[{"day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2021-10-25T00:00:00Z","publication":"Archive for Rational Mechanics and Analysis","citation":{"ista":"Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.","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","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7","chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.","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.","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906."},"article_type":"original","page":"1835–1906","abstract":[{"lang":"eng","text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"creator":"alisjak","content_type":"application/pdf","file_size":990529,"access_level":"open_access","file_name":"2021_Springer_Feliciangeli.pdf","success":1,"checksum":"672e9c21b20f1a50854b7c821edbb92f","date_updated":"2021-12-14T08:35:42Z","date_created":"2021-12-14T08:35:42Z","file_id":"10544","relation":"main_file"}],"_id":"10224","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"status":"public","title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","intvolume":" 242","month":"10","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"doi":"10.1007/s00205-021-01715-7","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":["2101.12566"],"isi":["000710850600001"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"file_date_updated":"2021-12-14T08:35:42Z","ec_funded":1,"author":[{"full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","first_name":"Dario"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"9787"}]},"date_created":"2021-11-07T23:01:26Z","date_updated":"2023-08-14T10:32:19Z","volume":242,"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","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer Nature"},{"date_published":"2021-10-30T00:00:00Z","citation":{"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.","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.","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","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.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021).","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."},"publication":"Genes","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"30","scopus_import":"1","file":[{"creator":"dernst","file_size":1335308,"content_type":"application/pdf","file_name":"2021_Genes_Vasic.pdf","access_level":"open_access","date_updated":"2022-05-16T07:02:27Z","date_created":"2022-05-16T07:02:27Z","success":1,"checksum":"256cb832a9c3051c7dc741f6423b8cbd","file_id":"11380","relation":"main_file"}],"oa_version":"Published Version","_id":"10281","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12","status":"public","title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","ddc":["570"],"issue":"11","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"}],"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"]},"project":[{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2073-4425"]},"month":"10","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."},{"full_name":"Haslinger, Denise","last_name":"Haslinger","first_name":"Denise","id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E"},{"last_name":"Knaus","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"last_name":"Schmeisser","first_name":"Michael J.","full_name":"Schmeisser, Michael J."},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"full_name":"Chiocchetti, Andreas G.","first_name":"Andreas G.","last_name":"Chiocchetti"}],"volume":12,"date_updated":"2023-08-14T11:46:12Z","date_created":"2021-11-14T23:01:24Z","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","department":[{"_id":"GaNo"}],"publisher":"MDPI","publication_status":"published","ec_funded":1,"file_date_updated":"2022-05-16T07:02:27Z","article_number":"1746"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10282","intvolume":" 233","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","status":"public","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.","lang":"eng"}],"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","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.","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","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."},"publication":"New Phytologist","page":"329-343","article_type":"original","date_published":"2021-11-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"05","pmid":1,"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.","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"last_name":"Kashkan","first_name":"Ivan","full_name":"Kashkan, Ivan"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan"},{"first_name":"Katarzyna","last_name":"Retzer","full_name":"Retzer, Katarzyna"},{"full_name":"Humpolíčková, Jana","last_name":"Humpolíčková","first_name":"Jana"},{"last_name":"Jayasree","first_name":"Aswathy","full_name":"Jayasree, Aswathy"},{"last_name":"Filepová","first_name":"Roberta","full_name":"Filepová, Roberta"},{"first_name":"Zuzana","last_name":"Vondráková","full_name":"Vondráková, Zuzana"},{"orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu"},{"first_name":"Debbie","last_name":"Rombaut","full_name":"Rombaut, Debbie"},{"full_name":"Jacobs, Thomas B.","last_name":"Jacobs","first_name":"Thomas B."},{"full_name":"Frilander, Mikko J.","first_name":"Mikko J.","last_name":"Frilander"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Kamil","last_name":"Růžička","full_name":"Růžička, Kamil"}],"volume":233,"date_updated":"2023-08-14T11:46:43Z","date_created":"2021-11-14T23:01:24Z","oa":1,"external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}],"quality_controlled":"1","isi":1,"doi":"10.1111/nph.17792","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"month":"11"},{"volume":245,"date_updated":"2023-08-14T11:43:55Z","date_created":"2021-11-07T23:01:24Z","related_material":{"record":[{"id":"8183","status":"public","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"9308"}]},"author":[{"full_name":"Avvakumov, Sergey","first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard"},{"last_name":"Skopenkov","first_name":"Arkadiy B.","full_name":"Skopenkov, Arkadiy B."},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2021","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.","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1007/s11856-021-2216-z","project":[{"grant_number":"P31312","_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1511.03501"],"isi":["000712942100013"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"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"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 245","title":"Eliminating higher-multiplicity intersections. III. Codimension 2","status":"public","_id":"10220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2021-10-30T00:00:00Z","page":"501–534 ","article_type":"original","citation":{"chicago":"Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z.","short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature, 2021, pp. 501–534, doi:10.1007/s11856-021-2216-z.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-021-2216-z","ieee":"S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” Israel Journal of Mathematics, vol. 245. Springer Nature, pp. 501–534, 2021.","ista":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.","ama":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534. doi:10.1007/s11856-021-2216-z"},"publication":"Israel Journal of Mathematics"},{"type":"research_data_reference","ec_funded":1,"abstract":[{"lang":"eng","text":"Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism."}],"publisher":"Dryad","department":[{"_id":"SyCr"}],"status":"public","ddc":["570"],"title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","_id":"13061","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2023-05-23T16:14:35Z","date_updated":"2023-08-14T11:45:28Z","related_material":{"record":[{"id":"10284","status":"public","relation":"used_in_publication"}]},"author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E"},{"last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher"},{"full_name":"Naiser, Filip","first_name":"Filip","last_name":"Naiser"},{"full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth","last_name":"Naderlinger"},{"full_name":"Matas, Jiri","last_name":"Matas","first_name":"Jiri"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"article_processing_charge":"No","month":"10","day":"29","project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"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.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021).","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.","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.","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.","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":[{"url":"https://doi.org/10.5061/dryad.7pvmcvdtj","open_access":"1"}],"doi":"10.5061/DRYAD.7PVMCVDTJ","date_published":"2021-10-29T00:00:00Z"},{"article_type":"original","publication":"eLife","citation":{"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.","ieee":"M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575","chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021)."},"date_published":"2021-11-17T00:00:00Z","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"day":"17","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","status":"public","intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10301","file":[{"relation":"main_file","file_id":"10302","checksum":"59318e9e41507cec83c2f4070e6ad540","success":1,"date_updated":"2021-11-18T07:02:02Z","date_created":"2021-11-18T07:02:02Z","access_level":"open_access","file_name":"elife-71575-v1.pdf","file_size":2477302,"content_type":"application/pdf","creator":"lgarciar"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.","lang":"eng"}],"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":["000720945900001"]},"language":[{"iso":"eng"}],"doi":"10.7554/elife.71575","month":"11","publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"GaNo"}],"year":"2021","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).","date_updated":"2023-08-14T11:50:50Z","date_created":"2021-11-18T06:59:45Z","volume":10,"author":[{"full_name":"Conde-Dusman, María J","last_name":"Conde-Dusman","first_name":"María J"},{"full_name":"Dey, Partha N","last_name":"Dey","first_name":"Partha N"},{"full_name":"Elía-Zudaire, Óscar","first_name":"Óscar","last_name":"Elía-Zudaire"},{"id":"33D1B084-F248-11E8-B48F-1D18A9856A87","first_name":"Luis E","last_name":"Garcia Rabaneda","full_name":"Garcia Rabaneda, Luis E"},{"full_name":"García-Lira, Carmen","last_name":"García-Lira","first_name":"Carmen"},{"last_name":"Grand","first_name":"Teddy","full_name":"Grand, Teddy"},{"last_name":"Briz","first_name":"Victor","full_name":"Briz, Victor"},{"first_name":"Eric R","last_name":"Velasco","full_name":"Velasco, Eric R"},{"last_name":"Andero Galí","first_name":"Raül","full_name":"Andero Galí, Raül"},{"first_name":"Sergio","last_name":"Niñerola","full_name":"Niñerola, Sergio"},{"last_name":"Barco","first_name":"Angel","full_name":"Barco, Angel"},{"first_name":"Pierre","last_name":"Paoletti","full_name":"Paoletti, Pierre"},{"full_name":"Wesseling, John F","last_name":"Wesseling","first_name":"John F"},{"first_name":"Fabrizio","last_name":"Gardoni","full_name":"Gardoni, Fabrizio"},{"first_name":"Steven J","last_name":"Tavalin","full_name":"Tavalin, Steven J"},{"full_name":"Perez-Otaño, Isabel","first_name":"Isabel","last_name":"Perez-Otaño"}],"article_number":"e71575","file_date_updated":"2021-11-18T07:02:02Z"},{"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2021-11-04T00:00:00Z","citation":{"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","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.","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","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","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).","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."},"publication":"EMBO Reports","article_type":"original","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","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_created":"2022-05-16T07:07:41Z","date_updated":"2022-05-16T07:07:41Z","success":1,"checksum":"74743baa6ef431ef60c3de3bc4da045a","file_id":"11381","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10283","intvolume":" 22","title":"Towards best practices in research: Role of academic core facilities","status":"public","ddc":["570"],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"month":"11","doi":"10.15252/embr.202153824","language":[{"iso":"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"},"oa":1,"external_id":{"isi":["000714350000001"]},"quality_controlled":"1","isi":1,"file_date_updated":"2022-05-16T07:07:41Z","article_number":"e53824","author":[{"last_name":"Restivo","first_name":"Leonardo","full_name":"Restivo, Leonardo"},{"last_name":"Gerlach","first_name":"Björn","full_name":"Gerlach, Björn"},{"last_name":"Tsoory","first_name":"Michael","full_name":"Tsoory, Michael"},{"full_name":"Bikovski, Lior","last_name":"Bikovski","first_name":"Lior"},{"full_name":"Badurek, Sylvia","first_name":"Sylvia","last_name":"Badurek"},{"full_name":"Pitzer, Claudia","last_name":"Pitzer","first_name":"Claudia"},{"last_name":"Kos-Braun","first_name":"Isabelle C.","full_name":"Kos-Braun, Isabelle C."},{"full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj"},{"last_name":"Ward","first_name":"Jonathan","full_name":"Ward, Jonathan"},{"full_name":"Schunn, Michael","last_name":"Schunn","first_name":"Michael","orcid":"0000-0003-4326-5300","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Noldus, Lucas P.J.J.","last_name":"Noldus","first_name":"Lucas P.J.J."},{"full_name":"Bespalov, Anton","first_name":"Anton","last_name":"Bespalov"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"}],"volume":22,"date_created":"2021-11-14T23:01:24Z","date_updated":"2023-08-14T11:47:35Z","year":"2021","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.","publisher":"EMBO Press","department":[{"_id":"PreCl"}],"publication_status":"published"},{"month":"03","publication_identifier":{"issn":["2399-3642"]},"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"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s42003-021-01808-9","language":[{"iso":"eng"}],"article_number":"304","file_date_updated":"2021-11-19T15:09:18Z","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","pmid":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Springer ","author":[{"id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun"},{"first_name":"Anna","last_name":"Frank","full_name":"Frank, Anna"},{"full_name":"Tanaka, Hideaki","first_name":"Hideaki","last_name":"Tanaka"},{"full_name":"Kawamoto, Akihiro","first_name":"Akihiro","last_name":"Kawamoto"},{"last_name":"El-Mohsnawy","first_name":"Eithar","full_name":"El-Mohsnawy, Eithar"},{"full_name":"Kato, Takayuki","last_name":"Kato","first_name":"Takayuki"},{"last_name":"Namba","first_name":"Keiichi","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."},{"full_name":"Kurisu, Genji","last_name":"Kurisu","first_name":"Genji"}],"date_created":"2021-11-19T11:37:29Z","date_updated":"2023-08-14T11:51:19Z","volume":4,"scopus_import":"1","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"day":"08","article_processing_charge":"No","has_accepted_license":"1","publication":"Communications Biology","citation":{"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.","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"},"article_type":"original","date_published":"2021-03-08T00:00:00Z","type":"journal_article","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."}],"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10310","ddc":["570"],"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","status":"public","intvolume":" 4","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":6030261,"file_name":"2021_CommBio_Çoruh.pdf","access_level":"open_access","date_updated":"2021-11-19T15:09:18Z","date_created":"2021-11-19T15:09:18Z","success":1,"checksum":"8ffd39f2bba7152a2441802ff313bf0b","file_id":"10318","relation":"main_file"}]},{"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"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.7554/elife.72132","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["2050-084X"]},"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).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"eLife Sciences Publications","author":[{"last_name":"Marconi","first_name":"Marco","full_name":"Marconi, Marco"},{"full_name":"Gallemi, Marçal","first_name":"Marçal","last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Krzysztof","last_name":"Wabnik","full_name":"Wabnik, Krzysztof"}],"date_created":"2021-11-11T10:05:18Z","date_updated":"2023-08-14T11:49:23Z","volume":10,"article_number":"72132","file_date_updated":"2022-05-13T09:00:29Z","publication":"eLife","citation":{"short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","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.","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.","ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132","apa":"Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132","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.","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."},"article_type":"original","date_published":"2021-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","_id":"10270","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","intvolume":" 10","oa_version":"Published Version","file":[{"file_id":"11372","relation":"main_file","success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","date_updated":"2022-05-13T09:00:29Z","date_created":"2022-05-13T09:00:29Z","access_level":"open_access","file_name":"2021_eLife_Marconi.pdf","creator":"dernst","file_size":14137503,"content_type":"application/pdf"}],"type":"journal_article","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."}]},{"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"11","doi":"10.1073/pnas.2102350118","language":[{"iso":"eng"}],"external_id":{"arxiv":["2103.00023"],"isi":["000720926900019"],"pmid":[" 34732570"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"project":[{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","article_number":"e2102350118","author":[{"full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","first_name":"George H"},{"id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","first_name":"Jose M","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M"},{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999"},{"first_name":"Sarath","last_name":"Sankar","full_name":"Sankar, Sarath"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"volume":118,"date_updated":"2023-08-14T11:50:10Z","date_created":"2021-11-17T13:24:24Z","pmid":1,"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.","year":"2021","publisher":"National Academy of Sciences","department":[{"_id":"BjHo"}],"publication_status":"published","article_processing_charge":"No","day":"03","scopus_import":"1","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"date_published":"2021-11-03T00:00:00Z","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."},"publication":"Proceedings of the National Academy of Sciences","article_type":"original","issue":"45","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10299","intvolume":" 118","status":"public","title":"Experimental observation of the origin and structure of elastoinertial turbulence"},{"type":"journal_article","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."}],"issue":"1","_id":"10280","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Metamachines of pluripotent colloids","status":"public","ddc":["530"],"intvolume":" 12","oa_version":"Published Version","file":[{"date_created":"2021-11-15T13:25:52Z","date_updated":"2021-11-15T13:25:52Z","checksum":"1c392b12b9b7b615d422d9fabe19cdb9","success":1,"relation":"main_file","file_id":"10292","file_size":6282703,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_NatComm_Aubret.pdf","access_level":"open_access"}],"scopus_import":"1","day":"04","article_processing_charge":"Yes","has_accepted_license":"1","publication":"Nature Communications","citation":{"ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6","apa":"Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","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.","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."},"article_type":"original","date_published":"2021-11-04T00:00:00Z","article_number":"6398","file_date_updated":"2021-11-15T13:25:52Z","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","pmid":1,"publication_status":"published","department":[{"_id":"JePa"}],"publisher":"Springer Nature","author":[{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","last_name":"Martinet","first_name":"Quentin","full_name":"Martinet, Quentin"},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A"}],"date_created":"2021-11-14T23:01:23Z","date_updated":"2023-08-14T11:48:37Z","volume":12,"month":"11","publication_identifier":{"eissn":["2041-1723"]},"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":["000714754400010"],"pmid":["34737315"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-021-26699-6","language":[{"iso":"eng"}]},{"date_published":"2021-11-01T00:00:00Z","article_type":"original","publication":"PLoS Biology","citation":{"ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 19(11), e3001431.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021.","mla":"Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:10.1371/journal.pbio.3001431.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021).","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pbio.3001431."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"date_updated":"2021-11-22T09:34:03Z","date_created":"2021-11-22T09:34:03Z","success":1,"checksum":"0c61b667f814fd9435b3ac42036fc36d","file_id":"10330","relation":"main_file","creator":"cchlebak","file_size":4069215,"content_type":"application/pdf","file_name":"2021_PLoSBio_Chauve.pdf","access_level":"open_access"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","intvolume":" 19","_id":"10322","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal.","lang":"eng"}],"issue":"11","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.3001431","isi":1,"quality_controlled":"1","external_id":{"isi":["000715818400001"],"pmid":["34723964"]},"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,"month":"11","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"date_updated":"2023-08-14T11:53:27Z","date_created":"2021-11-21T23:01:28Z","volume":19,"author":[{"full_name":"Chauve, Laetitia","first_name":"Laetitia","last_name":"Chauve"},{"full_name":"Hodge, Francesca","first_name":"Francesca","last_name":"Hodge"},{"full_name":"Murdoch, Sharlene","first_name":"Sharlene","last_name":"Murdoch"},{"full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah","last_name":"Masoudzadeh"},{"full_name":"Mann, Harry Jack","last_name":"Mann","first_name":"Harry Jack"},{"last_name":"Lopez-Clavijo","first_name":"Andrea","full_name":"Lopez-Clavijo, Andrea"},{"first_name":"Hanneke","last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke"},{"first_name":"Greg","last_name":"West","full_name":"West, Greg"},{"last_name":"Sousa","first_name":"Bebiana C.","full_name":"Sousa, Bebiana C."},{"full_name":"Segonds-Pichon, Anne","first_name":"Anne","last_name":"Segonds-Pichon"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"last_name":"Wingett","first_name":"Steven","full_name":"Wingett, Steven"},{"last_name":"Kienberger","first_name":"Hermine","full_name":"Kienberger, Hermine"},{"full_name":"Kleigrewe, Karin","first_name":"Karin","last_name":"Kleigrewe"},{"first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario"},{"last_name":"Wakelam","first_name":"Michael","full_name":"Wakelam, Michael"},{"last_name":"Casanueva","first_name":"Olivia","full_name":"Casanueva, Olivia"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13069"}]},"publication_status":"published","department":[{"_id":"MaDe"}],"publisher":"Public Library of Science","year":"2021","acknowledgement":"We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities.","pmid":1,"file_date_updated":"2021-11-22T09:34:03Z","article_number":"e3001431"},{"ec_funded":1,"file_date_updated":"2023-08-14T11:55:10Z","year":"2021","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions.","department":[{"_id":"HeEd"}],"publisher":"Taylor and Francis","publication_status":"published","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","first_name":"Anton"}],"date_updated":"2023-08-14T11:57:07Z","date_created":"2021-11-07T23:01:25Z","publication_identifier":{"issn":["1058-6458"],"eissn":["1944-950X"]},"month":"10","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":["2007.07783"],"isi":["000710893500001"]},"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Discretization in Geometry and Dynamics","grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1080/10586458.2021.1980459","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density.","lang":"eng"}],"_id":"10222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The beauty of random polytopes inscribed in the 2-sphere","ddc":["510"],"file":[{"content_type":"application/pdf","file_size":1966019,"creator":"dernst","file_name":"2023_ExperimentalMath_Akopyan.pdf","access_level":"open_access","date_created":"2023-08-14T11:55:10Z","date_updated":"2023-08-14T11:55:10Z","checksum":"3514382e3a1eb87fa6c61ad622874415","success":1,"relation":"main_file","file_id":"14053"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"25","citation":{"ama":"Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459","apa":"Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2021.1980459","ieee":"A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis, pp. 1–15, 2021.","ista":"Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15.","short":"A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15.","mla":"Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459.","chicago":"Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics. Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459."},"publication":"Experimental Mathematics","page":"1-15","article_type":"original","date_published":"2021-10-25T00:00:00Z"},{"doi":"10.3389/fmolb.2021.762005","language":[{"iso":"eng"}],"external_id":{"isi":["000717241700001"],"pmid":["34760928"]},"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,"month":"10","publication_identifier":{"eissn":["2296-889X"]},"author":[{"full_name":"Sučec, Iva","first_name":"Iva","last_name":"Sučec"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"}],"date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T11:55:04Z","volume":8,"year":"2021","acknowledgement":"We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).","pmid":1,"publication_status":"published","publisher":"Frontiers","department":[{"_id":"PaSc"}],"file_date_updated":"2021-11-23T15:06:58Z","article_number":"762005","date_published":"2021-10-25T00:00:00Z","publication":"Frontiers in Molecular Biosciences","citation":{"mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005.","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).","chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005.","ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021.","apa":"Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005"},"article_type":"original","day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":4700798,"content_type":"application/pdf","file_name":"2021_FrontiersMolBioSc_Sučec.pdf","access_level":"open_access","date_created":"2021-11-23T15:06:58Z","date_updated":"2021-11-23T15:06:58Z","success":1,"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","file_id":"10333","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10323","ddc":["547"],"status":"public","title":"How do chaperones bind (partly) unfolded client proteins?","intvolume":" 8","abstract":[{"lang":"eng","text":"Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity."}],"type":"journal_article"},{"doi":"10.1038/s41477-021-01011-y","language":[{"iso":"eng"}],"external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2055-0278"]},"month":"11","author":[{"full_name":"Xu, Enjun","first_name":"Enjun","last_name":"Xu"},{"first_name":"Liang","last_name":"Chai","full_name":"Chai, Liang"},{"first_name":"Shiqi","last_name":"Zhang","full_name":"Zhang, Shiqi"},{"full_name":"Yu, Ruixue","first_name":"Ruixue","last_name":"Yu"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"full_name":"Xu, Chongyi","last_name":"Xu","first_name":"Chongyi"},{"full_name":"Hu, Yuxin","last_name":"Hu","first_name":"Yuxin"}],"volume":7,"date_created":"2021-11-21T23:01:30Z","date_updated":"2023-08-14T11:54:02Z","pmid":1,"acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","year":"2021","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"publication_status":"published","date_published":"2021-11-11T00:00:00Z","citation":{"ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y","ieee":"E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y.","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y."},"publication":"Nature Plants","page":"1495–1504 ","article_type":"original","article_processing_charge":"No","day":"11","scopus_import":"1","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10326","intvolume":" 7","title":"Catabolism of strigolactones by a carboxylesterase","status":"public","abstract":[{"text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.","lang":"eng"}],"type":"journal_article"},{"month":"12","day":"25","article_processing_charge":"No","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":{"ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).","mla":"Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5547464"}],"doi":"10.5281/ZENODO.5519410","date_published":"2021-12-25T00:00:00Z","type":"research_data_reference","abstract":[{"text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.","lang":"eng"}],"status":"public","title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","ddc":["570"],"department":[{"_id":"MaDe"}],"publisher":"Zenodo","year":"2021","_id":"13069","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-14T11:53:26Z","date_created":"2023-05-23T16:40:56Z","oa_version":"Published Version","author":[{"last_name":"Chauve","first_name":"Laetitia","full_name":"Chauve, Laetitia"},{"last_name":"Hodge","first_name":"Francesca","full_name":"Hodge, Francesca"},{"full_name":"Murdoch, Sharlene","last_name":"Murdoch","first_name":"Sharlene"},{"last_name":"Masoudzadeh","first_name":"Fatemah","full_name":"Masoudzadeh, Fatemah"},{"first_name":"Harry-Jack","last_name":"Mann","full_name":"Mann, Harry-Jack"},{"last_name":"Lopez-Clavijo","first_name":"Andrea","full_name":"Lopez-Clavijo, Andrea"},{"last_name":"Okkenhaug","first_name":"Hanneke","full_name":"Okkenhaug, Hanneke"},{"full_name":"West, Greg","first_name":"Greg","last_name":"West"},{"full_name":"Sousa, Bebiana C.","first_name":"Bebiana C.","last_name":"Sousa"},{"first_name":"Anne","last_name":"Segonds-Pichon","full_name":"Segonds-Pichon, Anne"},{"first_name":"Cheryl","last_name":"Li","full_name":"Li, Cheryl"},{"last_name":"Wingett","first_name":"Steven","full_name":"Wingett, Steven"},{"full_name":"Kienberger, Hermine","last_name":"Kienberger","first_name":"Hermine"},{"last_name":"Kleigrewe","first_name":"Karin","full_name":"Kleigrewe, Karin"},{"full_name":"de Bono, Mario","first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"},{"first_name":"Michael","last_name":"Wakelam","full_name":"Wakelam, Michael"},{"last_name":"Casanueva","first_name":"Olivia","full_name":"Casanueva, Olivia"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10322"}]}},{"language":[{"iso":"eng"}],"conference":{"start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05","name":"FC: Financial Cryptography"},"doi":"10.1007/978-3-662-64331-0_1","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1128"}],"external_id":{"isi":["000712016200001"]},"oa":1,"month":"10","publication_identifier":{"eisbn":["978-3-662-64331-0"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"]},"date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T12:59:26Z","volume":"12675 ","author":[{"last_name":"Zamyatin","first_name":"Alexei","full_name":"Zamyatin, Alexei"},{"full_name":"Al-Bassam, Mustafa","last_name":"Al-Bassam","first_name":"Mustafa"},{"full_name":"Zindros, Dionysis","last_name":"Zindros","first_name":"Dionysis"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Pedro","last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro"},{"first_name":"Aggelos","last_name":"Kiayias","full_name":"Kiayias, Aggelos"},{"full_name":"Knottenbelt, William J.","first_name":"William J.","last_name":"Knottenbelt"}],"publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.","date_published":"2021-10-23T00:00:00Z","page":"3-36","publication":"25th International Conference on Financial Cryptography and Data Security","citation":{"chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In 25th International Conference on Financial Cryptography and Data Security, 12675:3–36. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_1.","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 3–36.","ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1"},"day":"23","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"SoK: Communication across distributed ledgers","_id":"10325","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains."}],"alternative_title":["LNCS"],"type":"conference"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.","lang":"eng"}],"_id":"10324","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Brick: Asynchronous incentive-compatible payment channels","status":"public","oa_version":"Preprint","scopus_import":"1","day":"23","article_processing_charge":"No","publication":"25th International Conference on Financial Cryptography and Data Security","citation":{"chicago":"Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th International Conference on Financial Cryptography and Data Security, 12675:209–30. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11.","short":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230.","mla":"Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.","apa":"Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11","ieee":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 209–230.","ista":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.","ama":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230. doi:10.1007/978-3-662-64331-0_11"},"page":"209-230","date_published":"2021-10-23T00:00:00Z","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ElKo"}],"author":[{"full_name":"Avarikioti, Zeta","first_name":"Zeta","last_name":"Avarikioti"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Wattenhofer, Roger","first_name":"Roger","last_name":"Wattenhofer"},{"full_name":"Zindros, Dionysis","last_name":"Zindros","first_name":"Dionysis"}],"date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T12:59:58Z","volume":"12675 ","month":"10","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"],"isbn":["9-783-6626-4330-3"],"eissn":["1611-3349"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.11360"}],"oa":1,"external_id":{"isi":["000712016200011"],"arxiv":["1905.11360"]},"isi":1,"quality_controlled":"1","conference":{"name":"FC: Financial Cryptography","start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05"},"doi":"10.1007/978-3-662-64331-0_11","language":[{"iso":"eng"}]},{"author":[{"full_name":"Lee, Jungmin","last_name":"Lee","first_name":"Jungmin"},{"full_name":"Vernet, Andyna","first_name":"Andyna","last_name":"Vernet"},{"first_name":"Nathalie","last_name":"Gruber","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","full_name":"Gruber, Nathalie"},{"full_name":"Kready, Kasia M.","last_name":"Kready","first_name":"Kasia M."},{"first_name":"Devin R.","last_name":"Burrill","full_name":"Burrill, Devin R."},{"full_name":"Way, Jeffrey C.","last_name":"Way","first_name":"Jeffrey C."},{"last_name":"Silver","first_name":"Pamela A.","full_name":"Silver, Pamela A."}],"date_updated":"2023-08-14T13:01:38Z","date_created":"2021-11-28T23:01:28Z","volume":34,"acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Oxford University Press","article_number":"gzab025","doi":"10.1093/protein/gzab025","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/protein/gzab025"}],"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"issn":["1741-0126"],"eissn":["1741-0134"]},"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10363","title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","status":"public","intvolume":" 34","abstract":[{"text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-01T00:00:00Z","publication":"Protein Engineering, Design and Selection","citation":{"apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., & Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzab025","ieee":"J. Lee et al., “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34. Oxford University Press, 2021.","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025.","ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 2021;34. doi:10.1093/protein/gzab025","chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection. Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025.","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021).","mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34, gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1"},{"year":"2021","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"CaHe"}],"author":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Lennon, Ana Maria","first_name":"Ana Maria","last_name":"Lennon"},{"full_name":"Mayor, Roberto","first_name":"Roberto","last_name":"Mayor"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"}],"date_created":"2021-11-28T23:01:30Z","date_updated":"2023-08-14T13:02:40Z","volume":168,"article_number":"203758","oa":1,"external_id":{"pmid":["34800748"],"isi":["000974771600028"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cdev.2021.203758","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.cdev.2021.203758","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["2667-2901"]},"_id":"10366","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Special rebranding issue: “Quantitative cell and developmental biology”","intvolume":" 168","oa_version":"Published Version","type":"journal_article","issue":"12","publication":"Cells and Development","citation":{"ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758","ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758."},"article_type":"letter_note","date_published":"2021-11-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No"},{"publication_identifier":{"eissn":["2041-1723"]},"month":"11","project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"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/s41467-021-27135-5","article_number":"6830","ec_funded":1,"file_date_updated":"2021-12-10T08:54:09Z","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","year":"2021","volume":12,"date_updated":"2023-08-14T13:18:46Z","date_created":"2021-12-05T23:01:40Z","related_material":{"record":[{"id":"13058","relation":"research_data","status":"public"}]},"author":[{"last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"},{"first_name":"Dmitrii","last_name":"Kamenev","full_name":"Kamenev, Dmitrii"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","first_name":"Dominik C","last_name":"Fachet","full_name":"Fachet, Dominik C"},{"last_name":"Lallemend","first_name":"Francois","full_name":"Lallemend, Francois"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"},{"full_name":"Hadjab, Saida","last_name":"Hadjab","first_name":"Saida"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"24","article_type":"original","citation":{"ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5","chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5."},"publication":"Nature Communications","date_published":"2021-11-24T00:00:00Z","type":"journal_article","abstract":[{"text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales.","lang":"eng"}],"intvolume":" 12","status":"public","ddc":["573"],"title":"Theory of branching morphogenesis by local interactions and global guidance","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10402","file":[{"file_id":"10529","relation":"main_file","date_created":"2021-12-10T08:54:09Z","date_updated":"2021-12-10T08:54:09Z","success":1,"checksum":"63c56ec75314a71e63e7dd2920b3c5b5","file_name":"2021_NatComm_Ucar.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":2303405}],"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10407","intvolume":" 13043","title":"Trojan-resilience without cryptography","status":"public","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2021-11-04T00:00:00Z","citation":{"ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14.","mla":"Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428."},"page":"397-428","ec_funded":1,"author":[{"full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"last_name":"Gałązka","first_name":"Małgorzata","full_name":"Gałązka, Małgorzata"},{"full_name":"Lizurej, Tomasz","first_name":"Tomasz","last_name":"Lizurej"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo","first_name":"Michelle X"}],"volume":13043,"date_updated":"2023-08-14T13:07:46Z","date_created":"2021-12-05T23:01:42Z","year":"2021","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"]},"month":"11","doi":"10.1007/978-3-030-90453-1_14","conference":{"name":"TCC: Theory of Cryptography Conference","end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08"},"language":[{"iso":"eng"}],"external_id":{"isi":["000728364000014"]},"main_file_link":[{"url":"https://eprint.iacr.org/2021/1224","open_access":"1"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"status":"public","title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","ddc":["570"],"intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10403","file":[{"file_size":13131322,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_eLife_Biane.pdf","access_level":"open_access","date_created":"2021-12-10T08:31:41Z","date_updated":"2021-12-10T08:31:41Z","checksum":"c7c33c3319428d56e332e22349c50ed3","success":1,"relation":"main_file","file_id":"10528"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits.","lang":"eng"}],"article_type":"original","publication":"eLife","citation":{"chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954.","short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954.","ieee":"C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954","ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954"},"date_published":"2021-11-03T00:00:00Z","scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"}],"acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","year":"2021","date_created":"2021-12-05T23:01:40Z","date_updated":"2023-08-14T13:12:07Z","volume":10,"author":[{"first_name":"Celia","last_name":"Biane","full_name":"Biane, Celia"},{"full_name":"Rückerl, Florian","first_name":"Florian","last_name":"Rückerl"},{"last_name":"Abrahamsson","first_name":"Therese","full_name":"Abrahamsson, Therese"},{"last_name":"Saint-Cloment","first_name":"Cécile","full_name":"Saint-Cloment, Cécile"},{"last_name":"Mariani","first_name":"Jean","full_name":"Mariani, Jean"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Digregorio","first_name":"David A.","full_name":"Digregorio, David A."},{"full_name":"Sherrard, Rachel M.","first_name":"Rachel M.","last_name":"Sherrard"},{"full_name":"Cathala, Laurence","first_name":"Laurence","last_name":"Cathala"}],"article_number":"e65954","file_date_updated":"2021-12-10T08:31:41Z","isi":1,"quality_controlled":"1","external_id":{"isi":["000715789500001"]},"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":"10.7554/eLife.65954","month":"11","publication_identifier":{"eissn":["2050-084X"]}},{"date_published":"2021-11-26T00:00:00Z","citation":{"ista":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252.","ieee":"R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021.","apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7","chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7.","mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021)."},"publication":"Communications Physics","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","file":[{"file_size":1068984,"content_type":"application/pdf","creator":"alisjak","access_level":"open_access","file_name":"2021_NatComm_Barfknecht.pdf","checksum":"9097319952cb9a3d96e7fd3aa9813a03","success":1,"date_updated":"2021-12-06T14:53:41Z","date_created":"2021-12-06T14:53:41Z","relation":"main_file","file_id":"10420"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10401","intvolume":" 4","title":"Generation of spin currents by a temperature gradient in a two-terminal device","ddc":["530"],"status":"public","issue":"1","abstract":[{"lang":"eng","text":"Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect."}],"type":"journal_article","doi":"10.1038/s42005-021-00753-7","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":["2101.02020"],"isi":["10.1038/s42005-021-00753-7"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","publication_identifier":{"eissn":["23993650"]},"month":"11","author":[{"first_name":"Rafael E.","last_name":"Barfknecht","full_name":"Barfknecht, Rafael E."},{"first_name":"Angela","last_name":"Foerster","full_name":"Foerster, Angela"},{"full_name":"Zinner, Nikolaj T.","last_name":"Zinner","first_name":"Nikolaj T."},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"}],"volume":4,"date_created":"2021-12-05T23:01:39Z","date_updated":"2023-08-14T13:04:34Z","acknowledgement":"The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z).","year":"2021","publisher":"Springer Nature","department":[{"_id":"MiLe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2021-12-06T14:53:41Z","article_number":"252"},{"month":"11","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.07667"}],"external_id":{"isi":["000722952000024"],"arxiv":["2110.07667"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"doi":"10.1111/cgf.14418","language":[{"iso":"eng"}],"year":"2021","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","publication_status":"published","publisher":"Wiley","department":[{"_id":"ToHe"}],"author":[{"first_name":"Stefan","last_name":"Sietzen","full_name":"Sietzen, Stefan"},{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Judy","last_name":"Borowski","full_name":"Borowski, Judy"},{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"full_name":"Waldner, Manuela","first_name":"Manuela","last_name":"Waldner"}],"date_updated":"2023-08-14T13:11:42Z","date_created":"2021-12-05T23:01:40Z","volume":40,"scopus_import":"1","day":"27","article_processing_charge":"No","publication":"Computer Graphics Forum","citation":{"ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418."},"article_type":"original","page":"253-264","date_published":"2021-11-27T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models."}],"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10404","title":"Interactive analysis of CNN robustness","status":"public","intvolume":" 40","oa_version":"Preprint"},{"publication_status":"published","publisher":"Annual Reviews","department":[{"_id":"CaHe"}],"acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","year":"2021","pmid":1,"date_created":"2021-12-05T23:01:41Z","date_updated":"2023-08-14T13:05:13Z","volume":55,"author":[{"full_name":"Mishra, Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","orcid":"0000-0002-6425-5788","first_name":"Nikhil","last_name":"Mishra"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000747220900010"],"pmid":["34460295"]},"language":[{"iso":"eng"}],"doi":"10.1146/annurev-genet-071819-103748","month":"08","publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"status":"public","title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","intvolume":" 55","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10406","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future."}],"article_type":"original","page":"209-233","publication":"Annual Review of Genetics","citation":{"short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748.","chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748","apa":"Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021.","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233."},"date_published":"2021-08-30T00:00:00Z","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"scopus_import":"1","day":"30","article_processing_charge":"No"},{"article_processing_charge":"No","month":"08","day":"25","date_published":"2021-08-25T00:00:00Z","doi":"10.5281/ZENODO.5257160","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5257161"}],"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":{"apa":"Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","ista":"Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160.","ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160.","short":"M.C. Ucar, (2021).","mla":"Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160."},"oa":1,"abstract":[{"text":"The zip file includes source data used in the main text of the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.","lang":"eng"}],"type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10402"}]},"author":[{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","full_name":"Ucar, Mehmet C"}],"oa_version":"Published Version","date_created":"2023-05-23T13:46:34Z","date_updated":"2023-08-14T13:18:46Z","_id":"13058","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","publisher":"Zenodo","department":[{"_id":"EdHa"}],"status":"public","title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","ddc":["570"]},{"external_id":{"isi":["000728363700008"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1158"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"conference":{"name":"TCC: Theory of Cryptography","start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11"},"doi":"10.1007/978-3-030-90456-2_8","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0455-5"],"issn":["0302-9743"],"eisbn":["978-3-030-90456-2"]},"acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen"},{"full_name":"Auerbach, Benedikt","last_name":"Auerbach","first_name":"Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425"},{"full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig"},{"full_name":"Cueto Noval, Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","last_name":"Cueto Noval"},{"full_name":"Klein, Karen","last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pascual Perez, Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","first_name":"Guillermo","last_name":"Pascual Perez"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"full_name":"Walter, Michael","first_name":"Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482"}],"date_updated":"2023-08-14T13:19:39Z","date_created":"2021-12-05T23:01:42Z","volume":13044,"ec_funded":1,"publication":"19th International Conference","citation":{"chicago":"Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In 19th International Conference, 13044:222–53. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90456-2_8.","mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” 19th International Conference, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:10.1007/978-3-030-90456-2_8.","short":"J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253.","ista":"Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.","ieee":"J. F. Alwen et al., “Grafting key trees: Efficient key management for overlapping groups,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.","apa":"Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In 19th International Conference (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90456-2_8","ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: 19th International Conference. Vol 13044. Springer Nature; 2021:222-253. doi:10.1007/978-3-030-90456-2_8"},"page":"222-253","date_published":"2021-11-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10408","title":"Grafting key trees: Efficient key management for overlapping groups","status":"public","intvolume":" 13044","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds log(N) keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting 2log(N) ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks."}]},{"month":"12","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000923819400004"],"arxiv":["2109.00011"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.00011"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.127.247001","article_number":"247001","ec_funded":1,"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","year":"2021","date_updated":"2023-08-14T13:19:13Z","date_created":"2021-12-10T07:51:33Z","volume":127,"author":[{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Berg, Erez","first_name":"Erez","last_name":"Berg"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/","relation":"press_release","description":"News on IST Webpage"}]},"keyword":["general physics and astronomy"],"scopus_import":"1","day":"09","article_processing_charge":"No","article_type":"original","publication":"Physical Review Letters","citation":{"mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:10.1103/physrevlett.127.247001.","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.247001.","ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.","ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021.","apa":"Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.247001"},"date_published":"2021-12-09T00:00:00Z","type":"journal_article","abstract":[{"text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase.","lang":"eng"}],"issue":"24","status":"public","title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","intvolume":" 127","_id":"10527","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"acknowledgement":"J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983).","year":"2021","department":[{"_id":"MaIb"}],"publisher":"Royal Society of Chemistry","publication_status":"published","author":[{"full_name":"Dong, Jingjin","first_name":"Jingjin","last_name":"Dong"},{"full_name":"Sami, Selim","last_name":"Sami","first_name":"Selim"},{"orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","first_name":"Daniel","full_name":"Balazs, Daniel"},{"full_name":"Alessandri, Riccardo","last_name":"Alessandri","first_name":"Riccardo"},{"last_name":"Jahani","first_name":"Fatimeh","full_name":"Jahani, Fatimeh"},{"full_name":"Qiu, Li","first_name":"Li","last_name":"Qiu"},{"full_name":"Marrink, Siewert J.","first_name":"Siewert J.","last_name":"Marrink"},{"first_name":"Remco W.A.","last_name":"Havenith","full_name":"Havenith, Remco W.A."},{"last_name":"Hummelen","first_name":"Jan C.","full_name":"Hummelen, Jan C."},{"first_name":"Maria A.","last_name":"Loi","full_name":"Loi, Maria A."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"}],"volume":9,"date_created":"2021-12-12T23:01:27Z","date_updated":"2023-08-17T06:18:44Z","file_date_updated":"2021-12-13T09:24:42Z","external_id":{"isi":["000688135700001"]},"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":"10.1039/d1tc02753k","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-7534"],"eissn":["2050-7526"]},"month":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10534","intvolume":" 9","title":"Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties","status":"public","ddc":["540"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10538","date_created":"2021-12-13T09:24:42Z","date_updated":"2021-12-13T09:24:42Z","checksum":"6b73c214ce54a6894a5854b4364413d7","success":1,"file_name":"2021_JMaterChemC_Dong.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4979390,"creator":"cchlebak"}],"type":"journal_article","issue":"45","abstract":[{"text":"For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications.","lang":"eng"}],"citation":{"ama":"Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k","ista":"Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.","apa":"Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k","ieee":"J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021.","mla":"Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:10.1039/d1tc02753k.","short":"J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225.","chicago":"Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k."},"publication":"Journal of Materials Chemistry C","page":"16217-16225","article_type":"original","date_published":"2021-12-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07"},{"type":"journal_article","abstract":[{"text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.","lang":"eng"}],"title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","ddc":["570"],"status":"public","intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10533","file":[{"file_id":"11384","relation":"main_file","success":1,"checksum":"22ed4c55fb550f6da02ae55c359be651","date_created":"2022-05-16T10:42:22Z","date_updated":"2022-05-16T10:42:22Z","access_level":"open_access","file_name":"2021_eLife_Choi.pdf","creator":"dernst","file_size":2715200,"content_type":"application/pdf"}],"oa_version":"Published Version","keyword":["genetics and molecular biology"],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"eLife","citation":{"ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","apa":"Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72676","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife Sciences Publications, 2021.","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676, eLife Sciences Publications, 2021, doi:10.7554/elife.72676.","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676."},"date_published":"2021-12-01T00:00:00Z","article_number":"e72676","file_date_updated":"2022-05-16T10:42:22Z","ec_funded":1,"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"eLife Sciences Publications","acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","year":"2021","pmid":1,"date_created":"2021-12-10T13:12:08Z","date_updated":"2023-08-17T06:21:08Z","volume":10,"author":[{"last_name":"Choi","first_name":"Jaemyung","full_name":"Choi, Jaemyung"},{"full_name":"Lyons, David B","last_name":"Lyons","first_name":"David B"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"}],"month":"12","publication_identifier":{"issn":["2050-084X"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin","_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746"}],"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":["000754832000001"],"pmid":["34850679"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/elife.72676"},{"publication_identifier":{"eissn":["2234-943X"]},"month":"11","doi":"10.3389/fonc.2021.765151","language":[{"iso":"eng"}],"external_id":{"pmid":["34868988"],"isi":["000726603400001"]},"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","file_date_updated":"2021-12-13T13:32:37Z","article_number":"765151","author":[{"full_name":"Stefanescu, Cristina","first_name":"Cristina","last_name":"Stefanescu"},{"first_name":"Merel","last_name":"Van Gogh","full_name":"Van Gogh, Merel"},{"full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek","first_name":"Marko"},{"last_name":"Heikenwalder","first_name":"Mathias","full_name":"Heikenwalder, Mathias"},{"last_name":"Borsig","first_name":"Lubor","full_name":"Borsig, Lubor"}],"volume":11,"date_created":"2021-12-12T23:01:27Z","date_updated":"2023-08-17T06:20:32Z","pmid":1,"year":"2021","acknowledgement":"The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich.","department":[{"_id":"DaSi"}],"publisher":"Frontiers","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","date_published":"2021-11-18T00:00:00Z","citation":{"ama":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 2021;11. doi:10.3389/fonc.2021.765151","ista":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151.","ieee":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” Frontiers in Oncology, vol. 11. Frontiers, 2021.","apa":"Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., & Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2021.765151","mla":"Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology, vol. 11, 765151, Frontiers, 2021, doi:10.3389/fonc.2021.765151.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","chicago":"Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology. Frontiers, 2021. https://doi.org/10.3389/fonc.2021.765151."},"publication":"Frontiers in Oncology","article_type":"original","abstract":[{"text":"TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"alisjak","file_size":9245199,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Frontiers_Stefanescu.pdf","success":1,"checksum":"56cbac80e6891ce750511a30161b7792","date_updated":"2021-12-13T13:32:37Z","date_created":"2021-12-13T13:32:37Z","file_id":"10539","relation":"main_file"}],"_id":"10536","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 11","status":"public","ddc":["610"],"title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms"},{"title":"Bosonization of fermionic many-body dynamics","status":"public","_id":"10537","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations."}],"article_type":"original","citation":{"ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” Annales Henri Poincaré. Springer Nature, 2021.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2021). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. Springer Nature. https://doi.org/10.1007/s00023-021-01136-y","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 2021. doi:10.1007/s00023-021-01136-y","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01136-y.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré (2021).","mla":"Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré, Springer Nature, 2021, doi:10.1007/s00023-021-01136-y."},"publication":"Annales Henri Poincaré","date_published":"2021-12-02T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"02","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782).","year":"2021","date_updated":"2023-08-17T06:19:14Z","date_created":"2021-12-12T23:01:28Z","author":[{"orcid":"0000-0002-1071-6091","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","first_name":"Niels P","full_name":"Benedikter, Niels P"},{"full_name":"Nam, Phan Thành","last_name":"Nam","first_name":"Phan Thành"},{"last_name":"Porta","first_name":"Marcello","full_name":"Porta, Marcello"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"ec_funded":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2103.08224","open_access":"1"}],"external_id":{"arxiv":["2103.08224"],"isi":["000725405700001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00023-021-01136-y","publication_identifier":{"issn":["1424-0637"]},"month":"12"},{"file_date_updated":"2021-12-16T14:58:08Z","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"},{"last_name":"Neukamm","first_name":"Stefan","full_name":"Neukamm, Stefan"}],"date_updated":"2023-08-17T06:23:21Z","date_created":"2021-12-16T12:12:33Z","volume":242,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441.","year":"2021","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","month":"06","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"doi":"10.1007/s00205-021-01686-9","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":["000668431200001"],"arxiv":["1908.02273"]},"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"text":"We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \\mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \\varepsilon >0, we establish homogenization error estimates of the order \\varepsilon in case d\\geqq 3, and of the order \\varepsilon |\\log \\varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \\varepsilon ^\\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\\alpha } regularity theory is available.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"file_id":"10558","relation":"main_file","success":1,"checksum":"cc830b739aed83ca2e32c4e0ce266a4c","date_updated":"2021-12-16T14:58:08Z","date_created":"2021-12-16T14:58:08Z","access_level":"open_access","file_name":"2021_ArchRatMechAnalysis_Fischer.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":1640121}],"oa_version":"Published Version","_id":"10549","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","status":"public","intvolume":" 242","day":"30","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"date_published":"2021-06-30T00:00:00Z","publication":"Archive for Rational Mechanics and Analysis","citation":{"mla":"Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:10.1007/s00205-021-01686-9.","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","chicago":"Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01686-9.","ama":"Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 2021;242(1):343-452. doi:10.1007/s00205-021-01686-9","ista":"Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452.","ieee":"J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” Archive for Rational Mechanics and Analysis, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021.","apa":"Fischer, J. L., & Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01686-9"},"article_type":"original","page":"343-452"},{"ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"year":"2021","acknowledgement":"We are grateful to Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. We would also like to thank Crypto 2021 and TCC 2021 reviewers for their detailed review and suggestions, which helped improve presentation considerably.","date_created":"2021-12-05T23:01:43Z","date_updated":"2023-08-17T06:21:38Z","volume":"13043 ","author":[{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"related_material":{"record":[{"id":"10044","status":"public","relation":"earlier_version"}]},"month":"11","publication_identifier":{"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://eprint.iacr.org/2021/926","open_access":"1"}],"external_id":{"isi":["000728364000017"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"TCC: Theory of Cryptography","end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08"},"doi":"10.1007/978-3-030-90453-1_17","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size S and treewidth w with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity. with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.","lang":"eng"}],"title":"On treewidth, separators and Yao’s garbling","status":"public","_id":"10409","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","day":"04","article_processing_charge":"No","page":"486-517","publication":"19th International Conference","citation":{"mla":"Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 486–517, doi:10.1007/978-3-030-90453-1_17.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In 19th International Conference, 13043:486–517. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_17.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: 19th International Conference. Vol 13043. Springer Nature; 2021:486-517. doi:10.1007/978-3-030-90453-1_17","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 486–517.","apa":"Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In 19th International Conference (Vol. 13043, pp. 486–517). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_17","ieee":"C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 486–517."},"date_published":"2021-11-04T00:00:00Z"},{"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","year":"2021","acknowledgement":"We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y. Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo, and C. Laumann. We acknowledge support from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899.","volume":104,"date_updated":"2023-08-17T06:22:49Z","date_created":"2021-12-14T20:46:07Z","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"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"}],"article_number":"062423","ec_funded":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2106.06344","open_access":"1"}],"external_id":{"arxiv":["2106.06344"],"isi":["000753659200004"]},"language":[{"iso":"eng"}],"doi":"10.1103/physreva.104.062423","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"month":"12","intvolume":" 104","title":"Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT)","status":"public","_id":"10545","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"6","abstract":[{"text":"Classical models with complex energy landscapes represent a perspective avenue for the near-term application of quantum simulators. Until now, many theoretical works studied the performance of quantum algorithms for models with a unique ground state. However, when the classical problem is in a so-called clustering phase, the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT model defined on simple hypergraphs. The degeneracy of classical ground state manifold translates into the emergence of an extensive number of Z2 symmetries, which remain intact even in the presence of a quantum transverse magnetic field. We establish a general duality approach that restricts the quantum problem to a given sector of conserved Z2 charges and use it to study how the outcome of the quantum adiabatic algorithm depends on the hypergraph geometry. We show that the tree hypergraph which corresponds to a classically solvable instance of the 3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters a second-order phase transition with a gap vanishing as a power-law in the problem size. The duality developed in this work provides a practical tool for studies of quantum models with classically degenerate energy manifold and reveals potential connections between glasses and gauge theories.","lang":"eng"}],"article_type":"original","citation":{"chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/physreva.104.062423.","short":"R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:10.1103/physreva.104.062423.","ieee":"R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT),” Physical Review A, vol. 104, no. 6. American Physical Society, 2021.","apa":"Medina Ramos, R. A., & Serbyn, M. (2021). Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.104.062423","ista":"Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 104(6), 062423.","ama":"Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 2021;104(6). doi:10.1103/physreva.104.062423"},"publication":"Physical Review A","date_published":"2021-12-14T00:00:00Z","article_processing_charge":"No","day":"14"},{"article_processing_charge":"No","day":"21","scopus_import":"1","date_published":"2021-07-21T00:00:00Z","citation":{"ama":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. All You Need is DAG. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:165-175. doi:10.1145/3465084.3467905","ieee":"I. Keidar, E. Kokoris Kogias, O. Naor, and A. Spiegelman, “All You Need is DAG,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 165–175.","apa":"Keidar, I., Kokoris Kogias, E., Naor, O., & Spiegelman, A. (2021). All You Need is DAG. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 165–175). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467905","ista":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. 2021. All You Need is DAG. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 165–175.","short":"I. Keidar, E. Kokoris Kogias, O. Naor, A. Spiegelman, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–175.","mla":"Keidar, Idit, et al. “All You Need Is DAG.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–75, doi:10.1145/3465084.3467905.","chicago":"Keidar, Idit, Eleftherios Kokoris Kogias, Oded Naor, and Alexander Spiegelman. “All You Need Is DAG.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 165–75. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467905."},"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","page":"165-175","abstract":[{"lang":"eng","text":"We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all values proposed by correct processes eventually get delivered. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication."}],"type":"conference","oa_version":"Preprint","_id":"10554","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"All You Need is DAG","status":"public","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"month":"07","doi":"10.1145/3465084.3467905","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2021-07-30","start_date":"2021-07-26","location":"Virtual, Italy"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000744439800016"],"arxiv":["2102.08325"]},"main_file_link":[{"url":"https://arxiv.org/abs/2102.08325","open_access":"1"}],"isi":1,"quality_controlled":"1","author":[{"first_name":"Idit","last_name":"Keidar","full_name":"Keidar, Idit"},{"full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"last_name":"Naor","first_name":"Oded","full_name":"Naor, Oded"},{"full_name":"Spiegelman, Alexander","first_name":"Alexander","last_name":"Spiegelman"}],"date_updated":"2023-08-17T06:24:44Z","date_created":"2021-12-16T13:21:13Z","year":"2021","acknowledgement":"Oded Naor is grateful to the Technion Hiroshi Fujiwara Cyber-Security Research Center for providing a research grant. Part of Oded’s work was done while at Novi Research. This work was funded by the Novi team at Facebook. We also wish to thank the Novi Research team for valuable feedback, and in particular George Danezis, Alberto Sonnino, and Dahlia Malkhi.\r\n","publisher":"Association for Computing Machinery","department":[{"_id":"ElKo"}],"publication_status":"published"},{"publication_identifier":{"issn":["2296-701X"]},"month":"03","doi":"10.3389/fevo.2021.626442","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":["000637736300001"]},"quality_controlled":"1","isi":1,"file_date_updated":"2021-12-20T10:44:20Z","article_number":"626442","author":[{"full_name":"Goehlich, Henry","first_name":"Henry","last_name":"Goehlich"},{"first_name":"Linda","last_name":"Sartoris","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","full_name":"Sartoris, Linda"},{"first_name":"Kim-Sara","last_name":"Wagner","full_name":"Wagner, Kim-Sara"},{"last_name":"Wendling","first_name":"Carolin C.","full_name":"Wendling, Carolin C."},{"full_name":"Roth, Olivia","last_name":"Roth","first_name":"Olivia"}],"volume":9,"date_updated":"2023-08-17T06:27:22Z","date_created":"2021-12-20T07:53:19Z","acknowledgement":"We are grateful for the help of Kristina Dauven, Andreas Ebner, Janina Röckner, and Paulina Urban for fish collection in the field and fish maintenance. Furthermore, we thank Fabian Wendt for setting up the aquaria system and Tatjana Liese, Paulina Urban, Jakob Gismann, and Thorsten Reusch for support with DNA extraction and analysis of pipefish population structure. The authors acknowledge support of Isabel Tanger, Agnes Piecyk, Jonas Müller, Grace Walls, Sebastian Albrecht, Julia Böge, and Julia Stefanschitz for their support in preparing cDNA and running of Fluidigm chips. A special thank goes to Diana Gill for general lab support, ordering materials and just being the good spirit of our molecular lab, to Till Bayer for bioinformatics support and to Melanie Heckwolf for fruitful discussion and feedback on the manuscript. HG is very grateful for inspirational office space with ocean view provided by Lisa Hentschel and family. This manuscript has been released as a pre-print at BIORXIV.","year":"2021","department":[{"_id":"SyCr"}],"publisher":"Frontiers Media","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"25","scopus_import":"1","keyword":["ecology","evolution","behavior and systematics","trans-generational plasticity","genetic adaptation","local adaptation","phenotypic plasticity","Baltic Sea","climate change","salinity","syngnathids"],"date_published":"2021-03-25T00:00:00Z","citation":{"ama":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 2021;9. doi:10.3389/fevo.2021.626442","ista":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. 2021. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 9, 626442.","apa":"Goehlich, H., Sartoris, L., Wagner, K.-S., Wendling, C. C., & Roth, O. (2021). Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. Frontiers Media. https://doi.org/10.3389/fevo.2021.626442","ieee":"H. Goehlich, L. Sartoris, K.-S. Wagner, C. C. Wendling, and O. Roth, “Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels,” Frontiers in Ecology and Evolution, vol. 9. Frontiers Media, 2021.","mla":"Goehlich, Henry, et al. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution, vol. 9, 626442, Frontiers Media, 2021, doi:10.3389/fevo.2021.626442.","short":"H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers in Ecology and Evolution 9 (2021).","chicago":"Goehlich, Henry, Linda Sartoris, Kim-Sara Wagner, Carolin C. Wendling, and Olivia Roth. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution. Frontiers Media, 2021. https://doi.org/10.3389/fevo.2021.626442."},"publication":"Frontiers in Ecology and Evolution","article_type":"original","abstract":[{"text":"Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.","lang":"eng"}],"type":"journal_article","file":[{"creator":"alisjak","content_type":"application/pdf","file_size":3175085,"access_level":"open_access","file_name":"2021_Frontiers_Goehlich.pdf","success":1,"checksum":"8d6e2b767bb0240a9b5a3a3555be51fd","date_created":"2021-12-20T10:44:20Z","date_updated":"2021-12-20T10:44:20Z","file_id":"10572","relation":"main_file"}],"oa_version":"Published Version","_id":"10568","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","status":"public","title":"Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels","ddc":["597"]},{"scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Crystals","citation":{"apa":"Lu, Y., Arshad, N., Irshad, M. S., Ahmed, I., Ahmad, S., Alshahrani, L. A., … Nauman, M. (2021). Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. MDPI. https://doi.org/10.3390/cryst11121509","ieee":"Y. Lu et al., “Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination,” Crystals, vol. 11, no. 12. MDPI, 2021.","ista":"Lu Y, Arshad N, Irshad MS, Ahmed I, Ahmad S, Alshahrani LA, Yousaf M, Sayed AE, Nauman M. 2021. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. 11(12), 1509.","ama":"Lu Y, Arshad N, Irshad MS, et al. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. 2021;11(12). doi:10.3390/cryst11121509","chicago":"Lu, Yuzheng, Naila Arshad, Muhammad Sultan Irshad, Iftikhar Ahmed, Shafiq Ahmad, Lina Abdullah Alshahrani, Muhammad Yousaf, Abdelaty Edrees Sayed, and Muhammad Nauman. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” Crystals. MDPI, 2021. https://doi.org/10.3390/cryst11121509.","short":"Y. Lu, N. Arshad, M.S. Irshad, I. Ahmed, S. Ahmad, L.A. Alshahrani, M. Yousaf, A.E. Sayed, M. Nauman, Crystals 11 (2021).","mla":"Lu, Yuzheng, et al. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” Crystals, vol. 11, no. 12, 1509, MDPI, 2021, doi:10.3390/cryst11121509."},"date_published":"2021-12-03T00:00:00Z","alternative_title":["Hybrid and Composite Crystalline Materials"],"type":"journal_article","abstract":[{"text":"A facile approach for developing an interfacial solar evaporator by heat localization of solar-thermal energy conversion at water-air liquid composed by in-situ polymerization of Fe2O3 nanoparticles (Fe2O3@PPy) deposited over a facial sponge is proposed. The demonstrated system consists of a floating solar receiver having a vertically cross-linked microchannel for wicking up saline water. The in situ polymerized Fe2O3@PPy interfacial layer promotes diffuse reflection and its rough black surface allows Omni-directional solar absorption (94%) and facilitates efficient thermal localization at the water/air interface and offers a defect-rich surface to promote heat localization (41.9 °C) and excellent thermal management due to cellulosic content. The self-floating composite foam reveals continuous vapors generation at a rate of 1.52 kg m−2 h−1 under one 1 kW m−2 and profound evaporating efficiency (95%) without heat losses that dissipates in its surroundings. Indeed, long-term evaporation experiments reveal the negligible disparity in continuous evaporation rate (33.84 kg m−2/8.3 h) receiving two sun solar intensity, and ensures the stability of the device under intense seawater conditions synchronized with excellent salt rejection potential. More importantly, Raman spectroscopy investigation validates the orange dye rejection via Fe2O3@PPy solar evaporator. The combined advantages of high efficiency, self-floating capability, multimedia rejection, low cost, and this configuration are promising for producing large-scale solar steam generating systems appropriate for commercial clean water yield due to their scalable fabrication.","lang":"eng"}],"issue":"12","status":"public","ddc":["620"],"title":"Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination","intvolume":" 11","_id":"10586","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"checksum":"668e9d777608ce0a3bc2e305133bd06b","success":1,"date_updated":"2022-01-03T09:46:53Z","date_created":"2022-01-03T09:46:53Z","relation":"main_file","file_id":"10591","content_type":"application/pdf","file_size":4569639,"creator":"alisjak","access_level":"open_access","file_name":"2021_Crystals_Yuzheng.pdf"}],"month":"12","publication_identifier":{"eissn":["2073-4352"]},"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":["000736602200001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/cryst11121509","article_number":"1509","file_date_updated":"2022-01-03T09:46:53Z","publication_status":"published","department":[{"_id":"KiMo"}],"publisher":"MDPI","acknowledgement":"The authors extend their appreciation to King Saud University for funding this work through Researchers Supporting Project number (RSP-2021/387), King Saud University, Riyadh, Saudi Arabia.","year":"2021","date_updated":"2023-08-17T06:31:20Z","date_created":"2022-01-02T23:01:34Z","volume":11,"author":[{"first_name":"Yuzheng","last_name":"Lu","full_name":"Lu, Yuzheng"},{"full_name":"Arshad, Naila","first_name":"Naila","last_name":"Arshad"},{"full_name":"Irshad, Muhammad Sultan","last_name":"Irshad","first_name":"Muhammad Sultan"},{"full_name":"Ahmed, Iftikhar","last_name":"Ahmed","first_name":"Iftikhar"},{"full_name":"Ahmad, Shafiq","last_name":"Ahmad","first_name":"Shafiq"},{"first_name":"Lina Abdullah","last_name":"Alshahrani","full_name":"Alshahrani, Lina Abdullah"},{"last_name":"Yousaf","first_name":"Muhammad","full_name":"Yousaf, Muhammad"},{"last_name":"Sayed","first_name":"Abdelaty Edrees","full_name":"Sayed, Abdelaty Edrees"},{"last_name":"Nauman","first_name":"Muhammad","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad"}]},{"file_date_updated":"2021-12-20T10:14:14Z","article_number":"jeb243647","volume":224,"date_updated":"2023-08-17T06:26:15Z","date_created":"2021-12-20T07:54:22Z","author":[{"full_name":"Szabo, B","last_name":"Szabo","first_name":"B"},{"full_name":"Mangione, R","last_name":"Mangione","first_name":"R"},{"last_name":"Rath","first_name":"M","full_name":"Rath, M"},{"full_name":"Pašukonis, A","last_name":"Pašukonis","first_name":"A"},{"last_name":"Reber","first_name":"SA","full_name":"Reber, SA"},{"full_name":"Oh, Jinook","first_name":"Jinook","last_name":"Oh","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","orcid":"0000-0001-7425-2372"},{"full_name":"Ringler, M","last_name":"Ringler","first_name":"M"},{"last_name":"Ringler","first_name":"E","full_name":"Ringler, E"}],"department":[{"_id":"SyCr"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"acknowledgement":"We are grateful to Véronique Helfer, Walter Hödl, Lisa Schretzmeyer and Julia Wotke, who assisted with fieldwork in French Guiana. This work was supported by the Austrian Science Fund (FWF) [P24788, T699 and P31518 to E.R.; P33728 to M.R.; J3827 to Thomas Bugnyar, Tecumseh Fitch and Ludwig Huber]; and by the Austrian Bundesministerium für Wissenschaft, Forschung und Wirtschaft [IS761001 to J.O. (Tecumseh Fitch, Thomas Bugnyar and Ludwig Huber)]. A.P. was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 835530. S.A.R. was supported by the HT faculty, Lund University. We thank the CNRS Nouragues Ecological Research Station, which benefited from the ‘Investissement d'Avenir’ grants managed by the Agence Nationale de la Recherche (AnaEE France ANR-11-INBS-0001; Labex CEBA ANR-10-LABX-25-01). Open access funding provided by University of Vienna. Deposited in PMC for immediate release.","year":"2021","publication_identifier":{"eissn":["1477-9145"],"issn":["0022-0949"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1242/jeb.243647","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":["34845497"],"isi":["000738259300013"]},"oa":1,"issue":"24","abstract":[{"text":"For animals to survive until reproduction, it is crucial that juveniles successfully detect potential predators and respond with appropriate behavior. The recognition of cues originating from predators can be innate or learned. Cues of various modalities might be used alone or in multi-modal combinations to detect and distinguish predators but studies investigating multi-modal integration in predator avoidance are scarce. Here, we used wild, naive tadpoles of the Neotropical poison frog Allobates femoralis ( Boulenger, 1884) to test their reaction to cues with two modalities from two different sympatrically occurring potential predators: heterospecific predatory Dendrobates tinctorius tadpoles and dragonfly larvae. We presented A. femoralis tadpoles with olfactory or visual cues, or a combination of the two, and compared their reaction to a water control in a between-individual design. In our trials, A. femoralis tadpoles reacted to multi-modal stimuli (a combination of visual and chemical information) originating from dragonfly larvae with avoidance but showed no reaction to uni-modal cues or cues from heterospecific tadpoles. In addition, visual cues from conspecifics increased swimming activity while cues from predators had no effect on tadpole activity. Our results show that A. femoralis tadpoles can innately recognize some predators and probably need both visual and chemical information to effectively avoid them. This is the first study looking at anti-predator behavior in poison frog tadpoles. We discuss how parental care might influence the expression of predator avoidance responses in tadpoles.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":607096,"file_name":"2021_JExpBio_Szabo.pdf","access_level":"open_access","date_updated":"2021-12-20T10:14:14Z","date_created":"2021-12-20T10:14:14Z","success":1,"checksum":"75d13a5ec8e3b90e3bc02bd8a9c17eef","file_id":"10571","relation":"main_file"}],"intvolume":" 224","title":"Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles","status":"public","ddc":["573"],"_id":"10569","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"No","day":"16","date_published":"2021-12-16T00:00:00Z","article_type":"original","citation":{"ama":"Szabo B, Mangione R, Rath M, et al. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. 2021;224(24). doi:10.1242/jeb.243647","ista":"Szabo B, Mangione R, Rath M, Pašukonis A, Reber S, Oh J, Ringler M, Ringler E. 2021. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. 224(24), jeb243647.","apa":"Szabo, B., Mangione, R., Rath, M., Pašukonis, A., Reber, S., Oh, J., … Ringler, E. (2021). Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.243647","ieee":"B. Szabo et al., “Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles,” Journal of Experimental Biology, vol. 224, no. 24. The Company of Biologists, 2021.","mla":"Szabo, B., et al. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” Journal of Experimental Biology, vol. 224, no. 24, jeb243647, The Company of Biologists, 2021, doi:10.1242/jeb.243647.","short":"B. Szabo, R. Mangione, M. Rath, A. Pašukonis, S. Reber, J. Oh, M. Ringler, E. Ringler, Journal of Experimental Biology 224 (2021).","chicago":"Szabo, B, R Mangione, M Rath, A Pašukonis, SA Reber, Jinook Oh, M Ringler, and E Ringler. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” Journal of Experimental Biology. The Company of Biologists, 2021. https://doi.org/10.1242/jeb.243647."},"publication":"Journal of Experimental Biology"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The choice of the boundary conditions in mechanical problems has to reflect the interaction of the considered material with the surface. Still the assumption of the no-slip condition is preferred in order to avoid boundary terms in the analysis and slipping effects are usually overlooked. Besides the “static slip models”, there are phenomena that are not accurately described by them, e.g. at the moment when the slip changes rapidly, the wall shear stress and the slip can exhibit a sudden overshoot and subsequent relaxation. When these effects become significant, the so-called dynamic slip phenomenon occurs. We develop a mathematical analysis of Navier–Stokes-like problems with a dynamic slip boundary condition, which requires a proper generalization of the Gelfand triplet and the corresponding function space setting."}],"issue":"11","status":"public","title":"On the dynamic slip boundary condition for Navier-Stokes-like problems","ddc":["510"],"intvolume":" 31","_id":"10575","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"11385","checksum":"8c0a9396335f0b70e1f5cbfe450a987a","success":1,"date_created":"2022-05-16T10:55:45Z","date_updated":"2022-05-16T10:55:45Z","access_level":"open_access","file_name":"2021_MathModelsMethods_Abbatiello.pdf","content_type":"application/pdf","file_size":795483,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"2165-2212","publication":"Mathematical Models and Methods in Applied Sciences","citation":{"short":"A. Abbatiello, M. Bulíček, E. Maringová, Mathematical Models and Methods in Applied Sciences 31 (2021) 2165–2212.","mla":"Abbatiello, Anna, et al. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 11, World Scientific Publishing, 2021, pp. 2165–212, doi:10.1142/S0218202521500470.","chicago":"Abbatiello, Anna, Miroslav Bulíček, and Erika Maringová. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” Mathematical Models and Methods in Applied Sciences. World Scientific Publishing, 2021. https://doi.org/10.1142/S0218202521500470.","ama":"Abbatiello A, Bulíček M, Maringová E. On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. 2021;31(11):2165-2212. doi:10.1142/S0218202521500470","ieee":"A. Abbatiello, M. Bulíček, and E. Maringová, “On the dynamic slip boundary condition for Navier-Stokes-like problems,” Mathematical Models and Methods in Applied Sciences, vol. 31, no. 11. World Scientific Publishing, pp. 2165–2212, 2021.","apa":"Abbatiello, A., Bulíček, M., & Maringová, E. (2021). On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. World Scientific Publishing. https://doi.org/10.1142/S0218202521500470","ista":"Abbatiello A, Bulíček M, Maringová E. 2021. On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. 31(11), 2165–2212."},"date_published":"2021-10-13T00:00:00Z","file_date_updated":"2022-05-16T10:55:45Z","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"World Scientific Publishing","year":"2021","acknowledgement":"The research of A. Abbatiello is supported by Einstein Foundation, Berlin. A. Abbatiello is also member of the Italian National Group for the Mathematical Physics (GNFM) of INdAM. M. Bulíček acknowledges the support of the project No. 20-11027X financed by Czech Science Foundation (GACR). M. Bulíček is member of the Jindřich Nečas Center for Mathematical Modelling. E. Maringová acknowledges support from Charles University Research program UNCE/SCI/023, the grant SVV-2020-260583 by the Ministry of Education, Youth and Sports, Czech Republic and from the Austrian Science Fund (FWF), grants P30000, W1245, and F65.","date_updated":"2023-08-17T06:29:01Z","date_created":"2021-12-26T23:01:27Z","volume":31,"author":[{"last_name":"Abbatiello","first_name":"Anna","full_name":"Abbatiello, Anna"},{"full_name":"Bulíček, Miroslav","first_name":"Miroslav","last_name":"Bulíček"},{"full_name":"Maringová, Erika","last_name":"Maringová","first_name":"Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4"}],"month":"10","publication_identifier":{"issn":["0218-2025"],"eissn":["1793-6314"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"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":["000722309400001"],"arxiv":["2009.09057"]},"language":[{"iso":"eng"}],"doi":"10.1142/S0218202521500470"},{"type":"journal_article","issue":"12","abstract":[{"text":"The understanding of material appearance perception is a complex problem due to interactions between material reflectance, surface geometry, and illumination. Recently, Serrano et al. collected the largest dataset to date with subjective ratings of material appearance attributes, including glossiness, metallicness, sharpness and contrast of reflections. In this work, we make use of their dataset to investigate for the first time the impact of the interactions between illumination, geometry, and eight different material categories in perceived appearance attributes. After an initial analysis, we select for further analysis the four material categories that cover the largest range for all perceptual attributes: fabric, plastic, ceramic, and metal. Using a cumulative link mixed model (CLMM) for robust regression, we discover interactions between these material categories and four representative illuminations and object geometries. We believe that our findings contribute to expanding the knowledge on material appearance perception and can be useful for many applications, such as scene design, where any particular material in a given shape can be aligned with dominant classes of illumination, so that a desired strength of appearance attributes can be achieved.","lang":"eng"}],"_id":"10574","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 37","status":"public","ddc":["000"],"title":"The effect of geometry and illumination on appearance perception of different material categories","file":[{"file_id":"10578","relation":"main_file","date_updated":"2021-12-27T13:51:08Z","date_created":"2021-12-27T13:51:08Z","success":1,"checksum":"244cfcac0479ca6e3444c098ab2860a1","file_name":"2021_VisComput_Chen.pdf","access_level":"open_access","creator":"cchlebak","file_size":5741094,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","citation":{"ama":"Chen B, Wang C, Piovarci M, et al. The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. 2021;37(12):2975-2987. doi:10.1007/s00371-021-02227-x","ista":"Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K, Serrano A. 2021. The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. 37(12), 2975–2987.","apa":"Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., Myszkowski, K., & Serrano, A. (2021). The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. Springer Nature. https://doi.org/10.1007/s00371-021-02227-x","ieee":"B. Chen et al., “The effect of geometry and illumination on appearance perception of different material categories,” Visual Computer, vol. 37, no. 12. Springer Nature, pp. 2975–2987, 2021.","mla":"Chen, Bin, et al. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” Visual Computer, vol. 37, no. 12, Springer Nature, 2021, pp. 2975–87, doi:10.1007/s00371-021-02227-x.","short":"B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, Visual Computer 37 (2021) 2975–2987.","chicago":"Chen, Bin, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, and Ana Serrano. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” Visual Computer. Springer Nature, 2021. https://doi.org/10.1007/s00371-021-02227-x."},"publication":"Visual Computer","page":"2975-2987","article_type":"original","date_published":"2021-12-01T00:00:00Z","file_date_updated":"2021-12-27T13:51:08Z","year":"2021","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie, grant agreement N∘ 765911 (RealVision) and from the European Research Council (ERC), grant agreement N∘ 804226 (PERDY). Open Access funding enabled and organized by Projekt DEAL.","department":[{"_id":"BeBi"}],"publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"orcid":"0000-0002-5062-4474","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","last_name":"Piovarci","first_name":"Michael","full_name":"Piovarci, Michael"},{"last_name":"Seidel","first_name":"Hans Peter","full_name":"Seidel, Hans Peter"},{"first_name":"Piotr","last_name":"Didyk","full_name":"Didyk, Piotr"},{"full_name":"Myszkowski, Karol","first_name":"Karol","last_name":"Myszkowski"},{"first_name":"Ana","last_name":"Serrano","full_name":"Serrano, Ana"}],"volume":37,"date_created":"2021-12-26T23:01:26Z","date_updated":"2023-08-17T06:29:34Z","publication_identifier":{"issn":["0178-2789"],"eissn":["1432-2315"]},"month":"12","external_id":{"isi":["000673536600003"]},"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":"10.1007/s00371-021-02227-x","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2021.11.025","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042","open_access":"1"}],"external_id":{"isi":["000735387500002"]},"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"month":"12","volume":184,"date_created":"2021-12-26T23:01:26Z","date_updated":"2023-08-17T06:28:25Z","author":[{"full_name":"Munjal, Akankshi","last_name":"Munjal","first_name":"Akankshi"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Tsai","first_name":"Tony Y.C.","full_name":"Tsai, Tony Y.C."},{"full_name":"Mitchison, Timothy J.","last_name":"Mitchison","first_name":"Timothy J."},{"full_name":"Megason, Sean G.","last_name":"Megason","first_name":"Sean G."}],"publisher":"Elsevier ; Cell Press","department":[{"_id":"EdHa"}],"publication_status":"published","year":"2021","acknowledgement":"We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and members of the Megason lab for useful comments on the manuscript and general feedback. We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on the right in the graphical abstract were created using BioRender. This work was supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by Human Frontiers Science Program LTF and NIH K99HD098918.","date_published":"2021-12-22T00:00:00Z","page":"6313-6325.e18","article_type":"original","citation":{"short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18.","mla":"Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell, vol. 184, no. 26, Elsevier ; Cell Press, 2021, p. 6313–6325.e18, doi:10.1016/j.cell.2021.11.025.","chicago":"Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.cell.2021.11.025.","ama":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 2021;184(26):6313-6325.e18. doi:10.1016/j.cell.2021.11.025","apa":"Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., & Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. Elsevier ; Cell Press. https://doi.org/10.1016/j.cell.2021.11.025","ieee":"A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” Cell, vol. 184, no. 26. Elsevier ; Cell Press, p. 6313–6325.e18, 2021.","ista":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 184(26), 6313–6325.e18."},"publication":"Cell","article_processing_charge":"No","day":"22","scopus_import":"1","oa_version":"Preprint","intvolume":" 184","title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10573","issue":"26","abstract":[{"text":"How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of actomyosin and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering.","lang":"eng"}],"type":"journal_article"},{"intvolume":" 17","ddc":["510"],"title":"Determinacy in discrete-bidding infinite-duration games","status":"public","_id":"10674","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"10690","relation":"main_file","success":1,"checksum":"b35586a50ed1ca8f44767de116d18d81","date_created":"2022-01-26T08:04:50Z","date_updated":"2022-01-26T08:04:50Z","access_level":"open_access","file_name":"2021_LMCS_AGHAJOHAR.pdf","creator":"alisjak","file_size":819878,"content_type":"application/pdf"}],"type":"journal_article","issue":"1","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets.","lang":"eng"}],"page":"10:1-10:23","article_type":"original","citation":{"mla":"Aghajohari, Milad, et al. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science, vol. 17, no. 1, International Federation for Computational Logic, 2021, p. 10:1-10:23, doi:10.23638/LMCS-17(1:10)2021.","short":"M. Aghajohari, G. Avni, T.A. Henzinger, Logical Methods in Computer Science 17 (2021) 10:1-10:23.","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science. International Federation for Computational Logic, 2021. https://doi.org/10.23638/LMCS-17(1:10)2021.","ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 2021;17(1):10:1-10:23. doi:10.23638/LMCS-17(1:10)2021","ista":"Aghajohari M, Avni G, Henzinger TA. 2021. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 17(1), 10:1-10:23.","apa":"Aghajohari, M., Avni, G., & Henzinger, T. A. (2021). Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. International Federation for Computational Logic. https://doi.org/10.23638/LMCS-17(1:10)2021","ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” Logical Methods in Computer Science, vol. 17, no. 1. International Federation for Computational Logic, p. 10:1-10:23, 2021."},"publication":"Logical Methods in Computer Science","date_published":"2021-02-03T00:00:00Z","keyword":["computer science","computer science and game theory","logic in computer science"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"03","publisher":"International Federation for Computational Logic","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship).\r\n","year":"2021","volume":17,"date_updated":"2023-08-17T06:56:42Z","date_created":"2022-01-25T16:32:13Z","author":[{"full_name":"Aghajohari, Milad","first_name":"Milad","last_name":"Aghajohari"},{"full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"file_date_updated":"2022-01-26T08:04:50Z","project":[{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000658724600010"],"arxiv":["1905.03588"]},"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":"10.23638/LMCS-17(1:10)2021","publication_identifier":{"eissn":["1860-5974"]},"month":"02"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"335-364","citation":{"short":"S. Chakraborty, C. Ganesh, M. Pancholi, P. Sarkar, in:, 27th International Conference on the Theory and Application of Cryptology and Information Security, Springer Nature, 2021, pp. 335–364.","mla":"Chakraborty, Suvradip, et al. “Reverse Firewalls for Adaptively Secure MPC without Setup.” 27th International Conference on the Theory and Application of Cryptology and Information Security, vol. 13091, Springer Nature, 2021, pp. 335–64, doi:10.1007/978-3-030-92075-3_12.","chicago":"Chakraborty, Suvradip, Chaya Ganesh, Mahak Pancholi, and Pratik Sarkar. “Reverse Firewalls for Adaptively Secure MPC without Setup.” In 27th International Conference on the Theory and Application of Cryptology and Information Security, 13091:335–64. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-92075-3_12.","ama":"Chakraborty S, Ganesh C, Pancholi M, Sarkar P. Reverse firewalls for adaptively secure MPC without setup. In: 27th International Conference on the Theory and Application of Cryptology and Information Security. Vol 13091. Springer Nature; 2021:335-364. doi:10.1007/978-3-030-92075-3_12","apa":"Chakraborty, S., Ganesh, C., Pancholi, M., & Sarkar, P. (2021). Reverse firewalls for adaptively secure MPC without setup. In 27th International Conference on the Theory and Application of Cryptology and Information Security (Vol. 13091, pp. 335–364). Virtual, Singapore: Springer Nature. https://doi.org/10.1007/978-3-030-92075-3_12","ieee":"S. Chakraborty, C. Ganesh, M. Pancholi, and P. Sarkar, “Reverse firewalls for adaptively secure MPC without setup,” in 27th International Conference on the Theory and Application of Cryptology and Information Security, Virtual, Singapore, 2021, vol. 13091, pp. 335–364.","ista":"Chakraborty S, Ganesh C, Pancholi M, Sarkar P. 2021. Reverse firewalls for adaptively secure MPC without setup. 27th International Conference on the Theory and Application of Cryptology and Information Security. ASIACRYPT: International Conference on Cryptology in Asia, LNCS, vol. 13091, 335–364."},"publication":"27th International Conference on the Theory and Application of Cryptology and Information Security","date_published":"2021-12-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We study Multi-party computation (MPC) in the setting of subversion, where the adversary tampers with the machines of honest parties. Our goal is to construct actively secure MPC protocols where parties are corrupted adaptively by an adversary (as in the standard adaptive security setting), and in addition, honest parties’ machines are compromised.\r\nThe idea of reverse firewalls (RF) was introduced at EUROCRYPT’15 by Mironov and Stephens-Davidowitz as an approach to protecting protocols against corruption of honest parties’ devices. Intuitively, an RF for a party P is an external entity that sits between P and the outside world and whose scope is to sanitize P ’s incoming and outgoing messages in the face of subversion of their computer. Mironov and Stephens-Davidowitz constructed a protocol for passively-secure two-party computation. At CRYPTO’20, Chakraborty, Dziembowski and Nielsen constructed a protocol for secure computation with firewalls that improved on this result, both by extending it to multi-party computation protocol, and considering active security in the presence of static corruptions. In this paper, we initiate the study of RF for MPC in the adaptive setting. We put forward a definition for adaptively secure MPC in the reverse firewall setting, explore relationships among the security notions, and then construct reverse firewalls for MPC in this stronger setting of adaptive security. We also resolve the open question of Chakraborty, Dziembowski and Nielsen by removing the need for a trusted setup in constructing RF for MPC. Towards this end, we construct reverse firewalls for adaptively secure augmented coin tossing and adaptively secure zero-knowledge protocols and obtain a constant round adaptively secure MPC protocol in the reverse firewall setting without setup. Along the way, we propose a new multi-party adaptively secure coin tossing protocol in the plain model, that is of independent interest."}],"intvolume":" 13091","status":"public","title":"Reverse firewalls for adaptively secure MPC without setup","_id":"10609","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","publication_identifier":{"eisbn":["978-3-030-92075-3"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-030-92074-6"]},"month":"12","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2021/1262","open_access":"1"}],"oa":1,"external_id":{"isi":["000927876200012"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-92075-3_12","conference":{"name":"ASIACRYPT: International Conference on Cryptology in Asia","start_date":"2021-12-06","location":"Virtual, Singapore","end_date":"2021-12-10"},"ec_funded":1,"department":[{"_id":"KrPi"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","volume":13091,"date_updated":"2023-08-17T06:34:41Z","date_created":"2022-01-09T23:01:27Z","author":[{"full_name":"Chakraborty, Suvradip","first_name":"Suvradip","last_name":"Chakraborty","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"full_name":"Ganesh, Chaya","first_name":"Chaya","last_name":"Ganesh"},{"first_name":"Mahak","last_name":"Pancholi","full_name":"Pancholi, Mahak"},{"full_name":"Sarkar, Pratik","last_name":"Sarkar","first_name":"Pratik"}]},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_eLife_Godard.pdf","creator":"alisjak","file_size":7769934,"content_type":"application/pdf","file_id":"10611","relation":"main_file","success":1,"checksum":"759c7a873d554c48a6639e6350746ca6","date_created":"2022-01-10T09:40:37Z","date_updated":"2022-01-10T09:40:37Z"}],"intvolume":" 10","ddc":["570"],"status":"public","title":"Combined effect of cell geometry and polarity domains determines the orientation of unequal division","_id":"10606","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Cell division orientation is thought to result from a competition between cell geometry and polarity domains controlling the position of the mitotic spindle during mitosis. Depending on the level of cell shape anisotropy or the strength of the polarity domain, one dominates the other and determines the orientation of the spindle. Whether and how such competition is also at work to determine unequal cell division (UCD), producing daughter cells of different size, remains unclear. Here, we show that cell geometry and polarity domains cooperate, rather than compete, in positioning the cleavage plane during UCDs in early ascidian embryos. We found that the UCDs and their orientation at the ascidian third cleavage rely on the spindle tilting in an anisotropic cell shape, and cortical polarity domains exerting different effects on spindle astral microtubules. By systematically varying mitotic cell shape, we could modulate the effect of attractive and repulsive polarity domains and consequently generate predicted daughter cell size asymmetries and position. We therefore propose that the spindle position during UCD is set by the combined activities of cell geometry and polarity domains, where cell geometry modulates the effect of cortical polarity domain(s).","lang":"eng"}],"type":"journal_article","date_published":"2021-12-21T00:00:00Z","article_type":"original","citation":{"chicago":"Godard, Benoit G, Remi Dumollard, Carl-Philipp J Heisenberg, and Alex Mcdougall. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.75639.","short":"B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021).","mla":"Godard, Benoit G., et al. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife, vol. 10, e75639, eLife Sciences Publications, 2021, doi:10.7554/eLife.75639.","ieee":"B. G. Godard, R. Dumollard, C.-P. J. Heisenberg, and A. Mcdougall, “Combined effect of cell geometry and polarity domains determines the orientation of unequal division,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Godard, B. G., Dumollard, R., Heisenberg, C.-P. J., & Mcdougall, A. (2021). Combined effect of cell geometry and polarity domains determines the orientation of unequal division. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.75639","ista":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. 2021. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 10, e75639.","ama":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 2021;10. doi:10.7554/eLife.75639"},"publication":"eLife","article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1","volume":10,"date_updated":"2023-08-17T06:32:44Z","date_created":"2022-01-09T23:01:26Z","author":[{"full_name":"Godard, Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G","last_name":"Godard"},{"full_name":"Dumollard, Remi","last_name":"Dumollard","first_name":"Remi"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Mcdougall","first_name":"Alex","full_name":"Mcdougall, Alex"}],"publisher":"eLife Sciences Publications","department":[{"_id":"CaHe"}],"publication_status":"published","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a collaborative grant from the French Government funding agency Agence National de la Recherche to McDougall (ANR 'MorCell': ANR-17-CE 13-0028) and the Austrian Science Fund to Heisenberg (FWF: I 3601-B27).","year":"2021","file_date_updated":"2022-01-10T09:40:37Z","article_number":"e75639","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"doi":"10.7554/eLife.75639","project":[{"call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601","_id":"2646861A-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":{"isi":["000733610100001"]},"publication_identifier":{"eissn":["2050-084X"]},"month":"12"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10607","intvolume":" 91","status":"public","title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","ddc":["610"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_Parkinsonism_Venezia.pdf","creator":"alisjak","file_size":6848513,"content_type":"application/pdf","file_id":"10612","relation":"main_file","success":1,"checksum":"360681585acb51e80d17c6b213c56b55","date_updated":"2022-01-10T13:41:40Z","date_created":"2022-01-10T13:41:40Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders."}],"citation":{"ista":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. 2021. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 91, 59–65.","ieee":"S. Venezia, W. Kaufmann, G. K. Wenning, and N. Stefanova, “Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease,” Parkinsonism & Related Disorders, vol. 91. Elsevier, pp. 59–65, 2021.","apa":"Venezia, S., Kaufmann, W., Wenning, G. K., & Stefanova, N. (2021). Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. Elsevier. https://doi.org/10.1016/j.parkreldis.2021.09.007","ama":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism & Related Disorders. 2021;91:59-65. doi:10.1016/j.parkreldis.2021.09.007","chicago":"Venezia, Serena, Walter Kaufmann, Gregor K. Wenning, and Nadia Stefanova. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders. Elsevier, 2021. https://doi.org/10.1016/j.parkreldis.2021.09.007.","mla":"Venezia, Serena, et al. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” Parkinsonism & Related Disorders, vol. 91, Elsevier, 2021, pp. 59–65, doi:10.1016/j.parkreldis.2021.09.007.","short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism & Related Disorders 91 (2021) 59–65."},"publication":"Parkinsonism & Related Disorders","page":"59-65","article_type":"original","date_published":"2021-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","pmid":1,"year":"2021","acknowledgement":"This study was supported by grants of the Austrian Science Fund (FWF) F4414 and W1206-08. Electron microscopy was performed at the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron Microscopy Facility.","publisher":"Elsevier","department":[{"_id":"EM-Fac"}],"publication_status":"published","author":[{"first_name":"Serena","last_name":"Venezia","full_name":"Venezia, Serena"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"full_name":"Wenning, Gregor K.","first_name":"Gregor K.","last_name":"Wenning"},{"first_name":"Nadia","last_name":"Stefanova","full_name":"Stefanova, Nadia"}],"volume":91,"date_updated":"2023-08-17T06:36:01Z","date_created":"2022-01-09T23:01:26Z","file_date_updated":"2022-01-10T13:41:40Z","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":["000701142900012"],"pmid":["34530328"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.parkreldis.2021.09.007","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1353-8020"],"eissn":["1873-5126"]},"month":"10"},{"date_published":"2021-12-23T00:00:00Z","article_type":"original","publication":"New Journal of Physics","citation":{"ama":"Ghazaryan A, Nica EM, Erten O, Ghaemi P. Shadow surface states in topological Kondo insulators. New Journal of Physics. 2021;23(12). doi:10.1088/1367-2630/ac4124","ieee":"A. Ghazaryan, E. M. Nica, O. Erten, and P. Ghaemi, “Shadow surface states in topological Kondo insulators,” New Journal of Physics, vol. 23, no. 12. IOP Publishing, 2021.","apa":"Ghazaryan, A., Nica, E. M., Erten, O., & Ghaemi, P. (2021). Shadow surface states in topological Kondo insulators. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac4124","ista":"Ghazaryan A, Nica EM, Erten O, Ghaemi P. 2021. Shadow surface states in topological Kondo insulators. New Journal of Physics. 23(12), 123042.","short":"A. Ghazaryan, E.M. Nica, O. Erten, P. Ghaemi, New Journal of Physics 23 (2021).","mla":"Ghazaryan, Areg, et al. “Shadow Surface States in Topological Kondo Insulators.” New Journal of Physics, vol. 23, no. 12, 123042, IOP Publishing, 2021, doi:10.1088/1367-2630/ac4124.","chicago":"Ghazaryan, Areg, Emilian M. Nica, Onur Erten, and Pouyan Ghaemi. “Shadow Surface States in Topological Kondo Insulators.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac4124."},"day":"23","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"relation":"main_file","file_id":"10632","date_created":"2022-01-17T10:01:58Z","date_updated":"2022-01-17T10:01:58Z","checksum":"0c3cb6816242fa8afd1cc87a5fe77821","success":1,"file_name":"2021_NewJourPhys_Ghazaryan.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2533102,"creator":"cchlebak"}],"oa_version":"Published Version","status":"public","ddc":["530"],"title":"Shadow surface states in topological Kondo insulators","intvolume":" 23","_id":"10628","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The surface states of 3D topological insulators in general have negligible quantum oscillations (QOs) when the chemical potential is tuned to the Dirac points. In contrast, we find that topological Kondo insulators (TKIs) can support surface states with an arbitrarily large Fermi surface (FS) when the chemical potential is pinned to the Dirac point. We illustrate that these FSs give rise to finite-frequency QOs, which can become comparable to the extremal area of the unhybridized bulk bands. We show that this occurs when the crystal symmetry is lowered from cubic to tetragonal in a minimal two-orbital model. We label such surface modes as 'shadow surface states'. Moreover, we show that the sufficient next-nearest neighbor out-of-plane hybridization leading to shadow surface states can be self-consistently stabilized for tetragonal TKIs. Consequently, shadow surface states provide an important example of high-frequency QOs beyond the context of cubic TKIs.","lang":"eng"}],"issue":"12","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1088/1367-2630/ac4124","quality_controlled":"1","isi":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"},"external_id":{"isi":["000734063700001"],"arxiv":["2012.11625"]},"oa":1,"month":"12","publication_identifier":{"issn":["1367-2630"]},"date_created":"2022-01-16T23:01:28Z","date_updated":"2023-08-17T06:54:54Z","volume":23,"author":[{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg"},{"full_name":"Nica, Emilian M.","first_name":"Emilian M.","last_name":"Nica"},{"full_name":"Erten, Onur","first_name":"Onur","last_name":"Erten"},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"IOP Publishing","year":"2021","acknowledgement":"PG acknowledges support from National Science Foundation Awards No. DMR-1824265 for this work. AG acknowledges support from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. EMN is supported by ASU startup grant. OE is in part supported by NSF-DMR-1904716.","file_date_updated":"2022-01-17T10:01:58Z","ec_funded":1,"article_number":"123042"},{"type":"journal_article","issue":"6","abstract":[{"text":"We combine experimental and theoretical approaches to explore excited rotational states of molecules embedded in helium nanodroplets using CS2 and I2 as examples. Laser-induced nonadiabatic molecular alignment is employed to measure spectral lines for rotational states extending beyond those initially populated at the 0.37 K droplet temperature. We construct a simple quantum-mechanical model, based on a linear rotor coupled to a single-mode bosonic bath, to determine the rotational energy structure in its entirety. The calculated and measured spectral lines are in good agreement. We show that the effect of the surrounding superfluid on molecular rotation can be rationalized by a single quantity, the angular momentum, transferred from the molecule to the droplet.","lang":"eng"}],"intvolume":" 104","status":"public","title":"Excited rotational states of molecules in a superfluid","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10631","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"30","article_type":"original","citation":{"ama":"Cherepanov I, Bighin G, Schouder CA, et al. Excited rotational states of molecules in a superfluid. Physical Review A. 2021;104(6). doi:10.1103/PhysRevA.104.L061303","ista":"Cherepanov I, Bighin G, Schouder CA, Chatterley AS, Albrechtsen SH, Muñoz AV, Christiansen L, Stapelfeldt H, Lemeshko M. 2021. Excited rotational states of molecules in a superfluid. Physical Review A. 104(6), L061303.","ieee":"I. Cherepanov et al., “Excited rotational states of molecules in a superfluid,” Physical Review A, vol. 104, no. 6. American Physical Society, 2021.","apa":"Cherepanov, I., Bighin, G., Schouder, C. A., Chatterley, A. S., Albrechtsen, S. H., Muñoz, A. V., … Lemeshko, M. (2021). Excited rotational states of molecules in a superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.104.L061303","mla":"Cherepanov, Igor, et al. “Excited Rotational States of Molecules in a Superfluid.” Physical Review A, vol. 104, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.104.L061303.","short":"I. Cherepanov, G. Bighin, C.A. Schouder, A.S. Chatterley, S.H. Albrechtsen, A.V. Muñoz, L. Christiansen, H. Stapelfeldt, M. Lemeshko, Physical Review A 104 (2021).","chicago":"Cherepanov, Igor, Giacomo Bighin, Constant A. Schouder, Adam S. Chatterley, Simon H. Albrechtsen, Alberto Viñas Muñoz, Lars Christiansen, Henrik Stapelfeldt, and Mikhail Lemeshko. “Excited Rotational States of Molecules in a Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.104.L061303."},"publication":"Physical Review A","date_published":"2021-12-30T00:00:00Z","article_number":"L061303","ec_funded":1,"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2021","acknowledgement":"I.C. acknowledges the support by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385. G.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.S acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl) and from The Villum Foundation through a Villum Investigator grant no. 25886.","volume":104,"date_updated":"2023-08-17T06:52:17Z","date_created":"2022-01-16T23:01:29Z","author":[{"id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","last_name":"Cherepanov","full_name":"Cherepanov, Igor"},{"first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"full_name":"Chatterley, Adam S.","first_name":"Adam S.","last_name":"Chatterley"},{"first_name":"Simon H.","last_name":"Albrechtsen","full_name":"Albrechtsen, Simon H."},{"first_name":"Alberto Viñas","last_name":"Muñoz","full_name":"Muñoz, Alberto Viñas"},{"last_name":"Christiansen","first_name":"Lars","full_name":"Christiansen, Lars"},{"last_name":"Stapelfeldt","first_name":"Henrik","full_name":"Stapelfeldt, Henrik"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"}],"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"month":"12","project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"http://128.84.4.18/abs/2107.00468","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2107.00468"],"isi":["000739618300001"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.104.L061303"},{"type":"conference","abstract":[{"text":"We thank Emmanuel Abbe and Min Ye for providing us the implementation of RPA decoding. D. Fathollahi and M. Mondelli are partially supported by the 2019 Lopez-Loreta Prize. N. Farsad is supported by Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC) and Canada Foundation for Innovation (CFI), John R. Evans Leader Fund. S. A. Hashemi is supported by a Postdoctoral Fellowship from NSERC.","lang":"eng"}],"status":"public","title":"Sparse multi-decoder recursive projection aggregation for Reed-Muller codes","_id":"10597","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"1082-1087","citation":{"short":"D. Fathollahi, N. Farsad, S.A. Hashemi, M. Mondelli, in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 1082–1087.","mla":"Fathollahi, Dorsa, et al. “Sparse Multi-Decoder Recursive Projection Aggregation for Reed-Muller Codes.” 2021 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 1082–87, doi:10.1109/isit45174.2021.9517887.","chicago":"Fathollahi, Dorsa, Nariman Farsad, Seyyed Ali Hashemi, and Marco Mondelli. “Sparse Multi-Decoder Recursive Projection Aggregation for Reed-Muller Codes.” In 2021 IEEE International Symposium on Information Theory, 1082–87. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/isit45174.2021.9517887.","ama":"Fathollahi D, Farsad N, Hashemi SA, Mondelli M. Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. In: 2021 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers; 2021:1082-1087. doi:10.1109/isit45174.2021.9517887","ieee":"D. Fathollahi, N. Farsad, S. A. Hashemi, and M. Mondelli, “Sparse multi-decoder recursive projection aggregation for Reed-Muller codes,” in 2021 IEEE International Symposium on Information Theory, Virtual, Melbourne, Australia, 2021, pp. 1082–1087.","apa":"Fathollahi, D., Farsad, N., Hashemi, S. A., & Mondelli, M. (2021). Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. In 2021 IEEE International Symposium on Information Theory (pp. 1082–1087). Virtual, Melbourne, Australia: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/isit45174.2021.9517887","ista":"Fathollahi D, Farsad N, Hashemi SA, Mondelli M. 2021. Sparse multi-decoder recursive projection aggregation for Reed-Muller codes. 2021 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 1082–1087."},"publication":"2021 IEEE International Symposium on Information Theory","date_published":"2021-09-01T00:00:00Z","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"MaMo"}],"publication_status":"published","year":"2021","date_updated":"2023-08-17T06:32:06Z","date_created":"2022-01-03T11:31:26Z","author":[{"last_name":"Fathollahi","first_name":"Dorsa","full_name":"Fathollahi, Dorsa"},{"full_name":"Farsad, Nariman","first_name":"Nariman","last_name":"Farsad"},{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"}],"publication_identifier":{"eisbn":["978-1-5386-8209-8"],"isbn":["978-1-5386-8210-4"]},"month":"09","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2011.12882"],"isi":["000701502201029"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.12882"}],"language":[{"iso":"eng"}],"doi":"10.1109/isit45174.2021.9517887","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2021-07-20","location":"Virtual, Melbourne, Australia","start_date":"2021-07-12"}}]