[{"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9946","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"month":"09","publication_identifier":{"issn":["2664-1690"]},"date_created":"2021-08-20T20:00:37Z","date_updated":"2023-08-14T07:20:29Z","author":[{"full_name":"Mühlböck, Fabian","first_name":"Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"9281","relation":"other","status":"public"},{"id":"10108","status":"public","relation":"shorter_version"}]},"publication_status":"published","publisher":"IST Austria","department":[{"_id":"ToHe"}],"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.","year":"2021","file_date_updated":"2021-09-03T12:34:28Z","date_published":"2021-09-01T00:00:00Z","page":"17","citation":{"short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.","ama":"Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946","ieee":"F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021.","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","keyword":["run-time verification","software engineering","implicit specification"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":"320453","creator":"fmuehlbo","access_level":"open_access","file_name":"differentialmonitoring-techreport.pdf","checksum":"0f9aafd59444cb6bdca6925d163ab946","date_created":"2021-08-20T19:59:44Z","date_updated":"2021-09-03T12:34:28Z","relation":"main_file","file_id":"9948"}],"status":"public","ddc":["005"],"title":"Differential monitoring","_id":"9946","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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."}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report"},{"_id":"10073","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 14","ddc":["540"],"status":"public","title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","file":[{"access_level":"open_access","file_name":"2021_Materials_Chang.pdf","content_type":"application/pdf","file_size":4404141,"creator":"cchlebak","relation":"main_file","file_id":"10140","checksum":"4929dfc673a3ae77c010b6174279cc1d","success":1,"date_updated":"2021-10-14T11:56:39Z","date_created":"2021-10-14T11:56:39Z"}],"oa_version":"Published Version","type":"journal_article","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"}],"citation":{"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.","short":"C. Chang, M. Ibáñez, Materials 14 (2021).","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.","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416","ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","ieee":"C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021.","apa":"Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416"},"publication":"Materials","article_type":"original","date_published":"2021-09-19T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"19","pmid":1,"year":"2021","acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","publisher":"MDPI","department":[{"_id":"MaIb"}],"publication_status":"published","author":[{"last_name":"Chang","first_name":"Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"}],"volume":14,"date_updated":"2023-08-14T08:00:01Z","date_created":"2021-10-03T22:01:23Z","article_number":"5416","file_date_updated":"2021-10-14T11:56:39Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000700689400001"],"pmid":["34576640"]},"project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"isi":1,"quality_controlled":"1","doi":"10.3390/ma14185416","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["1996-1944"]},"month":"09"},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/molbev/msab178","project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"oa":1,"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"06","date_created":"2021-10-21T07:49:12Z","date_updated":"2023-08-14T08:03:06Z","author":[{"full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi"},{"last_name":"Moldovan","first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"full_name":"Picard, Marion A L","first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press ","publication_status":"published","pmid":1,"year":"2021","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.","file_date_updated":"2022-05-06T09:47:18Z","date_published":"2021-06-19T00:00:00Z","article_type":"original","citation":{"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","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.","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","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.","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.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","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."},"publication":"Molecular Biology and Evolution","has_accepted_license":"1","article_processing_charge":"No","day":"19","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2022-05-06T09:47:18Z","date_created":"2022-05-06T09:47:18Z","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","success":1,"relation":"main_file","file_id":"11352","content_type":"application/pdf","file_size":1008594,"creator":"dernst","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","access_level":"open_access"}],"title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","ddc":["610"],"status":"public","_id":"10167","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000709050300001"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26360-2","publication_identifier":{"eissn":["2041-1723"]},"month":"10","department":[{"_id":"CaBe"}],"publisher":"Springer Nature","publication_status":"published","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.","year":"2021","volume":12,"date_created":"2021-10-20T14:40:32Z","date_updated":"2023-08-14T08:02:31Z","related_material":{"link":[{"relation":"earlier_version","description":"Preprint ","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159"}]},"author":[{"first_name":"Lisa-Marie","last_name":"Appel","full_name":"Appel, Lisa-Marie"},{"full_name":"Franke, Vedran","last_name":"Franke","first_name":"Vedran"},{"first_name":"Melania","last_name":"Bruno","full_name":"Bruno, Melania"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"first_name":"Aiste","last_name":"Kasiliauskaite","full_name":"Kasiliauskaite, Aiste"},{"first_name":"Tanja","last_name":"Kaufmann","full_name":"Kaufmann, Tanja"},{"full_name":"Schoeberl, Ursula E.","first_name":"Ursula E.","last_name":"Schoeberl"},{"last_name":"Puchinger","first_name":"Martin G.","full_name":"Puchinger, Martin G."},{"full_name":"Kostrhon, Sebastian","first_name":"Sebastian","last_name":"Kostrhon"},{"last_name":"Ebenwaldner","first_name":"Carmen","full_name":"Ebenwaldner, Carmen"},{"full_name":"Sebesta, Marek","last_name":"Sebesta","first_name":"Marek"},{"full_name":"Beltzung, Etienne","first_name":"Etienne","last_name":"Beltzung"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"full_name":"Lin, Gen","last_name":"Lin","first_name":"Gen"},{"full_name":"Vlasova, Anna","last_name":"Vlasova","first_name":"Anna"},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"},{"full_name":"Pavri, Rushad","last_name":"Pavri","first_name":"Rushad"},{"full_name":"Stark, Alexander","last_name":"Stark","first_name":"Alexander"},{"first_name":"Altuna","last_name":"Akalin","full_name":"Akalin, Altuna"},{"full_name":"Stefl, Richard","first_name":"Richard","last_name":"Stefl"},{"last_name":"Bernecky","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"last_name":"Slade","first_name":"Dea","full_name":"Slade, Dea"}],"article_number":"6078","file_date_updated":"2021-10-21T13:51:49Z","article_type":"original","citation":{"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.","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).","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","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.","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.","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"},"publication":"Nature Communications","date_published":"2021-10-19T00:00:00Z","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"has_accepted_license":"1","article_processing_charge":"No","day":"19","intvolume":" 12","ddc":["610"],"title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","status":"public","_id":"10163","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"d99fcd51aebde19c21314e3de0148007","success":1,"date_created":"2021-10-21T13:51:49Z","date_updated":"2021-10-21T13:51:49Z","relation":"main_file","file_id":"10169","content_type":"application/pdf","file_size":5111706,"creator":"cchlebak","access_level":"open_access","file_name":"2021_NatComm_Appel.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","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."}]},{"language":[{"iso":"eng"}],"doi":"10.1111/cgf.142626","isi":1,"quality_controlled":"1","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"external_id":{"isi":["000657959600017"]},"oa":1,"month":"05","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"date_updated":"2023-08-14T08:01:50Z","date_created":"2021-06-13T22:01:32Z","volume":40,"author":[{"full_name":"Rittig, Tobias","first_name":"Tobias","last_name":"Rittig"},{"full_name":"Sumin, Denis","first_name":"Denis","last_name":"Sumin"},{"full_name":"Babaei, Vahid","first_name":"Vahid","last_name":"Babaei"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"last_name":"Voloboy","first_name":"Alexey","full_name":"Voloboy, Alexey"},{"last_name":"Wilkie","first_name":"Alexander","full_name":"Wilkie, Alexander"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"},{"last_name":"Myszkowski","first_name":"Karol","full_name":"Myszkowski, Karol"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"},{"full_name":"Křivánek, Jaroslav","first_name":"Jaroslav","last_name":"Křivánek"}],"publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"Wiley","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).","year":"2021","file_date_updated":"2021-10-11T12:06:50Z","ec_funded":1,"date_published":"2021-05-01T00:00:00Z","article_type":"original","page":"205-219","publication":"Computer Graphics Forum","citation":{"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.","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.","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.","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","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.","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.","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"},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","file":[{"success":1,"checksum":"33271724215f54a75c39d2ed40f2c502","date_updated":"2021-10-11T12:06:50Z","date_created":"2021-10-11T12:06:50Z","file_id":"10120","relation":"main_file","creator":"bbickel","content_type":"application/pdf","file_size":26026501,"access_level":"open_access","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf"}],"status":"public","ddc":["004"],"title":"Neural acceleration of scattering-aware color 3D printing","intvolume":" 40","_id":"9547","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","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."}],"issue":"2","type":"journal_article"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2021-10-27T14:16:06Z","article_number":"abj0127","volume":7,"date_created":"2021-10-24T22:01:33Z","date_updated":"2023-08-14T08:04:42Z","author":[{"full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez","first_name":"Javier"},{"full_name":"Duan, Jiahua","last_name":"Duan","first_name":"Jiahua"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Kirill V.","last_name":"Voronin","full_name":"Voronin, Kirill V."},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ma, Weiliang","last_name":"Ma","first_name":"Weiliang"},{"last_name":"Bao","first_name":"Qiaoliang","full_name":"Bao, Qiaoliang"},{"last_name":"Volkov","first_name":"Valentyn S.","full_name":"Volkov, Valentyn S."},{"full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand","first_name":"Rainer"},{"full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y.","last_name":"Nikitin"},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"department":[{"_id":"NanoFab"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2021","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).","publication_identifier":{"eissn":["23752548"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abj0127","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"issue":"41","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"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":2441163,"creator":"cziletti","access_level":"open_access","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","success":1,"date_created":"2021-10-27T14:16:06Z","date_updated":"2021-10-27T14:16:06Z","relation":"main_file","file_id":"10189"}],"oa_version":"Published Version","intvolume":" 7","ddc":["530"],"title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","status":"public","_id":"10177","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","has_accepted_license":"1","day":"08","scopus_import":"1","date_published":"2021-10-08T00:00:00Z","article_type":"original","citation":{"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","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.","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","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.","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).","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."},"publication":"Science Advances"},{"citation":{"short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","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.","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.","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","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.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367."},"publication":"Nature","page":"364-367","article_type":"original","date_published":"2021-10-14T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"14","_id":"10146","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 598","title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV","status":"public","oa_version":"None","type":"journal_article","issue":"7880","abstract":[{"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.","lang":"eng"}],"external_id":{"pmid":["34616041"],"isi":["000704581600001"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-021-03927-z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"10","pmid":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.","year":"2021","department":[{"_id":"LeSa"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/"}]},"author":[{"full_name":"Vercellino, Irene","first_name":"Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"volume":598,"date_updated":"2023-08-14T08:01:21Z","date_created":"2021-10-17T22:01:17Z","ec_funded":1},{"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Journal of Mathematical Physics","citation":{"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","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.","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","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","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.","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","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."},"article_type":"original","date_published":"2021-10-01T00:00:00Z","type":"journal_article","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"}],"issue":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10176","status":"public","title":"Topological field theory on r-spin surfaces and the Arf-invariant","intvolume":" 62","oa_version":"Preprint","month":"10","publication_identifier":{"issn":["00222488"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.09978"}],"external_id":{"arxiv":["1802.09978"],"isi":["000755638500010"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1063/5.0037826","language":[{"iso":"eng"}],"article_number":"102302","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.”","year":"2021","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"MiLe"}],"author":[{"first_name":"Ingo","last_name":"Runkel","full_name":"Runkel, Ingo"},{"id":"7943226E-220E-11EA-94C7-D59F3DDC885E","orcid":"0000-0003-2834-5054","first_name":"Lorant","last_name":"Szegedy","full_name":"Szegedy, Lorant"}],"date_updated":"2023-08-14T08:04:12Z","date_created":"2021-10-24T22:01:32Z","volume":62},{"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.15252/embj.2021108714","isi":1,"quality_controlled":"1","external_id":{"pmid":["34661293"],"isi":["000708012800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2021-12-13T14:54:14Z","article_number":"e108714","volume":40,"date_created":"2021-10-24T22:01:34Z","date_updated":"2023-08-14T08:05:23Z","author":[{"full_name":"Bajaj, Sunanjay","first_name":"Sunanjay","last_name":"Bajaj"},{"last_name":"Bagley","first_name":"Joshua A.","full_name":"Bagley, Joshua A."},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vertesy","first_name":"Abel","full_name":"Vertesy, Abel"},{"full_name":"Nagumo Wong, Sakurako","last_name":"Nagumo Wong","first_name":"Sakurako"},{"full_name":"Krenn, Veronica","first_name":"Veronica","last_name":"Krenn"},{"last_name":"Lévi-Strauss","first_name":"Julie","full_name":"Lévi-Strauss, Julie"},{"full_name":"Knoblich, Juergen A.","last_name":"Knoblich","first_name":"Juergen A."}],"department":[{"_id":"Bio"}],"publisher":"Embo Press","publication_status":"published","pmid":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).","year":"2021","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"18","scopus_import":"1","date_published":"2021-10-18T00:00:00Z","article_type":"original","citation":{"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.","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).","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","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.","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","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021."},"publication":"EMBO Journal","issue":"23","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"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10541","date_created":"2021-12-13T14:54:14Z","date_updated":"2021-12-13T14:54:14Z","checksum":"78d2d02e775322297e774f72810a41a4","success":1,"file_name":"2021_EMBO_Bajaj.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7819881,"creator":"alisjak"}],"intvolume":" 40","ddc":["610"],"title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10179"},{"publication_identifier":{"eissn":["2041-1723"]},"month":"10","doi":"10.1038/s41467-021-26262-3","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2103.16986"],"isi":["000708601800015"]},"quality_controlled":"1","isi":1,"file_date_updated":"2021-11-03T11:31:24Z","article_number":"6063","author":[{"first_name":"Luca","last_name":"Sortino","full_name":"Sortino, Luca"},{"full_name":"Zotev, Panaiot G.","last_name":"Zotev","first_name":"Panaiot G."},{"last_name":"Phillips","first_name":"Catherine L.","full_name":"Phillips, Catherine L."},{"first_name":"Alistair J.","last_name":"Brash","full_name":"Brash, Alistair J."},{"full_name":"Cambiasso, Javier","first_name":"Javier","last_name":"Cambiasso"},{"full_name":"Marensi, Elena","first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","orcid":"0000-0001-7173-4923"},{"first_name":"A. Mark","last_name":"Fox","full_name":"Fox, A. Mark"},{"first_name":"Stefan A.","last_name":"Maier","full_name":"Maier, Stefan A."},{"first_name":"Riccardo","last_name":"Sapienza","full_name":"Sapienza, Riccardo"},{"last_name":"Tartakovskii","first_name":"Alexander I.","full_name":"Tartakovskii, Alexander I."}],"volume":12,"date_created":"2021-10-31T23:01:30Z","date_updated":"2023-08-14T08:12:12Z","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.","year":"2021","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","date_published":"2021-10-18T00:00:00Z","citation":{"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.","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).","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","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.","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","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."},"publication":"Nature Communications","article_type":"original","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"}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1434201,"creator":"cchlebak","file_name":"2021_NatComm_Sortino.pdf","access_level":"open_access","date_updated":"2021-11-03T11:31:24Z","date_created":"2021-11-03T11:31:24Z","checksum":"8580d128389860f732028c521cd5949e","success":1,"relation":"main_file","file_id":"10212"}],"_id":"10203","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","status":"public","ddc":["530"],"title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas"},{"article_number":"093043","file_date_updated":"2021-10-28T12:06:01Z","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","year":"2021","publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"IOP Publishing","author":[{"full_name":"Sahu, Preeti","first_name":"Preeti","last_name":"Sahu","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"last_name":"Schwarz","first_name":"J. M.","full_name":"Schwarz, J. M."},{"full_name":"Manning, M. Lisa","first_name":"M. Lisa","last_name":"Manning"}],"date_created":"2021-10-24T22:01:34Z","date_updated":"2023-08-14T08:10:31Z","volume":23,"month":"09","publication_identifier":{"eissn":["13672630"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1088/1367-2630/ac23f1","language":[{"iso":"eng"}],"type":"journal_article","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."}],"issue":"9","_id":"10178","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","status":"public","intvolume":" 23","file":[{"file_name":"2021_NewJPhys_Sahu.pdf","access_level":"open_access","creator":"cziletti","file_size":2215016,"content_type":"application/pdf","file_id":"10193","relation":"main_file","date_created":"2021-10-28T12:06:01Z","date_updated":"2021-10-28T12:06:01Z","success":1,"checksum":"ace603e8f0962b3ba55f23fa34f57764"}],"oa_version":"Published Version","scopus_import":"1","day":"29","article_processing_charge":"Yes","has_accepted_license":"1","publication":"New Journal of Physics","citation":{"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.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","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.","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","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.","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.","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"},"article_type":"original","date_published":"2021-09-29T00:00:00Z"},{"external_id":{"arxiv":["2012.10691"],"isi":["000705774800001"]},"main_file_link":[{"url":"https://arxiv.org/abs/2012.10691","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1007/s11228-021-00612-1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0927-6947"],"eissn":["1877-0541"]},"month":"10","year":"2021","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","author":[{"full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","last_name":"Ivanov"},{"full_name":"Lopushanski, Mariana S.","last_name":"Lopushanski","first_name":"Mariana S."}],"date_updated":"2023-08-14T08:11:38Z","date_created":"2021-10-24T22:01:35Z","citation":{"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.","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.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).","ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis.","ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” Set-Valued and Variational Analysis. Springer Nature, 2021.","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","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1"},"publication":"Set-Valued and Variational Analysis","article_type":"original","date_published":"2021-10-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"09","_id":"10181","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Rectifiable curves in proximally smooth sets","oa_version":"Published Version","type":"journal_article","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."}]},{"pmid":1,"year":"2021","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).","department":[{"_id":"CaHe"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"description":"Preprint","relation":"earlier_version","url":"https://doi.org/10.1101/2020.11.23.394171 "}]},"author":[{"full_name":"Pradhan, Saurabh J.","first_name":"Saurabh J.","last_name":"Pradhan"},{"full_name":"Reddy, Puli Chandramouli","last_name":"Reddy","first_name":"Puli Chandramouli"},{"last_name":"Smutny","first_name":"Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael"},{"full_name":"Sharma, Ankita","first_name":"Ankita","last_name":"Sharma"},{"last_name":"Sako","first_name":"Keisuke","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","full_name":"Sako, Keisuke"},{"last_name":"Oak","first_name":"Meghana S.","full_name":"Oak, Meghana S."},{"first_name":"Rini","last_name":"Shah","full_name":"Shah, Rini"},{"full_name":"Pal, Mrinmoy","first_name":"Mrinmoy","last_name":"Pal"},{"first_name":"Ojas","last_name":"Deshpande","full_name":"Deshpande, Ojas"},{"last_name":"Dsilva","first_name":"Greg","full_name":"Dsilva, Greg"},{"full_name":"Tang, Yin","first_name":"Yin","last_name":"Tang"},{"full_name":"Mishra, Rakesh","last_name":"Mishra","first_name":"Rakesh"},{"full_name":"Deshpande, Girish","first_name":"Girish","last_name":"Deshpande"},{"last_name":"Giraldez","first_name":"Antonio J.","full_name":"Giraldez, Antonio J."},{"first_name":"Mahendra","last_name":"Sonawane","full_name":"Sonawane, Mahendra"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Galande, Sanjeev","last_name":"Galande","first_name":"Sanjeev"}],"volume":12,"date_created":"2021-10-31T23:01:29Z","date_updated":"2023-08-14T10:32:48Z","article_number":"6094","file_date_updated":"2021-11-09T13:59:26Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000709050300016"],"pmid":["34667153"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-021-26234-7","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"month":"10","_id":"10202","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","status":"public","ddc":["570"],"file":[{"file_id":"10262","relation":"main_file","success":1,"checksum":"c40a69ae94435ecd3a30c9874a11ef2b","date_created":"2021-11-09T13:59:26Z","date_updated":"2021-11-09T13:59:26Z","access_level":"open_access","file_name":"2021_NatureComm_Pradhan.pdf","creator":"cziletti","content_type":"application/pdf","file_size":7144437}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","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."}],"citation":{"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.","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.","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","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.","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.","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)."},"publication":"Nature Communications","article_type":"original","date_published":"2021-10-19T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"19"},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2397203,"creator":"cchlebak","file_name":"2021_FrontiersMicrob_Qi.pdf","access_level":"open_access","date_created":"2021-11-11T10:54:40Z","date_updated":"2021-11-11T10:54:40Z","checksum":"d41321748e9588dd3cf03e9a7222127f","success":1,"relation":"main_file","file_id":"10272"}],"title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","status":"public","ddc":["610"],"intvolume":" 12","_id":"10271","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2021-10-20T00:00:00Z","article_type":"original","publication":"Frontiers in Microbiology","citation":{"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.","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.","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","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.","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.","short":"Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021)."},"day":"20","article_processing_charge":"No","has_accepted_license":"1","keyword":["microbiology"],"scopus_import":"1","date_created":"2021-11-11T10:39:37Z","date_updated":"2023-08-14T11:43:23Z","volume":12,"author":[{"id":"3B22D412-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6148-2416","first_name":"Qin","last_name":"Qi","full_name":"Qi, Qin"},{"full_name":"Angermayr, S. Andreas","first_name":"S. Andreas","last_name":"Angermayr"},{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"publication_status":"published","publisher":"Frontiers","year":"2021","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.","pmid":1,"file_date_updated":"2021-11-11T10:54:40Z","ec_funded":1,"article_number":"760017","language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2021.760017","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000715997300001"],"pmid":["34745067"]},"month":"10","publication_identifier":{"eissn":["1664-302X"]}},{"language":[{"iso":"eng"}],"doi":"10.1007/s00220-021-04239-z","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2012.13215"],"isi":["000712232700001"]},"oa":1,"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"10","volume":388,"date_updated":"2023-08-14T10:29:49Z","date_created":"2021-11-07T23:01:25Z","author":[{"last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","department":[{"_id":"LaEr"}],"publication_status":"published","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2021","file_date_updated":"2022-02-02T10:19:55Z","date_published":"2021-10-29T00:00:00Z","page":"1005–1048","article_type":"original","citation":{"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","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.","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","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.","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.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048.","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."},"publication":"Communications in Mathematical Physics","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"29","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2022-02-02T10:19:55Z","date_created":"2022-02-02T10:19:55Z","checksum":"a2c7b6f5d23b5453cd70d1261272283b","success":1,"relation":"main_file","file_id":"10715","content_type":"application/pdf","file_size":841426,"creator":"cchlebak","file_name":"2021_CommunMathPhys_Cipolloni.pdf","access_level":"open_access"}],"intvolume":" 388","ddc":["510"],"status":"public","title":"Eigenstate thermalization hypothesis for Wigner matrices","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10221","issue":"2","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)."}],"type":"journal_article"},{"isi":1,"quality_controlled":"1","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2101.12566"],"isi":["000710850600001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00205-021-01715-7","month":"10","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"year":"2021","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).","date_created":"2021-11-07T23:01:26Z","date_updated":"2023-08-14T10:32:19Z","volume":242,"author":[{"first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9787"}]},"file_date_updated":"2021-12-14T08:35:42Z","ec_funded":1,"article_type":"original","page":"1835–1906","publication":"Archive for Rational Mechanics and Analysis","citation":{"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","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.","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.","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","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.","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906.","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."},"date_published":"2021-10-25T00:00:00Z","scopus_import":"1","day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","status":"public","ddc":["530"],"title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","intvolume":" 242","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10224","file":[{"file_name":"2021_Springer_Feliciangeli.pdf","access_level":"open_access","creator":"alisjak","file_size":990529,"content_type":"application/pdf","file_id":"10544","relation":"main_file","date_updated":"2021-12-14T08:35:42Z","date_created":"2021-12-14T08:35:42Z","success":1,"checksum":"672e9c21b20f1a50854b7c821edbb92f"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"3"},{"ec_funded":1,"file_date_updated":"2022-05-16T07:02:27Z","article_number":"1746","author":[{"full_name":"Vasic, Verica","first_name":"Verica","last_name":"Vasic"},{"full_name":"Jones, Mattson S.O.","last_name":"Jones","first_name":"Mattson S.O."},{"full_name":"Haslinger, Denise","first_name":"Denise","last_name":"Haslinger","id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E"},{"last_name":"Knaus","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"first_name":"Michael J.","last_name":"Schmeisser","full_name":"Schmeisser, Michael J."},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"},{"full_name":"Chiocchetti, Andreas G.","first_name":"Andreas G.","last_name":"Chiocchetti"}],"volume":12,"date_updated":"2023-08-14T11:46:12Z","date_created":"2021-11-14T23:01:24Z","year":"2021","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.","publisher":"MDPI","department":[{"_id":"GaNo"}],"publication_status":"published","publication_identifier":{"eissn":["2073-4425"]},"month":"10","doi":"10.3390/genes12111746","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000834044200002"]},"project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"issue":"11","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"}],"type":"journal_article","alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"file":[{"relation":"main_file","file_id":"11380","date_created":"2022-05-16T07:02:27Z","date_updated":"2022-05-16T07:02:27Z","checksum":"256cb832a9c3051c7dc741f6423b8cbd","success":1,"file_name":"2021_Genes_Vasic.pdf","access_level":"open_access","file_size":1335308,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"10281","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","ddc":["570"],"title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2021-10-30T00:00:00Z","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.","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.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021).","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.","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","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.","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"},"publication":"Genes","article_type":"original"},{"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10282","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","status":"public","intvolume":" 233","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2021-11-05T00:00:00Z","publication":"New Phytologist","citation":{"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.","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.","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.","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.","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.","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"},"article_type":"original","page":"329-343","day":"05","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Ivan","last_name":"Kashkan","full_name":"Kashkan, Ivan"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"last_name":"Retzer","first_name":"Katarzyna","full_name":"Retzer, Katarzyna"},{"first_name":"Jana","last_name":"Humpolíčková","full_name":"Humpolíčková, Jana"},{"full_name":"Jayasree, Aswathy","first_name":"Aswathy","last_name":"Jayasree"},{"last_name":"Filepová","first_name":"Roberta","full_name":"Filepová, Roberta"},{"full_name":"Vondráková, Zuzana","last_name":"Vondráková","first_name":"Zuzana"},{"first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"first_name":"Debbie","last_name":"Rombaut","full_name":"Rombaut, Debbie"},{"full_name":"Jacobs, Thomas B.","first_name":"Thomas B.","last_name":"Jacobs"},{"first_name":"Mikko J.","last_name":"Frilander","full_name":"Frilander, Mikko J."},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Růžička, Kamil","first_name":"Kamil","last_name":"Růžička"}],"date_updated":"2023-08-14T11:46:43Z","date_created":"2021-11-14T23:01:24Z","volume":233,"year":"2021","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.","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","doi":"10.1111/nph.17792","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}],"oa":1,"external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]}},{"related_material":{"record":[{"id":"8183","relation":"earlier_version","status":"public"},{"relation":"earlier_version","status":"public","id":"9308"}]},"author":[{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey","full_name":"Avvakumov, Sergey"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard","first_name":"Isaac","full_name":"Mabillard, Isaac"},{"full_name":"Skopenkov, Arkadiy B.","last_name":"Skopenkov","first_name":"Arkadiy B."},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"volume":245,"date_created":"2021-11-07T23:01:24Z","date_updated":"2023-08-14T11:43:55Z","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.","year":"2021","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","publication_identifier":{"issn":["0021-2172"],"eissn":["1565-8511"]},"month":"10","doi":"10.1007/s11856-021-2216-z","language":[{"iso":"eng"}],"external_id":{"isi":["000712942100013"],"arxiv":["1511.03501"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"oa":1,"project":[{"grant_number":"P31312","_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory"}],"isi":1,"quality_controlled":"1","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."}],"type":"journal_article","oa_version":"Preprint","_id":"10220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 245","status":"public","title":"Eliminating higher-multiplicity intersections. III. Codimension 2","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2021-10-30T00:00:00Z","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.","short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 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","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.","ista":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.","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"},"publication":"Israel Journal of Mathematics","page":"501–534 ","article_type":"original"},{"title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","ddc":["570"],"status":"public","publisher":"Dryad","department":[{"_id":"SyCr"}],"_id":"13061","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-14T11:45:28Z","date_created":"2023-05-23T16:14:35Z","oa_version":"Published Version","author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull","full_name":"Pull, Christopher"},{"full_name":"Naiser, Filip","last_name":"Naiser","first_name":"Filip"},{"last_name":"Naderlinger","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth"},{"first_name":"Jiri","last_name":"Matas","full_name":"Matas, Jiri"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"id":"10284","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"text":"Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.","lang":"eng"}],"ec_funded":1,"project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"citation":{"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","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.","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.","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","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.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021).","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."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.7pvmcvdtj","open_access":"1"}],"doi":"10.5061/DRYAD.7PVMCVDTJ","date_published":"2021-10-29T00:00:00Z","day":"29","month":"10","article_processing_charge":"No"}]