[{"abstract":[{"text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"885b746051a7a6b6e24e3d2781a48fde","date_updated":"2021-06-28T11:35:30Z","date_created":"2021-06-28T11:35:30Z","file_id":"9609","relation":"main_file","creator":"asandaue","file_size":2500720,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_ELife_Bespalov.pdf"}],"intvolume":" 10","ddc":["570"],"status":"public","title":"Introduction to the EQIPD quality system","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9607","has_accepted_license":"1","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2021-05-24T00:00:00Z","article_type":"original","citation":{"ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294."},"publication":"eLife","file_date_updated":"2021-06-28T11:35:30Z","volume":10,"date_created":"2021-06-27T22:01:49Z","date_updated":"2023-08-10T13:36:50Z","author":[{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"full_name":"Bernard, René","first_name":"René","last_name":"Bernard"},{"full_name":"Gilis, Anja","last_name":"Gilis","first_name":"Anja"},{"last_name":"Gerlach","first_name":"Björn","full_name":"Gerlach, Björn"},{"first_name":"Javier","last_name":"Guillén","full_name":"Guillén, Javier"},{"first_name":"Vincent","last_name":"Castagné","full_name":"Castagné, Vincent"},{"last_name":"Lefevre","first_name":"Isabel A.","full_name":"Lefevre, Isabel A."},{"full_name":"Ducrey, Fiona","last_name":"Ducrey","first_name":"Fiona"},{"last_name":"Monk","first_name":"Lee","full_name":"Monk, Lee"},{"first_name":"Sandrine","last_name":"Bongiovanni","full_name":"Bongiovanni, Sandrine"},{"full_name":"Altevogt, Bruce","first_name":"Bruce","last_name":"Altevogt"},{"first_name":"María","last_name":"Arroyo-Araujo","full_name":"Arroyo-Araujo, María"},{"first_name":"Lior","last_name":"Bikovski","full_name":"Bikovski, Lior"},{"last_name":"De Bruin","first_name":"Natasja","full_name":"De Bruin, Natasja"},{"full_name":"Castaños-Vélez, Esmeralda","first_name":"Esmeralda","last_name":"Castaños-Vélez"},{"full_name":"Dityatev, Alexander","last_name":"Dityatev","first_name":"Alexander"},{"last_name":"Emmerich","first_name":"Christoph H.","full_name":"Emmerich, Christoph H."},{"full_name":"Fares, Raafat","last_name":"Fares","first_name":"Raafat"},{"last_name":"Ferland-Beckham","first_name":"Chantelle","full_name":"Ferland-Beckham, Chantelle"},{"full_name":"Froger-Colléaux, Christelle","last_name":"Froger-Colléaux","first_name":"Christelle"},{"full_name":"Gailus-Durner, Valerie","first_name":"Valerie","last_name":"Gailus-Durner"},{"last_name":"Hölter","first_name":"Sabine M.","full_name":"Hölter, Sabine M."},{"first_name":"Martine Cj","last_name":"Hofmann","full_name":"Hofmann, Martine Cj"},{"first_name":"Patricia","last_name":"Kabitzke","full_name":"Kabitzke, Patricia"},{"full_name":"Kas, Martien Jh","first_name":"Martien Jh","last_name":"Kas"},{"last_name":"Kurreck","first_name":"Claudia","full_name":"Kurreck, Claudia"},{"last_name":"Moser","first_name":"Paul","full_name":"Moser, Paul"},{"full_name":"Pietraszek, Malgorzata","last_name":"Pietraszek","first_name":"Malgorzata"},{"full_name":"Popik, Piotr","last_name":"Popik","first_name":"Piotr"},{"full_name":"Potschka, Heidrun","last_name":"Potschka","first_name":"Heidrun"},{"first_name":"Ernesto","last_name":"Prado Montes De Oca","full_name":"Prado Montes De Oca, Ernesto"},{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"last_name":"Riedel","first_name":"Gernot","full_name":"Riedel, Gernot"},{"full_name":"Ritskes-Hoitinga, Merel","last_name":"Ritskes-Hoitinga","first_name":"Merel"},{"full_name":"Samardzic, Janko","first_name":"Janko","last_name":"Samardzic"},{"full_name":"Schunn, Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","first_name":"Michael","last_name":"Schunn"},{"full_name":"Stöger, Claudia","first_name":"Claudia","last_name":"Stöger"},{"full_name":"Voikar, Vootele","first_name":"Vootele","last_name":"Voikar"},{"last_name":"Vollert","first_name":"Jan","full_name":"Vollert, Jan"},{"full_name":"Wever, Kimberley E.","last_name":"Wever","first_name":"Kimberley E."},{"first_name":"Kathleen","last_name":"Wuyts","full_name":"Wuyts, Kathleen"},{"full_name":"Macleod, Malcolm R.","last_name":"Macleod","first_name":"Malcolm R."},{"full_name":"Dirnagl, Ulrich","last_name":"Dirnagl","first_name":"Ulrich"},{"last_name":"Steckler","first_name":"Thomas","full_name":"Steckler, Thomas"}],"publisher":"eLife Sciences Publications","department":[{"_id":"PreCl"}],"publication_status":"published","pmid":1,"acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","year":"2021","publication_identifier":{"eissn":["2050084X"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.7554/eLife.63294","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"},"external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"oa":1},{"file_date_updated":"2021-06-28T08:04:22Z","article_number":"3804","author":[{"first_name":"Laura","last_name":"Santini","full_name":"Santini, Laura"},{"full_name":"Halbritter, Florian","last_name":"Halbritter","first_name":"Florian"},{"full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira","first_name":"Fabian"},{"full_name":"Suzuki, Toru","last_name":"Suzuki","first_name":"Toru"},{"last_name":"Asami","first_name":"Maki","full_name":"Asami, Maki"},{"full_name":"Ma, Xiaoyan","first_name":"Xiaoyan","last_name":"Ma"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"full_name":"Lackner, Andreas","last_name":"Lackner","first_name":"Andreas"},{"full_name":"Warr, Nick","last_name":"Warr","first_name":"Nick"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Laue, Ernest","first_name":"Ernest","last_name":"Laue"},{"last_name":"Farlik","first_name":"Matthias","full_name":"Farlik, Matthias"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"last_name":"Beyer","first_name":"Andreas","full_name":"Beyer, Andreas"},{"last_name":"Perry","first_name":"Anthony C.F.","full_name":"Perry, Anthony C.F."},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"}],"volume":12,"date_updated":"2023-08-10T13:53:23Z","date_created":"2021-06-27T22:01:46Z","acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","year":"2021","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"month":"07","doi":"10.1038/s41467-021-23510-4","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":["000667248600005"]},"isi":1,"quality_controlled":"1","issue":"1","abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2021-06-28T08:04:22Z","date_created":"2021-06-28T08:04:22Z","checksum":"75dd89d09945185b2d14b2434a0bcb50","success":1,"relation":"main_file","file_id":"9608","content_type":"application/pdf","file_size":2156554,"creator":"asandaue","file_name":"2021_NatureCommunications_Santini.pdf","access_level":"open_access"}],"_id":"9601","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","status":"public","title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2021-07-12T00:00:00Z","citation":{"ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4","ieee":"L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23510-4","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4.","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:10.1038/s41467-021-23510-4.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021)."},"publication":"Nature Communications","article_type":"original"},{"type":"journal_article","abstract":[{"lang":"eng","text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees."}],"ddc":["510"],"status":"public","title":"Erdős-Hajnal-type results for monotone paths","intvolume":" 151","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9602","oa_version":"Published Version","file":[{"checksum":"15fbc9064cd9d1c777ac0043b78c8f12","success":1,"date_created":"2021-06-28T13:33:23Z","date_updated":"2021-06-28T13:33:23Z","relation":"main_file","file_id":"9612","content_type":"application/pdf","file_size":418168,"creator":"asandaue","access_level":"open_access","file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf"}],"scopus_import":"1","day":"09","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"21-37","publication":"Journal of Combinatorial Theory. Series B","citation":{"short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.","mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp. 21–37, doi:10.1016/j.jctb.2021.05.004.","chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004.","ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021.","apa":"Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004","ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37."},"date_published":"2021-06-09T00:00:00Z","file_date_updated":"2021-06-28T13:33:23Z","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2021","acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","date_updated":"2023-08-10T13:38:00Z","date_created":"2021-06-27T22:01:47Z","volume":151,"author":[{"last_name":"Pach","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János"},{"full_name":"Tomon, István","last_name":"Tomon","first_name":"István"}],"month":"06","publication_identifier":{"issn":["0095-8956"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"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":["000702280800002"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.jctb.2021.05.004"},{"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9606","intvolume":" 103","status":"public","title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","issue":"6","abstract":[{"text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results.","lang":"eng"}],"type":"journal_article","date_published":"2021-06-01T00:00:00Z","citation":{"mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303.","short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303.","ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6). doi:10.1103/PhysRevA.103.L061303","ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","apa":"Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” Physical Review A, vol. 103, no. 6. American Physical Society, 2021."},"publication":"Physical Review A","article_type":"letter_note","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"first_name":"A.","last_name":"Tononi","full_name":"Tononi, A."},{"full_name":"Cappellaro, Alberto","first_name":"Alberto","last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359"},{"full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Salasnich","first_name":"L.","full_name":"Salasnich, L."}],"volume":103,"date_updated":"2023-08-10T13:37:25Z","date_created":"2021-06-27T22:01:49Z","acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","year":"2021","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","article_number":"L061303","doi":"10.1103/PhysRevA.103.L061303","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06491"}],"oa":1,"external_id":{"isi":["000662296700014"],"arxiv":["2009.06491"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"month":"06"},{"month":"07","publication_identifier":{"eissn":["22111247"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2021.109313","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","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"},"external_id":{"pmid":["34233180"],"isi":["000670188500004"]},"oa":1,"file_date_updated":"2021-07-19T13:32:17Z","ec_funded":1,"article_number":"109313","date_created":"2021-07-11T22:01:16Z","date_updated":"2023-08-10T14:09:39Z","volume":36,"author":[{"full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro"},{"full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","first_name":"Rouven"},{"last_name":"De Jesús-Cortés","first_name":"Héctor","full_name":"De Jesús-Cortés, Héctor"},{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes"},{"id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","first_name":"Balint","last_name":"Nagy","full_name":"Nagy, Balint"},{"full_name":"Reilly-Andújar, Francis","first_name":"Francis","last_name":"Reilly-Andújar"},{"full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","first_name":"Gloria"},{"full_name":"Cubero, Ryan J","last_name":"Cubero","first_name":"Ryan J","orcid":"0000-0003-0002-1867","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","last_name":"Schoot Uiterkamp","first_name":"Florianne E"},{"first_name":"Mark F.","last_name":"Bear","full_name":"Bear, Mark F."},{"last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/"}]},"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Elsevier","acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","year":"2021","pmid":1,"day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2021-07-06T00:00:00Z","article_type":"original","publication":"Cell Reports","citation":{"ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313","ieee":"A. Venturino et al., “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” Cell Reports, vol. 36, no. 1. Elsevier, 2021.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier, 2021. https://doi.org/10.1016/j.celrep.2021.109313."},"abstract":[{"lang":"eng","text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2021-07-19T13:32:17Z","date_created":"2021-07-19T13:32:17Z","success":1,"checksum":"f056255f6d01fd9a86b5387635928173","file_id":"9693","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":56388540,"file_name":"2021_CellReports_Venturino.pdf","access_level":"open_access"}],"ddc":["570"],"status":"public","title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","intvolume":" 36","_id":"9642","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"file_date_updated":"2021-06-28T14:06:24Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_number":"109274","author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena","full_name":"Contreras, Ximena"},{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole"},{"full_name":"Davaatseren, Amarbayasgalan","first_name":"Amarbayasgalan","last_name":"Davaatseren","id":"70ADC922-B424-11E9-99E3-BA18E6697425"},{"first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"full_name":"Sonntag, Johanna","first_name":"Johanna","last_name":"Sonntag","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Andersen","first_name":"Lill","full_name":"Andersen, Lill"},{"first_name":"Tina","last_name":"Bernthaler","full_name":"Bernthaler, Tina"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena","last_name":"Heger","full_name":"Heger, Anna-Magdalena"},{"first_name":"Randy L.","last_name":"Johnson","full_name":"Johnson, Randy L."},{"first_name":"Lindsay A.","last_name":"Schwarz","full_name":"Schwarz, Lindsay A."},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","description":"News on IST Homepage","relation":"press_release"}]},"date_updated":"2023-08-10T13:55:00Z","date_created":"2021-06-27T22:01:48Z","volume":35,"acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","year":"2021","publication_status":"published","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"publisher":"Cell Press","month":"06","publication_identifier":{"eissn":["22111247"]},"doi":"10.1016/j.celrep.2021.109274","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000664463600016"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"abstract":[{"text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.","lang":"eng"}],"issue":"12","type":"journal_article","oa_version":"Published Version","file":[{"creator":"asandaue","file_size":7653149,"content_type":"application/pdf","file_name":"2021_CellReports_Contreras.pdf","access_level":"open_access","date_updated":"2021-06-28T14:06:24Z","date_created":"2021-06-28T14:06:24Z","success":1,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77","file_id":"9613","relation":"main_file"}],"_id":"9603","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","intvolume":" 35","day":"22","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2021-06-22T00:00:00Z","publication":"Cell Reports","citation":{"chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274.","ieee":"X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274"},"article_type":"original"},{"ec_funded":1,"file_date_updated":"2021-09-23T14:00:05Z","volume":371,"date_created":"2021-06-29T12:04:05Z","date_updated":"2023-08-10T13:57:07Z","author":[{"full_name":"Bluvstein, D.","last_name":"Bluvstein","first_name":"D."},{"full_name":"Omran, A.","first_name":"A.","last_name":"Omran"},{"last_name":"Levine","first_name":"H.","full_name":"Levine, H."},{"full_name":"Keesling, A.","last_name":"Keesling","first_name":"A."},{"last_name":"Semeghini","first_name":"G.","full_name":"Semeghini, G."},{"full_name":"Ebadi, S.","last_name":"Ebadi","first_name":"S."},{"last_name":"Wang","first_name":"T. T.","full_name":"Wang, T. T."},{"orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios","full_name":"Michailidis, Alexios"},{"last_name":"Maskara","first_name":"N.","full_name":"Maskara, N."},{"first_name":"W. W.","last_name":"Ho","full_name":"Ho, W. W."},{"full_name":"Choi, S.","last_name":"Choi","first_name":"S."},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"first_name":"M.","last_name":"Greiner","full_name":"Greiner, M."},{"full_name":"Vuletić, V.","last_name":"Vuletić","first_name":"V."},{"full_name":"Lukin, M. D.","last_name":"Lukin","first_name":"M. D."}],"publisher":"AAAS","department":[{"_id":"MaSe"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.","year":"2021","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1126/science.abg2530","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2012.12276"],"isi":["000636043400048"],"pmid":["33632894"]},"oa":1,"issue":"6536","abstract":[{"lang":"eng","text":"The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science."}],"type":"journal_article","oa_version":"Preprint","file":[{"access_level":"open_access","file_name":"scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf","creator":"patrickd","content_type":"application/pdf","file_size":3671159,"file_id":"10040","relation":"main_file","success":1,"checksum":"0b356fd10ab9bb95177d4c047d4e9c1a","date_created":"2021-09-23T14:00:05Z","date_updated":"2021-09-23T14:00:05Z"}],"intvolume":" 371","title":"Controlling quantum many-body dynamics in driven Rydberg atom arrays","ddc":["539"],"status":"public","_id":"9618","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"No","day":"26","keyword":["Multidisciplinary"],"scopus_import":"1","date_published":"2021-03-26T00:00:00Z","page":"1355-1359","article_type":"original","citation":{"mla":"Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530.","short":"D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.","chicago":"Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530.","ama":"Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530","ista":"Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359.","apa":"Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530","ieee":"D. Bluvstein et al., “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021."},"publication":"Science"},{"file_date_updated":"2021-07-19T12:13:34Z","pmid":1,"year":"2021","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"last_name":"Gao","first_name":"Z","full_name":"Gao, Z"},{"last_name":"Chen","first_name":"Z","full_name":"Chen, Z"},{"last_name":"Cui","first_name":"Y","full_name":"Cui, Y"},{"full_name":"Ke, M","first_name":"M","last_name":"Ke"},{"full_name":"Xu, H","last_name":"Xu","first_name":"H"},{"full_name":"Xu, Q","first_name":"Q","last_name":"Xu"},{"full_name":"Chen, J","last_name":"Chen","first_name":"J"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Huang","first_name":"L","full_name":"Huang, L"},{"last_name":"Zhao","first_name":"H","full_name":"Zhao, H"},{"full_name":"Huang, D","first_name":"D","last_name":"Huang"},{"full_name":"Mai, S","last_name":"Mai","first_name":"S"},{"first_name":"T","last_name":"Xu","full_name":"Xu, T"},{"first_name":"X","last_name":"Liu","full_name":"Liu, X"},{"full_name":"Li, S","last_name":"Li","first_name":"S"},{"full_name":"Guan, Y","first_name":"Y","last_name":"Guan"},{"full_name":"Yang, W","first_name":"W","last_name":"Yang"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Petrášek","first_name":"J","full_name":"Petrášek, J"},{"last_name":"Zhang","first_name":"J","full_name":"Zhang, J"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"volume":33,"date_created":"2021-07-14T15:32:43Z","date_updated":"2023-08-10T14:01:41Z","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"month":"07","external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1093/plcell/koab183","language":[{"iso":"eng"}],"type":"journal_article","issue":"9","abstract":[{"text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.","lang":"eng"}],"_id":"9657","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 33","status":"public","title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","ddc":["580"],"file":[{"checksum":"6715712ec306c321f0204c817b7f8ae7","success":1,"date_updated":"2021-07-19T12:13:34Z","date_created":"2021-07-19T12:13:34Z","relation":"main_file","file_id":"9691","content_type":"application/pdf","file_size":10566921,"creator":"cziletti","access_level":"open_access","file_name":"2021_PlantCell_Gao.pdf"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"07","citation":{"mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183.","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","ieee":"Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183"},"publication":"Plant Cell","page":"2981–3003","article_type":"original","date_published":"2021-07-07T00:00:00Z"},{"author":[{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"date_updated":"2023-08-10T14:05:09Z","date_created":"2021-07-11T22:01:15Z","volume":12,"acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","file_date_updated":"2021-07-19T13:02:20Z","ec_funded":1,"article_number":"4009","doi":"10.1038/s41467-021-24271-w","language":[{"iso":"eng"}],"external_id":{"pmid":["34188036"],"isi":["000671752100003"]},"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,"quality_controlled":"1","isi":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"month":"06","publication_identifier":{"eissn":["20411723"]},"oa_version":"Published Version","file":[{"date_updated":"2021-07-19T13:02:20Z","date_created":"2021-07-19T13:02:20Z","checksum":"5767418926a7f7fb76151de29473dae0","success":1,"relation":"main_file","file_id":"9692","content_type":"application/pdf","file_size":628992,"creator":"cziletti","file_name":"2021_NatCoom_Tkadlec.pdf","access_level":"open_access"}],"_id":"9640","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["510"],"title":"Fast and strong amplifiers of natural selection","status":"public","intvolume":" 12","abstract":[{"text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2021-06-29T00:00:00Z","publication":"Nature Communications","citation":{"apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-24271-w","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w."},"article_type":"original","day":"29","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"title":"PIN-mediated polar auxin transport regulations in plant tropic responses","ddc":["580"],"status":"public","intvolume":" 232","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9656","file":[{"checksum":"6422a6eb329b52d96279daaee0fcf189","success":1,"date_created":"2021-10-07T13:42:47Z","date_updated":"2021-10-07T13:42:47Z","relation":"main_file","file_id":"10105","content_type":"application/pdf","file_size":1939800,"creator":"kschuh","access_level":"open_access","file_name":"2021_NewPhytologist_Han.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment."}],"issue":"2","article_type":"original","page":"510-522","publication":"New Phytologist","citation":{"ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522. doi:10.1111/nph.17617","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” New Phytologist, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. Wiley. https://doi.org/10.1111/nph.17617","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:10.1111/nph.17617.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617."},"date_published":"2021-10-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","year":"2021","pmid":1,"date_updated":"2023-08-10T14:02:41Z","date_created":"2021-07-14T15:29:14Z","volume":232,"author":[{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski"},{"last_name":"Qi","first_name":"Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin"},{"full_name":"Alotaibi, SS","first_name":"SS","last_name":"Alotaibi"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-10-07T13:42:47Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"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":{"pmid":["34254313"],"isi":["000680587100001"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.17617","month":"10","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]}},{"acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","year":"2021","publisher":"IOP Publishing","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"full_name":"Marchukov, Oleksandr V.","last_name":"Marchukov","first_name":"Oleksandr V."},{"full_name":"Hammer, Hans Werner","first_name":"Hans Werner","last_name":"Hammer"},{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"volume":23,"date_updated":"2023-08-10T13:58:09Z","date_created":"2021-07-18T22:01:22Z","article_number":"065009","ec_funded":1,"file_date_updated":"2021-07-19T11:47:16Z","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":["000664736300001"],"arxiv":["2102.04961"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.1088/1367-2630/ac0576","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["13672630"]},"month":"06","_id":"9679","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 23","ddc":["530"],"status":"public","title":"Morphology of three-body quantum states from machine learning","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3868445,"creator":"cziletti","access_level":"open_access","file_name":"2021_NewJPhys_Huber.pdf","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","success":1,"date_created":"2021-07-19T11:47:16Z","date_updated":"2021-07-19T11:47:16Z","relation":"main_file","file_id":"9690"}],"type":"journal_article","issue":"6","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"citation":{"ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” New Journal of Physics, vol. 23, no. 6. IOP Publishing, 2021.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:10.1088/1367-2630/ac0576.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576."},"publication":"New Journal of Physics","article_type":"original","date_published":"2021-06-23T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"23"},{"type":"journal_article","abstract":[{"text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis.","lang":"eng"}],"title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","status":"public","intvolume":" 23","_id":"9629","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","day":"21","article_processing_charge":"No","article_type":"original","page":"733–744","publication":"Nature Cell Biology","citation":{"chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021, pp. 733–744, doi:10.1038/s41556-021-00700-2.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","ieee":"Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744, 2021.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2"},"date_published":"2021-06-21T00:00:00Z","ec_funded":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","pmid":1,"date_updated":"2023-08-10T13:57:36Z","date_created":"2021-07-04T22:01:25Z","volume":23,"author":[{"first_name":"Qiutan","last_name":"Yang","full_name":"Yang, Qiutan"},{"full_name":"Xue, Shi-lei","first_name":"Shi-lei","last_name":"Xue","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chan, Chii Jou","first_name":"Chii Jou","last_name":"Chan"},{"full_name":"Rempfler, Markus","first_name":"Markus","last_name":"Rempfler"},{"first_name":"Dario","last_name":"Vischi","full_name":"Vischi, Dario"},{"last_name":"Maurer-Gutierrez","first_name":"Francisca","full_name":"Maurer-Gutierrez, Francisca"},{"full_name":"Hiiragi, Takashi","last_name":"Hiiragi","first_name":"Takashi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"last_name":"Liberali","first_name":"Prisca","full_name":"Liberali, Prisca"}],"month":"06","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"external_id":{"pmid":["34155381"],"isi":["000664016300003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41556-021-00700-2"},{"month":"06","publication_identifier":{"eissn":["2542-5293"]},"doi":"10.1016/j.mtphys.2021.100452","language":[{"iso":"eng"}],"external_id":{"isi":["000703159600010"]},"isi":1,"quality_controlled":"1","article_number":"100452","author":[{"full_name":"Su, Lizhong","first_name":"Lizhong","last_name":"Su"},{"first_name":"Tao","last_name":"Hong","full_name":"Hong, Tao"},{"full_name":"Wang, Dongyang","last_name":"Wang","first_name":"Dongyang"},{"last_name":"Wang","first_name":"Sining","full_name":"Wang, Sining"},{"last_name":"Qin","first_name":"Bingchao","full_name":"Qin, Bingchao"},{"last_name":"Zhang","first_name":"Mengmeng","full_name":"Zhang, Mengmeng"},{"full_name":"Gao, Xiang","first_name":"Xiang","last_name":"Gao"},{"full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"date_updated":"2023-08-10T13:56:31Z","date_created":"2021-07-04T22:01:24Z","volume":20,"year":"2021","acknowledgement":"This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements.","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"Elsevier","day":"03","article_processing_charge":"No","scopus_import":"1","date_published":"2021-06-03T00:00:00Z","publication":"Materials Today Physics","citation":{"ista":"Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452.","apa":"Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. Elsevier. https://doi.org/10.1016/j.mtphys.2021.100452","ieee":"L. Su et al., “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” Materials Today Physics, vol. 20. Elsevier, 2021.","ama":"Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 2021;20. doi:10.1016/j.mtphys.2021.100452","chicago":"Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics. Elsevier, 2021. https://doi.org/10.1016/j.mtphys.2021.100452.","mla":"Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics, vol. 20, 100452, Elsevier, 2021, doi:10.1016/j.mtphys.2021.100452.","short":"L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021)."},"article_type":"original","abstract":[{"lang":"eng","text":"SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors."}],"type":"journal_article","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9626","title":"Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation","status":"public","intvolume":" 20"},{"type":"journal_article","abstract":[{"text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.","lang":"eng"}],"issue":"1","ddc":["570"],"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","status":"public","intvolume":" 12","_id":"9778","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_name":"2021_NatureCommunications_Vandael.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3108845,"creator":"kschuh","relation":"main_file","file_id":"10563","date_created":"2021-12-17T11:34:50Z","date_updated":"2021-12-17T11:34:50Z","checksum":"6036a8cdae95e1707c2a04d54e325ff4","success":1}],"keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Nature Communications","citation":{"ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23153-5","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912.","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications, vol. 12, no. 1. Springer, 2021.","apa":"Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications, vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5."},"date_published":"2021-05-18T00:00:00Z","article_number":"2912","file_date_updated":"2021-12-17T11:34:50Z","ec_funded":1,"publication_status":"published","publisher":"Springer","department":[{"_id":"PeJo"}],"year":"2021","acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","date_updated":"2023-08-10T14:16:16Z","date_created":"2021-08-06T07:22:55Z","volume":12,"author":[{"full_name":"Vandael, David H","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676"},{"orcid":"0000-0003-0408-6094","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","first_name":"Yuji","full_name":"Okamoto, Yuji"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/","relation":"press_release","description":"News on IST Homepage"}]},"month":"05","publication_identifier":{"issn":["2041-1723"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"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":["000655481800014"]},"oa":1,"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-23153-5"},{"abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"11364","date_created":"2022-05-12T12:13:27Z","date_updated":"2022-05-12T12:13:27Z","checksum":"d3aef34cfb13e53bba4cf44d01680793","success":1,"file_name":"2021_TheoreticalComputerScience_Petrov.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2566504,"creator":"dernst"}],"oa_version":"Published Version","ddc":["004"],"title":"Long lived transients in gene regulation","status":"public","intvolume":" 893","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9647","day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-06-04T00:00:00Z","article_type":"original","page":"1-16","publication":"Theoretical Computer Science","citation":{"chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021.","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023"},"file_date_updated":"2022-05-12T12:13:27Z","date_created":"2021-07-11T22:01:18Z","date_updated":"2023-08-10T14:11:19Z","volume":893,"author":[{"last_name":"Petrov","first_name":"Tatjana","full_name":"Petrov, Tatjana"},{"full_name":"Igler, Claudia","first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sezgin, Ali","first_name":"Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","year":"2021","month":"06","publication_identifier":{"issn":["0304-3975"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2021.05.023","isi":1,"quality_controlled":"1","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"external_id":{"isi":["000710180500002"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1},{"month":"06","publication_identifier":{"eissn":["20734409"]},"external_id":{"pmid":["34201955"],"isi":["000678193300001"]},"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,"isi":1,"quality_controlled":"1","doi":"10.3390/cells10071593","language":[{"iso":"eng"}],"article_number":"1593","file_date_updated":"2021-08-04T14:01:30Z","year":"2021","acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","pmid":1,"publication_status":"published","publisher":"MDPI","department":[{"_id":"SaSi"}],"author":[{"first_name":"Nicole A.","last_name":"Muench","full_name":"Muench, Nicole A."},{"first_name":"Sonia","last_name":"Patel","full_name":"Patel, Sonia"},{"orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E","full_name":"Maes, Margaret E"},{"first_name":"Ryan J.","last_name":"Donahue","full_name":"Donahue, Ryan J."},{"first_name":"Akihiro","last_name":"Ikeda","full_name":"Ikeda, Akihiro"},{"full_name":"Nickells, Robert W.","last_name":"Nickells","first_name":"Robert W."}],"date_updated":"2023-08-10T14:14:53Z","date_created":"2021-08-01T22:01:22Z","volume":10,"scopus_import":"1","day":"25","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Cells","citation":{"chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071593.","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells, vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593"},"article_type":"original","date_published":"2021-06-25T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. "}],"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9761","ddc":["570"],"title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","status":"public","intvolume":" 10","oa_version":"Published Version","file":[{"file_id":"9768","relation":"main_file","date_updated":"2021-08-04T14:01:30Z","date_created":"2021-08-04T14:01:30Z","success":1,"checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","file_name":"2021_Cells_Muench.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":4555611}]},{"citation":{"ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.","apa":"Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021. https://doi.org/10.1016/j.nlm.2021.107486.","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486, Elsevier, 2021, doi:10.1016/j.nlm.2021.107486."},"publication":"Neurobiology of Learning and Memory","article_type":"original","date_published":"2021-06-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"30","_id":"9641","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 183","status":"public","ddc":["610"],"title":"The role of hippocampal mossy cells in novelty detection","file":[{"creator":"cziletti","content_type":"application/pdf","file_size":1994793,"file_name":"2021_NeurobLearnMemory_Fredes.pdf","access_level":"open_access","date_updated":"2021-07-19T13:46:06Z","date_created":"2021-07-19T13:46:06Z","success":1,"checksum":"8e8298a9e8c7df146ad23f32c2a63929","file_id":"9694","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"oa":1,"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.nlm.2021.107486","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10959564"],"issn":["10747427"]},"month":"06","pmid":1,"year":"2021","acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","department":[{"_id":"RySh"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"Felipe","last_name":"Fredes","full_name":"Fredes, Felipe"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"volume":183,"date_created":"2021-07-11T22:01:16Z","date_updated":"2023-08-10T14:10:37Z","article_number":"107486","ec_funded":1,"file_date_updated":"2021-07-19T13:46:06Z"},{"title":"Quantitative analysis of assertion violations in probabilistic programs","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9646","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude."}],"page":"1171-1186","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","citation":{"short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1171–86. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454102.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1171–1186). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454102","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1171–1186.","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186."},"date_published":"2021-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","year":"2021","date_updated":"2023-08-10T14:14:08Z","date_created":"2021-07-11T22:01:18Z","author":[{"last_name":"Wang","first_name":"Jinyi","full_name":"Wang, Jinyi"},{"full_name":"Sun, Yican","last_name":"Sun","first_name":"Yican"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"}],"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.14617"}],"external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2021-06-26","location":"Online","start_date":"2021-06-20","name":"PLDI: Programming Language Design and Implementation"},"doi":"10.1145/3453483.3454102","month":"06","publication_identifier":{"isbn":["9781450383912"]}},{"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","citation":{"mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–87, doi:10.1145/3453483.3454076.","short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 772–87. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454076.","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 772–787."},"page":"772-787","date_published":"2021-06-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9645","title":"Polynomial reachability witnesses via Stellensätze","status":"public","oa_version":"Submitted Version","month":"06","publication_identifier":{"isbn":["9781450383912"]},"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03183862/","open_access":"1"}],"oa":1,"external_id":{"isi":["000723661700050"]},"quality_controlled":"1","isi":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"Online","start_date":"2021-06-20","end_date":"2021-06-26","name":" PLDI: Programming Language Design and Implementation"},"doi":"10.1145/3453483.3454076","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","year":"2021","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei"},{"last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Mahdavi, Mohammad","first_name":"Mohammad","last_name":"Mahdavi"}],"date_updated":"2023-08-10T14:13:39Z","date_created":"2021-07-11T22:01:17Z"},{"month":"07","publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"external_id":{"pmid":["34264932"],"isi":["000677713500008"]},"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,"isi":1,"doi":"10.1371/journal.pcbi.1009124","language":[{"iso":"eng"}],"article_number":"e1009124","file_date_updated":"2021-08-05T12:06:49Z","year":"2021","acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Public Library of Science","author":[{"full_name":"Bartlett, Michael John","first_name":"Michael John","last_name":"Bartlett"},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","first_name":"Feyza N","last_name":"Arslan","full_name":"Arslan, Feyza N"},{"full_name":"Bankston, Adriana","last_name":"Bankston","first_name":"Adriana"},{"last_name":"Sarabipour","first_name":"Sarvenaz","full_name":"Sarabipour, Sarvenaz"}],"date_created":"2021-08-01T22:01:21Z","date_updated":"2023-08-10T14:16:46Z","volume":17,"scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"Yes","publication":"PLoS Computational Biology","citation":{"ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124","ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021.","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124."},"article_type":"letter_note","date_published":"2021-07-15T00:00:00Z","type":"journal_article","issue":"7","_id":"9759","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Ten simple rules to improve academic work- life balance","ddc":["613"],"intvolume":" 17","file":[{"date_updated":"2021-08-05T12:06:49Z","date_created":"2021-08-05T12:06:49Z","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","relation":"main_file","file_id":"9771","content_type":"application/pdf","file_size":693633,"creator":"cchlebak","file_name":"2021_PlosCompBio_Bartlett.pdf","access_level":"open_access"}],"oa_version":"Published Version"},{"quality_controlled":"1","isi":1,"project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020"}],"external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/acsami.1c09850","month":"08","publication_identifier":{"eissn":["19448252"],"issn":["19448244"]},"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"publisher":"American Chemical Society","year":"2021","acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","pmid":1,"date_updated":"2023-08-10T14:22:48Z","date_created":"2021-08-08T22:01:28Z","volume":13,"author":[{"last_name":"Zisis","first_name":"Themistoklis","full_name":"Zisis, Themistoklis"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan","full_name":"Schwarz, Jan"},{"full_name":"Balles, Miriam","first_name":"Miriam","last_name":"Balles"},{"full_name":"Kretschmer, Maibritt","last_name":"Kretschmer","first_name":"Maibritt"},{"full_name":"Nemethova, Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Nemethova"},{"full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","first_name":"Remy P"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"last_name":"Lange","first_name":"Janina","full_name":"Lange, Janina"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Zahler, Stefan","first_name":"Stefan","last_name":"Zahler"}],"file_date_updated":"2021-08-09T09:44:03Z","ec_funded":1,"article_type":"original","page":"35545–35560","publication":"ACS Applied Materials and Interfaces","citation":{"apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850."},"date_published":"2021-08-04T00:00:00Z","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","status":"public","ddc":["620","570"],"intvolume":" 13","_id":"9822","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9833","date_created":"2021-08-09T09:44:03Z","date_updated":"2021-08-09T09:44:03Z","checksum":"b043a91d9f9200e467b970b692687ed3","success":1,"file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","access_level":"open_access","file_size":7123293,"content_type":"application/pdf","creator":"asandaue"}],"type":"journal_article","abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"issue":"30"},{"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","ieee":"B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459765","ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765","chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459765.","short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021)."},"publication":"ACM Transactions on Graphics","date_published":"2021-08-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates."}],"intvolume":" 40","status":"public","ddc":["000"],"title":"PhotoApp: Photorealistic appearance editing of head portraits","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9819","oa_version":"Published Version","file":[{"file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf","access_level":"open_access","file_size":49840741,"content_type":"application/pdf","creator":"asandaue","relation":"main_file","file_id":"9834","date_updated":"2021-08-09T11:41:50Z","date_created":"2021-08-09T11:41:50Z","checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a","success":1}],"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"month":"08","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"},"oa":1,"external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"language":[{"iso":"eng"}],"doi":"10.1145/3450626.3459765","article_number":"44","file_date_updated":"2021-08-09T11:41:50Z","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2021","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","volume":40,"date_created":"2021-08-08T22:01:27Z","date_updated":"2023-08-10T14:25:08Z","author":[{"full_name":"Mallikarjun, B. R.","last_name":"Mallikarjun","first_name":"B. R."},{"full_name":"Tewari, Ayush","first_name":"Ayush","last_name":"Tewari"},{"last_name":"Dib","first_name":"Abdallah","full_name":"Dib, Abdallah"},{"full_name":"Weyrich, Tim","first_name":"Tim","last_name":"Weyrich"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Hans Peter","last_name":"Seidel","full_name":"Seidel, Hans Peter"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"full_name":"Chevallier, Louis","last_name":"Chevallier","first_name":"Louis"},{"full_name":"Elgharib, Mohamed A.","first_name":"Mohamed A.","last_name":"Elgharib"},{"full_name":"Theobalt, Christian","first_name":"Christian","last_name":"Theobalt"}]},{"file":[{"date_updated":"2021-08-09T11:52:14Z","date_created":"2021-08-09T11:52:14Z","success":1,"checksum":"ae4df60eb62f4491278588548d0c1f93","file_id":"9835","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_size":773921,"file_name":"2021_PLoSONE_Hledík.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"9816","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["610"],"title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","status":"public","intvolume":" 16","abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"issue":"7","type":"journal_article","date_published":"2021-07-29T00:00:00Z","publication":"PLoS ONE","citation":{"ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267."},"article_type":"original","day":"29","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","author":[{"full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112"},{"last_name":"Beiglböck","first_name":"Mathias","full_name":"Beiglböck, Mathias"},{"full_name":"Herdina, Anna Nele","first_name":"Anna Nele","last_name":"Herdina"},{"full_name":"Strassl, Robert","first_name":"Robert","last_name":"Strassl"},{"last_name":"Posch","first_name":"Martin","full_name":"Posch, Martin"}],"date_updated":"2023-08-10T14:26:32Z","date_created":"2021-08-08T22:01:26Z","volume":16,"year":"2021","acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","pmid":1,"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"file_date_updated":"2021-08-09T11:52:14Z","article_number":"e0255267","doi":"10.1371/journal.pone.0255267","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":{"isi":["000685248200095"],"pmid":["34324553"]},"quality_controlled":"1","isi":1,"month":"07","publication_identifier":{"eissn":["1932-6203"]}},{"file":[{"file_name":"2021_PLoSONE_Graff.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2706919,"creator":"asandaue","relation":"main_file","file_id":"9832","date_updated":"2021-08-09T09:25:41Z","date_created":"2021-08-09T09:25:41Z","checksum":"0277aa155d5db1febd2cb384768bba5f","success":1}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9821","title":"Persistent homology as a new method of the assessment of heart rate variability","status":"public","ddc":["006"],"intvolume":" 16","abstract":[{"text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode.","lang":"eng"}],"issue":"7","type":"journal_article","date_published":"2021-07-01T00:00:00Z","publication":"PLoS ONE","citation":{"mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:10.1371/journal.pone.0253851.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0253851.","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0253851","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851","ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021."},"article_type":"original","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","author":[{"first_name":"Grzegorz","last_name":"Graff","full_name":"Graff, Grzegorz"},{"full_name":"Graff, Beata","last_name":"Graff","first_name":"Beata"},{"full_name":"Pilarczyk, Pawel","first_name":"Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","first_name":"Grzegorz"},{"full_name":"Gąsecki, Dariusz","first_name":"Dariusz","last_name":"Gąsecki"},{"full_name":"Narkiewicz, Krzysztof","first_name":"Krzysztof","last_name":"Narkiewicz"}],"date_created":"2021-08-08T22:01:28Z","date_updated":"2023-08-10T14:21:42Z","volume":16,"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Public Library of Science","file_date_updated":"2021-08-09T09:25:41Z","article_number":"e0253851","doi":"10.1371/journal.pone.0253851","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":{"pmid":["34292957"],"isi":["000678124900050"]},"isi":1,"quality_controlled":"1","month":"07","publication_identifier":{"eissn":["19326203"]}},{"article_number":"125","year":"2021","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","publication_status":"published","author":[{"last_name":"Serrano","first_name":"Ana","full_name":"Serrano, Ana"},{"full_name":"Chen, Bin","first_name":"Bin","last_name":"Chen"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","orcid":"0000-0002-5062-4474","first_name":"Michael","last_name":"Piovarci","full_name":"Piovarci, Michael"},{"full_name":"Seidel, Hans Peter","last_name":"Seidel","first_name":"Hans Peter"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"last_name":"Myszkowski","first_name":"Karol","full_name":"Myszkowski, Karol"}],"volume":40,"date_created":"2021-08-08T22:01:28Z","date_updated":"2023-08-10T14:20:10Z","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"month":"08","external_id":{"isi":["000674930900090"]},"oa":1,"main_file_link":[{"url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1145/3450626.3459813","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9820","intvolume":" 40","status":"public","title":"The effect of shape and illumination on material perception: Model and applications","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. 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ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459813","chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021).","mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813."},"publication":"ACM Transactions on Graphics","article_type":"original","date_published":"2021-08-01T00:00:00Z"},{"date_published":"2021-08-01T00:00:00Z","citation":{"short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459816.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816","apa":"Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459816","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168."},"publication":"ACM Transactions on Graphics","article_type":"original","article_processing_charge":"Yes (in subscription journal)","day":"01","scopus_import":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9818","intvolume":" 40","title":"Mechanics-aware deformation of yarn pattern geometry","status":"public","issue":"4","abstract":[{"lang":"eng","text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales."}],"type":"journal_article","doi":"10.1145/3450626.3459816","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["000674930900132"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3450626.3459816"}],"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"month":"08","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/knitting-virtual-yarn/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"12358"},{"id":"9327","status":"public","relation":"software"}]},"author":[{"last_name":"Sperl","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg"},{"full_name":"Narain, Rahul","first_name":"Rahul","last_name":"Narain"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"volume":40,"date_updated":"2023-08-10T14:24:36Z","date_created":"2021-08-08T22:01:27Z","year":"2021","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","publisher":"Association for Computing Machinery","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"published","ec_funded":1,"article_number":"168"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9828","intvolume":" 69","title":"Fast and accurate amplitude demodulation of wideband signals","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"09","citation":{"chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021.","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899","ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899"},"publication":"IEEE Transactions on Signal Processing","page":"4039 - 4054","article_type":"original","date_published":"2021-06-09T00:00:00Z","year":"2021","acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","department":[{"_id":"GaTk"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","author":[{"full_name":"Gabrielaitis, Mantas","last_name":"Gabrielaitis","first_name":"Mantas","orcid":"0000-0002-7758-2016","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87"}],"volume":69,"date_created":"2021-08-08T22:01:31Z","date_updated":"2023-08-10T14:19:33Z","publication_identifier":{"eissn":["1941-0476"],"issn":["1053-587X"]},"month":"06","external_id":{"arxiv":["2102.04832"],"isi":["000682123900002"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"isi":1,"quality_controlled":"1","doi":"10.1109/TSP.2021.3087899","language":[{"iso":"eng"}]},{"month":"05","has_accepted_license":"1","oa":1,"tmp":{"name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT"},"citation":{"chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9327.","short":"G. 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Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9770","intvolume":" 104","status":"public","title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.","chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.024430.","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 2021;104(2). doi:10.1103/physrevb.104.024430","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” Physical Review B, vol. 104, no. 2. American Physical Society, 2021.","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430."},"publication":"Physical Review B","article_type":"original","date_published":"2021-07-01T00:00:00Z","article_number":"024430","ec_funded":1,"acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","year":"2021","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"},{"full_name":"Alpern, Hen","first_name":"Hen","last_name":"Alpern"},{"last_name":"Paltiel","first_name":"Yossi","full_name":"Paltiel, Yossi"},{"full_name":"Millo, Oded","last_name":"Millo","first_name":"Oded"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"}],"volume":104,"date_created":"2021-08-04T15:05:32Z","date_updated":"2023-08-10T14:27:07Z","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2101.05173"}],"oa":1,"external_id":{"arxiv":["2101.05173"],"isi":["000678780800003"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1103/physrevb.104.024430","language":[{"iso":"eng"}]},{"publisher":"Elsevier","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2021","volume":886,"date_created":"2021-08-08T22:01:31Z","date_updated":"2023-08-10T14:27:43Z","author":[{"first_name":"Bapi","last_name":"Chatterjee","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2742-4028","full_name":"Chatterjee, Bapi"},{"full_name":"Walulya, Ivan","last_name":"Walulya","first_name":"Ivan"},{"last_name":"Tsigas","first_name":"Philippas","full_name":"Tsigas, Philippas"}],"publication_identifier":{"issn":["0304-3975"]},"month":"09","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf","open_access":"1"}],"external_id":{"isi":["000694718900004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2021.06.041","type":"journal_article","abstract":[{"lang":"eng","text":"The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree."}],"intvolume":" 886","title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","status":"public","_id":"9827","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"scopus_import":"1","article_processing_charge":"No","day":"13","page":"27-48","article_type":"original","citation":{"short":"B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021) 27–48.","mla":"Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier, 2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041.","chicago":"Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.","ama":"Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48. doi:10.1016/j.tcs.2021.06.041","apa":"Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041","ieee":"B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol. 886. Elsevier, pp. 27–48, 2021.","ista":"Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48."},"publication":"Theoretical Computer Science","date_published":"2021-09-13T00:00:00Z"},{"day":"16","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2021-07-16T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.","ieee":"J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” Proceedings of the National Academy of Sciences, vol. 118, no. 29. National Academy of Sciences, 2021.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29), e2104445118.","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118"},"article_type":"original","abstract":[{"text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.","lang":"eng"}],"issue":"29","type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"19e84ad8c03c60222744ee8e16cd6998","date_updated":"2021-08-11T09:31:41Z","date_created":"2021-08-11T09:31:41Z","file_id":"9879","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_size":1898360,"access_level":"open_access","file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf"}],"_id":"9877","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","status":"public","ddc":["580","570"],"intvolume":" 118","month":"07","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.2104445118","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"isi":1,"quality_controlled":"1","file_date_updated":"2021-08-11T09:31:41Z","article_number":"e2104445118","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"full_name":"Ruan, Deling","last_name":"Ruan","first_name":"Deling"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"full_name":"Sharma, Manoj K.","last_name":"Sharma","first_name":"Manoj K."},{"full_name":"Sharma, Rita","first_name":"Rita","last_name":"Sharma"},{"last_name":"Ye","first_name":"XinYi","full_name":"Ye, XinYi"},{"last_name":"Nguyen","first_name":"Nicholas D.","full_name":"Nguyen, Nicholas D."},{"first_name":"Sukhranjan","last_name":"Nijjar","full_name":"Nijjar, Sukhranjan"},{"last_name":"Ronald","first_name":"Pamela C.","full_name":"Ronald, Pamela C."},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"date_updated":"2023-08-11T10:28:10Z","date_created":"2021-08-10T19:30:41Z","volume":118,"acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","year":"2021","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}]},{"article_number":"4808","file_date_updated":"2021-08-10T12:29:59Z","pmid":1,"acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).","year":"2021","publisher":"Springer Nature","department":[{"_id":"SaSi"}],"publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-32785-0","relation":"erratum"}]},"author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"last_name":"Dirkx","first_name":"Ellen","full_name":"Dirkx, Ellen"},{"full_name":"Sampaio-Pinto, Vasco","last_name":"Sampaio-Pinto","first_name":"Vasco"},{"last_name":"el Azzouzi","first_name":"Hamid","full_name":"el Azzouzi, Hamid"},{"full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","first_name":"Ryan J","last_name":"Cubero"},{"full_name":"Sorensen, Daniel W.","first_name":"Daniel W.","last_name":"Sorensen"},{"full_name":"Ottaviani, Lara","first_name":"Lara","last_name":"Ottaviani"},{"first_name":"Servé","last_name":"Olieslagers","full_name":"Olieslagers, Servé"},{"full_name":"Huibers, Manon M.","last_name":"Huibers","first_name":"Manon M."},{"full_name":"de Weger, Roel","first_name":"Roel","last_name":"de Weger"},{"first_name":"Sailay","last_name":"Siddiqi","full_name":"Siddiqi, Sailay"},{"full_name":"Moimas, Silvia","first_name":"Silvia","last_name":"Moimas"},{"last_name":"Torrini","first_name":"Consuelo","full_name":"Torrini, Consuelo"},{"full_name":"Zentillin, Lorena","last_name":"Zentillin","first_name":"Lorena"},{"first_name":"Luca","last_name":"Braga","full_name":"Braga, Luca"},{"full_name":"Nascimento, Diana S.","last_name":"Nascimento","first_name":"Diana S."},{"first_name":"Paula A.","last_name":"da Costa Martins","full_name":"da Costa Martins, Paula A."},{"last_name":"van Berlo","first_name":"Jop H.","full_name":"van Berlo, Jop H."},{"first_name":"Serena","last_name":"Zacchigna","full_name":"Zacchigna, Serena"},{"first_name":"Mauro","last_name":"Giacca","full_name":"Giacca, Mauro"},{"full_name":"De Windt, Leon J.","first_name":"Leon J.","last_name":"De Windt"}],"volume":12,"date_created":"2021-08-10T11:49:20Z","date_updated":"2023-08-11T10:27:03Z","publication_identifier":{"eissn":["2041-1723"]},"month":"08","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":["34376683"],"isi":["000683910200042"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-021-25211-4","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9874","intvolume":" 12","status":"public","ddc":["610","570"],"title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":4364333,"access_level":"open_access","file_name":"2021_NatureCommunications_Raso.pdf","success":1,"checksum":"48d8562e8229e4282f3f354b329722c5","date_updated":"2021-08-10T12:29:59Z","date_created":"2021-08-10T12:29:59Z","file_id":"9876","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","genbank":["GSE178867"],"article_processing_charge":"Yes","has_accepted_license":"1","day":"10","citation":{"chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.","mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications, vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.","short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808.","ieee":"A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4"},"publication":"Nature Communications","article_type":"original","date_published":"2021-08-10T00:00:00Z"},{"abstract":[{"text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_SciPostPhysics_Brauneis.pdf","creator":"asandaue","content_type":"application/pdf","file_size":1085300,"file_id":"9875","relation":"main_file","success":1,"checksum":"eaa847346b1a023d97bbb291779610ed","date_created":"2021-08-10T11:44:59Z","date_updated":"2021-08-10T11:44:59Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9769","title":"Impurities in a one-dimensional Bose gas: The flow equation approach","status":"public","ddc":["530"],"intvolume":" 11","day":"13","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-07-13T00:00:00Z","publication":"SciPost Physics","citation":{"short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021, doi:10.21468/scipostphys.11.1.008.","chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.1.008","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” SciPost Physics, vol. 11, no. 1. SciPost, 2021.","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008."},"article_type":"original","file_date_updated":"2021-08-10T11:44:59Z","ec_funded":1,"article_number":"008","author":[{"full_name":"Brauneis, Fabian","first_name":"Fabian","last_name":"Brauneis"},{"full_name":"Hammer, Hans-Werner","first_name":"Hans-Werner","last_name":"Hammer"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"date_created":"2021-08-04T15:00:55Z","date_updated":"2023-08-11T10:25:44Z","volume":11,"acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","year":"2021","publication_status":"published","publisher":"SciPost","department":[{"_id":"MiLe"}],"month":"07","publication_identifier":{"eissn":["2542-4653"]},"doi":"10.21468/scipostphys.11.1.008","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":["2101.10958"],"isi":["000680039500013"]},"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}]},{"citation":{"ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 2021;10. doi:10.7554/elife.68876","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876.","ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876","mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021, doi:10.7554/elife.68876.","short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021).","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876."},"publication":"eLife","article_type":"original","date_published":"2021-07-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"28","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9746","intvolume":" 10","title":"High potency of sequential therapy with only beta-lactam antibiotics","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs.","lang":"eng"}],"external_id":{"pmid":["34318749"],"isi":["000692027800001"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.7554/elife.68876","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"month":"07","pmid":1,"year":"2021","acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","publisher":"eLife Sciences Publications","department":[{"_id":"CaGu"}],"publication_status":"published","author":[{"last_name":"Batra","first_name":"Aditi","full_name":"Batra, Aditi"},{"last_name":"Römhild","first_name":"Roderich","orcid":"0000-0001-9480-5261","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","full_name":"Römhild, Roderich"},{"last_name":"Rousseau","first_name":"Emilie","full_name":"Rousseau, Emilie"},{"first_name":"Sören","last_name":"Franzenburg","full_name":"Franzenburg, Sören"},{"first_name":"Stefan","last_name":"Niemann","full_name":"Niemann, Stefan"},{"first_name":"Hinrich","last_name":"Schulenburg","full_name":"Schulenburg, Hinrich"}],"volume":10,"date_created":"2021-07-28T13:36:57Z","date_updated":"2023-08-11T10:26:29Z","article_number":"e68876"},{"volume":284,"date_updated":"2023-08-11T10:30:40Z","date_created":"2021-08-15T22:01:29Z","author":[{"first_name":"Glyn","last_name":"Nelson","full_name":"Nelson, Glyn"},{"full_name":"Boehm, Ulrike","first_name":"Ulrike","last_name":"Boehm"},{"last_name":"Bagley","first_name":"Steve","full_name":"Bagley, Steve"},{"full_name":"Bajcsy, Peter","first_name":"Peter","last_name":"Bajcsy"},{"first_name":"Johanna","last_name":"Bischof","full_name":"Bischof, Johanna"},{"last_name":"Brown","first_name":"Claire M.","full_name":"Brown, Claire M."},{"first_name":"Aurélien","last_name":"Dauphin","full_name":"Dauphin, Aurélien"},{"last_name":"Dobbie","first_name":"Ian M.","full_name":"Dobbie, Ian M."},{"full_name":"Eriksson, John E.","last_name":"Eriksson","first_name":"John E."},{"first_name":"Orestis","last_name":"Faklaris","full_name":"Faklaris, Orestis"},{"full_name":"Fernandez-Rodriguez, Julia","last_name":"Fernandez-Rodriguez","first_name":"Julia"},{"full_name":"Ferrand, Alexia","first_name":"Alexia","last_name":"Ferrand"},{"full_name":"Gelman, Laurent","last_name":"Gelman","first_name":"Laurent"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"full_name":"Hartmann, Hella","last_name":"Hartmann","first_name":"Hella"},{"full_name":"Kukat, Christian","last_name":"Kukat","first_name":"Christian"},{"full_name":"Laude, Alex","first_name":"Alex","last_name":"Laude"},{"full_name":"Mitkovski, Miso","last_name":"Mitkovski","first_name":"Miso"},{"full_name":"Munck, Sebastian","last_name":"Munck","first_name":"Sebastian"},{"first_name":"Alison J.","last_name":"North","full_name":"North, Alison J."},{"last_name":"Rasse","first_name":"Tobias M.","full_name":"Rasse, Tobias M."},{"full_name":"Resch-Genger, Ute","last_name":"Resch-Genger","first_name":"Ute"},{"full_name":"Schuetz, Lucas C.","first_name":"Lucas C.","last_name":"Schuetz"},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"full_name":"Strambio-De-Castillia, Caterina","first_name":"Caterina","last_name":"Strambio-De-Castillia"},{"full_name":"Swedlow, Jason R.","first_name":"Jason R.","last_name":"Swedlow"},{"last_name":"Alexopoulos","first_name":"Ioannis","full_name":"Alexopoulos, Ioannis"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"Karin"},{"full_name":"Avilov, Sergiy","first_name":"Sergiy","last_name":"Avilov"},{"full_name":"Bakker, Gert Jan","first_name":"Gert Jan","last_name":"Bakker"},{"last_name":"Bammann","first_name":"Rodrigo R.","full_name":"Bammann, Rodrigo R."},{"full_name":"Bassi, Andrea","first_name":"Andrea","last_name":"Bassi"},{"full_name":"Beckert, Hannes","first_name":"Hannes","last_name":"Beckert"},{"full_name":"Beer, Sebastian","first_name":"Sebastian","last_name":"Beer"},{"last_name":"Belyaev","first_name":"Yury","full_name":"Belyaev, Yury"},{"full_name":"Bierwagen, Jakob","first_name":"Jakob","last_name":"Bierwagen"},{"full_name":"Birngruber, Konstantin A.","last_name":"Birngruber","first_name":"Konstantin A."},{"first_name":"Manel","last_name":"Bosch","full_name":"Bosch, Manel"},{"first_name":"Juergen","last_name":"Breitlow","full_name":"Breitlow, Juergen"},{"full_name":"Cameron, Lisa A.","first_name":"Lisa A.","last_name":"Cameron"},{"full_name":"Chalfoun, Joe","first_name":"Joe","last_name":"Chalfoun"},{"full_name":"Chambers, James J.","first_name":"James J.","last_name":"Chambers"},{"full_name":"Chen, Chieh Li","last_name":"Chen","first_name":"Chieh Li"},{"full_name":"Conde-Sousa, Eduardo","last_name":"Conde-Sousa","first_name":"Eduardo"},{"first_name":"Alexander D.","last_name":"Corbett","full_name":"Corbett, Alexander D."},{"first_name":"Fabrice P.","last_name":"Cordelieres","full_name":"Cordelieres, Fabrice P."},{"full_name":"Nery, Elaine Del","last_name":"Nery","first_name":"Elaine Del"},{"full_name":"Dietzel, Ralf","first_name":"Ralf","last_name":"Dietzel"},{"full_name":"Eismann, Frank","first_name":"Frank","last_name":"Eismann"},{"first_name":"Elnaz","last_name":"Fazeli","full_name":"Fazeli, Elnaz"},{"full_name":"Felscher, Andreas","last_name":"Felscher","first_name":"Andreas"},{"first_name":"Hans","last_name":"Fried","full_name":"Fried, Hans"},{"first_name":"Nathalie","last_name":"Gaudreault","full_name":"Gaudreault, Nathalie"},{"full_name":"Goh, Wah Ing","last_name":"Goh","first_name":"Wah Ing"},{"last_name":"Guilbert","first_name":"Thomas","full_name":"Guilbert, Thomas"},{"full_name":"Hadleigh, Roland","first_name":"Roland","last_name":"Hadleigh"},{"last_name":"Hemmerich","first_name":"Peter","full_name":"Hemmerich, Peter"},{"first_name":"Gerhard A.","last_name":"Holst","full_name":"Holst, Gerhard A."},{"full_name":"Itano, Michelle S.","first_name":"Michelle S.","last_name":"Itano"},{"last_name":"Jaffe","first_name":"Claudia B.","full_name":"Jaffe, Claudia B."},{"full_name":"Jambor, Helena K.","first_name":"Helena K.","last_name":"Jambor"},{"full_name":"Jarvis, Stuart C.","first_name":"Stuart C.","last_name":"Jarvis"},{"full_name":"Keppler, Antje","last_name":"Keppler","first_name":"Antje"},{"first_name":"David","last_name":"Kirchenbuechler","full_name":"Kirchenbuechler, David"},{"last_name":"Kirchner","first_name":"Marcel","full_name":"Kirchner, Marcel"},{"full_name":"Kobayashi, Norio","first_name":"Norio","last_name":"Kobayashi"},{"first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"last_name":"Kunis","first_name":"Susanne","full_name":"Kunis, Susanne"},{"full_name":"Lacoste, Judith","last_name":"Lacoste","first_name":"Judith"},{"full_name":"Marcello, Marco","first_name":"Marco","last_name":"Marcello"},{"first_name":"Gabriel G.","last_name":"Martins","full_name":"Martins, Gabriel G."},{"full_name":"Metcalf, Daniel J.","last_name":"Metcalf","first_name":"Daniel J."},{"last_name":"Mitchell","first_name":"Claire A.","full_name":"Mitchell, Claire A."},{"full_name":"Moore, Joshua","first_name":"Joshua","last_name":"Moore"},{"first_name":"Tobias","last_name":"Mueller","full_name":"Mueller, Tobias"},{"full_name":"Nelson, Michael S.","first_name":"Michael S.","last_name":"Nelson"},{"last_name":"Ogg","first_name":"Stephen","full_name":"Ogg, Stephen"},{"full_name":"Onami, Shuichi","last_name":"Onami","first_name":"Shuichi"},{"full_name":"Palmer, Alexandra L.","last_name":"Palmer","first_name":"Alexandra L."},{"first_name":"Perrine","last_name":"Paul-Gilloteaux","full_name":"Paul-Gilloteaux, Perrine"},{"first_name":"Jaime A.","last_name":"Pimentel","full_name":"Pimentel, Jaime A."},{"first_name":"Laure","last_name":"Plantard","full_name":"Plantard, Laure"},{"last_name":"Podder","first_name":"Santosh","full_name":"Podder, Santosh"},{"first_name":"Elton","last_name":"Rexhepaj","full_name":"Rexhepaj, Elton"},{"first_name":"Arnaud","last_name":"Royon","full_name":"Royon, Arnaud"},{"full_name":"Saari, Markku A.","first_name":"Markku A.","last_name":"Saari"},{"first_name":"Damien","last_name":"Schapman","full_name":"Schapman, Damien"},{"last_name":"Schoonderwoert","first_name":"Vincent","full_name":"Schoonderwoert, Vincent"},{"first_name":"Britta","last_name":"Schroth-Diez","full_name":"Schroth-Diez, Britta"},{"last_name":"Schwartz","first_name":"Stanley","full_name":"Schwartz, Stanley"},{"full_name":"Shaw, Michael","first_name":"Michael","last_name":"Shaw"},{"full_name":"Spitaler, Martin","first_name":"Martin","last_name":"Spitaler"},{"full_name":"Stoeckl, Martin T.","last_name":"Stoeckl","first_name":"Martin T."},{"first_name":"Damir","last_name":"Sudar","full_name":"Sudar, Damir"},{"full_name":"Teillon, Jeremie","last_name":"Teillon","first_name":"Jeremie"},{"full_name":"Terjung, Stefan","last_name":"Terjung","first_name":"Stefan"},{"last_name":"Thuenauer","first_name":"Roland","full_name":"Thuenauer, Roland"},{"full_name":"Wilms, Christian D.","first_name":"Christian D.","last_name":"Wilms"},{"full_name":"Wright, Graham D.","last_name":"Wright","first_name":"Graham D."},{"full_name":"Nitschke, Roland","last_name":"Nitschke","first_name":"Roland"}],"department":[{"_id":"Bio"}],"publisher":"Wiley","publication_status":"published","year":"2021","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1111/jmi.13041","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/jmi.13041","open_access":"1"}],"external_id":{"isi":["000683702700001"]},"issue":"1","abstract":[{"text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 284","status":"public","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9911","article_processing_charge":"Yes","day":"11","scopus_import":"1","date_published":"2021-08-11T00:00:00Z","page":"56-73","article_type":"original","citation":{"mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041","ieee":"G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021."},"publication":"Journal of Microscopy"},{"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"month":"08","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"},"oa":1,"external_id":{"isi":["000689147400001"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms22168385","article_number":"8385","file_date_updated":"2021-08-16T09:29:17Z","department":[{"_id":"SiHi"}],"publisher":"MDPI","publication_status":"published","acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources.","year":"2021","volume":22,"date_updated":"2023-08-11T10:34:13Z","date_created":"2021-08-15T22:01:27Z","author":[{"first_name":"Iveta","last_name":"Yotova","full_name":"Yotova, Iveta"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."},{"orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Proestling, Katharina","first_name":"Katharina","last_name":"Proestling"},{"full_name":"Haslinger, Isabella","last_name":"Haslinger","first_name":"Isabella"},{"full_name":"Kuessel, Lorenz","last_name":"Kuessel","first_name":"Lorenz"},{"last_name":"Perricos","first_name":"Alexandra","full_name":"Perricos, Alexandra"},{"first_name":"Heinrich","last_name":"Husslein","full_name":"Husslein, Heinrich"},{"first_name":"René","last_name":"Wenzl","full_name":"Wenzl, René"}],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"04","article_type":"original","citation":{"ieee":"I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” International Journal of Molecular Sciences, vol. 22, no. 16. MDPI, 2021.","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22168385","ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385","chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22168385.","short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021).","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” International Journal of Molecular Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385."},"publication":"International Journal of Molecular Sciences","date_published":"2021-08-04T00:00:00Z","type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways."}],"intvolume":" 22","status":"public","ddc":["570"],"title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","_id":"9906","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":2646018,"access_level":"open_access","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","success":1,"checksum":"be7f0042607ca60549cb27513c19c6af","date_updated":"2021-08-16T09:29:17Z","date_created":"2021-08-16T09:29:17Z","file_id":"9922","relation":"main_file"}],"oa_version":"Published Version"},{"file":[{"file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","access_level":"open_access","creator":"asandaue","file_size":1079395,"content_type":"application/pdf","file_id":"9921","relation":"main_file","date_updated":"2021-08-16T09:14:36Z","date_created":"2021-08-16T09:14:36Z","success":1,"checksum":"a676d76f91b0dbe0504c63e469129c2a"}],"oa_version":"Published Version","intvolume":" 29","title":"The limits of normal approximation for adult height","ddc":["576"],"status":"public","_id":"9910","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","abstract":[{"text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait.","lang":"eng"}],"type":"journal_article","date_published":"2021-07-01T00:00:00Z","page":"1082-1091","article_type":"original","citation":{"mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:10.1038/s41431-021-00836-7.","short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091. doi:10.1038/s41431-021-00836-7","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-021-00836-7","ieee":"S. A. Slavskii et al., “The limits of normal approximation for adult height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021."},"publication":"European Journal of Human Genetics","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","scopus_import":"1","volume":29,"date_created":"2021-08-15T22:01:28Z","date_updated":"2023-08-11T10:33:42Z","author":[{"full_name":"Slavskii, Sergei A.","last_name":"Slavskii","first_name":"Sergei A."},{"first_name":"Ivan A.","last_name":"Kuznetsov","full_name":"Kuznetsov, Ivan A."},{"full_name":"Shashkova, Tatiana I.","first_name":"Tatiana I.","last_name":"Shashkova"},{"full_name":"Bazykin, Georgii A.","first_name":"Georgii A.","last_name":"Bazykin"},{"last_name":"Axenovich","first_name":"Tatiana I.","full_name":"Axenovich, Tatiana I."},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"first_name":"Yurii S.","last_name":"Aulchenko","full_name":"Aulchenko, Yurii S."}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","year":"2021","ec_funded":1,"file_date_updated":"2021-08-16T09:14:36Z","language":[{"iso":"eng"}],"doi":"10.1038/s41431-021-00836-7","project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"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"},"external_id":{"isi":["000625853200001"],"pmid":["33664501"]},"oa":1,"publication_identifier":{"issn":["10184813"],"eissn":["14765438"]},"month":"07"},{"month":"12","publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00023-021-01085-6","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"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":["1911.05112"],"isi":["000681531500001"]},"file_date_updated":"2022-05-12T12:50:27Z","ec_funded":1,"date_updated":"2023-08-11T10:31:48Z","date_created":"2021-08-15T22:01:29Z","volume":22,"author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H"},{"id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7327-856X","first_name":"Yuriy","last_name":"Nemish","full_name":"Nemish, Yuriy"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"year":"2021","acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2021-12-01T00:00:00Z","article_type":"original","page":"4205–4269","publication":"Annales Henri Poincaré ","citation":{"chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269.","mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:10.1007/s00023-021-01085-6.","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature, pp. 4205–4269, 2021.","apa":"Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . Springer Nature. https://doi.org/10.1007/s00023-021-01085-6","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269.","ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6"},"abstract":[{"text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries.","lang":"eng"}],"type":"journal_article","file":[{"checksum":"8d6bac0e2b0a28539608b0538a8e3b38","success":1,"date_created":"2022-05-12T12:50:27Z","date_updated":"2022-05-12T12:50:27Z","relation":"main_file","file_id":"11365","file_size":1162454,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2021_AnnHenriPoincare_Erdoes.pdf"}],"oa_version":"Published Version","title":"Scattering in quantum dots via noncommutative rational functions","status":"public","ddc":["510"],"intvolume":" 22","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9912"},{"year":"2021","acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","publisher":"AIP Publishing","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard"}],"volume":62,"date_updated":"2023-08-11T10:29:48Z","date_created":"2021-08-12T07:08:36Z","article_number":"083305","file_date_updated":"2021-10-27T12:57:06Z","external_id":{"isi":["000683960800003"],"arxiv":["2103.07975"]},"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,"quality_controlled":"1","isi":1,"doi":"10.1063/5.0053494","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"month":"08","_id":"9891","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 62","status":"public","ddc":["530"],"title":"Floating Wigner crystal and periodic jellium configurations","file":[{"file_id":"10188","relation":"main_file","date_updated":"2021-10-27T12:57:06Z","date_created":"2021-10-27T12:57:06Z","success":1,"checksum":"d035be2b894c4d50d90ac5ce252e27cd","file_name":"2021_JMathPhy_Lauritsen.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":4352640}],"oa_version":"Published Version","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations."}],"citation":{"ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305.","ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494","mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:10.1063/5.0053494.","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0053494."},"publication":"Journal of Mathematical Physics","article_type":"original","date_published":"2021-08-01T00:00:00Z","scopus_import":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"quality_controlled":"1","isi":1,"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":["000690558000001"]},"language":[{"iso":"eng"}],"doi":"10.3390/genes12081141","month":"07","publication_identifier":{"eissn":["20734425"]},"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"year":"2021","acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","date_created":"2021-08-15T22:01:28Z","date_updated":"2023-08-11T10:32:21Z","volume":12,"author":[{"last_name":"Zeng","first_name":"Yinwei","full_name":"Zeng, Yinwei"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge"},{"last_name":"Trinh","first_name":"Hoang Khai","full_name":"Trinh, Hoang Khai"},{"full_name":"Heugebaert, Thomas","first_name":"Thomas","last_name":"Heugebaert"},{"full_name":"Stevens, Christian V.","last_name":"Stevens","first_name":"Christian V."},{"full_name":"Garcia-Maquilon, Irene","last_name":"Garcia-Maquilon","first_name":"Irene"},{"last_name":"Rodriguez","first_name":"Pedro L.","full_name":"Rodriguez, Pedro L."},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Danny","last_name":"Geelen","full_name":"Geelen, Danny"}],"article_number":"1141","file_date_updated":"2021-08-16T09:02:40Z","article_type":"original","publication":"Genes","citation":{"mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021, doi:10.3390/genes12081141.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141.","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141","ieee":"Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021."},"date_published":"2021-07-27T00:00:00Z","scopus_import":"1","day":"27","has_accepted_license":"1","article_processing_charge":"Yes","status":"public","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","ddc":["580","570"],"intvolume":" 12","_id":"9909","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9919","date_created":"2021-08-16T09:02:40Z","date_updated":"2021-08-16T09:02:40Z","checksum":"3d99535618cf9a5b14d264408fa52e97","success":1,"file_name":"2021_Genes_Zeng.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1340305,"creator":"asandaue"}],"type":"journal_article","abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"issue":"8"},{"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":["000681815400001"],"pmid":["34361115"]},"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell"}],"isi":1,"quality_controlled":"1","doi":"10.3390/ijms22158350","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"month":"08","pmid":1,"acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","year":"2021","department":[{"_id":"MaLo"}],"publisher":"MDPI","publication_status":"published","author":[{"last_name":"Labajová","first_name":"Naďa","full_name":"Labajová, Naďa"},{"full_name":"Baranova, Natalia S.","first_name":"Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124"},{"full_name":"Jurásek, Miroslav","last_name":"Jurásek","first_name":"Miroslav"},{"full_name":"Vácha, Robert","first_name":"Robert","last_name":"Vácha"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"first_name":"Imrich","last_name":"Barák","full_name":"Barák, Imrich"}],"volume":22,"date_created":"2021-08-15T22:01:27Z","date_updated":"2023-08-11T10:34:44Z","article_number":"8350","ec_funded":1,"file_date_updated":"2021-08-16T09:35:56Z","citation":{"chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22158350.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” International Journal of Molecular Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” International Journal of Molecular Sciences, vol. 22, no. 15. MDPI, 2021.","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350"},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2021-08-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","_id":"9907","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 22","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","ddc":["570"],"status":"public","file":[{"relation":"main_file","file_id":"9923","checksum":"a4bc06e9a2c803ceff5a91f10b174054","success":1,"date_updated":"2021-08-16T09:35:56Z","date_created":"2021-08-16T09:35:56Z","access_level":"open_access","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","file_size":6132410,"content_type":"application/pdf","creator":"asandaue"}],"oa_version":"Published Version","type":"journal_article","issue":"15","abstract":[{"text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. ","lang":"eng"}]},{"scopus_import":"1","day":"30","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","publication":"Scientific Reports","citation":{"apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-95025-3.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3."},"date_published":"2021-07-30T00:00:00Z","type":"journal_article","abstract":[{"text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period.","lang":"eng"}],"issue":"1","status":"public","ddc":["570","610"],"title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9905","oa_version":"Published Version","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":3432001,"access_level":"open_access","file_name":"2021_ScientificReports_Rella.pdf","success":1,"checksum":"ac86892ed17e6724c7251844da5cef5c","date_updated":"2021-08-16T11:36:49Z","date_created":"2021-08-16T11:36:49Z","file_id":"9927","relation":"main_file"}],"month":"07","publication_identifier":{"eissn":["20452322"]},"isi":1,"quality_controlled":"1","project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"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":{"pmid":["34330988"],"isi":["000683329100001"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-021-95025-3","article_number":"15729","file_date_updated":"2021-08-16T11:36:49Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","year":"2021","pmid":1,"date_created":"2021-08-15T22:01:26Z","date_updated":"2023-08-11T10:42:58Z","volume":11,"author":[{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","last_name":"Rella","first_name":"Simon","full_name":"Rella, Simon"},{"full_name":"Kulikova, Yuliya A.","last_name":"Kulikova","first_name":"Yuliya A."},{"full_name":"Dermitzakis, Emmanouil T.","last_name":"Dermitzakis","first_name":"Emmanouil T."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Website","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/"}]}},{"_id":"9903","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 127","status":"public","title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","ddc":["539"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9904","checksum":"51218f302dcef99d90d1209809fcc874","success":1,"date_updated":"2021-08-13T09:28:08Z","date_created":"2021-08-13T09:28:08Z","access_level":"open_access","file_name":"PhysRevLett.127.060602_SOM.pdf","file_size":5064231,"content_type":"application/pdf","creator":"mserbyn"}],"type":"journal_article","issue":"6","abstract":[{"text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures.","lang":"eng"}],"citation":{"ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no. 6. American Physical Society, 2021.","apa":"Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.060602","ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602","chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602.","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:10.1103/physrevlett.127.060602.","short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021)."},"publication":"Physical Review Letters","article_type":"letter_note","date_published":"2021-08-06T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"06","acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","year":"2021","publisher":"American Physical Society","department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"publication_status":"published","author":[{"last_name":"Karle","first_name":"Volker","orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"}],"volume":127,"date_updated":"2023-08-11T10:43:27Z","date_created":"2021-08-13T09:27:39Z","article_number":"060602","ec_funded":1,"file_date_updated":"2021-08-13T09:28:08Z","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":["000684276000002"],"arxiv":["2102.13633"]},"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"isi":1,"quality_controlled":"1","doi":"10.1103/physrevlett.127.060602","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"08"},{"acknowledgement":"We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support.","year":"2021","publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"The Company of Biologists","author":[{"last_name":"Chaigne","first_name":"Agathe","full_name":"Chaigne, Agathe"},{"first_name":"Matthew B.","last_name":"Smith","full_name":"Smith, Matthew B."},{"first_name":"R. L.","last_name":"Cavestany","full_name":"Cavestany, R. L."},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chalut, Kevin J.","first_name":"Kevin J.","last_name":"Chalut"},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."}],"date_updated":"2023-08-11T10:55:36Z","date_created":"2021-08-22T22:01:20Z","volume":134,"article_number":"jcs255018","file_date_updated":"2021-08-23T07:32:20Z","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":["000681395800008"]},"isi":1,"quality_controlled":"1","doi":"10.1242/jcs.255018","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["00219533"],"eissn":["14779137"]},"_id":"9952","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Three-dimensional geometry controls division symmetry in stem cell colonies","intvolume":" 134","oa_version":"Published Version","file":[{"file_name":"2021_JournalOfCellScience_Chaigne.pdf","access_level":"open_access","creator":"asandaue","file_size":8651724,"content_type":"application/pdf","file_id":"9954","relation":"main_file","date_created":"2021-08-23T07:32:20Z","date_updated":"2021-08-23T07:32:20Z","success":1,"checksum":"f086f9d7cb63b2474c01921cb060c513"}],"type":"journal_article","abstract":[{"text":"Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry.","lang":"eng"}],"issue":"14","publication":"Journal of Cell Science","citation":{"short":"A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021).","mla":"Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:10.1242/jcs.255018.","chicago":"Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of Biologists, 2021. https://doi.org/10.1242/jcs.255018.","ama":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 2021;134(14). doi:10.1242/jcs.255018","apa":"Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.255018","ieee":"A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists, 2021.","ista":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018."},"article_type":"original","date_published":"2021-07-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)"},{"abstract":[{"text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems.","lang":"eng"}],"issue":"8","type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_Genes_Picard.pdf","content_type":"application/pdf","file_size":2297655,"creator":"asandaue","relation":"main_file","file_id":"9926","checksum":"744e60e56d290a96da3c91a9779f886f","success":1,"date_updated":"2021-08-16T09:49:35Z","date_created":"2021-08-16T09:49:35Z"}],"oa_version":"Published Version","title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","ddc":["570"],"status":"public","intvolume":" 12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9908","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2021-08-01T00:00:00Z","article_type":"review","publication":"Genes","citation":{"ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136.","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136","ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081136.","mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021)."},"file_date_updated":"2021-08-16T09:49:35Z","ec_funded":1,"article_number":"1136","date_updated":"2023-08-11T10:42:32Z","date_created":"2021-08-15T22:01:27Z","volume":12,"author":[{"orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A L","full_name":"Picard, Marion A L"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"},{"first_name":"Stéphanie","last_name":"Bertrand","full_name":"Bertrand, Stéphanie"},{"first_name":"Hector","last_name":"Escriva","full_name":"Escriva, Hector"}],"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"MDPI","year":"2021","month":"08","publication_identifier":{"eissn":["20734425"]},"language":[{"iso":"eng"}],"doi":"10.3390/genes12081136","isi":1,"quality_controlled":"1","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"external_id":{"isi":["000690475900001"]},"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},{"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9829","status":"public","title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","intvolume":" 15","abstract":[{"lang":"eng","text":"In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after."}],"issue":"7","type":"journal_article","date_published":"2021-07-06T00:00:00Z","publication":"ACS Nano","citation":{"chicago":"Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D. Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” ACS Nano. American Chemical Society, 2021. https://doi.org/10.1021/acsnano.1c03276.","short":"D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D. Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.","mla":"Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” ACS Nano, vol. 15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:10.1021/acsnano.1c03276.","apa":"Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E. K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.1c03276","ieee":"D. Baranov et al., “News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience,” ACS Nano, vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.","ista":"Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.","ama":"Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 2021;15(7):10743–10747. doi:10.1021/acsnano.1c03276"},"article_type":"original","page":"10743–10747","day":"06","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Baranov","first_name":"Dmitry","full_name":"Baranov, Dmitry"},{"first_name":"Tara","last_name":"Šverko","full_name":"Šverko, Tara"},{"full_name":"Moot, Taylor","first_name":"Taylor","last_name":"Moot"},{"last_name":"Keller","first_name":"Helena R.","full_name":"Keller, Helena R."},{"full_name":"Klein, Megan D.","last_name":"Klein","first_name":"Megan D."},{"full_name":"Vishnu, E. K.","first_name":"E. K.","last_name":"Vishnu"},{"orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","first_name":"Daniel","full_name":"Balazs, Daniel"},{"full_name":"Shulenberger, Katherine E.","first_name":"Katherine E.","last_name":"Shulenberger"}],"date_updated":"2023-08-11T10:55:08Z","date_created":"2021-08-08T22:01:31Z","volume":15,"year":"2021","acknowledgement":"K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for their feedback and support of the News in Nanocrystals initiative. The authors thank Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in the organization of the seminar, and Professors Brandi Cossairt (University of Washington) and Gordana Dukovic for their feedback on an earlier version of this manuscript. The authors thank all the seminar speakers and attendees for their interest and continuing participation in the seminar series.","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"doi":"10.1021/acsnano.1c03276","language":[{"iso":"eng"}],"external_id":{"pmid":["34228432"],"isi":["000679406500002"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1021/acsnano.1c03276","open_access":"1"}],"quality_controlled":"1","isi":1,"month":"07","publication_identifier":{"eissn":["1936086X"],"issn":["19360851"]}},{"title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","status":"public","ddc":["530"],"department":[{"_id":"JoFi"}],"publisher":"Zenodo","year":"2021","_id":"13057","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-11T10:44:21Z","date_created":"2023-05-23T13:42:27Z","oa_version":"Published Version","author":[{"full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628"},{"full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid"},{"last_name":"Szep","first_name":"Grisha","full_name":"Szep, Grisha"},{"first_name":"Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea"},{"full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9928"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction\". Additional raw data are available from the corresponding author on reasonable request."}],"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"},"citation":{"mla":"Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, (2021).","chicago":"Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.","apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., & Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103","ieee":"M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction.” Zenodo, 2021."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5592104"}],"doi":"10.5281/ZENODO.5592103","date_published":"2021-10-22T00:00:00Z","month":"10","day":"22","article_processing_charge":"No"},{"article_number":"5083","file_date_updated":"2021-09-08T12:57:06Z","pmid":1,"acknowledgement":"The authors are very grateful to Andrew Penn for advice and discussions on surface receptor labelling in slice tissue, dissociated culture transfection, and for providing tdTomato and BirAER expression plasmids. This work would not have been possible without support from the Biological Services teams at both the Laboratory of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression constructs, Veronica Chang for assistance with scFv-Clasp protein production, and Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa and Ole Paulsen for critical reading of the manuscript and constructive feedback. This work was supported by grants from the Medical Research Council (MC_U105174197) and BBSRC (BB/N002113/1).","year":"2021","department":[{"_id":"PeJo"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Watson, Jake","first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823"},{"full_name":"Pinggera, Alexandra","first_name":"Alexandra","last_name":"Pinggera"},{"last_name":"Ho","first_name":"Hinze","full_name":"Ho, Hinze"},{"full_name":"Greger, Ingo H.","first_name":"Ingo H.","last_name":"Greger"}],"volume":12,"date_updated":"2023-08-11T11:07:51Z","date_created":"2021-09-05T22:01:23Z","publication_identifier":{"eissn":["2041-1723"]},"month":"08","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":["34426577 "],"isi":["000687672000006"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-021-25281-4","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity."}],"_id":"9985","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","ddc":["612"],"status":"public","title":"AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions","file":[{"relation":"main_file","file_id":"9991","date_updated":"2021-09-08T12:57:06Z","date_created":"2021-09-08T12:57:06Z","checksum":"1bf4f6a561f96bc426d754de9cb57710","success":1,"file_name":"2021_NatureCommunications_Watson.pdf","access_level":"open_access","file_size":18310502,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"23","citation":{"mla":"Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications, vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:10.1038/s41467-021-25281-4.","short":"J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021).","chicago":"Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications. Nature Publishing Group, 2021. https://doi.org/10.1038/s41467-021-25281-4.","ama":"Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-25281-4","ista":"Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 12(1), 5083.","apa":"Watson, J., Pinggera, A., Ho, H., & Greger, I. H. (2021). AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-021-25281-4","ieee":"J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,” Nature Communications, vol. 12, no. 1. Nature Publishing Group, 2021."},"publication":"Nature Communications","article_type":"original","date_published":"2021-08-23T00:00:00Z"},{"external_id":{"isi":["000692534200001"],"arxiv":["2103.16468"]},"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,"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.21468/scipostphys.11.3.048","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["2666-9366"],"issn":["2542-4653"]},"year":"2021","publication_status":"published","publisher":"SciPost","department":[{"_id":"MaSe"}],"author":[{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671","first_name":"Stefano","last_name":"De Nicola","full_name":"De Nicola, Stefano"}],"date_updated":"2023-08-11T10:59:29Z","date_created":"2021-09-02T11:49:47Z","volume":11,"article_number":"048","file_date_updated":"2021-09-02T14:05:43Z","ec_funded":1,"publication":"SciPost Physics","citation":{"apa":"De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.3.048","ieee":"S. De Nicola, “Importance sampling scheme for the stochastic simulation of quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost, 2021.","ista":"De Nicola S. 2021. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 11(3), 048.","ama":"De Nicola S. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 2021;11(3). doi:10.21468/scipostphys.11.3.048","chicago":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.3.048.","short":"S. De Nicola, SciPost Physics 11 (2021).","mla":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics, vol. 11, no. 3, 048, SciPost, 2021, doi:10.21468/scipostphys.11.3.048."},"article_type":"original","date_published":"2021-09-02T00:00:00Z","keyword":["General Physics and Astronomy"],"day":"02","article_processing_charge":"No","has_accepted_license":"1","_id":"9981","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["519"],"title":"Importance sampling scheme for the stochastic simulation of quantum spin dynamics","status":"public","intvolume":" 11","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":373833,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_SciPostPhys_DeNicola.pdf","success":1,"checksum":"e4ec69d893e31811efc6093cb6ea8eb7","date_created":"2021-09-02T14:05:43Z","date_updated":"2021-09-02T14:05:43Z","file_id":"9984","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions\r\nfor further developments."}],"issue":"3"},{"acknowledgement":"We would like to thank Rati Gelashvili for very useful discussions, and the PODC anonymous reviewers for their careful reading of our paper, and for their useful remarks. This work is partially supported by the Polish National Science Center (NCN) grant UMO2017/25/B/ST6/02010.","_id":"9951","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","title":"Comparison dynamics in population protocols","status":"public","publication_status":"published","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Töpfer","first_name":"Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87","full_name":"Töpfer, Martin"},{"first_name":"Przemysław","last_name":"Uznański","full_name":"Uznański, Przemysław"}],"oa_version":"None","date_updated":"2023-08-11T10:56:04Z","date_created":"2021-08-22T22:01:20Z","type":"conference","abstract":[{"text":"There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.\r\n\r\nIn this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the \"correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model.","lang":"eng"}],"external_id":{"isi":["000744439800005"]},"citation":{"apa":"Alistarh, D.-A., Töpfer, M., & Uznański, P. (2021). Comparison dynamics in population protocols. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 55–65). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467915","ieee":"D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population protocols,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 55–65.","ista":"Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.","ama":"Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:55-65. doi:10.1145/3465084.3467915","chicago":"Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison Dynamics in Population Protocols.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 55–65. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467915.","short":"D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65.","mla":"Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65, doi:10.1145/3465084.3467915."},"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","page":"55-65","isi":1,"quality_controlled":"1","doi":"10.1145/3465084.3467915","date_published":"2021-07-21T00:00:00Z","conference":{"end_date":"2021-07-30","start_date":"2021-07-26","location":"Virtual, Italy","name":"PODC: Symposium on Principles of Distributed Computing"},"language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9781450385480"]},"month":"07","day":"21"},{"type":"journal_article","issue":"9","abstract":[{"text":"The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars.","lang":"eng"}],"intvolume":" 127","title":"Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9960","oa_version":"Submitted Version","article_processing_charge":"No","day":"27","article_type":"letter_note","citation":{"short":"N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M. Serbyn, Physical Review Letters 127 (2021).","mla":"Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters, vol. 127, no. 9, 090602, American Physical Society, 2021, doi:10.1103/PhysRevLett.127.090602.","chicago":"Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M. D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.127.090602.","ama":"Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 2021;127(9). doi:10.1103/PhysRevLett.127.090602","ieee":"N. Maskara et al., “Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving,” Physical Review Letters, vol. 127, no. 9. American Physical Society, 2021.","apa":"Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M. D., & Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.127.090602","ista":"Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M. 2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 127(9), 090602."},"publication":"Physical Review Letters","date_published":"2021-08-27T00:00:00Z","article_number":"090602","ec_funded":1,"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini, Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.); the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories and Gauge-Gravity Correspondence – Grant No. DE-SC0021013.","year":"2021","volume":127,"date_created":"2021-08-28T08:08:58Z","date_updated":"2023-08-11T10:57:51Z","author":[{"first_name":"N.","last_name":"Maskara","full_name":"Maskara, N."},{"full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"W. W.","last_name":"Ho","full_name":"Ho, W. W."},{"first_name":"D.","last_name":"Bluvstein","full_name":"Bluvstein, D."},{"full_name":"Choi, S.","first_name":"S.","last_name":"Choi"},{"full_name":"Lukin, M. D.","first_name":"M. D.","last_name":"Lukin"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"08","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000692200100002"],"arxiv":["2102.13160"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.13160"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.127.090602"},{"article_processing_charge":"No","day":"15","date_published":"2021-08-15T00:00:00Z","article_type":"letter_note","citation":{"chicago":"Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.104.L081112.","short":"M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021).","mla":"Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B, vol. 104, no. 8, L081112, American Physical Society, 2021, doi:10.1103/PhysRevB.104.L081112.","apa":"Sonner, M., Serbyn, M., Papić, Z., & Abanin, D. A. (2021). Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.104.L081112","ieee":"M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across the many-body localization transition in Floquet systems,” Physical Review B, vol. 104, no. 8. American Physical Society, 2021.","ista":"Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 104(8), L081112.","ama":"Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 2021;104(8). doi:10.1103/PhysRevB.104.L081112"},"publication":"Physical Review B","issue":"8","abstract":[{"text":"The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 104","title":"Thouless energy across the many-body localization transition in Floquet systems","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9961","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.104.L081112","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.15676"}],"external_id":{"arxiv":["2012.15676"],"isi":["000689734500009"]},"oa":1,"ec_funded":1,"article_number":"L081112","volume":104,"date_updated":"2023-08-11T10:57:09Z","date_created":"2021-08-28T16:44:55Z","author":[{"last_name":"Sonner","first_name":"Michael","full_name":"Sonner, Michael"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"}],"department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"We thank S. Garratt for useful comments on the manuscript. This work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A., Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1 and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations were performed on the Baobab cluster of the University\r\nof Geneva.","year":"2021"},{"citation":{"ista":"B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance fields. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 4791–4800.","apa":"B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., … Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (pp. 4791–4800). Nashville, TN, United States; Virtual: IEEE. https://doi.org/10.1109/CVPR46437.2021.00476","ieee":"M. B R et al., “Monocular reconstruction of neural face reflectance fields,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Nashville, TN, United States; Virtual, 2021, pp. 4791–4800.","ama":"B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance fields. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE; 2021:4791-4800. doi:10.1109/CVPR46437.2021.00476","chicago":"B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel, Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 4791–4800. IEEE, 2021. https://doi.org/10.1109/CVPR46437.2021.00476.","mla":"B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance Fields.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–800, doi:10.1109/CVPR46437.2021.00476.","short":"M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800."},"publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","page":"4791-4800","date_published":"2021-09-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","_id":"9957","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Monocular reconstruction of neural face reflectance fields","ddc":["000"],"status":"public","oa_version":"Preprint","file":[{"creator":"bbickel","file_size":4746649,"content_type":"application/pdf","file_name":"R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf","access_level":"open_access","date_updated":"2021-08-24T06:02:15Z","date_created":"2021-08-24T06:02:15Z","checksum":"961db0bde76dd87cf833930080bb9f38","file_id":"9958","relation":"main_file"}],"type":"conference","abstract":[{"lang":"eng","text":"The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects."}],"oa":1,"external_id":{"arxiv":["2008.10247"],"isi":["000739917304096"]},"isi":1,"quality_controlled":"1","doi":"10.1109/CVPR46437.2021.00476","conference":{"start_date":"2021-06-20","location":"Nashville, TN, United States; Virtual","end_date":"2021-06-25","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-166544509-2"],"issn":["1063-6919"]},"month":"09","year":"2021","acknowledgement":"We thank Tarun Yenamandra and Duarte David for helping us with the comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784). We also acknowledge support from InterDigital.","publisher":"IEEE","department":[{"_id":"BeBi"}],"publication_status":"published","author":[{"full_name":"B R, Mallikarjun","last_name":"B R","first_name":"Mallikarjun"},{"full_name":"Tewari, Ayush","first_name":"Ayush","last_name":"Tewari"},{"first_name":"Tae-Hyun","last_name":"Oh","full_name":"Oh, Tae-Hyun"},{"full_name":"Weyrich, Tim","first_name":"Tim","last_name":"Weyrich"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"full_name":"Seidel, Hans-Peter","first_name":"Hans-Peter","last_name":"Seidel"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"full_name":"Matusik, Wojciech","first_name":"Wojciech","last_name":"Matusik"},{"full_name":"Elgharib, Mohamed","last_name":"Elgharib","first_name":"Mohamed"},{"last_name":"Theobalt","first_name":"Christian","full_name":"Theobalt, Christian"}],"date_created":"2021-08-24T06:03:00Z","date_updated":"2023-08-11T11:08:35Z","file_date_updated":"2021-08-24T06:02:15Z"},{"type":"journal_article","abstract":[{"text":"In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors.","lang":"eng"}],"_id":"9973","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 387","status":"public","ddc":["621"],"title":"Complete gradient estimates of quantum Markov semigroups","file":[{"content_type":"application/pdf","file_size":505971,"creator":"cchlebak","file_name":"2021_CommunMathPhys_Wirth.pdf","access_level":"open_access","date_updated":"2021-09-08T09:46:34Z","date_created":"2021-09-08T07:34:24Z","checksum":"8a602f916b1c2b0dc1159708b7cb204b","relation":"main_file","file_id":"9990"}],"oa_version":"Published Version","scopus_import":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"30","citation":{"apa":"Wirth, M., & Zhang, H. (2021). Complete gradient estimates of quantum Markov semigroups. 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Zhang, Communications in Mathematical Physics 387 (2021) 761–791.","mla":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” Communications in Mathematical Physics, vol. 387, Springer Nature, 2021, pp. 761–791, doi:10.1007/s00220-021-04199-4."},"publication":"Communications in Mathematical Physics","page":"761–791","article_type":"original","date_published":"2021-08-30T00:00:00Z","ec_funded":1,"file_date_updated":"2021-09-08T09:46:34Z","year":"2021","acknowledgement":"Both authors would like to thank Jan Maas for fruitful discussions and helpful comments.","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"publication_status":"published","author":[{"full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth"},{"full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","last_name":"Zhang","first_name":"Haonan"}],"volume":387,"date_created":"2021-08-30T10:07:44Z","date_updated":"2023-08-11T11:09:07Z","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"08","external_id":{"isi":["000691214200001"],"arxiv":["2007.13506"]},"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,"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00220-021-04199-4","language":[{"iso":"eng"}]},{"oa_version":"Published Version","file":[{"date_updated":"2022-05-13T07:40:15Z","date_created":"2022-05-13T07:40:15Z","success":1,"checksum":"c430967746f653aa1ae84ee617f62b73","file_id":"11369","relation":"main_file","creator":"dernst","file_size":19707796,"content_type":"application/pdf","file_name":"2021_IOVS_Schmitt.pdf","access_level":"open_access"}],"status":"public","ddc":["570"],"title":"Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression","intvolume":" 62","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10000","abstract":[{"lang":"eng","text":"Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology."}],"issue":"10","type":"journal_article","date_published":"2021-08-16T00:00:00Z","article_type":"original","publication":"Investigative Ophthalmology and Visual Science","citation":{"ieee":"H. M. Schmitt et al., “Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression,” Investigative Ophthalmology and Visual Science, vol. 62, no. 10. Association for Research in Vision and Ophthalmology, 2021.","apa":"Schmitt, H. M., Fehrman, R. L., Maes, M. E., Yang, H., Guo, L. W., Schlamp, C. L., … Nickells, R. W. (2021). Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/IOVS.62.10.14","ista":"Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells RW. 2021. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 62(10), 14.","ama":"Schmitt HM, Fehrman RL, Maes ME, et al. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 2021;62(10). doi:10.1167/IOVS.62.10.14","chicago":"Schmitt, Heather M., Rachel L. Fehrman, Margaret E Maes, Huan Yang, Lian Wang Guo, Cassandra L. Schlamp, Heather R. Pelzel, and Robert W. Nickells. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology, 2021. https://doi.org/10.1167/IOVS.62.10.14.","short":"H.M. Schmitt, R.L. Fehrman, M.E. Maes, H. Yang, L.W. Guo, C.L. Schlamp, H.R. Pelzel, R.W. Nickells, Investigative Ophthalmology and Visual Science 62 (2021).","mla":"Schmitt, Heather M., et al. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology and Visual Science, vol. 62, no. 10, 14, Association for Research in Vision and Ophthalmology, 2021, doi:10.1167/IOVS.62.10.14."},"day":"16","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-08-14T06:35:17Z","date_created":"2021-09-12T22:01:23Z","volume":62,"author":[{"last_name":"Schmitt","first_name":"Heather M.","full_name":"Schmitt, Heather M."},{"full_name":"Fehrman, Rachel L.","last_name":"Fehrman","first_name":"Rachel L."},{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes"},{"full_name":"Yang, Huan","first_name":"Huan","last_name":"Yang"},{"full_name":"Guo, Lian Wang","first_name":"Lian Wang","last_name":"Guo"},{"last_name":"Schlamp","first_name":"Cassandra L.","full_name":"Schlamp, Cassandra L."},{"last_name":"Pelzel","first_name":"Heather R.","full_name":"Pelzel, Heather R."},{"last_name":"Nickells","first_name":"Robert W.","full_name":"Nickells, Robert W."}],"publication_status":"published","publisher":"Association for Research in Vision and Ophthalmology","department":[{"_id":"SaSi"}],"year":"2021","acknowledgement":"The authors thank Joel Dietz for maintaining the mice used in this study, Satoshi Kinoshita and the Translational Research Initiative in Pathology Laboratory at the University of Wisconsin-Madison for cutting retinal sections analyzed in this study, and Mark Banghart for statistical review of the data analysis. Supported by National Eye Institute Grants R01 EY012223 (RWN), R01 EY030123 (RWN), R01 EY029809 (LWG), R01 EY029809 (LWG) and a Vision Research CORE grant P30 EY016665, NRSA grant T32 GM081061, by an unrestricted research grant from Research to Prevent Blindness, Inc., and by a University of Wisconsin-Madison Vilas Life Cycle award and the Frederick A. Davis Research Chair (RWN). ","pmid":1,"file_date_updated":"2022-05-13T07:40:15Z","article_number":"14","language":[{"iso":"eng"}],"doi":"10.1167/IOVS.62.10.14","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["34398198"],"isi":["000695230000014"]},"month":"08","publication_identifier":{"issn":["0146-0404"],"eissn":["1552-5783"]}},{"article_type":"original","publication":"Selecta Mathematica","citation":{"ieee":"P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” Selecta Mathematica, vol. 27, no. 5. Springer Nature, 2021.","apa":"Koroteev, P., Pushkar, P., Smirnov, A. V., & Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-021-00698-3","ista":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87.","ama":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 2021;27(5). doi:10.1007/s00029-021-00698-3","chicago":"Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica. Springer Nature, 2021. https://doi.org/10.1007/s00029-021-00698-3.","short":"P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021).","mla":"Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica, vol. 27, no. 5, 87, Springer Nature, 2021, doi:10.1007/s00029-021-00698-3."},"date_published":"2021-08-30T00:00:00Z","scopus_import":"1","day":"30","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","ddc":["530"],"title":"Quantum K-theory of quiver varieties and many-body systems","status":"public","intvolume":" 27","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9998","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10010","checksum":"beadc5a722ffb48190e1e63ee2dbfee5","success":1,"date_updated":"2021-09-13T11:31:34Z","date_created":"2021-09-13T11:31:34Z","access_level":"open_access","file_name":"2021_SelectaMath_Koroteev.pdf","content_type":"application/pdf","file_size":584648,"creator":"cchlebak"}],"type":"journal_article","abstract":[{"text":"We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice.","lang":"eng"}],"issue":"5","quality_controlled":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"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":["000692795200001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00029-021-00698-3","month":"08","publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","acknowledgement":"First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2021","date_updated":"2023-08-14T06:34:14Z","date_created":"2021-09-12T22:01:22Z","volume":27,"author":[{"full_name":"Koroteev, Peter","first_name":"Peter","last_name":"Koroteev"},{"full_name":"Pushkar, Petr","id":"151DCEB6-9EC3-11E9-8480-ABECE5697425","last_name":"Pushkar","first_name":"Petr"},{"full_name":"Smirnov, Andrey V.","first_name":"Andrey V.","last_name":"Smirnov"},{"full_name":"Zeitlin, Anton M.","last_name":"Zeitlin","first_name":"Anton M."}],"article_number":"87","file_date_updated":"2021-09-13T11:31:34Z"},{"citation":{"apa":"Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.66483","ieee":"E. Pulgar et al., “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” eLife, vol. 10. eLife Sciences Publications, 2021.","ista":"Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.","ama":"Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 2021;10. doi:10.7554/eLife.66483","chicago":"Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.66483.","short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).","mla":"Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife, vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483."},"publication":"eLife","article_type":"original","date_published":"2021-08-27T00:00:00Z","scopus_import":"1","keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"27","_id":"9999","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","status":"public","ddc":["570"],"title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","oa_version":"Published Version","file":[{"file_id":"11371","relation":"main_file","date_updated":"2022-05-13T08:03:37Z","date_created":"2022-05-13T08:03:37Z","success":1,"checksum":"a3f82b0499cc822ac1eab48a01f3f57e","file_name":"2021_eLife_Pulgar.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":9010446}],"type":"journal_article","abstract":[{"lang":"eng","text":"The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site."}],"external_id":{"isi":["000700428500001"],"pmid":["34448451"]},"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,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.7554/eLife.66483","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"month":"08","pmid":1,"year":"2021","publisher":"eLife Sciences Publications","department":[{"_id":"CaHe"}],"publication_status":"published","author":[{"full_name":"Pulgar, Eduardo","first_name":"Eduardo","last_name":"Pulgar"},{"full_name":"Schwayer, Cornelia","last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guerrero","first_name":"Néstor","full_name":"Guerrero, Néstor"},{"last_name":"López","first_name":"Loreto","full_name":"López, Loreto"},{"full_name":"Márquez, Susana","first_name":"Susana","last_name":"Márquez"},{"full_name":"Härtel, Steffen","last_name":"Härtel","first_name":"Steffen"},{"full_name":"Soto, Rodrigo","last_name":"Soto","first_name":"Rodrigo"},{"full_name":"Heisenberg, Carl Philipp","first_name":"Carl Philipp","last_name":"Heisenberg"},{"first_name":"Miguel L.","last_name":"Concha","full_name":"Concha, Miguel L."}],"volume":10,"date_updated":"2023-08-14T06:53:33Z","date_created":"2021-09-12T22:01:23Z","article_number":"e66483","ec_funded":1,"file_date_updated":"2022-05-13T08:03:37Z"},{"article_processing_charge":"No","day":"07","keyword":["Computer science","Computational modeling","Markov processes","Probabilistic logic","Formal verification","Game Theory"],"scopus_import":"1","date_published":"2021-07-07T00:00:00Z","page":"1-13","citation":{"ieee":"K. Chatterjee, W. Dvorak, M. H. Henzinger, and A. Svozil, “Symbolic time and space tradeoffs for probabilistic verification,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021, pp. 1–13.","apa":"Chatterjee, K., Dvorak, W., Henzinger, M. H., & Svozil, A. (2021). Symbolic time and space tradeoffs for probabilistic verification. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470739","ista":"Chatterjee K, Dvorak W, Henzinger MH, Svozil A. 2021. Symbolic time and space tradeoffs for probabilistic verification. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","ama":"Chatterjee K, Dvorak W, Henzinger MH, Svozil A. Symbolic time and space tradeoffs for probabilistic verification. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470739","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorak, Monika H Henzinger, and Alexander Svozil. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470739.","short":"K. Chatterjee, W. Dvorak, M.H. Henzinger, A. Svozil, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13.","mla":"Chatterjee, Krishnendu, et al. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:10.1109/LICS52264.2021.9470739."},"publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","abstract":[{"text":"We present a faster symbolic algorithm for the following central problem in probabilistic verification: Compute the maximal end-component (MEC) decomposition of Markov decision processes (MDPs). This problem generalizes the SCC decomposition problem of graphs and closed recurrent sets of Markov chains. The model of symbolic algorithms is widely used in formal verification and model-checking, where access to the input model is restricted to only symbolic operations (e.g., basic set operations and computation of one-step neighborhood). For an input MDP with n vertices and m edges, the classical symbolic algorithm from the 1990s for the MEC decomposition requires O(n2) symbolic operations and O(1) symbolic space. The only other symbolic algorithm for the MEC decomposition requires O(nm−−√) symbolic operations and O(m−−√) symbolic space. A main open question is whether the worst-case O(n2) bound for symbolic operations can be beaten. We present a symbolic algorithm that requires O˜(n1.5) symbolic operations and O˜(n−−√) symbolic space. Moreover, the parametrization of our algorithm provides a trade-off between symbolic operations and symbolic space: for all 0<ϵ≤1/2 the symbolic algorithm requires O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space ( O˜ hides poly-logarithmic factors). Using our techniques we present faster algorithms for computing the almost-sure winning regions of ω -regular objectives for MDPs. We consider the canonical parity objectives for ω -regular objectives, and for parity objectives with d -priorities we present an algorithm that computes the almost-sure winning region with O˜(n2−ϵ) symbolic operations and O˜(nϵ) symbolic space, for all 0<ϵ≤1/2 .","lang":"eng"}],"type":"conference","oa_version":"Preprint","status":"public","title":"Symbolic time and space tradeoffs for probabilistic verification","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10002","publication_identifier":{"isbn":["978-1-6654-4896-3"],"issn":["1043-6871"],"eisbn":["978-1-6654-4895-6"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1109/LICS52264.2021.9470739","conference":{"end_date":"2021-07-02","location":"Rome, Italy","start_date":"2021-06-29","name":"LICS: Symposium on Logic in Computer Science"},"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2104.07466"],"isi":["000947350400089"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.07466"}],"ec_funded":1,"date_updated":"2023-08-14T06:51:33Z","date_created":"2021-09-12T22:01:24Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Wolfgang","last_name":"Dvorak","full_name":"Dvorak, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Svozil, Alexander","first_name":"Alexander","last_name":"Svozil"}],"department":[{"_id":"KrCh"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","acknowledgement":"The authors are grateful to the anonymous referees for their valuable comments. A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15–003. K. C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and by the ERC CoG 863818 (ForM-SMArt). For M. H. the research leading to these results has received funding from the European Research Council under the European Unions Seventh Framework Programme (FP/2007–2013) / ERC Grant Agreement no. 340506.","year":"2021"},{"type":"journal_article","abstract":[{"text":"In this paper, we introduce a random environment for the exclusion process in obtained by assigning a maximal occupancy to each site. This maximal occupancy is allowed to randomly vary among sites, and partial exclusion occurs. Under the assumption of ergodicity under translation and uniform ellipticity of the environment, we derive a quenched hydrodynamic limit in path space by strengthening the mild solution approach initiated in Nagy (2002) and Faggionato (2007). To this purpose, we prove, employing the technology developed for the random conductance model, a homogenization result in the form of an arbitrary starting point quenched invariance principle for a single particle in the same environment, which is a result of independent interest. The self-duality property of the partial exclusion process allows us to transfer this homogenization result to the particle system and, then, apply the tightness criterion in Redig et al. (2020).","lang":"eng"}],"title":"Hydrodynamics for the partial exclusion process in random environment","ddc":["519"],"status":"public","intvolume":" 142","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10024","file":[{"file_id":"11370","relation":"main_file","date_updated":"2022-05-13T07:55:50Z","date_created":"2022-05-13T07:55:50Z","success":1,"checksum":"56768c553d7218ee5714902ffec90ec4","file_name":"2021_StochasticProcessesAppl_Floreani.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2115791}],"oa_version":"Published Version","keyword":["hydrodynamic limit","random environment","random conductance model","arbitrary starting point quenched invariance principle","duality","mild solution"],"scopus_import":"1","day":"27","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","page":"124-158","publication":"Stochastic Processes and their Applications","citation":{"chicago":"Floreani, Simone, Frank Redig, and Federico Sau. “Hydrodynamics for the Partial Exclusion Process in Random Environment.” Stochastic Processes and Their Applications. Elsevier, 2021. https://doi.org/10.1016/j.spa.2021.08.006.","short":"S. Floreani, F. Redig, F. Sau, Stochastic Processes and Their Applications 142 (2021) 124–158.","mla":"Floreani, Simone, et al. “Hydrodynamics for the Partial Exclusion Process in Random Environment.” Stochastic Processes and Their Applications, vol. 142, Elsevier, 2021, pp. 124–58, doi:10.1016/j.spa.2021.08.006.","ieee":"S. Floreani, F. Redig, and F. Sau, “Hydrodynamics for the partial exclusion process in random environment,” Stochastic Processes and their Applications, vol. 142. Elsevier, pp. 124–158, 2021.","apa":"Floreani, S., Redig, F., & Sau, F. (2021). Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2021.08.006","ista":"Floreani S, Redig F, Sau F. 2021. Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and their Applications. 142, 124–158.","ama":"Floreani S, Redig F, Sau F. Hydrodynamics for the partial exclusion process in random environment. Stochastic Processes and their Applications. 2021;142:124-158. doi:10.1016/j.spa.2021.08.006"},"date_published":"2021-08-27T00:00:00Z","file_date_updated":"2022-05-13T07:55:50Z","ec_funded":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JaMa"}],"acknowledgement":"The authors would like to thank Marek Biskup and Alberto Chiarini for useful suggestions and Cristian Giardina, Frank den Hollander and Shubhamoy Nandan for inspiring discussions. S.F. acknowledges Simona Villa for her help in creating the picture. Furthermore, the authors thank two anonymous referees for the careful reading of the manuscript. S.F. acknowledges financial support from NWO, The Netherlands via the grant TOP1.17.019. F.S. acknowledges financial support from NWO via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.","year":"2021","date_created":"2021-09-19T22:01:25Z","date_updated":"2023-08-14T06:52:43Z","volume":142,"author":[{"full_name":"Floreani, Simone","first_name":"Simone","last_name":"Floreani"},{"full_name":"Redig, Frank","first_name":"Frank","last_name":"Redig"},{"full_name":"Sau, Federico","last_name":"Sau","first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425"}],"month":"08","publication_identifier":{"issn":["0304-4149"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"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":["1911.12564"],"isi":["000697748500005"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.spa.2021.08.006"},{"page":"1-13","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","citation":{"short":"K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:10.1109/LICS52264.2021.9470595.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470595.","ama":"Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470595","ieee":"K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021, pp. 1–13.","apa":"Chatterjee, K., & Doyen, L. (2021). Stochastic processes with expected stopping time. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470595","ista":"Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13."},"date_published":"2021-07-07T00:00:00Z","keyword":["Computer science","Heuristic algorithms","Memory management","Automata","Markov processes","Probability distribution","Complexity theory"],"scopus_import":"1","day":"07","article_processing_charge":"No","status":"public","title":"Stochastic processes with expected stopping time","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10004","oa_version":"Preprint","type":"conference","abstract":[{"text":"Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs.","lang":"eng"}],"isi":1,"quality_controlled":"1","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"main_file_link":[{"url":"https://arxiv.org/abs/2104.07278","open_access":"1"}],"oa":1,"external_id":{"isi":["000947350400036"],"arxiv":["2104.07278"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2021-07-02","start_date":"2021-06-29","location":"Rome, Italy","name":"LICS: Symposium on Logic in Computer Science"},"doi":"10.1109/LICS52264.2021.9470595","month":"07","publication_identifier":{"isbn":["978-1-6654-4896-3"],"issn":["1043-6871"],"eisbn":["978-1-6654-4895-6"]},"publication_status":"published","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"KrCh"}],"year":"2021","acknowledgement":"We are grateful to the anonymous reviewers of LICS 2021 and of a previous version of this paper for insightful comments that helped improving the presentation. This research was partially supported by the grant ERC CoG 863818 (ForM-SMArt).","date_updated":"2023-08-14T06:52:07Z","date_created":"2021-09-12T22:01:25Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"ec_funded":1},{"abstract":[{"lang":"eng","text":"This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1−1 μ+NPlog2log2NP), where N is the block length of the code and μ is the scaling exponent of polar codes for the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P=N2 , the latency of SSC decoding is O(N1−1/μ) , which is sublinear in the block length. This recovers a result from an earlier work. Second, in a fully-serial implementation where P=1 , the latency of SSC decoding scales as O(Nlog2log2N) . The multiplicative constant is also calculated: we show that the latency of SSC decoding when P=1 is given by (2+o(1))Nlog2log2N . Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P=N1/μ . The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations."}],"type":"conference","oa_version":"Preprint","_id":"10053","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-09-01T00:00:00Z","citation":{"ama":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. In: 2021 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers; 2021:2369-2374. doi:10.1109/ISIT45174.2021.9518153","ista":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2021. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. 2021 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 2369–2374.","ieee":"S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” in 2021 IEEE International Symposium on Information Theory, Melbourne, Australia, 2021, pp. 2369–2374.","apa":"Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., & Goldsmith, A. (2021). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. In 2021 IEEE International Symposium on Information Theory (pp. 2369–2374). Melbourne, Australia: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ISIT45174.2021.9518153","mla":"Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–74, doi:10.1109/ISIT45174.2021.9518153.","short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–2374.","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” In 2021 IEEE International Symposium on Information Theory, 2369–74. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/ISIT45174.2021.9518153."},"publication":"2021 IEEE International Symposium on Information Theory","page":"2369-2374","related_material":{"record":[{"relation":"later_version","status":"public","id":"10364"}]},"author":[{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco"},{"first_name":"Arman","last_name":"Fazeli","full_name":"Fazeli, Arman"},{"full_name":"Vardy, Alexander","first_name":"Alexander","last_name":"Vardy"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"full_name":"Goldsmith, Andrea","last_name":"Goldsmith","first_name":"Andrea"}],"date_created":"2021-09-27T14:33:14Z","date_updated":"2023-08-14T06:55:58Z","acknowledgement":"S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council\r\nof Canada (NSERC) and by Huawei. M. Mondelli is partially supported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by the National Science Foundation under Grant CCF-1764104.","year":"2021","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"MaMo"}],"publication_status":"published","publication_identifier":{"eisbn":["978-1-5386-8209-8"],"issn":["2157-8095"],"isbn":["978-1-5386-8210-4"]},"month":"09","doi":"10.1109/ISIT45174.2021.9518153","conference":{"end_date":"2021-07-20","location":"Melbourne, Australia","start_date":"2021-07-12","name":"ISIT: International Symposium on Information Theory"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000701502202078"],"arxiv":["2012.13378"]},"main_file_link":[{"url":"https://arxiv.org/abs/2012.13378","open_access":"1"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","isi":1},{"file":[{"access_level":"open_access","file_name":"1-s2.0-S000187082100431X-main.pdf","content_type":"application/pdf","file_size":840635,"creator":"qho","relation":"main_file","file_id":"10034","checksum":"f3c0086d41af11db31c00014efb38072","date_updated":"2021-09-21T15:58:52Z","date_created":"2021-09-21T15:58:52Z"}],"oa_version":"Published Version","_id":"10033","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["514"],"status":"public","title":"The Atiyah-Bott formula and connectivity in chiral Koszul duality","intvolume":" 392","abstract":[{"lang":"eng","text":"The ⊗*-monoidal structure on the category of sheaves on the Ran space is not pro-nilpotent in the sense of [3]. However, under some connectivity assumptions, we prove that Koszul duality induces an equivalence of categories and that this equivalence behaves nicely with respect to Verdier duality on the Ran space and integrating along the Ran space, i.e. taking factorization homology. Based on ideas sketched in [4], we show that these results also offer a simpler alternative to one of the two main steps in the proof of the Atiyah-Bott formula given in [7] and [5]."}],"type":"journal_article","date_published":"2021-09-21T00:00:00Z","publication":"Advances in Mathematics","citation":{"ama":"Ho QP. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 2021;392. doi:10.1016/j.aim.2021.107992","apa":"Ho, Q. P. (2021). The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107992","ieee":"Q. P. Ho, “The Atiyah-Bott formula and connectivity in chiral Koszul duality,” Advances in Mathematics, vol. 392. Elsevier, 2021.","ista":"Ho QP. 2021. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 392, 107992.","short":"Q.P. Ho, Advances in Mathematics 392 (2021).","mla":"Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” Advances in Mathematics, vol. 392, 107992, Elsevier, 2021, doi:10.1016/j.aim.2021.107992.","chicago":"Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107992."},"article_type":"original","day":"21","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","keyword":["Chiral algebras","Chiral homology","Factorization algebras","Koszul duality","Ran space"],"author":[{"full_name":"Ho, Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6889-1418","first_name":"Quoc P","last_name":"Ho"}],"date_created":"2021-09-21T15:58:59Z","date_updated":"2023-08-14T06:54:35Z","volume":392,"acknowledgement":"The author would like to express his gratitude to D. Gaitsgory, without whose tireless guidance and encouragement in pursuing this problem, this work would not have been possible. The author is grateful to his advisor B.C. Ngô for many years of patient guidance and support. This paper is revised while the author is a postdoc in Hausel group at IST Austria. We thank him and the group for providing a wonderful research environment. The author also gratefully acknowledges the support of the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization Homology,” Austrian Science Fund (FWF): M 2751.","year":"2021","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Elsevier","file_date_updated":"2021-09-21T15:58:52Z","article_number":"107992","doi":"10.1016/j.aim.2021.107992","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"},"external_id":{"isi":["000707040300031"],"arxiv":["1610.00212"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"26B96266-B435-11E9-9278-68D0E5697425","grant_number":"M02751","name":"Algebro-Geometric Applications of Factorization Homology","call_identifier":"FWF"}],"month":"09","publication_identifier":{"eissn":["1090-2082"],"issn":["0001-8708"]}},{"isi":1,"quality_controlled":"1","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":["000752287700005"],"pmid":["34353898"]},"language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0586-21.2021","month":"09","publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"publication_status":"published","publisher":"Society for Neuroscience","department":[{"_id":"RySh"}],"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Collaborative Sensory Research Center 1286 [to C.W. (A4) and T.M. (B5)] and under Germany’s Excellence Strategy Grant EXC 2067/1-390729940. We thank S. Gerke, A.J. Goldak, and C. Senger-Freitag for expert technical assistance; G. Hoch for developing image analysis routines; and S. Chepurwar and N. Strenzke for technical support and discussion regarding in vivo experiments. We also thank Dr. Christian Rosenmund, Dr. Katharina Grauel, and Dr. Stephan Sigrist for providing RIM-BP2 KO mice and Dr. Masahiko Watanabe for providing the anti-neurexin-antibody, and Dr. Toshihisa Ohtsuka for the anti-ELKS-antibody. J. Neef for help with the STED imaging and image analysis; E. Neher and S. Rizzoli for discussion and comments on the manuscript; K. Eguchi for help with the statistical analysis; and C. H. Huang and J. Neef for constant support and scientific discussion.","year":"2021","pmid":1,"date_created":"2021-09-27T14:33:13Z","date_updated":"2023-08-14T06:56:30Z","volume":41,"author":[{"first_name":"Tanvi","last_name":"Butola","full_name":"Butola, Tanvi"},{"first_name":"Theocharis","last_name":"Alvanos","full_name":"Alvanos, Theocharis"},{"last_name":"Hintze","first_name":"Anika","full_name":"Hintze, Anika"},{"full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","first_name":"Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"last_name":"Wichmann","first_name":"Carolin","full_name":"Wichmann, Carolin"},{"full_name":"Moser, Tobias","last_name":"Moser","first_name":"Tobias"}],"file_date_updated":"2022-05-31T09:10:15Z","article_type":"original","page":"7742-7767","publication":"Journal of Neuroscience","citation":{"chicago":"Butola, Tanvi, Theocharis Alvanos, Anika Hintze, Peter Koppensteiner, David Kleindienst, Ryuichi Shigemoto, Carolin Wichmann, and Tobias Moser. “RIM-Binding Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience. Society for Neuroscience, 2021. https://doi.org/10.1523/JNEUROSCI.0586-21.2021.","short":"T. Butola, T. Alvanos, A. Hintze, P. Koppensteiner, D. Kleindienst, R. Shigemoto, C. Wichmann, T. Moser, Journal of Neuroscience 41 (2021) 7742–7767.","mla":"Butola, Tanvi, et al. “RIM-Binding Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience, vol. 41, no. 37, Society for Neuroscience, 2021, pp. 7742–67, doi:10.1523/JNEUROSCI.0586-21.2021.","apa":"Butola, T., Alvanos, T., Hintze, A., Koppensteiner, P., Kleindienst, D., Shigemoto, R., … Moser, T. (2021). RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0586-21.2021","ieee":"T. Butola et al., “RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse,” Journal of Neuroscience, vol. 41, no. 37. Society for Neuroscience, pp. 7742–7767, 2021.","ista":"Butola T, Alvanos T, Hintze A, Koppensteiner P, Kleindienst D, Shigemoto R, Wichmann C, Moser T. 2021. RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. 41(37), 7742–7767.","ama":"Butola T, Alvanos T, Hintze A, et al. RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. 2021;41(37):7742-7767. doi:10.1523/JNEUROSCI.0586-21.2021"},"date_published":"2021-09-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1","status":"public","title":"RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse","ddc":["570"],"intvolume":" 41","_id":"10051","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"769ab627c7355a50ccfd445e43a5f351","date_updated":"2022-05-31T09:10:15Z","date_created":"2022-05-31T09:10:15Z","file_id":"11423","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":11571961,"access_level":"open_access","file_name":"2021_JourNeuroscience_Butola.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Rab-interacting molecule (RIM)-binding protein 2 (BP2) is a multidomain protein of the presynaptic active zone (AZ). By binding to RIM, bassoon (Bsn), and voltage-gated Ca2+ channels (CaV), it is considered to be a central organizer of the topography of CaV and release sites of synaptic vesicles (SVs) at the AZ. Here, we used RIM-BP2 knock-out (KO) mice and their wild-type (WT) littermates of either sex to investigate the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers (ANFs) with bushy cells (BCs) of the cochlear nucleus, a fast relay of the auditory pathway with high release probability. Disruption of RIM-BP2 lowered release probability altering short-term plasticity and reduced evoked EPSCs. Analysis of SV pool dynamics during high-frequency train stimulation indicated a reduction of SVs with high release probability but an overall normal size of the readily releasable SV pool (RRP). The Ca2+-dependent fast component of SV replenishment after RRP depletion was slowed. Ultrastructural analysis by superresolution light and electron microscopy revealed an impaired topography of presynaptic CaV and a reduction of docked and membrane-proximal SVs at the AZ. We conclude that RIM-BP2 organizes the topography of CaV, and promotes SV tethering and docking. This way RIM-BP2 is critical for establishing a high initial release probability as required to reliably signal sound onset information that we found to be degraded in BCs of RIM-BP2-deficient mice in vivo. SIGNIFICANCE STATEMENT: Rab-interacting molecule (RIM)-binding proteins (BPs) are key organizers of the active zone (AZ). Using a multidisciplinary approach to the calyceal endbulb of Held synapse that transmits auditory information at rates of up to hundreds of Hertz with submillisecond precision we demonstrate a requirement for RIM-BP2 for normal auditory signaling. Endbulb synapses lacking RIM-BP2 show a reduced release probability despite normal whole-terminal Ca2+ influx and abundance of the key priming protein Munc13-1, a reduced rate of SV replenishment, as well as an altered topography of voltage-gated (CaV)2.1 Ca2+ channels, and fewer docked and membrane proximal synaptic vesicles (SVs). This hampers transmission of sound onset information likely affecting downstream neural computations such as of sound localization.","lang":"eng"}],"issue":"37"},{"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Repeated idempotent elements are commonly used to characterise iterable behaviours in abstract models of computation. Therefore, given a monoid M, it is natural to ask how long a sequence of elements of M needs to be to ensure the presence of consecutive idempotent factors. This question is formalised through the notion of the Ramsey function R_M associated to M, obtained by mapping every k ∈ ℕ to the minimal integer R_M(k) such that every word u ∈ M^* of length R_M(k) contains k consecutive non-empty factors that correspond to the same idempotent element of M. In this work, we study the behaviour of the Ramsey function R_M by investigating the regular 𝒟-length of M, defined as the largest size L(M) of a submonoid of M isomorphic to the set of natural numbers {1,2, …, L(M)} equipped with the max operation. We show that the regular 𝒟-length of M determines the degree of R_M, by proving that k^L(M) ≤ R_M(k) ≤ (k|M|⁴)^L(M). To allow applications of this result, we provide the value of the regular 𝒟-length of diverse monoids. In particular, we prove that the full monoid of n × n Boolean matrices, which is used to express transition monoids of non-deterministic automata, has a regular 𝒟-length of (n²+n+2)/2."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10055","intvolume":" 187","ddc":["000"],"title":"A Ramsey theorem for finite monoids","status":"public","file":[{"date_updated":"2021-10-01T09:55:00Z","date_created":"2021-10-01T09:55:00Z","checksum":"17432a05733f408de300e17e390a90e4","success":1,"relation":"main_file","file_id":"10063","file_size":720250,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_LIPIcs_Jecker.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10","citation":{"chicago":"Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” In 38th International Symposium on Theoretical Aspects of Computer Science, Vol. 187. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.STACS.2021.44.","mla":"Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” 38th International Symposium on Theoretical Aspects of Computer Science, vol. 187, 44, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.STACS.2021.44.","short":"I.R. Jecker, in:, 38th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","ista":"Jecker IR. 2021. A Ramsey theorem for finite monoids. 38th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 187, 44.","apa":"Jecker, I. R. (2021). A Ramsey theorem for finite monoids. In 38th International Symposium on Theoretical Aspects of Computer Science (Vol. 187). Saarbrücken, Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2021.44","ieee":"I. R. Jecker, “A Ramsey theorem for finite monoids,” in 38th International Symposium on Theoretical Aspects of Computer Science, Saarbrücken, Germany, 2021, vol. 187.","ama":"Jecker IR. A Ramsey theorem for finite monoids. In: 38th International Symposium on Theoretical Aspects of Computer Science. Vol 187. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.STACS.2021.44"},"publication":"38th International Symposium on Theoretical Aspects of Computer Science","date_published":"2021-03-10T00:00:00Z","article_number":"44","ec_funded":1,"file_date_updated":"2021-10-01T09:55:00Z","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. I wish to thank Michaël Cadilhac, Emmanuel Filiot and Charles Paperman for their valuable insights concerning Green’s relations.","year":"2021","publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Jecker, Ismael R","last_name":"Jecker","first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425"}],"volume":187,"date_updated":"2023-08-14T07:03:23Z","date_created":"2021-09-27T14:33:15Z","publication_identifier":{"isbn":["978-3-9597-7180-1"],"issn":["1868-8969"]},"month":"03","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":["000635691700044"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"doi":"10.4230/LIPIcs.STACS.2021.44","conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","location":"Saarbrücken, Germany","start_date":"2021-03-16","end_date":"2021-03-19"},"language":[{"iso":"eng"}]},{"date_published":"2021-09-28T00:00:00Z","article_type":"original","citation":{"chicago":"Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum, and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-98411-z.","short":"M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021).","mla":"Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports, vol. 11, 19238, Springer Nature, 2021, doi:10.1038/s41598-021-98411-z.","apa":"Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., & Baud, D. (2021). Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-98411-z","ieee":"M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy,” Scientific Reports, vol. 11. Springer Nature, 2021.","ista":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 11, 19238.","ama":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 2021;11. doi:10.1038/s41598-021-98411-z"},"publication":"Scientific Reports","article_processing_charge":"Yes","has_accepted_license":"1","day":"28","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_ScientificReports_Robinson.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":6970368,"file_id":"10091","relation":"main_file","success":1,"checksum":"f002ec22f609f58e1263b79e7f79601e","date_updated":"2021-10-05T14:56:48Z","date_created":"2021-10-05T14:56:48Z"}],"intvolume":" 11","status":"public","ddc":["618"],"title":"Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10069","abstract":[{"lang":"eng","text":"The extent to which women differ in the course of blood cell counts throughout pregnancy, and the importance of these changes to pregnancy outcomes has not been well defined. Here, we develop a series of statistical analyses of repeated measures data to reveal the degree to which women differ in the course of pregnancy, predict the changes that occur, and determine the importance of these changes for post-partum hemorrhage (PPH) which is one of the leading causes of maternal mortality. We present a prospective cohort of 4082 births recorded at the University Hospital, Lausanne, Switzerland between 2009 and 2014 where full labour records could be obtained, along with complete blood count data taken at hospital admission. We find significant differences, at a [Formula: see text] level, among women in how blood count values change through pregnancy for mean corpuscular hemoglobin, mean corpuscular volume, mean platelet volume, platelet count and red cell distribution width. We find evidence that almost all complete blood count values show trimester-specific associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53), high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels (OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester 3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences among women in the course of blood cell counts throughout pregnancy have an important role in shaping pregnancy outcome and tracking blood count value changes through pregnancy improves identification of women at increased risk of postpartum hemorrhage. This study provides greater understanding of the complex changes in blood count values that occur through pregnancy and provides indicators to guide the stratification of patients into risk groups."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41598-021-98411-z","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":["34584125"],"isi":["000701575500083"]},"oa":1,"publication_identifier":{"eissn":["2045-2322"]},"month":"09","volume":11,"date_updated":"2023-08-14T07:05:15Z","date_created":"2021-10-03T22:01:21Z","author":[{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"last_name":"Patxot","first_name":"Marion","full_name":"Patxot, Marion"},{"full_name":"Stojanov, Miloš","last_name":"Stojanov","first_name":"Miloš"},{"first_name":"Sabine","last_name":"Blum","full_name":"Blum, Sabine"},{"first_name":"David","last_name":"Baud","full_name":"Baud, David"}],"department":[{"_id":"MaRo"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the study and all the midwives and doctors for the computerized obstetrical data.","file_date_updated":"2021-10-05T14:56:48Z","article_number":"19238"},{"scopus_import":"1","keyword":["condensed matter - mesoscale and nanoscale physics","condensed matter - strongly correlated electrons","multidisciplinary"],"article_processing_charge":"No","day":"01","citation":{"apa":"Zhou, H., Xie, T., Ghazaryan, A., Holder, T., Ehrets, J. R., Spanton, E. M., … Young, A. F. (2021). Half and quarter metals in rhombohedral trilayer graphene. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03938-w","ieee":"H. Zhou et al., “Half and quarter metals in rhombohedral trilayer graphene,” Nature. Springer Nature, 2021.","ista":"Zhou H, Xie T, Ghazaryan A, Holder T, Ehrets JR, Spanton EM, Taniguchi T, Watanabe K, Berg E, Serbyn M, Young AF. 2021. Half and quarter metals in rhombohedral trilayer graphene. Nature.","ama":"Zhou H, Xie T, Ghazaryan A, et al. Half and quarter metals in rhombohedral trilayer graphene. Nature. 2021. doi:10.1038/s41586-021-03938-w","chicago":"Zhou, Haoxin, Tian Xie, Areg Ghazaryan, Tobias Holder, James R. Ehrets, Eric M. Spanton, Takashi Taniguchi, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03938-w.","short":"H. Zhou, T. Xie, A. Ghazaryan, T. Holder, J.R. Ehrets, E.M. Spanton, T. Taniguchi, K. Watanabe, E. Berg, M. Serbyn, A.F. Young, Nature (2021).","mla":"Zhou, Haoxin, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature, Springer Nature, 2021, doi:10.1038/s41586-021-03938-w."},"publication":"Nature","article_type":"original","date_published":"2021-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Ferromagnetism is most common in transition metal compounds but may also arise in low-density two-dimensional electron systems, with signatures observed in silicon, III-V semiconductor systems, and graphene moiré heterostructures. Here we show that gate-tuned van Hove singularities in rhombohedral trilayer graphene drive the spontaneous ferromagnetic polarization of the electron system into one or more spin- and valley flavors. Using capacitance measurements on graphite-gated van der Waals heterostructures, we find a cascade of density- and electronic displacement field tuned phase transitions marked by negative electronic compressibility. The transitions define the boundaries between phases where quantum oscillations have either four-fold, two-fold, or one-fold degeneracy, associated with a spin and valley degenerate normal metal, spin-polarized `half-metal', and spin and valley polarized `quarter metal', respectively. For electron doping, the salient features are well captured by a phenomenological Stoner model with a valley-anisotropic Hund's coupling, likely arising from interactions at the lattice scale. For hole filling, we observe a richer phase diagram featuring a delicate interplay of broken symmetries and transitions in the Fermi surface topology. Finally, by rotational alignment of a hexagonal boron nitride substrate to induce a moiré superlattice, we find that the superlattice perturbs the preexisting isospin order only weakly, leaving the basic phase diagram intact while catalyzing the formation of topologically nontrivial gapped states whenever itinerant half- or quarter metal states occur at half- or quarter superlattice band filling. Our results show that rhombohedral trilayer graphene is an ideal platform for well-controlled tests of many-body theory and reveal magnetism in moiré materials to be fundamentally itinerant in nature."}],"_id":"10025","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Half and quarter metals in rhombohedral trilayer graphene","status":"public","oa_version":"Preprint","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"09","external_id":{"isi":["000706977400002"],"arxiv":["2104.00653"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2104.00653","open_access":"1"}],"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/s41586-021-03938-w","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"The authors acknowledge discussions with A. Macdonald, L. Fu, F. Wang and M. Zaletel. AFY acknowledges support of the National Science Foundation under DMR1654186, and the Gordon and Betty Moore Foundation under award GBMF9471. The authors acknowledge the use of the research facilities within the California NanoSystems Institute, supported by the University of California, Santa Barbara and the University of California, Office of the President.\r\nK.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant Number JPMXP0112101001 and JSPS KAKENHI, Grant Number JP20H00354. EB and TH were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement\r\nNo. 754411.\r\n","year":"2021","publisher":"Springer Nature","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-021-04181-z","relation":"erratum"}]},"author":[{"first_name":"Haoxin","last_name":"Zhou","full_name":"Zhou, Haoxin"},{"first_name":"Tian","last_name":"Xie","full_name":"Xie, Tian"},{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg"},{"full_name":"Holder, Tobias","last_name":"Holder","first_name":"Tobias"},{"full_name":"Ehrets, James R.","last_name":"Ehrets","first_name":"James R."},{"first_name":"Eric M.","last_name":"Spanton","full_name":"Spanton, Eric M."},{"full_name":"Taniguchi, Takashi","last_name":"Taniguchi","first_name":"Takashi"},{"first_name":"Kenji","last_name":"Watanabe","full_name":"Watanabe, Kenji"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"first_name":"Andrea F.","last_name":"Young","full_name":"Young, Andrea F."}],"date_created":"2021-09-19T22:01:25Z","date_updated":"2023-08-14T07:04:06Z"},{"article_processing_charge":"No","day":"17","scopus_import":"1","date_published":"2021-09-17T00:00:00Z","page":"431-450","citation":{"ieee":"S. Blackshear et al., “Reactive key-loss protection in blockchains,” in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450.","apa":"Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya, I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains. In FC 2021 Workshops (Vol. 12676, pp. 431–450). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-63958-0_34","ista":"Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I, Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography and Data Security, LNCS, vol. 12676, 431–450.","ama":"Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection in blockchains. In: FC 2021 Workshops. Vol 12676. Springer Nature; 2021:431-450. doi:10.1007/978-3-662-63958-0_34","chicago":"Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In FC 2021 Workshops, 12676:431–50. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-63958-0_34.","short":"S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya, E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer Nature, 2021, pp. 431–450.","mla":"Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” FC 2021 Workshops, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:10.1007/978-3-662-63958-0_34."},"publication":"FC 2021 Workshops","abstract":[{"lang":"eng","text":"We present a novel approach for blockchain asset owners to reclaim their funds in case of accidental private-key loss or transfer to a mistyped address. Our solution can be deployed upon failure or absence of proactively implemented backup mechanisms, such as secret sharing and cold storage. The main advantages against previous proposals is it does not require any prior action from users and works with both single-key and multi-sig accounts. We achieve this by a 3-phase Commit()→Reveal()→Claim()−or−Challenge() smart contract that enables accessing funds of addresses for which the spending key is not available. We provide an analysis of the threat and incentive models and formalize the concept of reactive KEy-Loss Protection (KELP)."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","title":"Reactive key-loss protection in blockchains","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10076","publication_identifier":{"eisbn":["978-3-662-63958-0"],"issn":["0302-9743"],"isbn":["978-3-6626-3957-3"],"eissn":["1611-3349"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-63958-0_34","conference":{"name":"FC: International Conference on Financial Cryptography and Data Security","location":"Virtual","start_date":"2021-03-01","end_date":"2021-03-05"},"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/","open_access":"1"}],"oa":1,"external_id":{"isi":["000713005000034"]},"volume":"12676 ","date_created":"2021-10-03T22:01:24Z","date_updated":"2023-08-14T07:06:16Z","author":[{"last_name":"Blackshear","first_name":"Sam","full_name":"Blackshear, Sam"},{"last_name":"Chalkias","first_name":"Konstantinos","full_name":"Chalkias, Konstantinos"},{"last_name":"Chatzigiannis","first_name":"Panagiotis","full_name":"Chatzigiannis, Panagiotis"},{"first_name":"Riyaz","last_name":"Faizullabhoy","full_name":"Faizullabhoy, Riyaz"},{"full_name":"Khaburzaniya, Irakliy","last_name":"Khaburzaniya","first_name":"Irakliy"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"last_name":"Lind","first_name":"Joshua","full_name":"Lind, Joshua"},{"last_name":"Wong","first_name":"David","full_name":"Wong, David"},{"first_name":"Tim","last_name":"Zakian","full_name":"Zakian, Tim"}],"department":[{"_id":"ElKo"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"The authors would like to thank all anonymous reviewers of FC21 WTSC workshop for comments and suggestions that greatly improved the quality of this paper.","year":"2021"},{"department":[{"_id":"JaMa"}],"publisher":"Elsevier","publication_status":"published","acknowledgement":"The authors are grateful to Professor Kazuhiro Kuwae for kindly providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They wish to express their deepest gratitude to an anonymous Reviewer, whose punctual remarks and comments greatly improved the accessibility and overall quality of the initial submission. This work was completed while L.D.S. was a member of the Institut für Angewandte Mathematik of the University of Bonn. He acknowledges funding of his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center) 1060 - project number 211504053. He also acknowledges funding of his current position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465.","year":"2021","volume":281,"date_created":"2021-10-03T22:01:21Z","date_updated":"2023-08-14T07:05:44Z","author":[{"full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","first_name":"Lorenzo"},{"full_name":"Suzuki, Kohei","first_name":"Kohei","last_name":"Suzuki"}],"article_number":"109234","ec_funded":1,"project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01492"}],"oa":1,"external_id":{"isi":["000703896600005"],"arxiv":["2008.01492"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2021.109234","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"month":"09","intvolume":" 281","title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10070","oa_version":"Preprint","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties for generalized intrinsic distances on strongly local Dirichlet spaces possibly without square field operator. We present many non-smooth and infinite-dimensional examples. As an application, we prove the integral Varadhan short-time asymptotic with respect to a given distance function for a large class of strongly local Dirichlet forms."}],"article_type":"original","citation":{"ama":"Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 2021;281(11). doi:10.1016/j.jfa.2021.109234","ieee":"L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces,” Journal of Functional Analysis, vol. 281, no. 11. Elsevier, 2021.","apa":"Dello Schiavo, L., & Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109234","ista":"Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 281(11), 109234.","short":"L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).","mla":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis, vol. 281, no. 11, 109234, Elsevier, 2021, doi:10.1016/j.jfa.2021.109234.","chicago":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109234."},"publication":"Journal of Functional Analysis","date_published":"2021-09-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15"},{"publisher":"Wiley","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","volume":33,"date_created":"2021-10-11T20:07:24Z","date_updated":"2023-08-14T07:25:27Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12885"}]},"author":[{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu"},{"orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","first_name":"Mariano","full_name":"Calcabrini, Mariano"},{"last_name":"Yu","first_name":"Yuan","full_name":"Yu, Yuan"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"last_name":"Chang","first_name":"Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng"},{"last_name":"Costanzo","first_name":"Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso"},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias"},{"full_name":"Lee, Seungho","last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"last_name":"Cojocaru‐Mirédin","first_name":"Oana","full_name":"Cojocaru‐Mirédin, Oana"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"article_number":"2106858","ec_funded":1,"file_date_updated":"2022-02-03T13:16:14Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"quality_controlled":"1","isi":1,"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":["000709899300001"],"pmid":["34626034"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"doi":"10.1002/adma.202106858","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"month":"12","intvolume":" 33","status":"public","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","ddc":["620"],"_id":"10123","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10720","checksum":"990bccc527c64d85cf1c97885110b5f4","success":1,"date_updated":"2022-02-03T13:16:14Z","date_created":"2022-02-03T13:16:14Z","access_level":"open_access","file_name":"2021_AdvancedMaterials_Liu.pdf","content_type":"application/pdf","file_size":5595666,"creator":"cchlebak"}],"type":"journal_article","issue":"52","abstract":[{"lang":"eng","text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials."}],"article_type":"original","citation":{"chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley, 2021. https://doi.org/10.1002/adma.202106858.","mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33, no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858","ieee":"Y. Liu et al., “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33, no. 52. Wiley, 2021.","ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 2021;33(52). doi:10.1002/adma.202106858"},"publication":"Advanced Materials","date_published":"2021-12-29T00:00:00Z","keyword":["mechanical engineering","mechanics of materials","general materials science"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"29"},{"month":"09","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"doi":"10.1016/J.JBC.2021.101094","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":{"isi":["000706409200006"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2021-10-11T12:20:58Z","ec_funded":1,"article_number":"101094","author":[{"first_name":"Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat"},{"last_name":"Barratt","first_name":"Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","full_name":"Barratt, Stephen"},{"last_name":"Flynn","first_name":"Sean M.","full_name":"Flynn, Sean M."},{"full_name":"Begum, Farida","first_name":"Farida","last_name":"Begum"},{"last_name":"Skehel","first_name":"Mark","full_name":"Skehel, Mark"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","first_name":"Mario","full_name":"De Bono, Mario"}],"date_updated":"2023-08-14T07:24:09Z","date_created":"2021-10-10T22:01:23Z","volume":297,"acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","year":"2021","publication_status":"published","publisher":"Elsevier","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-09-01T00:00:00Z","publication":"Journal of Biological Chemistry","citation":{"chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry. Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry, vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., & de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier. https://doi.org/10.1016/J.JBC.2021.101094","ieee":"M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” Journal of Biological Chemistry, vol. 297, no. 3. Elsevier, 2021.","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094"},"article_type":"original","abstract":[{"lang":"eng","text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":1680010,"file_name":"2021_JBC_Artan.pdf","access_level":"open_access","date_updated":"2021-10-11T12:20:58Z","date_created":"2021-10-11T12:20:58Z","success":1,"checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","file_id":"10121","relation":"main_file"}],"_id":"10117","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["612"],"status":"public","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","intvolume":" 297"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-88494-9_12","conference":{"name":"RV: Runtime Verification","start_date":"2021-10-11","location":"Virtual","end_date":"2021-10-14"},"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000719383800012"]},"publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-030-88494-9"],"isbn":["978-3-030-88493-2"],"eissn":["1611-3349"]},"month":"10","volume":12974,"date_updated":"2023-08-14T07:20:30Z","date_created":"2021-10-07T23:30:10Z","related_material":{"record":[{"relation":"extended_version","status":"public","id":"9946"}]},"author":[{"orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","first_name":"Fabian","full_name":"Mühlböck, Fabian"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae 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.","file_date_updated":"2021-10-07T23:32:18Z","place":"Cham","date_published":"2021-10-06T00:00:00Z","page":"231-243","citation":{"chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In International Conference on Runtime Verification, 12974:231–43. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:10.1007/978-3-030-88494-9_12.","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_12","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12"},"publication":"International Conference on Runtime Verification","has_accepted_license":"1","article_processing_charge":"No","day":"06","keyword":["run-time verification","software engineering","implicit specification"],"scopus_import":"1","oa_version":"Preprint","file":[{"checksum":"554c7fdb259eda703a8b6328a6dad55a","success":1,"date_created":"2021-10-07T23:32:18Z","date_updated":"2021-10-07T23:32:18Z","relation":"main_file","file_id":"10109","file_size":350632,"content_type":"application/pdf","creator":"fmuehlbo","access_level":"open_access","file_name":"differentialmonitoring-cameraready-openaccess.pdf"}],"intvolume":" 12974","ddc":["005"],"status":"public","title":"Differential monitoring","_id":"10108","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"},{"doi":"10.7554/eLife.68238","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":{"isi":["000695716100001"],"pmid":["34499028"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"09","publication_identifier":{"eissn":["2050-084X"]},"author":[{"first_name":"Thanh","last_name":"Vuong-Brender","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Vuong-Brender, Thanh"},{"full_name":"Flynn, Sean","first_name":"Sean","last_name":"Flynn"},{"id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E","first_name":"Yvonne","last_name":"Vallis","full_name":"Vallis, Yvonne"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"De Bono","full_name":"De Bono, Mario"}],"date_updated":"2023-08-14T07:23:39Z","date_created":"2021-10-10T22:01:22Z","volume":10,"acknowledgement":"The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).","year":"2021","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"MaDe"}],"file_date_updated":"2021-10-11T14:15:07Z","ec_funded":1,"article_number":"e68238","date_published":"2021-09-17T00:00:00Z","publication":"eLife","citation":{"ama":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 2021;10. doi:10.7554/eLife.68238","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","ieee":"T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Vuong-Brender, T., Flynn, S., Vallis, Y., & de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.68238","mla":"Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife, vol. 10, e68238, eLife Sciences Publications, 2021, doi:10.7554/eLife.68238.","short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).","chicago":"Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.68238."},"article_type":"original","day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2021_eLife_VuongBrender.pdf","access_level":"open_access","file_size":1774624,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10122","date_updated":"2021-10-11T14:15:07Z","date_created":"2021-10-11T14:15:07Z","checksum":"b465e172d2b1f57aa26a2571a085d052","success":1}],"_id":"10116","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["610"],"status":"public","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","intvolume":" 10","abstract":[{"text":"The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior.","lang":"eng"}],"type":"journal_article"},{"day":"17","has_accepted_license":"1","article_processing_charge":"Yes","keyword":["virology","infectious diseases"],"date_published":"2021-09-17T00:00:00Z","article_type":"original","publication":"Viruses","citation":{"ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","apa":"Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI. https://doi.org/10.3390/v13091853","ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no. 9. MDPI, 2021.","mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021, doi:10.3390/v13091853.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses. MDPI, 2021. https://doi.org/10.3390/v13091853."},"abstract":[{"lang":"eng","text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses."}],"issue":"9","type":"journal_article","file":[{"relation":"main_file","file_id":"10115","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","success":1,"date_created":"2021-10-08T10:38:15Z","date_updated":"2021-10-08T10:38:15Z","access_level":"open_access","file_name":"2021_Viruses_Obr.pdf","file_size":4146796,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","ddc":["616"],"status":"public","intvolume":" 13","_id":"10103","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","publication_identifier":{"issn":["1999-4915"]},"language":[{"iso":"eng"}],"doi":"10.3390/v13091853","quality_controlled":"1","isi":1,"project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445"}],"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":["34578434"],"isi":["000699841100001"]},"oa":1,"file_date_updated":"2021-10-08T10:38:15Z","article_number":"1853","date_created":"2021-10-07T09:13:29Z","date_updated":"2023-08-14T07:21:51Z","volume":13,"author":[{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin","full_name":"Obr, Martin"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."}],"publication_status":"published","publisher":"MDPI","department":[{"_id":"FlSc"}],"acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","year":"2021","pmid":1},{"type":"journal_article","abstract":[{"lang":"eng","text":"The search for novel entangled phases of matter has lead to the recent discovery of a new class of “entanglement transitions,” exemplified by random tensor networks and monitored quantum circuits. Most known examples can be understood as some classical ordering transitions in an underlying statistical mechanics model, where entanglement maps onto the free-energy cost of inserting a domain wall. In this paper we study the possibility of entanglement transitions driven by physics beyond such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired variational Ansätze, we investigate under what conditions on the variational parameters these Ansätze can capture an entanglement transition. We study the entanglement scaling of short-range restricted Boltzmann machine (RBM) quantum states with random phases. For uncorrelated random phases, we analytically demonstrate the absence of an entanglement transition and reveal subtle finite-size effects in finite-size numerical simulations. Introducing phases with correlations decaying as 1/r^α in real space, we observe three regions with a different scaling of entanglement entropy depending on the exponent α. We study the nature of the transition between these regions, finding numerical evidence for critical behavior. Our work establishes the presence of long-range correlated phases in RBM-based wave functions as a required ingredient for entanglement transitions."}],"issue":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10067","title":"Entanglement transitions from restricted Boltzmann machines","status":"public","intvolume":" 104","oa_version":"Preprint","day":"30","article_processing_charge":"No","publication":"Physical Review B","citation":{"ama":"Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 2021;104(10). doi:10.1103/physrevb.104.104205","ista":"Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 104(10), 104205.","ieee":"R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from restricted Boltzmann machines,” Physical Review B, vol. 104, no. 10. American Physical Society, 2021.","apa":"Medina Ramos, R. A., Vasseur, R., & Serbyn, M. (2021). Entanglement transitions from restricted Boltzmann machines. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.104205","mla":"Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B, vol. 104, no. 10, 104205, American Physical Society, 2021, doi:10.1103/physrevb.104.104205.","short":"R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).","chicago":"Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.104205."},"article_type":"original","date_published":"2021-09-30T00:00:00Z","article_number":"104205","ec_funded":1,"year":"2021","acknowledgement":"We would like to thank S. De Nicola, P. Brighi, and V. Karle for fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges support from the US Department of Energy, Office of Science, Basic Energy Sciences, under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through a Sloan Research Fellowship.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"author":[{"full_name":"Medina Ramos, Raimel A","last_name":"Medina Ramos","first_name":"Raimel A","orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"first_name":"Romain","last_name":"Vasseur","full_name":"Vasseur, Romain"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"date_updated":"2023-08-14T07:24:47Z","date_created":"2021-10-02T09:03:42Z","volume":104,"month":"09","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"external_id":{"isi":["000704414400002"],"arxiv":["2107.05735"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.05735"}],"quality_controlled":"1","isi":1,"project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"doi":"10.1103/physrevb.104.104205","language":[{"iso":"eng"}]},{"author":[{"full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian","last_name":"Mühlböck"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"}],"related_material":{"record":[{"id":"9281","status":"public","relation":"other"},{"relation":"shorter_version","status":"public","id":"10108"}]},"date_updated":"2023-08-14T07:20:29Z","date_created":"2021-08-20T20:00:37Z","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","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IST Austria","file_date_updated":"2021-09-03T12:34:28Z","doi":"10.15479/AT:ISTA:9946","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"month":"09","publication_identifier":{"issn":["2664-1690"]},"file":[{"relation":"main_file","file_id":"9948","date_created":"2021-08-20T19:59:44Z","date_updated":"2021-09-03T12:34:28Z","checksum":"0f9aafd59444cb6bdca6925d163ab946","file_name":"differentialmonitoring-techreport.pdf","access_level":"open_access","content_type":"application/pdf","file_size":"320453","creator":"fmuehlbo"}],"oa_version":"Published Version","_id":"9946","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["005"],"status":"public","title":"Differential monitoring","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"date_published":"2021-09-01T00:00:00Z","citation":{"chicago":"Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.","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.","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.","ama":"Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946"},"page":"17","day":"01","article_processing_charge":"No","has_accepted_license":"1","keyword":["run-time verification","software engineering","implicit specification"]},{"author":[{"full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"}],"date_created":"2021-10-03T22:01:23Z","date_updated":"2023-08-14T08:00:01Z","volume":14,"acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"MDPI","file_date_updated":"2021-10-14T11:56:39Z","article_number":"5416","doi":"10.3390/ma14185416","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["34576640"],"isi":["000700689400001"]},"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,"isi":1,"quality_controlled":"1","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"}],"month":"09","publication_identifier":{"eissn":["1996-1944"]},"oa_version":"Published Version","file":[{"file_id":"10140","relation":"main_file","success":1,"checksum":"4929dfc673a3ae77c010b6174279cc1d","date_created":"2021-10-14T11:56:39Z","date_updated":"2021-10-14T11:56:39Z","access_level":"open_access","file_name":"2021_Materials_Chang.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":4404141}],"_id":"10073","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["540"],"title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","intvolume":" 14","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"}],"issue":"18","type":"journal_article","date_published":"2021-09-19T00:00:00Z","publication":"Materials","citation":{"chicago":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14185416.","short":"C. Chang, M. Ibáñez, Materials 14 (2021).","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.","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","ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416"},"article_type":"original","day":"19","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1"},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11352","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","success":1,"date_updated":"2022-05-06T09:47:18Z","date_created":"2022-05-06T09:47:18Z","access_level":"open_access","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","file_size":1008594,"content_type":"application/pdf","creator":"dernst"}],"title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","status":"public","ddc":["610"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10167","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","date_published":"2021-06-19T00:00:00Z","article_type":"original","citation":{"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.","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."},"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","date_updated":"2023-08-14T08:03:06Z","date_created":"2021-10-21T07:49:12Z","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N"},{"last_name":"Moldovan","first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A L","full_name":"Picard, Marion A L"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"publisher":"Oxford University Press ","department":[{"_id":"BeVi"}],"publication_status":"published","pmid":1,"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","year":"2021","file_date_updated":"2022-05-06T09:47:18Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/molbev/msab178","project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"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":{"pmid":["34146097"],"isi":["000741368600009"]},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"06"},{"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":[{"last_name":"Appel","first_name":"Lisa-Marie","full_name":"Appel, Lisa-Marie"},{"full_name":"Franke, Vedran","first_name":"Vedran","last_name":"Franke"},{"first_name":"Melania","last_name":"Bruno","full_name":"Bruno, Melania"},{"full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya","first_name":"Irina"},{"first_name":"Aiste","last_name":"Kasiliauskaite","full_name":"Kasiliauskaite, Aiste"},{"full_name":"Kaufmann, Tanja","last_name":"Kaufmann","first_name":"Tanja"},{"first_name":"Ursula E.","last_name":"Schoeberl","full_name":"Schoeberl, Ursula E."},{"full_name":"Puchinger, Martin G.","first_name":"Martin G.","last_name":"Puchinger"},{"full_name":"Kostrhon, Sebastian","first_name":"Sebastian","last_name":"Kostrhon"},{"full_name":"Ebenwaldner, Carmen","last_name":"Ebenwaldner","first_name":"Carmen"},{"first_name":"Marek","last_name":"Sebesta","full_name":"Sebesta, Marek"},{"full_name":"Beltzung, Etienne","last_name":"Beltzung","first_name":"Etienne"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"last_name":"Lin","first_name":"Gen","full_name":"Lin, Gen"},{"first_name":"Anna","last_name":"Vlasova","full_name":"Vlasova, Anna"},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"},{"last_name":"Pavri","first_name":"Rushad","full_name":"Pavri, Rushad"},{"full_name":"Stark, Alexander","first_name":"Alexander","last_name":"Stark"},{"full_name":"Akalin, Altuna","first_name":"Altuna","last_name":"Akalin"},{"full_name":"Stefl, Richard","first_name":"Richard","last_name":"Stefl"},{"full_name":"Bernecky, Carrie A","last_name":"Bernecky","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina","last_name":"Djinovic-Carugo"},{"last_name":"Slade","first_name":"Dea","full_name":"Slade, Dea"}],"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","file_date_updated":"2021-10-21T13:51:49Z","article_number":"6078","language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26360-2","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"},"external_id":{"isi":["000709050300001"]},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"10","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_NatComm_Appel.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":5111706,"file_id":"10169","relation":"main_file","success":1,"checksum":"d99fcd51aebde19c21314e3de0148007","date_updated":"2021-10-21T13:51:49Z","date_created":"2021-10-21T13:51:49Z"}],"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","issue":"1","abstract":[{"text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.","lang":"eng"}],"type":"journal_article","date_published":"2021-10-19T00:00:00Z","article_type":"original","citation":{"ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","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","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","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.","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)."},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"19","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"]},{"language":[{"iso":"eng"}],"doi":"10.1111/cgf.142626","isi":1,"quality_controlled":"1","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"oa":1,"external_id":{"isi":["000657959600017"]},"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","last_name":"Babaei","first_name":"Vahid"},{"first_name":"Piotr","last_name":"Didyk","full_name":"Didyk, Piotr"},{"last_name":"Voloboy","first_name":"Alexey","full_name":"Voloboy, Alexey"},{"last_name":"Wilkie","first_name":"Alexander","full_name":"Wilkie, Alexander"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"last_name":"Myszkowski","first_name":"Karol","full_name":"Myszkowski, Karol"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"full_name":"Křivánek, Jaroslav","first_name":"Jaroslav","last_name":"Křivánek"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"BeBi"}],"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":{"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.","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.","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","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.","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","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."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":26026501,"creator":"bbickel","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf","access_level":"open_access","date_created":"2021-10-11T12:06:50Z","date_updated":"2021-10-11T12:06:50Z","checksum":"33271724215f54a75c39d2ed40f2c502","success":1,"relation":"main_file","file_id":"10120"}],"oa_version":"Submitted Version","ddc":["004"],"status":"public","title":"Neural acceleration of scattering-aware color 3D printing","intvolume":" 40","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9547","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"},{"day":"08","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-10-08T00:00:00Z","article_type":"original","publication":"Science Advances","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","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","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.","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.","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).","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.","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."},"abstract":[{"lang":"eng","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."}],"issue":"41","type":"journal_article","file":[{"date_created":"2021-10-27T14:16:06Z","date_updated":"2021-10-27T14:16:06Z","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","success":1,"relation":"main_file","file_id":"10189","content_type":"application/pdf","file_size":2441163,"creator":"cziletti","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["530"],"status":"public","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","intvolume":" 7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10177","month":"10","publication_identifier":{"eissn":["23752548"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abj0127","isi":1,"quality_controlled":"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":{"isi":["000704912700024"],"arxiv":["2103.10852"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2021-10-27T14:16:06Z","article_number":"abj0127","date_updated":"2023-08-14T08:04:42Z","date_created":"2021-10-24T22:01:33Z","volume":7,"author":[{"last_name":"Martín-Sánchez","first_name":"Javier","full_name":"Martín-Sánchez, Javier"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"last_name":"Voronin","first_name":"Kirill V.","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"},{"first_name":"Weiliang","last_name":"Ma","full_name":"Ma, Weiliang"},{"last_name":"Bao","first_name":"Qiaoliang","full_name":"Bao, Qiaoliang"},{"first_name":"Valentyn S.","last_name":"Volkov","full_name":"Volkov, Valentyn S."},{"last_name":"Hillenbrand","first_name":"Rainer","full_name":"Hillenbrand, Rainer"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"American Association for the Advancement of Science","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).","year":"2021"},{"citation":{"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","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.","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","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367.","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."},"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","status":"public","title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV","oa_version":"None","type":"journal_article","issue":"7880","abstract":[{"lang":"eng","text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain."}],"external_id":{"pmid":["34616041"],"isi":["000704581600001"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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":{"issn":["0028-0836"],"eissn":["1476-4687"]},"month":"10","pmid":1,"year":"2021","acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","department":[{"_id":"LeSa"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","relation":"press_release","description":"News on IST Webpage"}]},"author":[{"first_name":"Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"volume":598,"date_updated":"2023-08-14T08:01:21Z","date_created":"2021-10-17T22:01:17Z","ec_funded":1},{"author":[{"last_name":"Runkel","first_name":"Ingo","full_name":"Runkel, Ingo"},{"full_name":"Szegedy, Lorant","orcid":"0000-0003-2834-5054","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","last_name":"Szegedy","first_name":"Lorant"}],"volume":62,"date_updated":"2023-08-14T08:04:12Z","date_created":"2021-10-24T22:01:32Z","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","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","publication_status":"published","article_number":"102302","doi":"10.1063/5.0037826","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1802.09978","open_access":"1"}],"external_id":{"isi":["000755638500010"],"arxiv":["1802.09978"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["00222488"]},"month":"10","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10176","intvolume":" 62","title":"Topological field theory on r-spin surfaces and the Arf-invariant","status":"public","issue":"10","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2021-10-01T00:00:00Z","citation":{"mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:10.1063/5.0037826.","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0037826.","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","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","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."},"publication":"Journal of Mathematical Physics","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"article_type":"original","citation":{"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.","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).","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.","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021.","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","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"},"publication":"EMBO Journal","date_published":"2021-10-18T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"18","intvolume":" 40","ddc":["610"],"status":"public","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10179","file":[{"date_updated":"2021-12-13T14:54:14Z","date_created":"2021-12-13T14:54:14Z","checksum":"78d2d02e775322297e774f72810a41a4","success":1,"relation":"main_file","file_id":"10541","file_size":7819881,"content_type":"application/pdf","creator":"alisjak","file_name":"2021_EMBO_Bajaj.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"23","abstract":[{"lang":"eng","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."}],"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":["34661293"],"isi":["000708012800001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15252/embj.2021108714","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"month":"10","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","volume":40,"date_updated":"2023-08-14T08:05:23Z","date_created":"2021-10-24T22:01:34Z","author":[{"full_name":"Bajaj, Sunanjay","last_name":"Bajaj","first_name":"Sunanjay"},{"first_name":"Joshua A.","last_name":"Bagley","full_name":"Bagley, Joshua A."},{"last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"full_name":"Vertesy, Abel","last_name":"Vertesy","first_name":"Abel"},{"last_name":"Nagumo Wong","first_name":"Sakurako","full_name":"Nagumo Wong, Sakurako"},{"full_name":"Krenn, Veronica","last_name":"Krenn","first_name":"Veronica"},{"first_name":"Julie","last_name":"Lévi-Strauss","full_name":"Lévi-Strauss, Julie"},{"first_name":"Juergen A.","last_name":"Knoblich","full_name":"Knoblich, Juergen A."}],"article_number":"e108714","file_date_updated":"2021-12-13T14:54:14Z"},{"_id":"10203","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["530"],"title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","intvolume":" 12","file":[{"checksum":"8580d128389860f732028c521cd5949e","success":1,"date_updated":"2021-11-03T11:31:24Z","date_created":"2021-11-03T11:31:24Z","relation":"main_file","file_id":"10212","file_size":1434201,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2021_NatComm_Sortino.pdf"}],"oa_version":"Published Version","type":"journal_article","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"}],"publication":"Nature Communications","citation":{"ista":"Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063.","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.","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","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","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.","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)."},"article_type":"original","date_published":"2021-10-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","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","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"author":[{"first_name":"Luca","last_name":"Sortino","full_name":"Sortino, Luca"},{"full_name":"Zotev, Panaiot G.","last_name":"Zotev","first_name":"Panaiot G."},{"first_name":"Catherine L.","last_name":"Phillips","full_name":"Phillips, Catherine L."},{"last_name":"Brash","first_name":"Alistair J.","full_name":"Brash, Alistair J."},{"first_name":"Javier","last_name":"Cambiasso","full_name":"Cambiasso, Javier"},{"full_name":"Marensi, Elena","last_name":"Marensi","first_name":"Elena","orcid":"0000-0001-7173-4923","id":"0BE7553A-1004-11EA-B805-18983DDC885E"},{"last_name":"Fox","first_name":"A. Mark","full_name":"Fox, A. Mark"},{"last_name":"Maier","first_name":"Stefan A.","full_name":"Maier, Stefan A."},{"full_name":"Sapienza, Riccardo","first_name":"Riccardo","last_name":"Sapienza"},{"first_name":"Alexander I.","last_name":"Tartakovskii","full_name":"Tartakovskii, Alexander I."}],"date_created":"2021-10-31T23:01:30Z","date_updated":"2023-08-14T08:12:12Z","volume":12,"article_number":"6063","file_date_updated":"2021-11-03T11:31:24Z","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":["000708601800015"],"arxiv":["2103.16986"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-021-26262-3","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["2041-1723"]}},{"publication_identifier":{"eissn":["13672630"]},"month":"09","quality_controlled":"1","isi":1,"external_id":{"arxiv":["2102.05397"],"isi":["000702042400001"]},"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,"language":[{"iso":"eng"}],"doi":"10.1088/1367-2630/ac23f1","article_number":"093043","file_date_updated":"2021-10-28T12:06:01Z","department":[{"_id":"EdHa"}],"publisher":"IOP Publishing","publication_status":"published","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","volume":23,"date_updated":"2023-08-14T08:10:31Z","date_created":"2021-10-24T22:01:34Z","author":[{"full_name":"Sahu, Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","last_name":"Sahu","first_name":"Preeti"},{"full_name":"Schwarz, J. M.","first_name":"J. M.","last_name":"Schwarz"},{"full_name":"Manning, M. Lisa","last_name":"Manning","first_name":"M. Lisa"}],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"29","article_type":"original","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.","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.","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","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"},"publication":"New Journal of Physics","date_published":"2021-09-29T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"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.","lang":"eng"}],"intvolume":" 23","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","status":"public","ddc":["570"],"_id":"10178","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":2215016,"creator":"cziletti","file_name":"2021_NewJPhys_Sahu.pdf","access_level":"open_access","date_created":"2021-10-28T12:06:01Z","date_updated":"2021-10-28T12:06:01Z","checksum":"ace603e8f0962b3ba55f23fa34f57764","success":1,"relation":"main_file","file_id":"10193"}],"oa_version":"Published Version"},{"scopus_import":"1","article_processing_charge":"No","day":"09","article_type":"original","citation":{"short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).","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.","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.","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1","ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” Set-Valued and Variational Analysis. Springer Nature, 2021.","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","ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis."},"publication":"Set-Valued and Variational Analysis","date_published":"2021-10-09T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"status":"public","title":"Rectifiable curves in proximally smooth sets","_id":"10181","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","publication_identifier":{"issn":["0927-6947"],"eissn":["1877-0541"]},"month":"10","quality_controlled":"1","isi":1,"external_id":{"isi":["000705774800001"],"arxiv":["2012.10691"]},"main_file_link":[{"url":"https://arxiv.org/abs/2012.10691","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11228-021-00612-1","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","year":"2021","date_created":"2021-10-24T22:01:35Z","date_updated":"2023-08-14T08:11:38Z","author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"full_name":"Lopushanski, Mariana S.","first_name":"Mariana S.","last_name":"Lopushanski"}]},{"isi":1,"quality_controlled":"1","external_id":{"isi":["000709050300016"],"pmid":["34667153"]},"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,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26234-7","publication_identifier":{"eissn":["20411723"]},"month":"10","publisher":"Springer Nature","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"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).","year":"2021","volume":12,"date_updated":"2023-08-14T10:32:48Z","date_created":"2021-10-31T23:01:29Z","related_material":{"link":[{"description":"Preprint","relation":"earlier_version","url":"https://doi.org/10.1101/2020.11.23.394171 "}]},"author":[{"full_name":"Pradhan, Saurabh J.","last_name":"Pradhan","first_name":"Saurabh J."},{"full_name":"Reddy, Puli Chandramouli","first_name":"Puli Chandramouli","last_name":"Reddy"},{"full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","first_name":"Michael","last_name":"Smutny"},{"full_name":"Sharma, Ankita","last_name":"Sharma","first_name":"Ankita"},{"full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako","first_name":"Keisuke"},{"full_name":"Oak, Meghana S.","first_name":"Meghana S.","last_name":"Oak"},{"full_name":"Shah, Rini","first_name":"Rini","last_name":"Shah"},{"full_name":"Pal, Mrinmoy","last_name":"Pal","first_name":"Mrinmoy"},{"first_name":"Ojas","last_name":"Deshpande","full_name":"Deshpande, Ojas"},{"first_name":"Greg","last_name":"Dsilva","full_name":"Dsilva, Greg"},{"full_name":"Tang, Yin","last_name":"Tang","first_name":"Yin"},{"first_name":"Rakesh","last_name":"Mishra","full_name":"Mishra, Rakesh"},{"full_name":"Deshpande, Girish","first_name":"Girish","last_name":"Deshpande"},{"first_name":"Antonio J.","last_name":"Giraldez","full_name":"Giraldez, Antonio J."},{"last_name":"Sonawane","first_name":"Mahendra","full_name":"Sonawane, Mahendra"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"}],"article_number":"6094","file_date_updated":"2021-11-09T13:59:26Z","article_type":"original","citation":{"mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7.","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).","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.","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","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"},"publication":"Nature Communications","date_published":"2021-10-19T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"19","intvolume":" 12","ddc":["570"],"status":"public","title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10202","oa_version":"Published Version","file":[{"file_size":7144437,"content_type":"application/pdf","creator":"cziletti","file_name":"2021_NatureComm_Pradhan.pdf","access_level":"open_access","date_created":"2021-11-09T13:59:26Z","date_updated":"2021-11-09T13:59:26Z","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","success":1,"relation":"main_file","file_id":"10262"}],"type":"journal_article","issue":"1","abstract":[{"text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.","lang":"eng"}]},{"publication_identifier":{"eissn":["1664-302X"]},"month":"10","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"]},"oa":1,"project":[{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"}],"quality_controlled":"1","isi":1,"doi":"10.3389/fmicb.2021.760017","language":[{"iso":"eng"}],"article_number":"760017","ec_funded":1,"file_date_updated":"2021-11-11T10:54:40Z","pmid":1,"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.","year":"2021","publisher":"Frontiers","publication_status":"published","author":[{"full_name":"Qi, Qin","id":"3B22D412-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6148-2416","first_name":"Qin","last_name":"Qi"},{"full_name":"Angermayr, S. Andreas","first_name":"S. Andreas","last_name":"Angermayr"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach"}],"volume":12,"date_updated":"2023-08-14T11:43:23Z","date_created":"2021-11-11T10:39:37Z","scopus_import":"1","keyword":["microbiology"],"has_accepted_license":"1","article_processing_charge":"No","day":"20","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)."},"publication":"Frontiers in Microbiology","article_type":"original","date_published":"2021-10-20T00:00:00Z","type":"journal_article","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"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10271","intvolume":" 12","title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","status":"public","ddc":["610"],"file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":2397203,"access_level":"open_access","file_name":"2021_FrontiersMicrob_Qi.pdf","success":1,"checksum":"d41321748e9588dd3cf03e9a7222127f","date_created":"2021-11-11T10:54:40Z","date_updated":"2021-11-11T10:54:40Z","file_id":"10272","relation":"main_file"}],"oa_version":"Published Version"},{"external_id":{"isi":["000712232700001"],"arxiv":["2012.13215"]},"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,"isi":1,"quality_controlled":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"doi":"10.1007/s00220-021-04239-z","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"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"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J"}],"date_updated":"2023-08-14T10:29:49Z","date_created":"2021-11-07T23:01:25Z","volume":388,"file_date_updated":"2022-02-02T10:19:55Z","publication":"Communications in Mathematical Physics","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","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.","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","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048.","mla":"Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z.","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."},"article_type":"original","page":"1005–1048","date_published":"2021-10-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10221","status":"public","title":"Eigenstate thermalization hypothesis for Wigner matrices","ddc":["510"],"intvolume":" 388","file":[{"access_level":"open_access","file_name":"2021_CommunMathPhys_Cipolloni.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":841426,"file_id":"10715","relation":"main_file","success":1,"checksum":"a2c7b6f5d23b5453cd70d1261272283b","date_created":"2022-02-02T10:19:55Z","date_updated":"2022-02-02T10:19:55Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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).","lang":"eng"}],"issue":"2"},{"doi":"10.1007/s00205-021-01715-7","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":{"arxiv":["2101.12566"],"isi":["000710850600001"]},"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"month":"10","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"9787"}]},"author":[{"full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"volume":242,"date_created":"2021-11-07T23:01:26Z","date_updated":"2023-08-14T10:32:19Z","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).","year":"2021","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2021-12-14T08:35:42Z","date_published":"2021-10-25T00:00:00Z","citation":{"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","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.","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","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.","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.","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."},"publication":"Archive for Rational Mechanics and Analysis","page":"1835–1906","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","scopus_import":"1","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_created":"2021-12-14T08:35:42Z","date_updated":"2021-12-14T08:35:42Z","success":1,"checksum":"672e9c21b20f1a50854b7c821edbb92f"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10224","intvolume":" 242","title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","ddc":["530"],"status":"public","issue":"3","abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"type":"journal_article"},{"date_published":"2021-10-30T00:00:00Z","publication":"Genes","citation":{"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).","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.","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","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."},"article_type":"original","day":"30","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":1335308,"creator":"dernst","file_name":"2021_Genes_Vasic.pdf","access_level":"open_access","date_created":"2022-05-16T07:02:27Z","date_updated":"2022-05-16T07:02:27Z","checksum":"256cb832a9c3051c7dc741f6423b8cbd","success":1,"relation":"main_file","file_id":"11380"}],"oa_version":"Published Version","_id":"10281","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","ddc":["570"],"status":"public","intvolume":" 12","abstract":[{"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","lang":"eng"}],"issue":"11","type":"journal_article","alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"doi":"10.3390/genes12111746","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":{"isi":["000834044200002"]},"isi":1,"quality_controlled":"1","project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"month":"10","publication_identifier":{"eissn":["2073-4425"]},"author":[{"full_name":"Vasic, Verica","last_name":"Vasic","first_name":"Verica"},{"full_name":"Jones, Mattson S.O.","last_name":"Jones","first_name":"Mattson S.O."},{"id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E","last_name":"Haslinger","first_name":"Denise","full_name":"Haslinger, Denise"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","last_name":"Knaus","full_name":"Knaus, Lisa"},{"last_name":"Schmeisser","first_name":"Michael J.","full_name":"Schmeisser, Michael J."},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"first_name":"Andreas G.","last_name":"Chiocchetti","full_name":"Chiocchetti, Andreas G."}],"date_created":"2021-11-14T23:01:24Z","date_updated":"2023-08-14T11:46:12Z","volume":12,"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.","year":"2021","publication_status":"published","publisher":"MDPI","department":[{"_id":"GaNo"}],"file_date_updated":"2022-05-16T07:02:27Z","ec_funded":1,"article_number":"1746"},{"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","publisher":"Wiley","department":[{"_id":"JiFr"}],"author":[{"full_name":"Kashkan, Ivan","last_name":"Kashkan","first_name":"Ivan"},{"first_name":"Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika"},{"first_name":"Katarzyna","last_name":"Retzer","full_name":"Retzer, Katarzyna"},{"first_name":"Jana","last_name":"Humpolíčková","full_name":"Humpolíčková, Jana"},{"last_name":"Jayasree","first_name":"Aswathy","full_name":"Jayasree, Aswathy"},{"full_name":"Filepová, Roberta","first_name":"Roberta","last_name":"Filepová"},{"last_name":"Vondráková","first_name":"Zuzana","full_name":"Vondráková, Zuzana"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"},{"full_name":"Rombaut, Debbie","first_name":"Debbie","last_name":"Rombaut"},{"first_name":"Thomas B.","last_name":"Jacobs","full_name":"Jacobs, Thomas B."},{"full_name":"Frilander, Mikko J.","first_name":"Mikko J.","last_name":"Frilander"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"last_name":"Růžička","first_name":"Kamil","full_name":"Růžička, Kamil"}],"date_created":"2021-11-14T23:01:24Z","date_updated":"2023-08-14T11:46:43Z","volume":233,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2","open_access":"1"}],"oa":1,"external_id":{"pmid":["34637542"],"isi":["000714678100001"]},"quality_controlled":"1","isi":1,"doi":"10.1111/nph.17792","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"_id":"10282","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","status":"public","intvolume":" 233","oa_version":"Preprint","type":"journal_article","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."}],"publication":"New Phytologist","citation":{"short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792.","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.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792","ieee":"I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233. Wiley, pp. 329–343, 2021.","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."},"article_type":"original","page":"329-343","date_published":"2021-11-05T00:00:00Z","scopus_import":"1","day":"05","article_processing_charge":"No"},{"status":"public","title":"Eliminating higher-multiplicity intersections. III. Codimension 2","intvolume":" 245","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10220","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"article_type":"original","page":"501–534 ","publication":"Israel Journal of Mathematics","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"},"date_published":"2021-10-30T00:00:00Z","scopus_import":"1","day":"30","article_processing_charge":"No","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","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","date_created":"2021-11-07T23:01:24Z","date_updated":"2023-08-14T11:43:55Z","volume":245,"author":[{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey"},{"full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard","first_name":"Isaac"},{"full_name":"Skopenkov, Arkadiy B.","first_name":"Arkadiy B.","last_name":"Skopenkov"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"8183","status":"public","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"9308"}]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory","_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312"}],"external_id":{"arxiv":["1511.03501"],"isi":["000712942100013"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11856-021-2216-z","month":"10","publication_identifier":{"issn":["0021-2172"],"eissn":["1565-8511"]}},{"month":"10","day":"29","article_processing_charge":"No","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)"},"citation":{"chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. https://doi.org/10.5061/DRYAD.7PVMCVDTJ.","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).","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.","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","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.","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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7pvmcvdtj"}],"oa":1,"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"doi":"10.5061/DRYAD.7PVMCVDTJ","date_published":"2021-10-29T00:00:00Z","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,"license":"https://creativecommons.org/publicdomain/zero/1.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13061","year":"2021","ddc":["570"],"title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","status":"public","department":[{"_id":"SyCr"}],"publisher":"Dryad","author":[{"full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","first_name":"Christopher","full_name":"Pull, Christopher"},{"full_name":"Naiser, Filip","last_name":"Naiser","first_name":"Filip"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","first_name":"Elisabeth"},{"full_name":"Matas, Jiri","first_name":"Jiri","last_name":"Matas"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"related_material":{"record":[{"id":"10284","status":"public","relation":"used_in_publication"}]},"date_created":"2023-05-23T16:14:35Z","date_updated":"2023-08-14T11:45:28Z","oa_version":"Published Version"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10301","ddc":["570"],"status":"public","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","intvolume":" 10","file":[{"date_created":"2021-11-18T07:02:02Z","date_updated":"2021-11-18T07:02:02Z","success":1,"checksum":"59318e9e41507cec83c2f4070e6ad540","file_id":"10302","relation":"main_file","creator":"lgarciar","content_type":"application/pdf","file_size":2477302,"file_name":"elife-71575-v1.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement."}],"publication":"eLife","citation":{"chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575","ieee":"M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021.","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575.","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575"},"article_type":"original","date_published":"2021-11-17T00:00:00Z","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"day":"17","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","year":"2021","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"GaNo"}],"author":[{"full_name":"Conde-Dusman, María J","last_name":"Conde-Dusman","first_name":"María J"},{"first_name":"Partha N","last_name":"Dey","full_name":"Dey, Partha N"},{"full_name":"Elía-Zudaire, Óscar","first_name":"Óscar","last_name":"Elía-Zudaire"},{"full_name":"Garcia Rabaneda, Luis E","first_name":"Luis E","last_name":"Garcia Rabaneda","id":"33D1B084-F248-11E8-B48F-1D18A9856A87"},{"last_name":"García-Lira","first_name":"Carmen","full_name":"García-Lira, Carmen"},{"last_name":"Grand","first_name":"Teddy","full_name":"Grand, Teddy"},{"full_name":"Briz, Victor","first_name":"Victor","last_name":"Briz"},{"first_name":"Eric R","last_name":"Velasco","full_name":"Velasco, Eric R"},{"first_name":"Raül","last_name":"Andero Galí","full_name":"Andero Galí, Raül"},{"first_name":"Sergio","last_name":"Niñerola","full_name":"Niñerola, Sergio"},{"full_name":"Barco, Angel","first_name":"Angel","last_name":"Barco"},{"full_name":"Paoletti, Pierre","last_name":"Paoletti","first_name":"Pierre"},{"first_name":"John F","last_name":"Wesseling","full_name":"Wesseling, John F"},{"first_name":"Fabrizio","last_name":"Gardoni","full_name":"Gardoni, Fabrizio"},{"first_name":"Steven J","last_name":"Tavalin","full_name":"Tavalin, Steven J"},{"first_name":"Isabel","last_name":"Perez-Otaño","full_name":"Perez-Otaño, Isabel"}],"date_updated":"2023-08-14T11:50:50Z","date_created":"2021-11-18T06:59:45Z","volume":10,"article_number":"e71575","file_date_updated":"2021-11-18T07:02:02Z","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":["000720945900001"]},"isi":1,"quality_controlled":"1","doi":"10.7554/elife.71575","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["2050-084X"]}},{"date_published":"2021-11-04T00:00:00Z","article_type":"original","citation":{"chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824.","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021).","ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824"},"publication":"EMBO Reports","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"04","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":488583,"file_name":"2021_EmboReports_Restivo.pdf","access_level":"open_access","date_updated":"2022-05-16T07:07:41Z","date_created":"2022-05-16T07:07:41Z","success":1,"checksum":"74743baa6ef431ef60c3de3bc4da045a","file_id":"11381","relation":"main_file"}],"intvolume":" 22","ddc":["570"],"status":"public","title":"Towards best practices in research: Role of academic core facilities","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10283","abstract":[{"text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.15252/embr.202153824","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000714350000001"]},"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"month":"11","volume":22,"date_updated":"2023-08-14T11:47:35Z","date_created":"2021-11-14T23:01:24Z","author":[{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"full_name":"Gerlach, Björn","last_name":"Gerlach","first_name":"Björn"},{"full_name":"Tsoory, Michael","last_name":"Tsoory","first_name":"Michael"},{"full_name":"Bikovski, Lior","last_name":"Bikovski","first_name":"Lior"},{"last_name":"Badurek","first_name":"Sylvia","full_name":"Badurek, Sylvia"},{"first_name":"Claudia","last_name":"Pitzer","full_name":"Pitzer, Claudia"},{"full_name":"Kos-Braun, Isabelle C.","last_name":"Kos-Braun","first_name":"Isabelle C."},{"last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj"},{"last_name":"Ward","first_name":"Jonathan","full_name":"Ward, Jonathan"},{"first_name":"Michael","last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael"},{"full_name":"Noldus, Lucas P.J.J.","first_name":"Lucas P.J.J.","last_name":"Noldus"},{"first_name":"Anton","last_name":"Bespalov","full_name":"Bespalov, Anton"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"}],"publisher":"EMBO Press","department":[{"_id":"PreCl"}],"publication_status":"published","acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","year":"2021","file_date_updated":"2022-05-16T07:07:41Z","article_number":"e53824"},{"publisher":"Springer ","department":[{"_id":"LeSa"}],"publication_status":"published","pmid":1,"acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","year":"2021","volume":4,"date_created":"2021-11-19T11:37:29Z","date_updated":"2023-08-14T11:51:19Z","author":[{"full_name":"Çoruh, Mehmet Orkun","orcid":"0000-0002-3219-2022","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","last_name":"Çoruh","first_name":"Mehmet Orkun"},{"first_name":"Anna","last_name":"Frank","full_name":"Frank, Anna"},{"last_name":"Tanaka","first_name":"Hideaki","full_name":"Tanaka, Hideaki"},{"last_name":"Kawamoto","first_name":"Akihiro","full_name":"Kawamoto, Akihiro"},{"last_name":"El-Mohsnawy","first_name":"Eithar","full_name":"El-Mohsnawy, Eithar"},{"full_name":"Kato, Takayuki","last_name":"Kato","first_name":"Takayuki"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Gerle, Christoph","last_name":"Gerle","first_name":"Christoph"},{"full_name":"Nowaczyk, Marc M.","last_name":"Nowaczyk","first_name":"Marc M."},{"last_name":"Kurisu","first_name":"Genji","full_name":"Kurisu, Genji"}],"article_number":"304","file_date_updated":"2021-11-19T15:09:18Z","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":{"pmid":["33686186"],"isi":["000627440700001"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-021-01808-9","publication_identifier":{"issn":["2399-3642"]},"month":"03","intvolume":" 4","status":"public","ddc":["570"],"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","_id":"10310","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":6030261,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_CommBio_Çoruh.pdf","access_level":"open_access","date_updated":"2021-11-19T15:09:18Z","date_created":"2021-11-19T15:09:18Z","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"relation":"main_file","file_id":"10318"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700."}],"article_type":"original","citation":{"ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","ieee":"M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021.","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9."},"publication":"Communications Biology","date_published":"2021-03-08T00:00:00Z","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"08"},{"month":"11","publication_identifier":{"issn":["2050-084X"]},"doi":"10.7554/elife.72132","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":{"pmid":["34723798"],"isi":["000734671200001"]},"quality_controlled":"1","isi":1,"file_date_updated":"2022-05-13T09:00:29Z","article_number":"72132","author":[{"full_name":"Marconi, Marco","first_name":"Marco","last_name":"Marconi"},{"full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","first_name":"Marçal"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Wabnik, Krzysztof","first_name":"Krzysztof","last_name":"Wabnik"}],"date_created":"2021-11-11T10:05:18Z","date_updated":"2023-08-14T11:49:23Z","volume":10,"year":"2021","acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","pmid":1,"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"eLife Sciences Publications","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-11-01T00:00:00Z","publication":"eLife","citation":{"ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","apa":"Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132.","mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences Publications, 2021, doi:10.7554/elife.72132.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021)."},"article_type":"original","abstract":[{"lang":"eng","text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development."}],"type":"journal_article","file":[{"file_id":"11372","relation":"main_file","success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","date_created":"2022-05-13T09:00:29Z","date_updated":"2022-05-13T09:00:29Z","access_level":"open_access","file_name":"2021_eLife_Marconi.pdf","creator":"dernst","file_size":14137503,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"10270","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","intvolume":" 10"},{"article_number":"e2102350118","author":[{"first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H"},{"full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul","full_name":"Varshney, Atul"},{"first_name":"Sarath","last_name":"Sankar","full_name":"Sankar, Sarath"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"date_created":"2021-11-17T13:24:24Z","date_updated":"2023-08-14T11:50:10Z","volume":118,"year":"2021","acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","pmid":1,"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","month":"11","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.2102350118","language":[{"iso":"eng"}],"external_id":{"isi":["000720926900019"],"pmid":[" 34732570"],"arxiv":["2103.00023"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188"}],"abstract":[{"lang":"eng","text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number."}],"issue":"45","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10299","status":"public","title":"Experimental observation of the origin and structure of elastoinertial turbulence","intvolume":" 118","day":"03","article_processing_charge":"No","scopus_import":"1","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"date_published":"2021-11-03T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021.","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118."},"article_type":"original"},{"date_published":"2021-11-04T00:00:00Z","article_type":"original","citation":{"mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26699-6.","ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6"},"publication":"Nature Communications","article_processing_charge":"Yes","has_accepted_license":"1","day":"04","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2021_NatComm_Aubret.pdf","access_level":"open_access","file_size":6282703,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10292","date_updated":"2021-11-15T13:25:52Z","date_created":"2021-11-15T13:25:52Z","checksum":"1c392b12b9b7b615d422d9fabe19cdb9","success":1}],"intvolume":" 12","status":"public","ddc":["530"],"title":"Metamachines of pluripotent colloids","_id":"10280","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","abstract":[{"lang":"eng","text":"Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26699-6","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":{"isi":["000714754400010"],"pmid":["34737315"]},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"11","volume":12,"date_created":"2021-11-14T23:01:23Z","date_updated":"2023-08-14T11:48:37Z","author":[{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"last_name":"Martinet","first_name":"Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","full_name":"Martinet, Quentin"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A"}],"department":[{"_id":"JePa"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112.","year":"2021","file_date_updated":"2021-11-15T13:25:52Z","article_number":"6398"}]