23:01:29Z","article_number":"L061303","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","name":"A path-integral approach to composite impurities","grant_number":"M02641"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"I. Cherepanov, G. Bighin, C.A. Schouder, A.S. Chatterley, S.H. Albrechtsen, A.V. Muñoz, L. Christiansen, H. Stapelfeldt, M. Lemeshko, Physical Review A 104 (2021).","ieee":"I. Cherepanov et al., “Excited rotational states of molecules in a superfluid,” Physical Review A, vol. 104, no. 6. American Physical Society, 2021.","ama":"Cherepanov I, Bighin G, Schouder CA, et al. Excited rotational states of molecules in a superfluid. Physical Review A. 2021;104(6). doi:10.1103/PhysRevA.104.L061303","apa":"Cherepanov, I., Bighin, G., Schouder, C. A., Chatterley, A. S., Albrechtsen, S. H., Muñoz, A. V., … Lemeshko, M. (2021). Excited rotational states of molecules in a superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.104.L061303","mla":"Cherepanov, Igor, et al. “Excited Rotational States of Molecules in a Superfluid.” Physical Review A, vol. 104, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.104.L061303.","ista":"Cherepanov I, Bighin G, Schouder CA, Chatterley AS, Albrechtsen SH, Muñoz AV, Christiansen L, Stapelfeldt H, Lemeshko M. 2021. Excited rotational states of molecules in a superfluid. Physical Review A. 104(6), L061303.","chicago":"Cherepanov, Igor, Giacomo Bighin, Constant A. Schouder, Adam S. Chatterley, Simon H. Albrechtsen, Alberto Viñas Muñoz, Lars Christiansen, Henrik Stapelfeldt, and Mikhail Lemeshko. “Excited Rotational States of Molecules in a Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.104.L061303."},"title":"Excited rotational states of molecules in a superfluid","author":[{"last_name":"Cherepanov","full_name":"Cherepanov, Igor","first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"first_name":"Adam S.","full_name":"Chatterley, Adam S.","last_name":"Chatterley"},{"first_name":"Simon H.","full_name":"Albrechtsen, Simon H.","last_name":"Albrechtsen"},{"full_name":"Muñoz, Alberto Viñas","last_name":"Muñoz","first_name":"Alberto Viñas"},{"first_name":"Lars","last_name":"Christiansen","full_name":"Christiansen, Lars"},{"first_name":"Henrik","last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"article_processing_charge":"No","external_id":{"arxiv":["2107.00468"],"isi":["000739618300001"]}},{"year":"2021","isi":1,"publication":"2021 IEEE International Symposium on Information Theory","day":"01","page":"1082-1087","date_created":"2022-01-03T11:31:26Z","date_published":"2021-09-01T00:00:00Z","doi":"10.1109/isit45174.2021.9517887","oa":1,"publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","citation":{"ista":"Fathollahi D, Farsad N, Hashemi SA, Mondelli M. 2021. Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. 2021 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 1082–1087.","chicago":"Fathollahi, Dorsa, Nariman Farsad, Seyyed Ali Hashemi, and Marco Mondelli. “Sparse Multi-Decoder Recursive Projection Aggregation for Reed-Muller Codes.” In 2021 IEEE International Symposium on Information Theory, 1082–87. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/isit45174.2021.9517887.","ieee":"D. Fathollahi, N. Farsad, S. A. Hashemi, and M. Mondelli, “Sparse multi-decoder recursive projection aggregation for Reed-Muller codes,” in 2021 IEEE International Symposium on Information Theory, Virtual, Melbourne, Australia, 2021, pp. 1082–1087.","short":"D. Fathollahi, N. Farsad, S.A. Hashemi, M. Mondelli, in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 1082–1087.","ama":"Fathollahi D, Farsad N, Hashemi SA, Mondelli M. Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. In: 2021 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers; 2021:1082-1087. doi:10.1109/isit45174.2021.9517887","apa":"Fathollahi, D., Farsad, N., Hashemi, S. A., & Mondelli, M. (2021). Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. In 2021 IEEE International Symposium on Information Theory (pp. 1082–1087). Virtual, Melbourne, Australia: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/isit45174.2021.9517887","mla":"Fathollahi, Dorsa, et al. “Sparse Multi-Decoder Recursive Projection Aggregation for Reed-Muller Codes.” 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 1082–87, doi:10.1109/isit45174.2021.9517887."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["2011.12882"],"isi":["000701502201029"]},"author":[{"last_name":"Fathollahi","full_name":"Fathollahi, Dorsa","first_name":"Dorsa"},{"last_name":"Farsad","full_name":"Farsad, Nariman","first_name":"Nariman"},{"first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"title":"Sparse multi-decoder recursive projection aggregation for Reed-Muller codes","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-5386-8210-4"],"eisbn":["978-1-5386-8209-8"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We thank Emmanuel Abbe and Min Ye for providing us the implementation of RPA decoding. D. Fathollahi and M. Mondelli are partially supported by the 2019 Lopez-Loreta Prize. N. Farsad is supported by Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC) and Canada Foundation for Innovation (CFI), John R. Evans Leader Fund. S. A. Hashemi is supported by a Postdoctoral Fellowship from NSERC."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2011.12882","open_access":"1"}],"scopus_import":"1","month":"09","date_updated":"2023-08-17T06:32:06Z","department":[{"_id":"MaMo"}],"_id":"10597","conference":{"location":"Virtual, Melbourne, Australia","end_date":"2021-07-20","start_date":"2021-07-12","name":"ISIT: International Symposium on Information Theory"},"type":"conference","status":"public"},{"main_file_link":[{"url":"https://arxiv.org/abs/2103.08187","open_access":"1"}],"abstract":[{"text":"Adversarial training is an effective method to train deep learning models that are resilient to norm-bounded perturbations, with the cost of nominal performance drop. While adversarial training appears to enhance the robustness and safety of a deep model deployed in open-world decision-critical applications, counterintuitively, it induces undesired behaviors in robot learning settings. In this paper, we show theoretically and experimentally that neural controllers obtained via adversarial training are subjected to three types of defects, namely transient, systematic, and conditional errors. We first generalize adversarial training to a safety-domain optimization scheme allowing for more generic specifications. We then prove that such a learning process tends to cause certain error profiles. We support our theoretical results by a thorough experimental safety analysis in a robot-learning task. Our results suggest that adversarial training is not yet ready for robot learning.","lang":"eng"}],"oa_version":"None","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","related_material":{"record":[{"relation":"dissertation_contains","id":"11362","status":"public"}]},"publication_status":"published","publication_identifier":{"eisbn":["978-1-7281-9077-8"],"isbn":["978-1-7281-9078-5"],"eissn":["2577-087X"],"issn":["1050-4729"]},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"conference":{"location":"Xi'an, China","end_date":"2021-06-05","start_date":"2021-05-30","name":"ICRA: International Conference on Robotics and Automation"},"type":"conference","status":"public","_id":"10666","series_title":"ICRA","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_updated":"2023-08-17T06:58:38Z","ddc":["000"],"oa":1,"quality_controlled":"1","acknowledgement":"M.L. and T.A.H. are supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H. and D.R. are supported by Boeing and R.G. by Horizon-2020 ECSEL Project grant no. 783163 (iDev40).","page":"4140-4147","date_created":"2022-01-25T15:44:54Z","date_published":"2021-01-01T00:00:00Z","doi":"10.1109/ICRA48506.2021.9561036","year":"2021","has_accepted_license":"1","isi":1,"publication":"2021 IEEE International Conference on Robotics and Automation","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"external_id":{"isi":["000765738803040"],"arxiv":["2103.08187"]},"article_processing_charge":"No","author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"title":"Adversarial training is not ready for robot learning","citation":{"ama":"Lechner M, Hasani R, Grosu R, Rus D, Henzinger TA. Adversarial training is not ready for robot learning. In: 2021 IEEE International Conference on Robotics and Automation. ICRA. ; 2021:4140-4147. doi:10.1109/ICRA48506.2021.9561036","apa":"Lechner, M., Hasani, R., Grosu, R., Rus, D., & Henzinger, T. A. (2021). Adversarial training is not ready for robot learning. In 2021 IEEE International Conference on Robotics and Automation (pp. 4140–4147). Xi’an, China. https://doi.org/10.1109/ICRA48506.2021.9561036","ieee":"M. Lechner, R. Hasani, R. Grosu, D. Rus, and T. A. Henzinger, “Adversarial training is not ready for robot learning,” in 2021 IEEE International Conference on Robotics and Automation, Xi’an, China, 2021, pp. 4140–4147.","short":"M. Lechner, R. Hasani, R. Grosu, D. Rus, T.A. Henzinger, in:, 2021 IEEE International Conference on Robotics and Automation, 2021, pp. 4140–4147.","mla":"Lechner, Mathias, et al. “Adversarial Training Is Not Ready for Robot Learning.” 2021 IEEE International Conference on Robotics and Automation, 2021, pp. 4140–47, doi:10.1109/ICRA48506.2021.9561036.","ista":"Lechner M, Hasani R, Grosu R, Rus D, Henzinger TA. 2021. Adversarial training is not ready for robot learning. 2021 IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and AutomationICRA, 4140–4147.","chicago":"Lechner, Mathias, Ramin Hasani, Radu Grosu, Daniela Rus, and Thomas A Henzinger. “Adversarial Training Is Not Ready for Robot Learning.” In 2021 IEEE International Conference on Robotics and Automation, 4140–47. ICRA, 2021. https://doi.org/10.1109/ICRA48506.2021.9561036."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0010-437X"],"eissn":["1570-5846"]},"issue":"7","volume":157,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper, we investigate the distribution of the maximum of partial sums of families of m -periodic complex-valued functions satisfying certain conditions. We obtain precise uniform estimates for the distribution function of this maximum in a near-optimal range. Our results apply to partial sums of Kloosterman sums and other families of ℓ -adic trace functions, and are as strong as those obtained by Bober, Goldmakher, Granville and Koukoulopoulos for character sums. In particular, we improve on the recent work of the third author for Birch sums. However, unlike character sums, we are able to construct families of m -periodic complex-valued functions which satisfy our conditions, but for which the Pólya–Vinogradov inequality is sharp."}],"intvolume":" 157","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.03266"}],"date_updated":"2023-08-17T06:59:16Z","department":[{"_id":"TiBr"}],"_id":"10711","keyword":["Algebra and Number Theory"],"status":"public","type":"journal_article","article_type":"original","publication":"Compositio Mathematica","day":"28","year":"2021","isi":1,"date_created":"2022-02-01T08:10:43Z","date_published":"2021-06-28T00:00:00Z","doi":"10.1112/s0010437x21007351","page":"1610-1651","acknowledgement":"We would like to thank the anonymous referees for carefully reading the paper and for their remarks and suggestions.","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Autissier, Pascal, Dante Bonolis, and Youness Lamzouri. “The Distribution of the Maximum of Partial Sums of Kloosterman Sums and Other Trace Functions.” Compositio Mathematica. Cambridge University Press, 2021. https://doi.org/10.1112/s0010437x21007351.","ista":"Autissier P, Bonolis D, Lamzouri Y. 2021. The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. 157(7), 1610–1651.","mla":"Autissier, Pascal, et al. “The Distribution of the Maximum of Partial Sums of Kloosterman Sums and Other Trace Functions.” Compositio Mathematica, vol. 157, no. 7, Cambridge University Press, 2021, pp. 1610–51, doi:10.1112/s0010437x21007351.","short":"P. Autissier, D. Bonolis, Y. Lamzouri, Compositio Mathematica 157 (2021) 1610–1651.","ieee":"P. Autissier, D. Bonolis, and Y. Lamzouri, “The distribution of the maximum of partial sums of Kloosterman sums and other trace functions,” Compositio Mathematica, vol. 157, no. 7. Cambridge University Press, pp. 1610–1651, 2021.","apa":"Autissier, P., Bonolis, D., & Lamzouri, Y. (2021). The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/s0010437x21007351","ama":"Autissier P, Bonolis D, Lamzouri Y. The distribution of the maximum of partial sums of Kloosterman sums and other trace functions. Compositio Mathematica. 2021;157(7):1610-1651. doi:10.1112/s0010437x21007351"},"title":"The distribution of the maximum of partial sums of Kloosterman sums and other trace functions","article_processing_charge":"No","external_id":{"arxiv":["1909.03266"],"isi":["000667289300001"]},"author":[{"last_name":"Autissier","full_name":"Autissier, Pascal","first_name":"Pascal"},{"last_name":"Bonolis","full_name":"Bonolis, Dante","first_name":"Dante","id":"6A459894-5FDD-11E9-AF35-BB24E6697425"},{"last_name":"Lamzouri","full_name":"Lamzouri, Youness","first_name":"Youness"}]},{"type":"journal_article","article_type":"letter_note","keyword":["multidisciplinary"],"status":"public","_id":"10809","department":[{"_id":"MaIb"}],"date_updated":"2023-08-17T07:00:35Z","scopus_import":"1","intvolume":" 371","month":"02","abstract":[{"text":"Thermoelectric materials are engines that convert heat into an electrical current. Intuitively, the efficiency of this process depends on how many electrons (charge carriers) can move and how easily they do so, how much energy those moving electrons transport, and how easily the temperature gradient is maintained. In terms of material properties, an excellent thermoelectric material requires a high electrical conductivity σ, a high Seebeck coefficient S (a measure of the induced thermoelectric voltage as a function of temperature gradient), and a low thermal conductivity κ. The challenge is that these three properties are strongly interrelated in a conflicting manner (1). On page 722 of this issue, Roychowdhury et al. (2) have found a way to partially break these ties in silver antimony telluride (AgSbTe2) with the addition of cadmium (Cd) cations, which increase the ordering in this inherently disordered thermoelectric material.","lang":"eng"}],"oa_version":"None","pmid":1,"volume":371,"issue":"6530","publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"pmid":["33574201"],"isi":["000617551600027"]},"author":[{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"title":"Tidying up the mess","citation":{"chicago":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abg0886.","ista":"Liu Y, Ibáñez M. 2021. Tidying up the mess. Science. 371(6530), 678–679.","mla":"Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science, vol. 371, no. 6530, American Association for the Advancement of Science, 2021, pp. 678–79, doi:10.1126/science.abg0886.","ama":"Liu Y, Ibáñez M. Tidying up the mess. Science. 2021;371(6530):678-679. doi:10.1126/science.abg0886","apa":"Liu, Y., & Ibáñez, M. (2021). Tidying up the mess. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abg0886","ieee":"Y. Liu and M. Ibáñez, “Tidying up the mess,” Science, vol. 371, no. 6530. American Association for the Advancement of Science, pp. 678–679, 2021.","short":"Y. Liu, M. Ibáñez, Science 371 (2021) 678–679."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"American Association for the Advancement of Science","page":"678-679","date_created":"2022-03-03T09:51:48Z","doi":"10.1126/science.abg0886","date_published":"2021-02-12T00:00:00Z","year":"2021","isi":1,"publication":"Science","day":"12"},{"article_number":"1827","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Li M, Zhang Y, Zhang T, Zuo Y, Xiao K, Arbiol J, Llorca J, Liu Y, Cabot A. 2021. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. 11(7), 1827.","chicago":"Li, Mengyao, Yu Zhang, Ting Zhang, Yong Zuo, Ke Xiao, Jordi Arbiol, Jordi Llorca, Yu Liu, and Andreu Cabot. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” Nanomaterials. MDPI, 2021. https://doi.org/10.3390/nano11071827.","ieee":"M. Li et al., “Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping,” Nanomaterials, vol. 11, no. 7. MDPI, 2021.","short":"M. Li, Y. Zhang, T. Zhang, Y. Zuo, K. Xiao, J. Arbiol, J. Llorca, Y. Liu, A. Cabot, Nanomaterials 11 (2021).","apa":"Li, M., Zhang, Y., Zhang, T., Zuo, Y., Xiao, K., Arbiol, J., … Cabot, A. (2021). Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. MDPI. https://doi.org/10.3390/nano11071827","ama":"Li M, Zhang Y, Zhang T, et al. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. 2021;11(7). doi:10.3390/nano11071827","mla":"Li, Mengyao, et al. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” Nanomaterials, vol. 11, no. 7, 1827, MDPI, 2021, doi:10.3390/nano11071827."},"title":"Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping","article_processing_charge":"No","external_id":{"isi":["000676570000001"]},"author":[{"last_name":"Li","full_name":"Li, Mengyao","first_name":"Mengyao"},{"last_name":"Zhang","full_name":"Zhang, Yu","first_name":"Yu"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"full_name":"Zuo, Yong","last_name":"Zuo","first_name":"Yong"},{"last_name":"Xiao","full_name":"Xiao, Ke","first_name":"Ke"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"acknowledgement":"M.L., Y.Z., T.Z. and K.X. thank the China Scholarship Council for their scholarship\r\nsupport. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and\r\ninnovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. thanks the ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and G.C. 2017 SGR 128. ICN2 acknowledges funding from the Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO ENE2017-85087-C3.","oa":1,"quality_controlled":"1","publisher":"MDPI","publication":"Nanomaterials","day":"14","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2022-03-18T09:45:02Z","date_published":"2021-07-14T00:00:00Z","doi":"10.3390/nano11071827","_id":"10858","keyword":["General Materials Science","General Chemical Engineering"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["540"],"date_updated":"2023-08-17T07:08:30Z","department":[{"_id":"MaIb"}],"file_date_updated":"2022-03-18T09:53:15Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The cost-effective conversion of low-grade heat into electricity using thermoelectric devices requires developing alternative materials and material processing technologies able to reduce the currently high device manufacturing costs. In this direction, thermoelectric materials that do not rely on rare or toxic elements such as tellurium or lead need to be produced using high-throughput technologies not involving high temperatures and long processes. Bi2Se3 is an obvious possible Te-free alternative to Bi2Te3 for ambient temperature thermoelectric applications, but its performance is still low for practical applications, and additional efforts toward finding proper dopants are required. Here, we report a scalable method to produce Bi2Se3 nanosheets at low synthesis temperatures. We studied the influence of different dopants on the thermoelectric properties of this material. Among the elements tested, we demonstrated that Sn doping resulted in the best performance. Sn incorporation resulted in a significant improvement to the Bi2Se3 Seebeck coefficient and a reduction in the thermal conductivity in the direction of the hot-press axis, resulting in an overall 60% improvement in the thermoelectric figure of merit of Bi2Se3."}],"intvolume":" 11","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f28a8b5cf80f5605828359bb398463b0","file_id":"10859","success":1,"date_updated":"2022-03-18T09:53:15Z","file_size":4867547,"creator":"dernst","date_created":"2022-03-18T09:53:15Z","file_name":"2021_Nanomaterials_Li.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2079-4991"]},"ec_funded":1,"issue":"7","volume":11},{"_id":"10834","article_type":"original","type":"journal_article","status":"public","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"date_updated":"2023-08-17T07:01:14Z","department":[{"_id":"MiSi"}],"abstract":[{"lang":"eng","text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis."}],"pmid":1,"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.03.24.005835","open_access":"1"}],"month":"05","intvolume":" 31","publication_identifier":{"issn":["0960-9822"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":31,"issue":"10","citation":{"mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:10.1016/j.cub.2021.02.043.","short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8.","ieee":"S. Stahnke et al., “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” Current Biology, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.","ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 2021;31(10):2051-2064.e8. doi:10.1016/j.cub.2021.02.043","apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2021.02.043","chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.043.","ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Stahnke, Stephanie","last_name":"Stahnke","first_name":"Stephanie"},{"last_name":"Döring","full_name":"Döring, Hermann","first_name":"Hermann"},{"first_name":"Charly","full_name":"Kusch, Charly","last_name":"Kusch"},{"full_name":"de Gorter, David J.J.","last_name":"de Gorter","first_name":"David J.J."},{"first_name":"Sebastian","last_name":"Dütting","full_name":"Dütting, Sebastian"},{"last_name":"Guledani","full_name":"Guledani, Aleks","first_name":"Aleks"},{"full_name":"Pleines, Irina","last_name":"Pleines","first_name":"Irina"},{"last_name":"Schnoor","full_name":"Schnoor, Michael","first_name":"Michael"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"full_name":"Geffers, Robert","last_name":"Geffers","first_name":"Robert"},{"first_name":"Manfred","full_name":"Rohde, Manfred","last_name":"Rohde"},{"first_name":"Mathias","last_name":"Müsken","full_name":"Müsken, Mathias"},{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"last_name":"Nieswandt","full_name":"Nieswandt, Bernhard","first_name":"Bernhard"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"full_name":"Stradal, Theresia E.B.","last_name":"Stradal","first_name":"Theresia E.B."}],"article_processing_charge":"No","external_id":{"pmid":["33711252"],"isi":["000654652200002"]},"title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","publisher":"Elsevier","quality_controlled":"1","oa":1,"isi":1,"year":"2021","day":"24","publication":"Current Biology","page":"2051-2064.e8","date_published":"2021-05-24T00:00:00Z","doi":"10.1016/j.cub.2021.02.043","date_created":"2022-03-08T07:51:04Z"},{"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring in low-space MPC,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 469–479.","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.","ama":"Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space MPC. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:469–479. doi:10.1145/3465084.3467937","apa":"Czumaj, A., Davies, P., & Parter, M. (2021). Improved deterministic (Δ+1) coloring in low-space MPC. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 469–479). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467937","mla":"Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479, doi:10.1145/3465084.3467937.","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.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 469–479. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467937."},"title":"Improved deterministic (Δ+1) coloring in low-space MPC","author":[{"first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","last_name":"Davies","id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter"},{"first_name":"Merav","last_name":"Parter","full_name":"Parter, Merav"}],"article_processing_charge":"No","external_id":{"isi":["000744439800048"]},"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.","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"day":"21","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","isi":1,"year":"2021","date_published":"2021-07-21T00:00:00Z","doi":"10.1145/3465084.3467937","date_created":"2021-08-17T18:14:15Z","page":"469–479","_id":"9935","status":"public","type":"conference","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","location":"Virtual, Italy","end_date":"2021-07-30","start_date":"2021-07-26"},"date_updated":"2023-08-17T07:11:03Z","department":[{"_id":"DaAl"}],"oa_version":"Submitted Version","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."}],"month":"07","main_file_link":[{"url":"http://wrap.warwick.ac.uk/153753","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-8548-0"]},"publication_status":"published","ec_funded":1},{"keyword":["Applied Mathematics","Geometry and Topology","Analysis"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10856","file_date_updated":"2022-03-18T09:31:59Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2023-08-17T07:07:58Z","intvolume":" 9","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We study the properties of the maximal volume k-dimensional sections of the n-dimensional cube [−1, 1]n. We obtain a first order necessary condition for a k-dimensional subspace to be a local maximizer of the volume of such sections, which we formulate in a geometric way. We estimate the length of the projection of a vector of the standard basis of Rn onto a k-dimensional subspace that maximizes the volume of the intersection. We \u001cnd the optimal upper bound on the volume of a planar section of the cube [−1, 1]n , n ≥ 2.","lang":"eng"}],"issue":"1","volume":9,"language":[{"iso":"eng"}],"file":[{"date_updated":"2022-03-18T09:31:59Z","file_size":789801,"creator":"dernst","date_created":"2022-03-18T09:31:59Z","file_name":"2021_AnalysisMetricSpaces_Ivanov.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7e615ac8489f5eae580b6517debfdc53","file_id":"10857","success":1}],"publication_status":"published","publication_identifier":{"issn":["2299-3274"]},"title":"On the volume of sections of the cube","article_processing_charge":"No","external_id":{"arxiv":["2004.02674"],"isi":["000734286800001"]},"author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"},{"first_name":"Igor","last_name":"Tsiutsiurupa","full_name":"Tsiutsiurupa, Igor"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"G. Ivanov, I. Tsiutsiurupa, Analysis and Geometry in Metric Spaces 9 (2021) 1–18.","ieee":"G. Ivanov and I. Tsiutsiurupa, “On the volume of sections of the cube,” Analysis and Geometry in Metric Spaces, vol. 9, no. 1. De Gruyter, pp. 1–18, 2021.","apa":"Ivanov, G., & Tsiutsiurupa, I. (2021). On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. De Gruyter. https://doi.org/10.1515/agms-2020-0103","ama":"Ivanov G, Tsiutsiurupa I. On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. 2021;9(1):1-18. doi:10.1515/agms-2020-0103","mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” Analysis and Geometry in Metric Spaces, vol. 9, no. 1, De Gruyter, 2021, pp. 1–18, doi:10.1515/agms-2020-0103.","ista":"Ivanov G, Tsiutsiurupa I. 2021. On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. 9(1), 1–18.","chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” Analysis and Geometry in Metric Spaces. De Gruyter, 2021. https://doi.org/10.1515/agms-2020-0103."},"oa":1,"publisher":"De Gruyter","quality_controlled":"1","acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-\r\n2019-1926. G.I.was supported also by the SwissNational Science Foundation grant 200021-179133. The authors are very grateful to the anonymous reviewer for valuable remarks.","date_created":"2022-03-18T09:25:14Z","doi":"10.1515/agms-2020-0103","date_published":"2021-01-29T00:00:00Z","page":"1-18","publication":"Analysis and Geometry in Metric Spaces","day":"29","year":"2021","isi":1,"has_accepted_license":"1"},{"year":"2021","isi":1,"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","day":"21","page":"481–491","date_created":"2021-08-17T18:11:16Z","date_published":"2021-07-21T00:00:00Z","doi":"10.1145/3465084.3467903","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.","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","citation":{"mla":"Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel Computation.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491, doi:10.1145/3465084.3467903.","ama":"Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel computation. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:481–491. doi:10.1145/3465084.3467903","apa":"Czumaj, A., Davies, P., & Parter, M. (2021). Component stability in low-space massively parallel computation. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 481–491). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467903","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.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively parallel computation,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 481–491.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in Low-Space Massively Parallel Computation.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 481–491. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467903.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2106.01880"],"isi":["000744439800049"]},"article_processing_charge":"No","author":[{"first_name":"Artur","full_name":"Czumaj, Artur","last_name":"Czumaj"},{"first_name":"Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter"},{"full_name":"Parter, Merav","last_name":"Parter","first_name":"Merav"}],"title":"Component stability in low-space massively parallel computation","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","publication_identifier":{"isbn":["9781450385480"]},"language":[{"iso":"eng"}],"ec_funded":1,"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"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.01880"}],"month":"07","date_updated":"2023-08-17T07:11:32Z","department":[{"_id":"DaAl"}],"_id":"9933","conference":{"start_date":"2021-07-26","location":"Virtual, Italy","end_date":"2021-07-30","name":"PODC: Principles of Distributed Computing"},"type":"conference","status":"public"},{"citation":{"mla":"Lenz, Daniel, et al. “Self-Adjoint Extensions of Bipartite Hamiltonians.” Proceedings of the Edinburgh Mathematical Society, vol. 64, no. 3, Cambridge University Press, 2021, pp. 443–47, doi:10.1017/S0013091521000080.","ama":"Lenz D, Weinmann T, Wirth M. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 2021;64(3):443-447. doi:10.1017/S0013091521000080","apa":"Lenz, D., Weinmann, T., & Wirth, M. (2021). Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. Cambridge University Press. https://doi.org/10.1017/S0013091521000080","ieee":"D. Lenz, T. Weinmann, and M. Wirth, “Self-adjoint extensions of bipartite Hamiltonians,” Proceedings of the Edinburgh Mathematical Society, vol. 64, no. 3. Cambridge University Press, pp. 443–447, 2021.","short":"D. Lenz, T. Weinmann, M. Wirth, Proceedings of the Edinburgh Mathematical Society 64 (2021) 443–447.","chicago":"Lenz, Daniel, Timon Weinmann, and Melchior Wirth. “Self-Adjoint Extensions of Bipartite Hamiltonians.” Proceedings of the Edinburgh Mathematical Society. Cambridge University Press, 2021. https://doi.org/10.1017/S0013091521000080.","ista":"Lenz D, Weinmann T, Wirth M. 2021. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 64(3), 443–447."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1912.03670"],"isi":["000721363700003"]},"author":[{"last_name":"Lenz","full_name":"Lenz, Daniel","first_name":"Daniel"},{"first_name":"Timon","last_name":"Weinmann","full_name":"Weinmann, Timon"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","last_name":"Wirth","full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241"}],"title":"Self-adjoint extensions of bipartite Hamiltonians","year":"2021","isi":1,"publication":"Proceedings of the Edinburgh Mathematical Society","day":"01","page":"443-447","date_created":"2021-07-04T22:01:24Z","doi":"10.1017/S0013091521000080","date_published":"2021-08-01T00:00:00Z","acknowledgement":"M. W. gratefully acknowledges financial support by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes). T.W. thanks PAO Gazprom Neft, the Euler International Mathematical Institute in Saint Petersburg and ORISA GmbH for their financial support in the form of scholarships during his Master's and Bachelor's studies respectively. The authors want to thank Mark Malamud for pointing out the reference [1] to them. This work was supported by the Ministry of Science and Higher Education of the Russian Federation, agreement No 075-15-2019-1619.","oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","date_updated":"2023-08-17T07:12:05Z","department":[{"_id":"JaMa"}],"_id":"9627","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1464-3839"],"issn":["0013-0915"]},"language":[{"iso":"eng"}],"issue":"3","volume":64,"abstract":[{"lang":"eng","text":"We compute the deficiency spaces of operators of the form 𝐻𝐴⊗̂ 𝐼+𝐼⊗̂ 𝐻𝐵, for symmetric 𝐻𝐴 and self-adjoint 𝐻𝐵. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of 𝐻𝐵 having discrete, non-degenerate spectrum."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/S0013091521000080"}],"scopus_import":"1","intvolume":" 64","month":"08"},{"page":"885-979","date_created":"2020-05-28T16:48:20Z","date_published":"2021-05-03T00:00:00Z","doi":"10.1007/s00222-021-01041-5","year":"2021","has_accepted_license":"1","isi":1,"publication":"Inventiones Mathematicae","day":"03","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"We thank Christian Hainzl for helpful discussions and a referee for very careful reading of the paper and many helpful suggestions. NB and RS were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 694227). Part of the research of NB was conducted on the RZD18 Nice–Milan–Vienna–Moscow. NB thanks Elliott H. Lieb and Peter Otte for explanations about the Luttinger model. PTN has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP acknowledges financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, grant agreement No. 802901). BS gratefully acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS (grant agreement No. 834782). All authors acknowledge support for workshop participation from Mathematisches Forschungsinstitut Oberwolfach (Leibniz Association). NB, PTN, BS, and RS acknowledge support for workshop participation from Fondation des Treilles.","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2005.08933"],"isi":["000646573600001"]},"author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P","last_name":"Benedikter"},{"last_name":"Nam","full_name":"Nam, Phan Thành","first_name":"Phan Thành"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"title":"Correlation energy of a weakly interacting Fermi gas","citation":{"chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas.” Inventiones Mathematicae. Springer, 2021. https://doi.org/10.1007/s00222-021-01041-5.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. 225, 885–979.","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas.” Inventiones Mathematicae, vol. 225, Springer, 2021, pp. 885–979, doi:10.1007/s00222-021-01041-5.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas,” Inventiones Mathematicae, vol. 225. Springer, pp. 885–979, 2021.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Inventiones Mathematicae 225 (2021) 885–979.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. 2021;225:885-979. doi:10.1007/s00222-021-01041-5","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2021). Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. Springer. https://doi.org/10.1007/s00222-021-01041-5"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"volume":225,"publication_status":"published","publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2022-05-16T12:23:40Z","file_name":"2021_InventMath_Benedikter.pdf","creator":"dernst","date_updated":"2022-05-16T12:23:40Z","file_size":1089319,"checksum":"f38c79dfd828cdc7f49a34b37b83d376","file_id":"11386","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 225","month":"05","abstract":[{"text":"We derive rigorously the leading order of the correlation energy of a Fermi gas in a scaling regime of high density and weak interaction. The result verifies the prediction of the random-phase approximation. Our proof refines the method of collective bosonization in three dimensions. We approximately diagonalize an effective Hamiltonian describing approximately bosonic collective excitations around the Hartree–Fock state, while showing that gapless and non-collective excitations have only a negligible effect on the ground state energy.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2022-05-16T12:23:40Z","department":[{"_id":"RoSe"}],"date_updated":"2023-08-21T06:30:30Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7901"},{"oa":1,"publisher":"EDP Sciences","quality_controlled":"1","year":"2021","publication":"Astronomy & Astrophysics","day":"02","date_created":"2023-08-03T10:11:09Z","date_published":"2021-12-02T00:00:00Z","doi":"10.1051/0004-6361/202140506","article_number":"A58","citation":{"chicago":"Laplace, E., S. Justham, M. Renzo, Ylva Louise Linsdotter Götberg, R. Farmer, D. Vartanyan, and S. E. de Mink. “Different to the Core: The Pre-Supernova Structures of Massive Single and Binary-Stripped Stars.” Astronomy & Astrophysics. EDP Sciences, 2021. https://doi.org/10.1051/0004-6361/202140506.","ista":"Laplace E, Justham S, Renzo M, Götberg YLL, Farmer R, Vartanyan D, de Mink SE. 2021. Different to the core: The pre-supernova structures of massive single and binary-stripped stars. Astronomy & Astrophysics. 656, A58.","mla":"Laplace, E., et al. “Different to the Core: The Pre-Supernova Structures of Massive Single and Binary-Stripped Stars.” Astronomy & Astrophysics, vol. 656, A58, EDP Sciences, 2021, doi:10.1051/0004-6361/202140506.","ama":"Laplace E, Justham S, Renzo M, et al. Different to the core: The pre-supernova structures of massive single and binary-stripped stars. Astronomy & Astrophysics. 2021;656. doi:10.1051/0004-6361/202140506","apa":"Laplace, E., Justham, S., Renzo, M., Götberg, Y. L. L., Farmer, R., Vartanyan, D., & de Mink, S. E. (2021). Different to the core: The pre-supernova structures of massive single and binary-stripped stars. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202140506","ieee":"E. Laplace et al., “Different to the core: The pre-supernova structures of massive single and binary-stripped stars,” Astronomy & Astrophysics, vol. 656. EDP Sciences, 2021.","short":"E. Laplace, S. Justham, M. Renzo, Y.L.L. Götberg, R. Farmer, D. Vartanyan, S.E. de Mink, Astronomy & Astrophysics 656 (2021)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2102.05036"]},"author":[{"full_name":"Laplace, E.","last_name":"Laplace","first_name":"E."},{"full_name":"Justham, S.","last_name":"Justham","first_name":"S."},{"last_name":"Renzo","full_name":"Renzo, M.","first_name":"M."},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg"},{"first_name":"R.","last_name":"Farmer","full_name":"Farmer, R."},{"first_name":"D.","full_name":"Vartanyan, D.","last_name":"Vartanyan"},{"first_name":"S. E.","last_name":"de Mink","full_name":"de Mink, S. E."}],"title":"Different to the core: The pre-supernova structures of massive single and binary-stripped stars","abstract":[{"text":"The majority of massive stars live in binary or multiple systems and will interact with a companion during their lifetimes, which helps to explain the observed diversity of core-collapse supernovae. Donor stars in binary systems can lose most of their hydrogen-rich envelopes through mass transfer. As a result, not only are the surface properties affected, but so is the core structure. However, most calculations of the core-collapse properties of massive stars rely on single-star models. We present a systematic study of the difference between the pre-supernova structures of single stars and stars of the same initial mass (11–21 M⊙) that have been stripped due to stable post-main-sequence mass transfer at solar metallicity. We present the pre-supernova core composition with novel diagrams that give an intuitive representation of the isotope distribution. As shown in previous studies, at the edge of the carbon-oxygen core, the binary-stripped star models contain an extended gradient of carbon, oxygen, and neon. This layer remains until core collapse and is more extended in mass for higher initial stellar masses. It originates from the receding of the convective helium core during core helium burning in binary-stripped stars, which does not occur in single-star models. We find that this same evolutionary phase leads to systematic differences in the final density and nuclear energy generation profiles. Binary-stripped star models have systematically higher total masses of carbon at the moment of core collapse compared to single-star models, which likely results in systematically different supernova yields. In about half of our models, the silicon-burning and oxygen-rich layers merge after core silicon burning. We discuss the implications of our findings for the “explodability”, supernova observations, and nucleosynthesis of these stars. Our models are publicly available and can be readily used as input for detailed supernova simulations.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/202140506"}],"scopus_import":"1","intvolume":" 656","month":"12","publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"language":[{"iso":"eng"}],"volume":656,"_id":"13455","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","date_updated":"2023-08-21T11:49:15Z"},{"month":"08","intvolume":" 31","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2009.06917","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We study systems of nonlinear partial differential equations of parabolic type, in which the elliptic operator is replaced by the first-order divergence operator acting on a flux function, which is related to the spatial gradient of the unknown through an additional implicit equation. This setting, broad enough in terms of applications, significantly expands the paradigm of nonlinear parabolic problems. Formulating four conditions concerning the form of the implicit equation, we first show that these conditions describe a maximal monotone p-coercive graph. We then establish the global-in-time and large-data existence of a (weak) solution and its uniqueness. To this end, we adopt and significantly generalize Minty’s method of monotone mappings. A unified theory, containing several novel tools, is developed in a way to be tractable from the point of view of numerical approximations.","lang":"eng"}],"issue":"09","volume":31,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0218-2025"],"eissn":["1793-6314"]},"publication_status":"published","status":"public","keyword":["Nonlinear parabolic systems","implicit constitutive theory","weak solutions","existence","uniqueness"],"article_type":"original","type":"journal_article","_id":"10005","department":[{"_id":"JuFi"}],"date_updated":"2023-09-04T11:43:45Z","publisher":"World Scientific","quality_controlled":"1","oa":1,"acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 18-12719S financed by the Czech\r\nScience foundation (GAČR). E. Maringová acknowledges support from Charles University Research program \r\nUNCE/SCI/023, the grant SVV-2020-260583 by the Ministry of Education, Youth and Sports, Czech Republic\r\nand from the Austrian Science Fund (FWF), grants P30000, W1245, and F65. M. Bulíček and J. Málek are\r\nmembers of the Nečas Center for Mathematical Modelling.\r\n","date_published":"2021-08-25T00:00:00Z","doi":"10.1142/S0218202521500457","date_created":"2021-09-12T22:01:25Z","day":"25","publication":"Mathematical Models and Methods in Applied Sciences","isi":1,"year":"2021","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"title":"On nonlinear problems of parabolic type with implicit constitutive equations involving flux","author":[{"first_name":"Miroslav","last_name":"Bulíček","full_name":"Bulíček, Miroslav"},{"last_name":"Maringová","full_name":"Maringová, Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","first_name":"Erika"},{"first_name":"Josef","full_name":"Málek, Josef","last_name":"Málek"}],"external_id":{"arxiv":["2009.06917"],"isi":["000722222900004"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bulíček, Miroslav, et al. “On Nonlinear Problems of Parabolic Type with Implicit Constitutive Equations Involving Flux.” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 09, World Scientific, 2021, doi:10.1142/S0218202521500457.","short":"M. Bulíček, E. Maringová, J. Málek, Mathematical Models and Methods in Applied Sciences 31 (2021).","ieee":"M. Bulíček, E. Maringová, and J. Málek, “On nonlinear problems of parabolic type with implicit constitutive equations involving flux,” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 09. World Scientific, 2021.","ama":"Bulíček M, Maringová E, Málek J. On nonlinear problems of parabolic type with implicit constitutive equations involving flux. Mathematical Models and Methods in Applied Sciences. 2021;31(09). doi:10.1142/S0218202521500457","apa":"Bulíček, M., Maringová, E., & Málek, J. (2021). On nonlinear problems of parabolic type with implicit constitutive equations involving flux. Mathematical Models and Methods in Applied Sciences. World Scientific. https://doi.org/10.1142/S0218202521500457","chicago":"Bulíček, Miroslav, Erika Maringová, and Josef Málek. “On Nonlinear Problems of Parabolic Type with Implicit Constitutive Equations Involving Flux.” Mathematical Models and Methods in Applied Sciences. World Scientific, 2021. https://doi.org/10.1142/S0218202521500457.","ista":"Bulíček M, Maringová E, Málek J. 2021. On nonlinear problems of parabolic type with implicit constitutive equations involving flux. Mathematical Models and Methods in Applied Sciences. 31(09)."}},{"type":"conference","conference":{"start_date":"2021-07-26","location":"Virtual, Italy","end_date":"2021-07-30","name":"PODC: Principles of Distributed Computing"},"status":"public","keyword":["optimal","state machine replication","fallback","asynchrony","byzantine faults"],"_id":"10553","department":[{"_id":"ElKo"}],"date_updated":"2023-09-04T11:42:10Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.03181"}],"month":"07","abstract":[{"lang":"eng","text":"The popularity of permissioned blockchain systems demands BFT SMR protocols that are efficient under good network conditions (synchrony) and robust under bad network conditions (asynchrony). The state-of-the-art partially synchronous BFT SMR protocols provide optimal linear communication cost per decision under synchrony and good leaders, but lose liveness under asynchrony. On the other hand, the state-of-the-art asynchronous BFT SMR protocols are live even under asynchrony, but always pay quadratic cost even under synchrony. In this paper, we propose a BFT SMR protocol that achieves the best of both worlds -- optimal linear cost per decision under good networks and leaders, optimal quadratic cost per decision under bad networks, and remains always live."}],"oa_version":"Preprint","publication_identifier":{"isbn":["9-781-4503-8548-0"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"},{"first_name":"Zhuolun","last_name":"Xiang","full_name":"Xiang, Zhuolun"}],"article_processing_charge":"No","external_id":{"arxiv":["2103.03181"],"isi":["000744439800018"]},"title":"Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol","citation":{"mla":"Gelashvili, Rati, et al. “Brief Announcement: Be Prepared When Network Goes Bad: An Asynchronous View-Change Protocol.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 187–90, doi:10.1145/3465084.3467941.","short":"R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, Z. Xiang, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 187–190.","ieee":"R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, and Z. Xiang, “Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 187–190.","apa":"Gelashvili, R., Kokoris Kogias, E., Spiegelman, A., & Xiang, Z. (2021). Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 187–190). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467941","ama":"Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:187-190. doi:10.1145/3465084.3467941","chicago":"Gelashvili, Rati, Eleftherios Kokoris Kogias, Alexander Spiegelman, and Zhuolun Xiang. “Brief Announcement: Be Prepared When Network Goes Bad: An Asynchronous View-Change Protocol.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 187–90. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467941.","ista":"Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. 2021. Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 187–190."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"page":"187-190","date_published":"2021-07-21T00:00:00Z","doi":"10.1145/3465084.3467941","date_created":"2021-12-16T13:20:19Z","isi":1,"year":"2021","day":"21","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.126.040602.","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602.","mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” Physical Review Letters, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:10.1103/physrevlett.126.040602.","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 2021;126(4). doi:10.1103/physrevlett.126.040602","apa":"De Nicola, S., Michailidis, A., & Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.126.040602","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” Physical Review Letters, vol. 126, no. 4. American Physical Society, 2021."},"title":"Entanglement view of dynamical quantum phase transitions","author":[{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","last_name":"De Nicola"},{"orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"article_processing_charge":"Yes","external_id":{"isi":["000613148200001"],"arxiv":["2008.04894"]},"article_number":"040602","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"day":"29","publication":"Physical Review Letters","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1103/physrevlett.126.040602","date_published":"2021-01-29T00:00:00Z","date_created":"2021-02-01T09:20:00Z","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"ddc":["530"],"date_updated":"2023-09-05T12:08:58Z","department":[{"_id":"MaSe"}],"file_date_updated":"2021-02-03T12:47:04Z","_id":"9048","status":"public","keyword":["General Physics and Astronomy"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"2021_PhysicalRevLett_DeNicola.pdf","date_created":"2021-02-03T12:47:04Z","file_size":398075,"date_updated":"2021-02-03T12:47:04Z","creator":"dernst","success":1,"file_id":"9074","checksum":"d9acbc502390ed7a97e631d23ae19ecd","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","volume":126,"issue":"4","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology."}],"month":"01","intvolume":" 126"},{"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9368","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T12:20:27Z","main_file_link":[{"url":"https://doi.org/10.1093/plphys/kiab199","open_access":"1"}],"month":"04","intvolume":" 186","abstract":[{"lang":"eng","text":"The quality control system for messenger RNA (mRNA) is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic growth and development, we employed a forward genetic approach to screen for suppressors of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1 (HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein that is responsible for ribosomal rescue and thereby assures the quality and fidelity of mRNA molecules during translation. Genetic analysis further revealed that a dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts, which were truncated but functional, and thus rescued the growth and developmental defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing insights into the mechanism of mRNA quality control."}],"pmid":1,"oa_version":"Published Version","issue":"4","volume":186,"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"author":[{"full_name":"Kong, W","last_name":"Kong","first_name":"W"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Q","full_name":"Zhao, Q","last_name":"Zhao"},{"full_name":"Lin, DL","last_name":"Lin","first_name":"DL"},{"full_name":"Xu, ZH","last_name":"Xu","first_name":"ZH"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"HW","full_name":"Xue, HW","last_name":"Xue"}],"external_id":{"pmid":["33930167"],"isi":["000703922000025"]},"article_processing_charge":"No","title":"mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth","citation":{"ista":"Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 186(4), 2003–2020.","chicago":"Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plphys/kiab199.","ama":"Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 2021;186(4):2003-2020. doi:10.1093/plphys/kiab199","apa":"Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., & Xue, H. (2021). mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiab199","short":"W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology 186 (2021) 2003–2020.","ieee":"W. Kong et al., “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth,” Plant Physiology, vol. 186, no. 4. American Society of Plant Biologists, pp. 2003–2020, 2021.","mla":"Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology, vol. 186, no. 4, American Society of Plant Biologists, 2021, pp. 2003–20, doi:10.1093/plphys/kiab199."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"American Society of Plant Biologists","oa":1,"acknowledgement":"We gratefully acknowledge the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria) and Hana Semeradova (IST Austria) for helpful discussions. The study was supported by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W. X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25 (to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015).","page":"2003-2020","doi":"10.1093/plphys/kiab199","date_published":"2021-04-30T00:00:00Z","date_created":"2021-05-03T13:28:20Z","isi":1,"year":"2021","day":"30","publication":"Plant Physiology"},{"oa":1,"quality_controlled":"1","publisher":"Canadian Mathematical Society","acknowledgement":"The author was supported by the Swiss National Science Foundation grant 200021_179133. The author acknowledges the financial support from the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no. 075-15-2019-1926.","page":"942-963","date_created":"2022-03-18T09:55:59Z","date_published":"2021-12-18T00:00:00Z","doi":"10.4153/s000843952000096x","year":"2021","isi":1,"publication":"Canadian Mathematical Bulletin","day":"18","external_id":{"isi":["000730165300021"],"arxiv":["1804.10055"]},"article_processing_charge":"No","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","full_name":"Ivanov, Grigory","last_name":"Ivanov"}],"title":"Tight frames and related geometric problems","citation":{"chicago":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” Canadian Mathematical Bulletin. Canadian Mathematical Society, 2021. https://doi.org/10.4153/s000843952000096x.","ista":"Ivanov G. 2021. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 64(4), 942–963.","mla":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” Canadian Mathematical Bulletin, vol. 64, no. 4, Canadian Mathematical Society, 2021, pp. 942–63, doi:10.4153/s000843952000096x.","apa":"Ivanov, G. (2021). Tight frames and related geometric problems. Canadian Mathematical Bulletin. Canadian Mathematical Society. https://doi.org/10.4153/s000843952000096x","ama":"Ivanov G. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 2021;64(4):942-963. doi:10.4153/s000843952000096x","ieee":"G. Ivanov, “Tight frames and related geometric problems,” Canadian Mathematical Bulletin, vol. 64, no. 4. Canadian Mathematical Society, pp. 942–963, 2021.","short":"G. Ivanov, Canadian Mathematical Bulletin 64 (2021) 942–963."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/1804.10055","open_access":"1"}],"scopus_import":"1","intvolume":" 64","month":"12","abstract":[{"text":"A tight frame is the orthogonal projection of some orthonormal basis of Rn onto Rk. We show that a set of vectors is a tight frame if and only if the set of all cross products of these vectors is a tight frame. We reformulate a range of problems on the volume of projections (or sections) of regular polytopes in terms of tight frames and write a first-order necessary condition for local extrema of these problems. As applications, we prove new results for the problem of maximization of the volume of zonotopes.","lang":"eng"}],"oa_version":"Preprint","issue":"4","volume":64,"publication_status":"published","publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["General Mathematics","Tight frame","Grassmannian","zonotope"],"status":"public","_id":"10860","department":[{"_id":"UlWa"}],"date_updated":"2023-09-05T12:43:09Z"},{"_id":"9290","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-05T13:03:34Z","ddc":["580"],"file_date_updated":"2021-04-01T10:53:42Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Polar subcellular localization of the PIN exporters of the phytohormone auxin is a key determinant of directional, intercellular auxin transport and thus a central topic of both plant cell and developmental biology. Arabidopsis mutants lacking PID, a kinase that phosphorylates PINs, or the MAB4/MEL proteins of unknown molecular function display PIN polarity defects and phenocopy pin mutants, but mechanistic insights into how these factors convey PIN polarity are missing. Here, by combining protein biochemistry with quantitative live-cell imaging, we demonstrate that PINs, MAB4/MELs, and AGC kinases interact in the same complex at the plasma membrane. MAB4/MELs are recruited to the plasma membrane by the PINs and in concert with the AGC kinases maintain PIN polarity through limiting lateral diffusion-based escape of PINs from the polar domain. The PIN-MAB4/MEL-PID protein complex has self-reinforcing properties thanks to positive feedback between AGC kinase-mediated PIN phosphorylation and MAB4/MEL recruitment. We thus uncover the molecular mechanism by which AGC kinases and MAB4/MEL proteins regulate PIN localization and plant development.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"oa_version":"Published Version","intvolume":" 31","month":"03","publication_status":"published","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-04-01T10:53:42Z","file_size":4324371,"creator":"dernst","date_created":"2021-04-01T10:53:42Z","file_name":"2021_CurrentBiology_Glanc.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9303","checksum":"b1723040ecfd8c81194185472eb62546","success":1}],"ec_funded":1,"issue":"9","volume":31,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"citation":{"ista":"Glanc M, Van Gelderen K, Hörmayer L, Tan S, Naramoto S, Zhang X, Domjan D, Vcelarova L, Hauschild R, Johnson AJ, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnar G, Fendrych M, De Rybel B, Offringa R, Friml J. 2021. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 31(9), 1918–1930.","chicago":"Glanc, Matous, K Van Gelderen, Lukas Hörmayer, Shutang Tan, S Naramoto, Xixi Zhang, David Domjan, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.028.","apa":"Glanc, M., Van Gelderen, K., Hörmayer, L., Tan, S., Naramoto, S., Zhang, X., … Friml, J. (2021). AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2021.02.028","ama":"Glanc M, Van Gelderen K, Hörmayer L, et al. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 2021;31(9):1918-1930. doi:10.1016/j.cub.2021.02.028","short":"M. Glanc, K. Van Gelderen, L. Hörmayer, S. Tan, S. Naramoto, X. Zhang, D. Domjan, L. Vcelarova, R. Hauschild, A.J. Johnson, E. de Koning, M. van Dop, E. Rademacher, S. Janson, X. Wei, G. Molnar, M. Fendrych, B. De Rybel, R. Offringa, J. Friml, Current Biology 31 (2021) 1918–1930.","ieee":"M. Glanc et al., “AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells,” Current Biology, vol. 31, no. 9. Elsevier, pp. 1918–1930, 2021.","mla":"Glanc, Matous, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology, vol. 31, no. 9, Elsevier, 2021, pp. 1918–30, doi:10.1016/j.cub.2021.02.028."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000653077800004"],"pmid":["33705718"]},"author":[{"last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"Van Gelderen, K","last_name":"Van Gelderen","first_name":"K"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"S","full_name":"Naramoto, S","last_name":"Naramoto"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"first_name":"David","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","last_name":"Domjan","orcid":"0000-0003-2267-106X","full_name":"Domjan, David"},{"last_name":"Vcelarova","full_name":"Vcelarova, L","first_name":"L"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"first_name":"E","last_name":"de Koning","full_name":"de Koning, E"},{"first_name":"M","last_name":"van Dop","full_name":"van Dop, M"},{"first_name":"E","last_name":"Rademacher","full_name":"Rademacher, E"},{"first_name":"S","last_name":"Janson","full_name":"Janson, S"},{"full_name":"Wei, X","last_name":"Wei","first_name":"X"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"first_name":"B","full_name":"De Rybel, B","last_name":"De Rybel"},{"first_name":"R","full_name":"Offringa, R","last_name":"Offringa"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells","acknowledgement":"We acknowledge Ben Scheres, Christian Luschnig, and Claus Schwechheimer for sharing published material. We thank Monika Hrtyan and Dorota Jaworska at IST Austria and Gerda Lamers and Ward de Winter at IBL Netherlands for technical assistance; Corinna Hartinger, Jakub Hajný, Lesia Rodriguez, Mingyue Li, and Lindy Abas for experimental support; and the Bioimaging Facility at IST Austria and the Bioimaging Core at VIB for imaging support. We are grateful to Christian Luschnig, Lindy Abas, and Roman Pleskot for valuable discussions. We also acknowledge the EMBO for supporting M.G. with a long-term fellowship ( ALTF 1005-2019 ) during the finalization and revision of this manuscript in the laboratory of B.D.R., and we thank R. Pierik for allowing K.V.G. to work on this manuscript during a postdoc in his laboratory at Utrecht University. This work was supported by grants from the European Research Council under the European Union’s Seventh Framework Programme (ERC grant agreements 742985 to J.F., 714055 to B.D.R., and 803048 to M.F.), the Austrian Science Fund (FWF; I 3630-B25 to J.F.), Chemical Sciences (partly) financed by the Dutch Research Council (NWO-CW TOP 700.58.301 to R.O.), the Dutch Research Council (NWO-VICI 865.17.002 to R. Pierik), Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan (KAKENHI grant 17K17595 to S.N.), the Ministry of Education, Youth and Sports of the Czech Republic (MŠMT project NPUI-LO1417 ), and a China Scholarship Council (to X.W.).","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2021","has_accepted_license":"1","isi":1,"publication":"Current Biology","day":"10","page":"1918-1930","date_created":"2021-03-26T12:09:33Z","date_published":"2021-03-10T00:00:00Z","doi":"10.1016/j.cub.2021.02.028"},{"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["33157019"],"isi":["000614361000039"]},"author":[{"first_name":"MM","last_name":"Marquès-Bueno","full_name":"Marquès-Bueno, MM"},{"first_name":"L","last_name":"Armengot","full_name":"Armengot, L"},{"first_name":"LC","full_name":"Noack, LC","last_name":"Noack"},{"first_name":"J","last_name":"Bareille","full_name":"Bareille, J"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237"},{"first_name":"MP","last_name":"Platre","full_name":"Platre, MP"},{"first_name":"V","last_name":"Bayle","full_name":"Bayle, V"},{"last_name":"Liu","full_name":"Liu, M","first_name":"M"},{"last_name":"Opdenacker","full_name":"Opdenacker, D","first_name":"D"},{"first_name":"S","last_name":"Vanneste","full_name":"Vanneste, S"},{"first_name":"BK","last_name":"Möller","full_name":"Möller, BK"},{"first_name":"ZL","full_name":"Nimchuk, ZL","last_name":"Nimchuk"},{"last_name":"Beeckman","full_name":"Beeckman, T","first_name":"T"},{"last_name":"Caño-Delgado","full_name":"Caño-Delgado, AI","first_name":"AI"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Y","last_name":"Jaillais","full_name":"Jaillais, Y"}],"title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","citation":{"mla":"Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology, vol. 31, no. 1, Elsevier, 2021, doi:10.1016/j.cub.2020.10.011.","apa":"Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey, L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2020.10.011","ama":"Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 2021;31(1). doi:10.1016/j.cub.2020.10.011","ieee":"M. Marquès-Bueno et al., “Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” Current Biology, vol. 31, no. 1. Elsevier, 2021.","short":"M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey, M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk, T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021).","chicago":"Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey, MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2020.10.011.","ista":"Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T, Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 31(1)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank the SiCE group for discussions and comments; S. Yalovsky, B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A. Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences (UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre, and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon and A. Page at the Protein Science Facility (PSF) for assistance with protein purification and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013. Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID: ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie COFUND and Research Foundation Flanders for a postdoctoral fellowship.","date_created":"2020-12-01T13:39:46Z","doi":"10.1016/j.cub.2020.10.011","date_published":"2021-01-11T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Current Biology","day":"11","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"8824","file_date_updated":"2021-02-04T11:37:50Z","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T13:03:15Z","ddc":["570"],"intvolume":" 31","month":"01","abstract":[{"lang":"eng","text":"Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface."}],"oa_version":"Published Version","pmid":1,"issue":"1","volume":31,"publication_status":"published","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2021-02-04T11:37:50Z","file_size":3458646,"date_created":"2021-02-04T11:37:50Z","file_name":"2021_CurrentBiology_MarquesBueno.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"30b3393d841fb2b1e2b22fb42b5c8fff","file_id":"9090","success":1}]},{"_id":"9301","status":"public","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"article_type":"original","type":"journal_article","date_updated":"2023-09-05T13:27:18Z","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered.","lang":"eng"}],"month":"04","intvolume":" 118","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.11447775"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","issue":"14","volume":118,"article_number":"e2021893118","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2021893118.","ista":"Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H, Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 118(14), e2021893118.","mla":"Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118","ama":"Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 2021;118(14). doi:10.1073/pnas.2021893118","ieee":"C. Prehal et al., “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings of the National Academy of Sciences, vol. 118, no. 14. National Academy of Sciences, 2021.","short":"C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences 118 (2021)."},"title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"first_name":"Aleksej","full_name":"Samojlov, Aleksej","last_name":"Samojlov"},{"full_name":"Nachtnebel, Manfred","last_name":"Nachtnebel","first_name":"Manfred"},{"id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","first_name":"Ludek","last_name":"Lovicar","full_name":"Lovicar, Ludek","orcid":"0000-0001-6206-4200"},{"last_name":"Kriechbaum","full_name":"Kriechbaum, Manfred","first_name":"Manfred"},{"first_name":"Heinz","full_name":"Amenitsch, Heinz","last_name":"Amenitsch"},{"last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"}],"external_id":{"isi":["000637398300050"]},"article_processing_charge":"No","acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou, C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis, C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively. We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption measurements, and acknowledge Graz University of Technology for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F. is indebted to Institute of Science and Technology Austria (IST Austria) for support. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"day":"06","publication":"Proceedings of the National Academy of Sciences","isi":1,"year":"2021","date_published":"2021-04-06T00:00:00Z","doi":"10.1073/pnas.2021893118","date_created":"2021-03-31T07:00:01Z"},{"article_number":"050550","title":"Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes","author":[{"full_name":"Maffre, Marion","last_name":"Maffre","first_name":"Marion"},{"first_name":"Roza","last_name":"Bouchal","full_name":"Bouchal, Roza"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Niklas","last_name":"Lindahl","full_name":"Lindahl, Niklas"},{"full_name":"Johansson, Patrik","last_name":"Johansson","first_name":"Patrik"},{"first_name":"Frédéric","last_name":"Favier","full_name":"Favier, Frédéric"},{"last_name":"Fontaine","full_name":"Fontaine, Olivier","first_name":"Olivier"},{"full_name":"Bélanger, Daniel","last_name":"Bélanger","first_name":"Daniel"}],"external_id":{"isi":["000657724200001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M. Maffre, R. Bouchal, S.A. Freunberger, N. Lindahl, P. Johansson, F. Favier, O. Fontaine, D. Bélanger, Journal of The Electrochemical Society 168 (2021).","ieee":"M. Maffre et al., “Investigation of electrochemical and chemical processes occurring at positive potentials in ‘Water-in-Salt’ electrolytes,” Journal of The Electrochemical Society, vol. 168, no. 5. IOP Publishing, 2021.","ama":"Maffre M, Bouchal R, Freunberger SA, et al. Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. 2021;168(5). doi:10.1149/1945-7111/ac0300","apa":"Maffre, M., Bouchal, R., Freunberger, S. A., Lindahl, N., Johansson, P., Favier, F., … Bélanger, D. (2021). Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. IOP Publishing. https://doi.org/10.1149/1945-7111/ac0300","mla":"Maffre, Marion, et al. “Investigation of Electrochemical and Chemical Processes Occurring at Positive Potentials in ‘Water-in-Salt’ Electrolytes.” Journal of The Electrochemical Society, vol. 168, no. 5, 050550, IOP Publishing, 2021, doi:10.1149/1945-7111/ac0300.","ista":"Maffre M, Bouchal R, Freunberger SA, Lindahl N, Johansson P, Favier F, Fontaine O, Bélanger D. 2021. Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. 168(5), 050550.","chicago":"Maffre, Marion, Roza Bouchal, Stefan Alexander Freunberger, Niklas Lindahl, Patrik Johansson, Frédéric Favier, Olivier Fontaine, and Daniel Bélanger. “Investigation of Electrochemical and Chemical Processes Occurring at Positive Potentials in ‘Water-in-Salt’ Electrolytes.” Journal of The Electrochemical Society. IOP Publishing, 2021. https://doi.org/10.1149/1945-7111/ac0300."},"publisher":"IOP Publishing","quality_controlled":"1","doi":"10.1149/1945-7111/ac0300","date_published":"2021-05-01T00:00:00Z","date_created":"2021-06-03T09:58:38Z","day":"01","publication":"Journal of The Electrochemical Society","isi":1,"year":"2021","status":"public","keyword":["Renewable Energy","Sustainability and the Environment","Electrochemistry","Materials Chemistry","Electronic","Optical and Magnetic Materials","Surfaces","Coatings and Films","Condensed Matter Physics"],"type":"journal_article","_id":"9447","department":[{"_id":"StFr"}],"date_updated":"2023-09-05T13:25:30Z","month":"05","intvolume":" 168","oa_version":"None","abstract":[{"lang":"eng","text":"Lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) based water-in-salt electrolytes (WiSEs) has recently emerged as a new promising class of electrolytes, primarily owing to their wide electrochemical stability windows (~3–4 V), that by far exceed the thermodynamic stability window of water (1.23 V). Upon increasing the salt concentration towards superconcentration the onset of the oxygen evolution reaction (OER) shifts more significantly than the hydrogen evolution reaction (HER) does. The OER shift has been explained by the accumulation of hydrophobic anions blocking water access to the electrode surface, hence by double layer theory. Here we demonstrate that the processes during oxidation are much more complex, involving OER, carbon and salt decomposition by OER intermediates, and salt precipitation upon local oversaturation. The positive shift in the onset potential of oxidation currents was elucidated by combining several advanced analysis techniques: rotating ring-disk electrode voltammetry, online electrochemical mass spectrometry, and X-ray photoelectron spectroscopy, using both dilute and superconcentrated electrolytes. The results demonstrate the importance of reactive OER intermediates and surface films for electrolyte and electrode stability and motivate further studies of the nature of the electrode."}],"volume":168,"issue":"5","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1945-7111"],"issn":["0013-4651"]},"publication_status":"published"},{"day":"05","publication":"Journal of Cell Biology","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-04-05T00:00:00Z","doi":"10.1083/jcb.202006081","date_created":"2021-02-05T10:08:04Z","quality_controlled":"1","publisher":"Rockefeller University Press","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 220(4), e202006081.","chicago":"Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner, Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” Journal of Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202006081.","short":"A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB, A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021).","ieee":"A. F. Leithner et al., “Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse,” Journal of Cell Biology, vol. 220, no. 4. Rockefeller University Press, 2021.","ama":"Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 2021;220(4). doi:10.1083/jcb.202006081","apa":"Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K., TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202006081","mla":"Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” Journal of Cell Biology, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021, doi:10.1083/jcb.202006081."},"title":"Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse","author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"full_name":"Altenburger, LM","last_name":"Altenburger","first_name":"LM"},{"last_name":"Hauschild","full_name":"Hauschild, R","first_name":"R"},{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","last_name":"Assen","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119"},{"first_name":"K","full_name":"Rottner, K","last_name":"Rottner"},{"first_name":"Stradal","full_name":"TEB, Stradal","last_name":"TEB"},{"last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, A","first_name":"A"},{"full_name":"Stein, JV","last_name":"Stein","first_name":"JV"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"article_processing_charge":"No","external_id":{"isi":["000626365700001"],"pmid":["33533935"]},"article_number":"e202006081","file":[{"date_created":"2022-05-12T14:16:21Z","file_name":"2021_JournCellBiology_Leithner.pdf","creator":"dernst","date_updated":"2022-05-12T14:16:21Z","file_size":5102328,"file_id":"11367","checksum":"843ebc153847c8626e13c9c5ce71d533","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"publication_status":"published","issue":"4","volume":220,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality.","lang":"eng"}],"month":"04","intvolume":" 220","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-05T13:57:53Z","department":[{"_id":"MiSi"}],"file_date_updated":"2022-05-12T14:16:21Z","_id":"9094","status":"public","article_type":"original","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"}},{"project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"author":[{"first_name":"Ileana L.","last_name":"Hanganu-Opatz","full_name":"Hanganu-Opatz, Ileana L."},{"full_name":"Butt, Simon J. B.","last_name":"Butt","first_name":"Simon J. B."},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Marco García","full_name":"De Marco García, Natalia V.","first_name":"Natalia V."},{"last_name":"Cardin","full_name":"Cardin, Jessica A.","first_name":"Jessica A."},{"first_name":"Bradley","last_name":"Voytek","full_name":"Voytek, Bradley"},{"last_name":"Muotri","full_name":"Muotri, Alysson R.","first_name":"Alysson R."}],"article_processing_charge":"No","external_id":{"isi":["000616763400002"],"pmid":["33431633"]},"title":"The logic of developing neocortical circuits in health and disease","citation":{"mla":"Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits in Health and Disease.” The Journal of Neuroscience, vol. 41, no. 5, Society for Neuroscience, 2021, pp. 813–22, doi:10.1523/jneurosci.1655-20.2020.","apa":"Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N. V., Cardin, J. A., Voytek, B., & Muotri, A. R. (2021). The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1655-20.2020","ama":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 2021;41(5):813-822. doi:10.1523/jneurosci.1655-20.2020","short":"I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A. Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822.","ieee":"I. L. Hanganu-Opatz et al., “The logic of developing neocortical circuits in health and disease,” The Journal of Neuroscience, vol. 41, no. 5. Society for Neuroscience, pp. 813–822, 2021.","chicago":"Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri. “The Logic of Developing Neocortical Circuits in Health and Disease.” The Journal of Neuroscience. Society for Neuroscience, 2021. https://doi.org/10.1523/jneurosci.1655-20.2020.","ista":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA, Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 41(5), 813–822."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Society for Neuroscience","oa":1,"acknowledgement":"Work in the I.L.H.-O. laboratory was supported by European Research Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1, Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and 102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G. Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons Foundation SFARI Research Award, and National Institutes of Health/National Institute of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National Institutes of Health, National Institute of General Medical Sciences R01GM134363-01, and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the University of California San Diego School of Medicine.","page":"813-822","doi":"10.1523/jneurosci.1655-20.2020","date_published":"2021-02-03T00:00:00Z","date_created":"2021-02-03T12:23:51Z","has_accepted_license":"1","isi":1,"year":"2021","day":"03","publication":"The Journal of Neuroscience","type":"journal_article","article_type":"original","status":"public","keyword":["General Neuroscience"],"_id":"9073","file_date_updated":"2022-05-27T06:59:55Z","department":[{"_id":"SiHi"}],"date_updated":"2023-09-05T14:03:17Z","ddc":["570"],"scopus_import":"1","month":"02","intvolume":" 41","abstract":[{"text":"The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":41,"issue":"5","ec_funded":1,"publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"publication_status":"published","file":[{"date_updated":"2022-05-27T06:59:55Z","file_size":1031150,"creator":"dernst","date_created":"2022-05-27T06:59:55Z","file_name":"2021_JourNeuroscience_Hanganu.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"578fd7ed1a0aef74bce61bea2d987b33","file_id":"11414","success":1}],"language":[{"iso":"eng"}]},{"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"title":"Optimal combination of linear and spectral estimators for generalized linear models","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000685721000001"],"arxiv":["2008.03326"]},"author":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"first_name":"Christos","last_name":"Thrampoulidis","full_name":"Thrampoulidis, Christos"},{"full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan","first_name":"Ramji"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics, Springer, 2021, doi:10.1007/s10208-021-09531-x.","short":"M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics (2021).","ieee":"M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination of linear and spectral estimators for generalized linear models,” Foundations of Computational Mathematics. Springer, 2021.","apa":"Mondelli, M., Thrampoulidis, C., & Venkataramanan, R. (2021). Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-021-09531-x","ama":"Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. 2021. doi:10.1007/s10208-021-09531-x","chicago":"Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics. Springer, 2021. https://doi.org/10.1007/s10208-021-09531-x.","ista":"Mondelli M, Thrampoulidis C, Venkataramanan R. 2021. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics."},"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"M. Mondelli would like to thank Andrea Montanari for helpful discussions. All the authors would like to thank the anonymous reviewers for their helpful comments.","date_created":"2021-11-03T10:59:08Z","doi":"10.1007/s10208-021-09531-x","date_published":"2021-08-17T00:00:00Z","publication":"Foundations of Computational Mathematics","day":"17","year":"2021","has_accepted_license":"1","isi":1,"keyword":["Applied Mathematics","Computational Theory and Mathematics","Computational Mathematics","Analysis"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10211","department":[{"_id":"MaMo"}],"file_date_updated":"2021-12-13T15:47:54Z","ddc":["510"],"date_updated":"2023-09-05T14:13:57Z","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We study the problem of recovering an unknown signal 𝑥𝑥 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator 𝑥𝑥^L and a spectral estimator 𝑥𝑥^s. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine 𝑥𝑥^L and 𝑥𝑥^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of 𝑥𝑥^L and 𝑥𝑥^s, given the limiting distribution of the signal 𝑥𝑥. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form 𝜃𝑥𝑥^L+𝑥𝑥^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s), we design and analyze an approximate message passing algorithm whose iterates give 𝑥𝑥^L and approach 𝑥𝑥^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately.","lang":"eng"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"9ea12dd8045a0678000a3a59295221cb","file_id":"10542","file_size":2305731,"date_updated":"2021-12-13T15:47:54Z","creator":"alisjak","file_name":"2021_Springer_Mondelli.pdf","date_created":"2021-12-13T15:47:54Z"}],"publication_status":"published","publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]}},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric."}],"intvolume":" 66","month":"07","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"c848986091e56699dc12de85adb1e39c","file_id":"9795","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","date_created":"2021-08-06T09:52:29Z","file_size":983307,"date_updated":"2021-08-06T09:52:29Z","creator":"kschuh"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"ec_funded":1,"issue":"1","volume":66,"_id":"8940","keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["516"],"date_updated":"2023-09-05T15:02:40Z","file_date_updated":"2021-08-06T09:52:29Z","department":[{"_id":"HeEd"}],"acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Discrete & Computational Geometry","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2020-12-12T11:07:02Z","doi":"10.1007/s00454-020-00250-8","date_published":"2021-07-01T00:00:00Z","page":"386-434","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 66(1), 386–434.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00250-8.","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete & Computational Geometry 66 (2021) 386–434.","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” Discrete & Computational Geometry, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 2021;66(1):386-434. doi:10.1007/s00454-020-00250-8","apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00250-8","mla":"Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:10.1007/s00454-020-00250-8."},"title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000597770300001"]},"author":[{"last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel","first_name":"Jean-Daniel"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs"}]},{"title":"The BCS energy gap at low density","author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000617531900001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” Letters in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01358-5.","ista":"Lauritsen AB. 2021. The BCS energy gap at low density. Letters in Mathematical Physics. 111, 20.","mla":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” Letters in Mathematical Physics, vol. 111, 20, Springer Nature, 2021, doi:10.1007/s11005-021-01358-5.","apa":"Lauritsen, A. B. (2021). The BCS energy gap at low density. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01358-5","ama":"Lauritsen AB. The BCS energy gap at low density. Letters in Mathematical Physics. 2021;111. doi:10.1007/s11005-021-01358-5","ieee":"A. B. Lauritsen, “The BCS energy gap at low density,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021.","short":"A.B. Lauritsen, Letters in Mathematical Physics 111 (2021)."},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"20","doi":"10.1007/s11005-021-01358-5","date_published":"2021-02-12T00:00:00Z","date_created":"2021-02-15T09:27:14Z","day":"12","publication":"Letters in Mathematical Physics","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Most of this work was done as part of the author’s master’s thesis. The author would like to thank Jan Philip Solovej for his supervision of this process.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria)","department":[{"_id":"GradSch"}],"file_date_updated":"2021-02-15T09:31:07Z","ddc":["510"],"date_updated":"2023-09-05T15:17:16Z","status":"public","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9121","volume":111,"file":[{"date_created":"2021-02-15T09:31:07Z","file_name":"2021_LettersMathPhysics_Lauritsen.pdf","creator":"dernst","date_updated":"2021-02-15T09:31:07Z","file_size":329332,"file_id":"9122","checksum":"eaf1b3ff5026f120f0929a5c417dc842","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"publication_status":"published","month":"02","intvolume":" 111","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We show that the energy gap for the BCS gap equation is\r\nΞ=μ(8e−2+o(1))exp(π2μ−−√a)\r\nin the low density limit μ→0. Together with the similar result for the critical temperature by Hainzl and Seiringer (Lett Math Phys 84: 99–107, 2008), this shows that, in the low density limit, the ratio of the energy gap and critical temperature is a universal constant independent of the interaction potential V. The results hold for a class of potentials with negative scattering length a and no bound states."}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” Networks and Spatial Economics, vol. 21, no. 2, Springer Nature, 2021, pp. 291–323, doi:10.1007/s11067-021-09517-w.","ama":"Izuchukwu C, Shehu Y. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. 2021;21(2):291-323. doi:10.1007/s11067-021-09517-w","apa":"Izuchukwu, C., & Shehu, Y. (2021). New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. Springer Nature. https://doi.org/10.1007/s11067-021-09517-w","short":"C. Izuchukwu, Y. Shehu, Networks and Spatial Economics 21 (2021) 291–323.","ieee":"C. Izuchukwu and Y. Shehu, “New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity,” Networks and Spatial Economics, vol. 21, no. 2. Springer Nature, pp. 291–323, 2021.","chicago":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” Networks and Spatial Economics. Springer Nature, 2021. https://doi.org/10.1007/s11067-021-09517-w.","ista":"Izuchukwu C, Shehu Y. 2021. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. 21(2), 291–323."},"title":"New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000625002100001"]},"author":[{"full_name":"Izuchukwu, Chinedu","last_name":"Izuchukwu","first_name":"Chinedu"},{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","last_name":"Shehu","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139"}],"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication":"Networks and Spatial Economics","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-03-10T12:18:47Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1007/s11067-021-09517-w","page":"291-323","acknowledgement":"The authors sincerely thank the Editor-in-Chief and anonymous referees for their careful reading, constructive comments and fruitful suggestions that help improve the manuscript. The research of the first author is supported by the National Research Foundation (NRF) South Africa (S& F-DSI/NRF Free Standing Postdoctoral Fellowship; Grant Number: 120784). The first author also acknowledges the financial support from DSI/NRF, South Africa Center of Excellence in Mathematical and Statistical Sciences (CoE-MaSS) Postdoctoral Fellowship. The second author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160). Open Access funding provided by Institute of Science and Technology (IST Austria).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","ddc":["510"],"date_updated":"2023-09-05T15:32:32Z","department":[{"_id":"VlKo"}],"file_date_updated":"2021-08-11T12:44:16Z","_id":"9234","keyword":["Computer Networks and Communications","Software","Artificial Intelligence"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"checksum":"22b4253a2e5da843622a2df713784b4c","file_id":"9884","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-11T12:44:16Z","file_name":"2021_NetworksSpatialEconomics_Shehu.pdf","creator":"kschuh","date_updated":"2021-08-11T12:44:16Z","file_size":834964}],"publication_status":"published","publication_identifier":{"issn":["1566-113X"],"eissn":["1572-9427"]},"ec_funded":1,"issue":"2","volume":21,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this paper, we present two new inertial projection-type methods for solving multivalued variational inequality problems in finite-dimensional spaces. We establish the convergence of the sequence generated by these methods when the multivalued mapping associated with the problem is only required to be locally bounded without any monotonicity assumption. Furthermore, the inertial techniques that we employ in this paper are quite different from the ones used in most papers. Moreover, based on the weaker assumptions on the inertial factor in our methods, we derive several special cases of our methods. Finally, we present some experimental results to illustrate the profits that we gain by introducing the inertial extrapolation steps."}],"intvolume":" 21","month":"06","scopus_import":"1"},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"title":"Probabilistic convergence and stability of random mapper graphs","author":[{"last_name":"Brown","full_name":"Brown, Adam","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425"},{"last_name":"Bobrowski","full_name":"Bobrowski, Omer","first_name":"Omer"},{"last_name":"Munch","full_name":"Munch, Elizabeth","first_name":"Elizabeth"},{"first_name":"Bei","last_name":"Wang","full_name":"Wang, Bei"}],"external_id":{"arxiv":["1909.03488"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Brown, Adam, Omer Bobrowski, Elizabeth Munch, and Bei Wang. “Probabilistic Convergence and Stability of Random Mapper Graphs.” Journal of Applied and Computational Topology. Springer Nature, 2021. https://doi.org/10.1007/s41468-020-00063-x.","ista":"Brown A, Bobrowski O, Munch E, Wang B. 2021. Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. 5(1), 99–140.","mla":"Brown, Adam, et al. “Probabilistic Convergence and Stability of Random Mapper Graphs.” Journal of Applied and Computational Topology, vol. 5, no. 1, Springer Nature, 2021, pp. 99–140, doi:10.1007/s41468-020-00063-x.","apa":"Brown, A., Bobrowski, O., Munch, E., & Wang, B. (2021). Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00063-x","ama":"Brown A, Bobrowski O, Munch E, Wang B. Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. 2021;5(1):99-140. doi:10.1007/s41468-020-00063-x","short":"A. Brown, O. Bobrowski, E. Munch, B. Wang, Journal of Applied and Computational Topology 5 (2021) 99–140.","ieee":"A. Brown, O. Bobrowski, E. Munch, and B. Wang, “Probabilistic convergence and stability of random mapper graphs,” Journal of Applied and Computational Topology, vol. 5, no. 1. Springer Nature, pp. 99–140, 2021."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"AB was supported in part by the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Sklodowska-Curie GrantAgreement No. 754411 and NSF IIS-1513616. OB was supported in part by the Israel Science Foundation, Grant 1965/19. BW was supported in part by NSF IIS-1513616 and DBI-1661375. EM was supported in part by NSF CMMI-1800466, DMS-1800446, and CCF-1907591.We would like to thank the Institute for Mathematics and its Applications for hosting a workshop titled Bridging Statistics and Sheaves in May 2018, where this work was conceived.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1007/s41468-020-00063-x","date_published":"2021-03-01T00:00:00Z","date_created":"2021-02-11T14:41:02Z","page":"99-140","day":"01","publication":"Journal of Applied and Computational Topology","has_accepted_license":"1","year":"2021","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9111","department":[{"_id":"HeEd"}],"file_date_updated":"2021-02-11T14:43:59Z","ddc":["510"],"date_updated":"2023-09-05T15:37:56Z","month":"03","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We study the probabilistic convergence between the mapper graph and the Reeb graph of a topological space X equipped with a continuous function f:X→R. We first give a categorification of the mapper graph and the Reeb graph by interpreting them in terms of cosheaves and stratified covers of the real line R. We then introduce a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium on point-based graphics, 2007), referred to as the enhanced mapper graph, and demonstrate that such a construction approximates the Reeb graph of (X,f) when it is applied to points randomly sampled from a probability density function concentrated on (X,f). Our techniques are based on the interleaving distance of constructible cosheaves and topological estimation via kernel density estimates. Following Munch and Wang (In: 32nd international symposium on computational geometry, volume 51 of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany, pp 53:1–53:16, 2016), we first show that the mapper graph of (X,f), a constructible R-space (with a fixed open cover), approximates the Reeb graph of the same space. We then construct an isomorphism between the mapper of (X,f) to the mapper of a super-level set of a probability density function concentrated on (X,f). Finally, building on the approach of Bobrowski et al. (Bernoulli 23(1):288–328, 2017b), we show that, with high probability, we can recover the mapper of the super-level set given a sufficiently large sample. Our work is the first to consider the mapper construction using the theory of cosheaves in a probabilistic setting. It is part of an ongoing effort to combine sheaf theory, probability, and statistics, to support topological data analysis with random data.","lang":"eng"}],"issue":"1","volume":5,"ec_funded":1,"file":[{"checksum":"3f02e9d47c428484733da0f588a3c069","file_id":"9112","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-02-11T14:43:59Z","file_name":"2020_JourApplCompTopology_Brown.pdf","creator":"dernst","date_updated":"2021-02-11T14:43:59Z","file_size":2090265}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"publication_status":"published"},{"volume":75,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13062"}]},"issue":"5","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b90fb5767d623602046fed03725e16ca","file_id":"9886","success":1,"date_updated":"2021-08-11T13:39:19Z","file_size":734102,"creator":"kschuh","date_created":"2021-08-11T13:39:19Z","file_name":"2021_Evolution_Szep.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 75","abstract":[{"text":"This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2021-08-11T13:39:19Z","department":[{"_id":"NiBa"}],"date_updated":"2023-09-05T15:44:06Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"_id":"9252","page":"1030-1045","doi":"10.1111/evo.14210","date_published":"2021-05-01T00:00:00Z","date_created":"2021-03-20T08:22:10Z","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Evolution","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","author":[{"full_name":"Szep, Eniko","last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000636966300001"]},"title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","citation":{"short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210","ama":"Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210","mla":"Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:10.1111/evo.14210.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14210."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"issue":"5","volume":75,"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235","open_access":"1"}],"month":"04","intvolume":" 75","abstract":[{"lang":"eng","text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since."}],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"date_updated":"2023-09-05T15:44:33Z","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"_id":"9374","page":"978-988","date_published":"2021-04-19T00:00:00Z","doi":"10.1111/evo.14235","date_created":"2021-05-06T04:34:47Z","isi":1,"year":"2021","day":"19","publication":"Evolution","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","author":[{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."},{"full_name":"Servedio, Maria R.","last_name":"Servedio","first_name":"Maria R."},{"last_name":"Smadja","full_name":"Smadja, Carole M.","first_name":"Carole M."},{"first_name":"Claudia","full_name":"Bank, Claudia","last_name":"Bank"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Samuel M.","full_name":"Flaxman, Samuel M.","last_name":"Flaxman"},{"full_name":"Giraud, Tatiana","last_name":"Giraud","first_name":"Tatiana"},{"full_name":"Hopkins, Robin","last_name":"Hopkins","first_name":"Robin"},{"first_name":"Erica L.","full_name":"Larson, Erica L.","last_name":"Larson"},{"first_name":"Martine E.","last_name":"Maan","full_name":"Maan, Martine E."},{"full_name":"Meier, Joana","last_name":"Meier","first_name":"Joana"},{"full_name":"Merrill, Richard","last_name":"Merrill","first_name":"Richard"},{"full_name":"Noor, Mohamed A. F.","last_name":"Noor","first_name":"Mohamed A. F."},{"first_name":"Daniel","full_name":"Ortiz‐Barrientos, Daniel","last_name":"Ortiz‐Barrientos"},{"last_name":"Qvarnström","full_name":"Qvarnström, Anna","first_name":"Anna"}],"article_processing_charge":"No","external_id":{"isi":["000647224000001"]},"title":"Homage to Felsenstein 1981, or why are there so few/many species?","citation":{"mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235","short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","ieee":"R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"abstract":[{"text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.8gtht76p1","open_access":"1"}],"oa":1,"publisher":"Dryad","month":"03","year":"2021","day":"02","date_created":"2023-05-23T16:17:02Z","date_published":"2021-03-02T00:00:00Z","related_material":{"record":[{"id":"9252","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/DRYAD.8GTHT76P1","_id":"13062","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","date_updated":"2023-09-05T15:44:05Z","citation":{"mla":"Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","author":[{"full_name":"Szep, Eniko","last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","department":[{"_id":"NiBa"}]},{"publication_status":"published","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10839","checksum":"d5611f243ceb63a0e091d6662ebd9cda","success":1,"creator":"dernst","date_updated":"2022-03-08T11:31:30Z","file_size":1726548,"date_created":"2022-03-08T11:31:30Z","file_name":"2021_MolecularEcology_Westram.pdf"}],"issue":"15","volume":30,"abstract":[{"text":"Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 30","month":"08","date_updated":"2023-09-05T16:02:19Z","ddc":["570"],"file_date_updated":"2022-03-08T11:31:30Z","department":[{"_id":"BeVi"}],"_id":"10838","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"status":"public","year":"2021","has_accepted_license":"1","isi":1,"publication":"Molecular Ecology","day":"01","page":"3797-3814","date_created":"2022-03-08T11:28:32Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1111/mec.15861","acknowledgement":"We thank everyone who helped with fieldwork, snail processing and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark Ravinet for helpful discussions, and to three anonymous reviewers for their constructive comments. This work was supported by the Natural Environment Research Council (NE/K014021/1), the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628), and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017). A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno. 754411/797747 and no. 706376, respectively.","oa":1,"quality_controlled":"1","publisher":"Wiley","citation":{"ista":"Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 30(15), 3797–3814.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15861.","ama":"Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 2021;30(15):3797-3814. doi:10.1111/mec.15861","apa":"Westram, A. M., Faria, R., Johannesson, K., & Butlin, R. (2021). Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15861","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 3797–3814.","ieee":"A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid zones to understand the genomic basis of adaptive divergence,” Molecular Ecology, vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.","mla":"Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” Molecular Ecology, vol. 30, no. 15, Wiley, 2021, pp. 3797–814, doi:10.1111/mec.15861."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000669439700001"],"pmid":["33638231"]},"author":[{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence"},{"pmid":1,"oa_version":"Published Version","abstract":[{"text":"• The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored.\r\n• We use complementary pharmacological and genetic approaches to block CINNAMATE‐4‐HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes.\r\n• Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in auxin transport. The upstream accumulation in cis‐cinnamic acid was found to likely cause polar auxin transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem‐mediated auxin transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, auxin homeostasis.\r\n• Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of auxin distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development.","lang":"eng"}],"intvolume":" 230","month":"03","main_file_link":[{"open_access":"1","url":"https://biblio.ugent.be/publication/8703799/file/8703800.pdf"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"issue":"6","volume":230,"_id":"9288","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-05T15:46:55Z","department":[{"_id":"JiFr"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"New Phytologist","day":"17","year":"2021","isi":1,"date_created":"2021-03-26T12:09:01Z","date_published":"2021-03-17T00:00:00Z","doi":"10.1111/nph.17349","page":"2275-2291","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"El Houari, I, C Van Beirs, HE Arents, Huibin Han, A Chanoca, D Opdenacker, J Pollier, et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17349.","ista":"El Houari I, Van Beirs C, Arents H, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. 2021. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 230(6), 2275–2291.","mla":"El Houari, I., et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” New Phytologist, vol. 230, no. 6, Wiley, 2021, pp. 2275–91, doi:10.1111/nph.17349.","apa":"El Houari, I., Van Beirs, C., Arents, H., Han, H., Chanoca, A., Opdenacker, D., … Vanholme, B. (2021). Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. Wiley. https://doi.org/10.1111/nph.17349","ama":"El Houari I, Van Beirs C, Arents H, et al. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 2021;230(6):2275-2291. doi:10.1111/nph.17349","ieee":"I. El Houari et al., “Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport,” New Phytologist, vol. 230, no. 6. Wiley, pp. 2275–2291, 2021.","short":"I. El Houari, C. Van Beirs, H. Arents, H. Han, A. Chanoca, D. Opdenacker, J. Pollier, V. Storme, W. Steenackers, M. Quareshy, R. Napier, T. Beeckman, J. Friml, B. De Rybel, W. Boerjan, B. Vanholme, New Phytologist 230 (2021) 2275–2291."},"title":"Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport","article_processing_charge":"No","external_id":{"pmid":["33728703"],"isi":["000639552400001"]},"author":[{"first_name":"I","last_name":"El Houari","full_name":"El Houari, I"},{"first_name":"C","full_name":"Van Beirs, C","last_name":"Van Beirs"},{"full_name":"Arents, HE","last_name":"Arents","first_name":"HE"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chanoca","full_name":"Chanoca, A","first_name":"A"},{"full_name":"Opdenacker, D","last_name":"Opdenacker","first_name":"D"},{"full_name":"Pollier, J","last_name":"Pollier","first_name":"J"},{"first_name":"V","last_name":"Storme","full_name":"Storme, V"},{"last_name":"Steenackers","full_name":"Steenackers, W","first_name":"W"},{"first_name":"M","last_name":"Quareshy","full_name":"Quareshy, M"},{"first_name":"R","last_name":"Napier","full_name":"Napier, R"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"B","full_name":"De Rybel, B","last_name":"De Rybel"},{"full_name":"Boerjan, W","last_name":"Boerjan","first_name":"W"},{"first_name":"B","last_name":"Vanholme","full_name":"Vanholme, B"}]},{"scopus_import":"1","month":"05","intvolume":" 76","oa_version":"Published Version","pmid":1,"volume":76,"issue":"5","publication_identifier":{"issn":["0105-4538"],"eissn":["1398-9995"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"9526f9554112fc027c9f7fa540c488cd","file_id":"10837","creator":"dernst","file_size":626081,"date_updated":"2022-03-08T11:23:16Z","file_name":"2021_Allergy_Pranger.pdf","date_created":"2022-03-08T11:23:16Z"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Immunology","Immunology and Allergy"],"_id":"10836","department":[{"_id":"Bio"}],"file_date_updated":"2022-03-08T11:23:16Z","date_updated":"2023-09-05T15:58:53Z","ddc":["570"],"quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) grants MCCA W1248-B30 and SFB F4606-B28 to EJJ. CP received a short-term research fellowship of the European Federation of Immunological Societies (EFIS-IL) for a research visit at Biocruces Bizkaia Health Research Institute, Barakaldo, Spain. VKK received an EFIS-IL short-term research fellowship for a research visit at King’s College London. The research was funded by the National Institute for Health Research (NIHR) Biomedical Research Centre (BRC) based at Guy's and St Thomas' NHS Foundation Trust and King's College London (IS-BRC-1215-20006) (SNK). The authors acknowledge support by the Medical Research Council (MR/L023091/1) (SNK); Breast Cancer Now (147; KCL-BCN-Q3)(SNK); Cancer Research UK (C30122/A11527; C30122/A15774) (SNK); Cancer Research UK King's Health Partners Centre at King's College London (C604/A25135) (SNK); CRUK/NIHR in England/DoH for Scotland, Wales and Northern Ireland Experimental Cancer Medicine Centre (C10355/A15587) (SNK). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. Additionally, this work was funded by Instituto de Salud Carlos III through the project \"PI16/01223\" (Co-funded by European Regional Development Fund; “A way to make Europe”) to FB and by the Department of Health, Basque Government through the project “2019111031” to OZ. OZ is recipient of a Sara Borrell 2017 post-doctoral contract “CD17/00128” funded by Instituto de Salud Carlos III (Co-funded by European Social Fund; “Investing in your future”).","page":"1553-1556","doi":"10.1111/all.14604","date_published":"2021-05-01T00:00:00Z","date_created":"2022-03-08T11:19:05Z","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Allergy","author":[{"first_name":"Christina L.","full_name":"Pranger, Christina L.","last_name":"Pranger"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer"},{"first_name":"Verena K.","last_name":"Köhler","full_name":"Köhler, Verena K."},{"first_name":"Isabella","last_name":"Pali‐Schöll","full_name":"Pali‐Schöll, Isabella"},{"last_name":"Fiocchi","full_name":"Fiocchi, Alessandro","first_name":"Alessandro"},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis"},{"first_name":"Olatz","last_name":"Zenarruzabeitia","full_name":"Zenarruzabeitia, Olatz"},{"first_name":"Francisco","full_name":"Borrego, Francisco","last_name":"Borrego"},{"first_name":"Erika","last_name":"Jensen‐Jarolim","full_name":"Jensen‐Jarolim, Erika"}],"article_processing_charge":"No","external_id":{"pmid":["32990982"],"isi":["000577708800001"]},"title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","citation":{"mla":"Pranger, Christina L., et al. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” Allergy, vol. 76, no. 5, Wiley, 2021, pp. 1553–56, doi:10.1111/all.14604.","apa":"Pranger, C. L., Singer, J., Köhler, V. K., Pali‐Schöll, I., Fiocchi, A., Karagiannis, S. N., … Jensen‐Jarolim, E. (2021). PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. Wiley. https://doi.org/10.1111/all.14604","ama":"Pranger CL, Singer J, Köhler VK, et al. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 2021;76(5):1553-1556. doi:10.1111/all.14604","short":"C.L. Pranger, J. Singer, V.K. Köhler, I. Pali‐Schöll, A. Fiocchi, S.N. Karagiannis, O. Zenarruzabeitia, F. Borrego, E. Jensen‐Jarolim, Allergy 76 (2021) 1553–1556.","ieee":"C. L. Pranger et al., “PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance,” Allergy, vol. 76, no. 5. Wiley, pp. 1553–1556, 2021.","chicago":"Pranger, Christina L., Judit Singer, Verena K. Köhler, Isabella Pali‐Schöll, Alessandro Fiocchi, Sophia N. Karagiannis, Olatz Zenarruzabeitia, Francisco Borrego, and Erika Jensen‐Jarolim. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” Allergy. Wiley, 2021. https://doi.org/10.1111/all.14604.","ista":"Pranger CL, Singer J, Köhler VK, Pali‐Schöll I, Fiocchi A, Karagiannis SN, Zenarruzabeitia O, Borrego F, Jensen‐Jarolim E. 2021. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 76(5), 1553–1556."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ke, M, Z Ma, D Wang, Y Sun, C Wen, D Huang, Z Chen, et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.16915.","ista":"Ke M, Ma Z, Wang D, Sun Y, Wen C, Huang D, Chen Z, Yang L, Tan S, Li R, Friml J, Miao Y, Chen X. 2021. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 229(2), 963–978.","mla":"Ke, M., et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” New Phytologist, vol. 229, no. 2, Wiley, 2021, pp. 963–78, doi:10.1111/nph.16915.","ama":"Ke M, Ma Z, Wang D, et al. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 2021;229(2):963-978. doi:10.1111/nph.16915","apa":"Ke, M., Ma, Z., Wang, D., Sun, Y., Wen, C., Huang, D., … Chen, X. (2021). Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.16915","short":"M. Ke, Z. Ma, D. Wang, Y. Sun, C. Wen, D. Huang, Z. Chen, L. Yang, S. Tan, R. Li, J. Friml, Y. Miao, X. Chen, New Phytologist 229 (2021) 963–978.","ieee":"M. Ke et al., “Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana,” New Phytologist, vol. 229, no. 2. Wiley, pp. 963–978, 2021."},"title":"Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana","author":[{"first_name":"M","full_name":"Ke, M","last_name":"Ke"},{"first_name":"Z","last_name":"Ma","full_name":"Ma, Z"},{"first_name":"D","last_name":"Wang","full_name":"Wang, D"},{"last_name":"Sun","full_name":"Sun, Y","first_name":"Y"},{"full_name":"Wen, C","last_name":"Wen","first_name":"C"},{"last_name":"Huang","full_name":"Huang, D","first_name":"D"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"last_name":"Yang","full_name":"Yang, L","first_name":"L"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan"},{"first_name":"R","full_name":"Li, R","last_name":"Li"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Miao","full_name":"Miao, Y","first_name":"Y"},{"first_name":"X","full_name":"Chen, X","last_name":"Chen"}],"article_processing_charge":"No","external_id":{"pmid":["32901934"],"isi":["000573568000001"]},"acknowledgement":"This work was supported by the National Key Research andDevelopment Programme of China (2017YFA0506100), theNational Natural Science Foundation of China (31870170 and31701168), and the Fok Ying Tung Education Foundation(161027) to XC; NTU startup grant (M4081533) and NIM/01/2016 (NTU, Singapore) to YM. We thank Lei Shi andZhongquan Lin for microscopy assistance.","quality_controlled":"1","publisher":"Wiley","oa":1,"day":"01","publication":"New Phytologist","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-01-01T00:00:00Z","doi":"10.1111/nph.16915","date_created":"2020-10-05T12:45:36Z","page":"963-978","_id":"8608","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"date_updated":"2023-09-05T16:06:24Z","department":[{"_id":"JiFr"}],"file_date_updated":"2021-02-04T09:53:16Z","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"To adapt to the diverse array of biotic and abiotic cues, plants have evolved sophisticated mechanisms to sense changes in environmental conditions and modulate their growth. Growth-promoting hormones and defence signalling fine tune plant development antagonistically. During host-pathogen interactions, this defence-growth trade-off is mediated by the counteractive effects of the defence hormone salicylic acid (SA) and the growth hormone auxin. Here we revealed an underlying mechanism of SA regulating auxin signalling by constraining the plasma membrane dynamics of PIN2 auxin efflux transporter in Arabidopsis thaliana roots. The lateral diffusion of PIN2 proteins is constrained by SA signalling, during which PIN2 proteins are condensed into hyperclusters depending on REM1.2-mediated nanodomain compartmentalisation. Furthermore, membrane nanodomain compartmentalisation by SA or Remorin (REM) assembly significantly suppressed clathrin-mediated endocytosis. Consequently, SA-induced heterogeneous surface condensation disrupted asymmetric auxin distribution and the resultant gravitropic response. Our results demonstrated a defence-growth trade-off mechanism by which SA signalling crosstalked with auxin transport by concentrating membrane-resident PIN2 into heterogeneous compartments."}],"month":"01","intvolume":" 229","scopus_import":"1","file":[{"date_updated":"2021-02-04T09:53:16Z","file_size":3674502,"creator":"dernst","date_created":"2021-02-04T09:53:16Z","file_name":"2021_NewPhytologist_Ke.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9085","checksum":"d36b6a8c6fafab66264e0d27114dae63","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"publication_status":"published","volume":229,"issue":"2"},{"oa":1,"quality_controlled":"1","publisher":"World Scientific","year":"2021","isi":1,"publication":"Reviews in Mathematical Physics","day":"01","date_created":"2020-05-28T16:47:55Z","date_published":"2021-01-01T00:00:00Z","doi":"10.1142/s0129055x20600090","article_number":"2060009","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"citation":{"mla":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” Reviews in Mathematical Physics, vol. 33, no. 1, 2060009, World Scientific, 2021, doi:10.1142/s0129055x20600090.","apa":"Benedikter, N. P. (2021). Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. World Scientific. https://doi.org/10.1142/s0129055x20600090","ama":"Benedikter NP. Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. 2021;33(1). doi:10.1142/s0129055x20600090","short":"N.P. Benedikter, Reviews in Mathematical Physics 33 (2021).","ieee":"N. P. Benedikter, “Bosonic collective excitations in Fermi gases,” Reviews in Mathematical Physics, vol. 33, no. 1. World Scientific, 2021.","chicago":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” Reviews in Mathematical Physics. World Scientific, 2021. https://doi.org/10.1142/s0129055x20600090.","ista":"Benedikter NP. 2021. Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. 33(1), 2060009."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1910.08190"],"isi":["000613313200010"]},"article_processing_charge":"No","author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P","last_name":"Benedikter","full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091"}],"title":"Bosonic collective excitations in Fermi gases","abstract":[{"text":"Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.08190"}],"scopus_import":"1","intvolume":" 33","month":"01","publication_status":"published","publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","volume":33,"_id":"7900","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-05T16:07:40Z","department":[{"_id":"RoSe"}]}]