[{"publisher":"Springer Nature","supplementarymaterial":"yes","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41598-024-67787-z","_id":"17389","publication_identifier":{"issn":["2045-2322"]},"pmid":1,"publication":"Scientific Reports","arxiv":1,"project":[{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"has_accepted_license":"1","oa":1,"article_processing_charge":"Yes","department":[{"_id":"GeKa"}],"das_tickbox":"1","citation":{"chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>Scientific Reports</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41598-024-67787-z\">https://doi.org/10.1038/s41598-024-67787-z</a>.","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>Scientific Reports</i>. 2024;14. doi:<a href=\"https://doi.org/10.1038/s41598-024-67787-z\">10.1038/s41598-024-67787-z</a>","ieee":"B. Severin <i>et al.</i>, “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” <i>Scientific Reports</i>, vol. 14. Springer Nature, 2024.","short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, Scientific Reports 14 (2024).","ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, de Kruijf M, Carballido MJ, Svab S, Kuhlmann AV, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. 2024. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. Scientific Reports. 14, 17281.","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>Scientific Reports</i>, vol. 14, 17281, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41598-024-67787-z\">10.1038/s41598-024-67787-z</a>.","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (2024). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-024-67787-z\">https://doi.org/10.1038/s41598-024-67787-z</a>"},"volume":14,"month":"07","publication_status":"published","date_published":"2024-07-27T00:00:00Z","article_type":"original","related_material":{"record":[{"status":"public","id":"10066","relation":"earlier_version"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Severin, B.","first_name":"B.","last_name":"Severin"},{"full_name":"Lennon, D. T.","last_name":"Lennon","first_name":"D. T."},{"full_name":"Camenzind, L. C.","first_name":"L. C.","last_name":"Camenzind"},{"full_name":"Vigneau, F.","first_name":"F.","last_name":"Vigneau"},{"first_name":"F.","last_name":"Fedele","full_name":"Fedele, F."},{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"first_name":"A.","last_name":"Ballabio","full_name":"Ballabio, A."},{"last_name":"Chrastina","first_name":"D.","full_name":"Chrastina, D."},{"full_name":"Isella, G.","first_name":"G.","last_name":"Isella"},{"last_name":"de Kruijf","first_name":"M.","full_name":"de Kruijf, M."},{"last_name":"Carballido","first_name":"M. J.","full_name":"Carballido, M. J."},{"first_name":"S.","last_name":"Svab","full_name":"Svab, S."},{"full_name":"Kuhlmann, A. V.","first_name":"A. V.","last_name":"Kuhlmann"},{"full_name":"Geyer, S.","first_name":"S.","last_name":"Geyer"},{"full_name":"Froning, F. N. M.","last_name":"Froning","first_name":"F. N. M."},{"full_name":"Moon, H.","last_name":"Moon","first_name":"H."},{"full_name":"Osborne, M. A.","first_name":"M. A.","last_name":"Osborne"},{"last_name":"Sejdinovic","first_name":"D.","full_name":"Sejdinovic, D."},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"},{"last_name":"Zumbühl","first_name":"D. M.","full_name":"Zumbühl, D. M."},{"first_name":"G. A. D.","last_name":"Briggs","full_name":"Briggs, G. A. D."},{"last_name":"Ares","first_name":"N.","full_name":"Ares, N."}],"ddc":["530"],"acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant (EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the NCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units of IST Austria through resources provided by the nanofabrication facility, the FWF-I 05060 and the FWF-P 30207 project.","date_created":"2024-08-05T08:50:51Z","dataavailabilitystatement":"The data acquired by the algorithm during experiments is available from the corresponding author upon reasonable request.","file_date_updated":"2024-08-05T08:52:14Z","doi":"10.1038/s41598-024-67787-z","status":"public","type":"journal_article","acknowledged_ssus":[{"_id":"NanoFab"}],"researchdata_availability":"upon request","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"27","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","date_updated":"2026-10-02T11:04:33Z","abstract":[{"text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions and each device realisation requires a different tuning protocol. We demonstrate that it is possible to automate the tuning of a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate Ge/SiGe heterostructure double quantum dot device from scratch with the same algorithm. We achieve tuning times of 30, 10, and 92 min, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices, allowing for the characterization of the regions where double quantum dot regimes are found. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning.","lang":"eng"}],"article_number":"17281","file":[{"file_name":"2024_ScientificReports_Severin.pdf","date_updated":"2024-08-05T08:52:14Z","access_level":"open_access","date_created":"2024-08-05T08:52:14Z","file_id":"17390","creator":"dernst","success":1,"content_type":"application/pdf","checksum":"0b34b89e5f4f3f7b32ffadf104394594","file_size":2255741,"relation":"main_file"}],"intvolume":"        14","year":"2024","external_id":{"isi":["001281273100062"],"pmid":["39068242"],"arxiv":["2107.12975"]},"quality_controlled":"1","isi":1},{"year":"2023","external_id":{"isi":["000995271600104"],"pmid":["37198326"]},"quality_controlled":"1","keyword":["Multidisciplinary"],"isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2025-04-23T08:56:48Z","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","day":"17","file":[{"relation":"main_file","file_size":3055077,"file_id":"13047","success":1,"content_type":"application/pdf","checksum":"8c1b769693ff4288df8376e59ad1176d","creator":"dernst","date_created":"2023-05-22T07:57:37Z","file_name":"2023_ScientificReports_Zavadakova.pdf","date_updated":"2023-05-22T07:57:37Z","access_level":"open_access"}],"article_number":"7959","abstract":[{"text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.","lang":"eng"}],"intvolume":"        13","file_date_updated":"2023-05-22T07:57:37Z","doi":"10.1038/s41598-023-35162-z","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"author":[{"full_name":"Zavadakova, Anna","last_name":"Zavadakova","first_name":"Anna"},{"full_name":"Vistejnova, Lucie","first_name":"Lucie","last_name":"Vistejnova"},{"full_name":"Belinova, Tereza","last_name":"Belinova","first_name":"Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368"},{"last_name":"Tichanek","first_name":"Filip","full_name":"Tichanek, Filip"},{"last_name":"Bilikova","first_name":"Dagmar","full_name":"Bilikova, Dagmar"},{"full_name":"Mouton, Peter R.","last_name":"Mouton","first_name":"Peter R."}],"acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","issue":"1","date_created":"2023-05-19T11:12:25Z","month":"05","date_published":"2023-05-17T00:00:00Z","publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-023-37265-z","relation":"erratum"}]},"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"Bio"}],"article_processing_charge":"No","citation":{"ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>.","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” <i>Scientific Reports</i>, vol. 13, no. 1. Springer Nature, 2023.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &#38; Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>.","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023)."},"volume":13,"has_accepted_license":"1","oa":1,"publisher":"Springer Nature","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41598-023-35162-z","publication_identifier":{"issn":["2045-2322"]},"_id":"13033","pmid":1,"publication":"Scientific Reports"},{"article_processing_charge":"No","volume":13,"citation":{"chicago":"Bronstein, Alex M., and Ailie Marx. “Water Stabilizes an Alternate Turn Conformation in Horse Heart Myoglobin.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-32821-z\">https://doi.org/10.1038/s41598-023-32821-z</a>.","ama":"Bronstein AM, Marx A. Water stabilizes an alternate turn conformation in horse heart myoglobin. <i>Scientific Reports</i>. 2023;13. doi:<a href=\"https://doi.org/10.1038/s41598-023-32821-z\">10.1038/s41598-023-32821-z</a>","ieee":"A. M. Bronstein and A. Marx, “Water stabilizes an alternate turn conformation in horse heart myoglobin,” <i>Scientific Reports</i>, vol. 13. Springer Nature, 2023.","apa":"Bronstein, A. M., &#38; Marx, A. (2023). Water stabilizes an alternate turn conformation in horse heart myoglobin. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-32821-z\">https://doi.org/10.1038/s41598-023-32821-z</a>","mla":"Bronstein, Alex M., and Ailie Marx. “Water Stabilizes an Alternate Turn Conformation in Horse Heart Myoglobin.” <i>Scientific Reports</i>, vol. 13, 6094, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-32821-z\">10.1038/s41598-023-32821-z</a>.","ista":"Bronstein AM, Marx A. 2023. Water stabilizes an alternate turn conformation in horse heart myoglobin. Scientific Reports. 13, 6094.","short":"A.M. Bronstein, A. Marx, Scientific Reports 13 (2023)."},"date_published":"2023-04-13T00:00:00Z","publication_status":"published","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","fulldoi":"https://doi.org/10.1038/s41598-023-32821-z","scopus_import":"1","publisher":"Springer Nature","publication":"Scientific Reports","pmid":1,"_id":"18207","publication_identifier":{"issn":["2045-2322"]},"oa":1,"extern":"1","has_accepted_license":"1","title":"Water stabilizes an alternate turn conformation in horse heart myoglobin","date_updated":"2024-10-09T10:39:26Z","day":"13","language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"        13","abstract":[{"lang":"eng","text":"Comparison of myoglobin structures reveals that protein isolated from horse heart consistently adopts an alternate turn conformation in comparison to its homologues. Analysis of hundreds of high-resolution structures discounts crystallization conditions or the surrounding amino acid protein environment as explaining this difference, that is also not captured by the AlphaFold prediction. Rather, a water molecule is identified as stabilizing the conformation in the horse heart structure, which immediately reverts to the whale conformation in molecular dynamics simulations excluding that structural water."}],"article_number":"6094","external_id":{"pmid":["37055458"]},"year":"2023","quality_controlled":"1","author":[{"last_name":"Bronstein","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","full_name":"Bronstein, Alexander"},{"first_name":"Ailie","last_name":"Marx","full_name":"Marx, Ailie"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-10-08T12:46:41Z","main_file_link":[{"url":"https://doi.org/10.1038/s41598-023-32821-z","open_access":"1"}],"type":"journal_article","status":"public","doi":"10.1038/s41598-023-32821-z"},{"external_id":{"isi":["000788639400032"],"pmid":["35477739"]},"year":"2022","isi":1,"quality_controlled":"1","date_updated":"2026-04-15T08:51:09Z","title":"Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia","day":"27","language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"        12","file":[{"access_level":"open_access","date_updated":"2022-05-02T09:05:20Z","file_name":"2022_ScientificReports_Dranenko.pdf","date_created":"2022-05-02T09:05:20Z","creator":"dernst","success":1,"content_type":"application/pdf","checksum":"12601b8a5c6b83bb618f92bcb963ecc9","file_id":"11349","file_size":3564155,"relation":"main_file"}],"abstract":[{"text":"Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.","lang":"eng"}],"article_number":"6868","type":"journal_article","file_date_updated":"2022-05-02T09:05:20Z","status":"public","doi":"10.1038/s41598-022-10827-3","ddc":["570"],"author":[{"last_name":"Dranenko","first_name":"NO","full_name":"Dranenko, NO"},{"full_name":"Tutukina, MN","first_name":"MN","last_name":"Tutukina"},{"last_name":"Gelfand","first_name":"MS","full_name":"Gelfand, MS"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","date_created":"2022-05-02T07:08:42Z","acknowledgement":"The project was initiated with Aygul Minnegalieva and Yulia Yakovleva at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya, and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also thank Peter Vlasov for fruitful discussions.This study was supported by the Russian Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. ","date_published":"2022-04-27T00:00:00Z","publication_status":"published","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","department":[{"_id":"FyKo"}],"article_processing_charge":"No","volume":12,"citation":{"apa":"Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &#38; Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>","ista":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 12, 6868.","mla":"Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>, vol. 12, 6868, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>.","short":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022).","ieee":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” <i>Scientific Reports</i>, vol. 12. Springer Nature, 2022.","chicago":"Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>.","ama":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific Reports</i>. 2022;12. doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>"},"ec_funded":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181"}],"oa":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1038/s41598-022-10827-3","scopus_import":"1","publisher":"Springer Nature","publication":"Scientific Reports","publication_identifier":{"issn":["2045-2322"]},"_id":"11344","pmid":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","publication_status":"published","date_published":"2022-06-02T00:00:00Z","month":"06","volume":12,"citation":{"short":"C. Currin, S.V. Vera, A. Khaledi-Nasab, Scientific Reports 12 (2022).","ista":"Currin C, Vera SV, Khaledi-Nasab A. 2022. Depolarization of echo chambers by random dynamical nudge. Scientific Reports. 12, 9234.","apa":"Currin, C., Vera, S. V., &#38; Khaledi-Nasab, A. (2022). Depolarization of echo chambers by random dynamical nudge. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-12494-w\">https://doi.org/10.1038/s41598-022-12494-w</a>","mla":"Currin, Christopher, et al. “Depolarization of Echo Chambers by Random Dynamical Nudge.” <i>Scientific Reports</i>, vol. 12, 9234, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-12494-w\">10.1038/s41598-022-12494-w</a>.","ieee":"C. Currin, S. V. Vera, and A. Khaledi-Nasab, “Depolarization of echo chambers by random dynamical nudge,” <i>Scientific Reports</i>, vol. 12. Springer Nature, 2022.","chicago":"Currin, Christopher, Sebastián Vallejo Vera, and Ali Khaledi-Nasab. “Depolarization of Echo Chambers by Random Dynamical Nudge.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-12494-w\">https://doi.org/10.1038/s41598-022-12494-w</a>.","ama":"Currin C, Vera SV, Khaledi-Nasab A. Depolarization of echo chambers by random dynamical nudge. <i>Scientific Reports</i>. 2022;12. doi:<a href=\"https://doi.org/10.1038/s41598-022-12494-w\">10.1038/s41598-022-12494-w</a>"},"article_processing_charge":"No","department":[{"_id":"TiVo"}],"oa":1,"has_accepted_license":"1","publication":"Scientific Reports","_id":"12225","publication_identifier":{"issn":["2045-2322"]},"pmid":1,"fulldoi":"https://doi.org/10.1038/s41598-022-12494-w","publisher":"Springer Nature","scopus_import":"1","isi":1,"keyword":["Multidisciplinary"],"quality_controlled":"1","external_id":{"isi":["000805561200024"],"pmid":["35654942"]},"year":"2022","intvolume":"        12","article_number":"9234","abstract":[{"text":"In social networks, users often engage with like-minded peers. This selective exposure to opinions might result in echo chambers, i.e., political fragmentation and social polarization of user interactions. When echo chambers form, opinions have a bimodal distribution with two peaks on opposite sides. In certain issues, where either extreme positions contain a degree of misinformation, neutral consensus is preferable for promoting discourse. In this paper, we use an opinion dynamics model that naturally forms echo chambers in order to find a feedback mechanism that bridges these communities and leads to a neutral consensus. We introduce the <jats:italic>random dynamical nudge</jats:italic> (RDN), which presents each agent with input from a random selection of other agents’ opinions and does not require surveillance of every person’s opinions. Our computational results in two different models suggest that the RDN leads to a unimodal distribution of opinions centered around the neutral consensus. Furthermore, the RDN is effective both for preventing the formation of echo chambers and also for depolarizing existing echo chambers. Due to the simple and robust nature of the RDN, social media networks might be able to implement a version of this self-feedback mechanism, when appropriate, to prevent the segregation of online communities on complex social issues.","lang":"eng"}],"file":[{"access_level":"open_access","file_name":"2022_ScientificReports_Currin.pdf","date_updated":"2023-01-27T08:56:18Z","creator":"dernst","content_type":"application/pdf","success":1,"checksum":"e024a75f14ce5667795a31e44a259c52","file_id":"12418","date_created":"2023-01-27T08:56:18Z","file_size":3625627,"relation":"main_file"}],"day":"02","title":"Depolarization of echo chambers by random dynamical nudge","date_updated":"2023-08-04T09:26:30Z","oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1038/s41598-022-12494-w","status":"public","file_date_updated":"2023-01-27T08:56:18Z","date_created":"2023-01-16T09:48:30Z","acknowledgement":"CBC and AKN would like to thank Neuromatch Academy https://www.neuromatchacademy.org for introducing the authors to each other. We thank Dr. Krešimir Josic (University of Houston) , Fabian Baumann (Humboldt University) and Dr. Igor M. Sokolov (Humboldt University) for carefully reading the early versions of the manuscript and providing constructive feedback. CBC is supported by the German Deutscher Akademischer Austauschdienst (DAAD, https://daad.de), the South African National Research Foundation (NRF, https://nrf.ac.za), the University of Cape Town (UCT, https://uct.ac.za), and the NOMIS Foundation through the NOMIS Fellowships at IST Austria program (https://nomisfoundation.ch). SVV appreciate the generosity of Tecnológico de Monterrey for covering the publication fee.","author":[{"full_name":"Currin, Christopher","first_name":"Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","last_name":"Currin","orcid":"0000-0002-4809-5059"},{"last_name":"Vera","first_name":"Sebastián Vallejo","full_name":"Vera, Sebastián Vallejo"},{"last_name":"Khaledi-Nasab","first_name":"Ali","full_name":"Khaledi-Nasab, Ali"}],"ddc":["570"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"month":"12","publication_status":"published","date_published":"2022-12-20T00:00:00Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","citation":{"ieee":"L. Ackerman-Schraier, A. A. Rosenberg, A. Marx, and A. M. Bronstein, “Machine learning approaches demonstrate that protein structures carry information about their genetic coding,” <i>Scientific Reports</i>, vol. 12. Springer Nature, 2022.","short":"L. Ackerman-Schraier, A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Reports 12 (2022).","apa":"Ackerman-Schraier, L., Rosenberg, A. A., Marx, A., &#38; Bronstein, A. M. (2022). Machine learning approaches demonstrate that protein structures carry information about their genetic coding. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-25874-z\">https://doi.org/10.1038/s41598-022-25874-z</a>","ista":"Ackerman-Schraier L, Rosenberg AA, Marx A, Bronstein AM. 2022. Machine learning approaches demonstrate that protein structures carry information about their genetic coding. Scientific Reports. 12, 21968.","mla":"Ackerman-Schraier, Linor, et al. “Machine Learning Approaches Demonstrate That Protein Structures Carry Information about Their Genetic Coding.” <i>Scientific Reports</i>, vol. 12, 21968, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-25874-z\">10.1038/s41598-022-25874-z</a>.","chicago":"Ackerman-Schraier, Linor, Aviv A. Rosenberg, Ailie Marx, and Alex M. Bronstein. “Machine Learning Approaches Demonstrate That Protein Structures Carry Information about Their Genetic Coding.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-25874-z\">https://doi.org/10.1038/s41598-022-25874-z</a>.","ama":"Ackerman-Schraier L, Rosenberg AA, Marx A, Bronstein AM. Machine learning approaches demonstrate that protein structures carry information about their genetic coding. <i>Scientific Reports</i>. 2022;12. doi:<a href=\"https://doi.org/10.1038/s41598-022-25874-z\">10.1038/s41598-022-25874-z</a>"},"volume":12,"OA_place":"publisher","extern":"1","oa":1,"publisher":"Springer Nature","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41598-022-25874-z","_id":"18220","publication_identifier":{"issn":["2045-2322"]},"pmid":1,"publication":"Scientific Reports","year":"2022","external_id":{"pmid":["36539476"]},"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"20","title":"Machine learning approaches demonstrate that protein structures carry information about their genetic coding","date_updated":"2024-10-14T09:46:06Z","abstract":[{"lang":"eng","text":"Synonymous codons translate into the same amino acid. Although the identity of synonymous codons is often considered inconsequential to the final protein structure, there is mounting evidence for an association between the two. Our study examined this association using regression and classification models, finding that codon sequences predict protein backbone dihedral angles with a lower error than amino acid sequences, and that models trained with true dihedral angles have better classification of synonymous codons given structural information than models trained with random dihedral angles. Using this classification approach, we investigated local codon–codon dependencies and tested whether synonymous codon identity can be predicted more accurately from codon context than amino acid context alone, and most specifically which codon context position carries the most predictive power."}],"article_number":"21968","DOAJ_listed":"1","intvolume":"        12","OA_type":"gold","status":"public","doi":"10.1038/s41598-022-25874-z","type":"journal_article","author":[{"first_name":"Linor","last_name":"Ackerman-Schraier","full_name":"Ackerman-Schraier, Linor"},{"full_name":"Rosenberg, Aviv A.","first_name":"Aviv A.","last_name":"Rosenberg"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"},{"first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41598-022-25874-z"}],"date_created":"2024-10-08T12:52:29Z"},{"year":"2019","quality_controlled":"1","day":"14","title":"Thermodynamic signatures of Weyl fermions in NbP","date_updated":"2021-01-12T08:11:36Z","language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"         9","article_number":"2095","abstract":[{"text":"We present a high magnetic field study of NbP—a member of the monopnictide Weyl semimetal (WSM) family. While the monoarsenides (NbAs and TaAs) have topologically distinct left and right-handed Weyl fermi surfaces, NbP is argued to be “topologically trivial” due to the fact that all pairs of Weyl nodes are encompassed by a single Fermi surface. We use torque magnetometry to measure the magnetic response of NbP up to 60 tesla and uncover a Berry paramagnetic response, characteristic of the topological Weyl nodes, across the entire field range. At the quantum limit B* (≈32 T), τ/B experiences a change in slope when the chemical potential enters the last Landau level. Our calculations confirm that this magnetic response arises from band topology of the Weyl pocket, even though the Fermi surface encompasses both Weyl nodes at zero magnetic field. We also find that the magnetic field pulls the chemical potential to the chiral n = 0 Landau level in the quantum limit, providing a disorder-free way of accessing chiral Weyl fermions in systems that are “not quite” WSMs in zero magnetic field.","lang":"eng"}],"file":[{"file_size":3256400,"relation":"main_file","file_name":"2019_ScientificReports_Modic.pdf","date_updated":"2020-07-14T12:47:48Z","access_level":"open_access","date_created":"2019-11-20T12:24:13Z","file_id":"7086","creator":"dernst","content_type":"application/pdf","checksum":"3b5a7b316e1ff22aa0f89e8d1f1ace91"}],"type":"journal_article","doi":"10.1038/s41598-018-38161-7","file_date_updated":"2020-07-14T12:47:48Z","status":"public","author":[{"full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","last_name":"Modic","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"full_name":"Meng, Tobias","first_name":"Tobias","last_name":"Meng"},{"first_name":"Filip","last_name":"Ronning","full_name":"Ronning, Filip"},{"first_name":"Eric D.","last_name":"Bauer","full_name":"Bauer, Eric D."},{"full_name":"Moll, Philip J. W.","last_name":"Moll","first_name":"Philip J. W."},{"full_name":"Ramshaw, B. J.","first_name":"B. J.","last_name":"Ramshaw"}],"ddc":["530"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2019-11-19T13:00:35Z","issue":"1","date_published":"2019-02-14T00:00:00Z","publication_status":"published","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","article_processing_charge":"No","volume":9,"citation":{"ama":"Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. Thermodynamic signatures of Weyl fermions in NbP. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-38161-7\">10.1038/s41598-018-38161-7</a>","chicago":"Modic, Kimberly A, Tobias Meng, Filip Ronning, Eric D. Bauer, Philip J. W. Moll, and B. J. Ramshaw. “Thermodynamic Signatures of Weyl Fermions in NbP.” <i>Scientific Reports</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41598-018-38161-7\">https://doi.org/10.1038/s41598-018-38161-7</a>.","ista":"Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. 2019. Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. 9(1), 2095.","mla":"Modic, Kimberly A., et al. “Thermodynamic Signatures of Weyl Fermions in NbP.” <i>Scientific Reports</i>, vol. 9, no. 1, 2095, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-018-38161-7\">10.1038/s41598-018-38161-7</a>.","apa":"Modic, K. A., Meng, T., Ronning, F., Bauer, E. D., Moll, P. J. W., &#38; Ramshaw, B. J. (2019). Thermodynamic signatures of Weyl fermions in NbP. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-38161-7\">https://doi.org/10.1038/s41598-018-38161-7</a>","short":"K.A. Modic, T. Meng, F. Ronning, E.D. Bauer, P.J.W. Moll, B.J. Ramshaw, Scientific Reports 9 (2019).","ieee":"K. A. Modic, T. Meng, F. Ronning, E. D. Bauer, P. J. W. Moll, and B. J. Ramshaw, “Thermodynamic signatures of Weyl fermions in NbP,” <i>Scientific Reports</i>, vol. 9, no. 1. Springer Nature, 2019."},"oa":1,"has_accepted_license":"1","extern":"1","fulldoi":"https://doi.org/10.1038/s41598-018-38161-7","publisher":"Springer Nature","publication":"Scientific Reports","_id":"7057","publication_identifier":{"issn":["2045-2322"]}},{"intvolume":"         8","article_number":"2724","abstract":[{"text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting.","lang":"eng"}],"file":[{"checksum":"e642080fcbde9584c63544f587c74f03","creator":"dernst","content_type":"application/pdf","success":1,"file_id":"8619","date_created":"2020-10-06T16:35:16Z","access_level":"open_access","date_updated":"2020-10-06T16:35:16Z","file_name":"2018_ScientificReports_Gregor.pdf","relation":"main_file","file_size":2818077}],"day":"09","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","date_updated":"2024-10-21T06:02:43Z","language":[{"iso":"eng"}],"oa_version":"Published Version","isi":1,"keyword":["Multidisciplinary"],"quality_controlled":"1","external_id":{"isi":["000424630400037"],"pmid":["29426833"]},"year":"2018","date_created":"2020-10-06T16:33:37Z","author":[{"full_name":"Gregor, Carola","first_name":"Carola","last_name":"Gregor"},{"full_name":"Sidenstein, Sven C.","last_name":"Sidenstein","first_name":"Sven C."},{"last_name":"Andresen","first_name":"Martin","full_name":"Andresen, Martin"},{"last_name":"Sahl","first_name":"Steffen J.","full_name":"Sahl, Steffen J."},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"first_name":"Stefan W.","last_name":"Hell","full_name":"Hell, Stefan W."}],"ddc":["570"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","status":"public","file_date_updated":"2020-10-06T16:35:16Z","doi":"10.1038/s41598-018-19947-1","volume":8,"citation":{"ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>.","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>.","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38; Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>","ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>, vol. 8. Springer Nature, 2018."},"article_processing_charge":"No","department":[{"_id":"JoDa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","date_published":"2018-02-09T00:00:00Z","publication_status":"published","month":"02","publication":"Scientific Reports","_id":"8618","publication_identifier":{"issn":["2045-2322"]},"pmid":1,"fulldoi":"https://doi.org/10.1038/s41598-018-19947-1","scopus_import":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1"},{"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","oa":1,"pubrep_id":"803","publisher":"Nature Publishing Group","scopus_import":"1","fulldoi":"https://doi.org/10.1038/srep41906","_id":"1110","publication_identifier":{"issn":["2045-2322"]},"publication":"Scientific Reports","month":"02","publication_status":"published","date_published":"2017-02-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"article_processing_charge":"No","ec_funded":1,"citation":{"ama":"Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. <i>Scientific Reports</i>. 2017;7. doi:<a href=\"https://doi.org/10.1038/srep41906\">10.1038/srep41906</a>","chicago":"Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta, Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” <i>Scientific Reports</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/srep41906\">https://doi.org/10.1038/srep41906</a>.","mla":"Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” <i>Scientific Reports</i>, vol. 7, 41906, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/srep41906\">10.1038/srep41906</a>.","ista":"Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 7, 41906.","apa":"Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli, C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep41906\">https://doi.org/10.1038/srep41906</a>","short":"B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev, L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports 7 (2017).","ieee":"B. Kuhn <i>et al.</i>, “Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,” <i>Scientific Reports</i>, vol. 7. Nature Publishing Group, 2017."},"volume":7,"file_date_updated":"2018-12-12T10:18:09Z","doi":"10.1038/srep41906","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Kuhn","first_name":"Benjamin","full_name":"Kuhn, Benjamin"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"last_name":"Errafi","first_name":"Sanae","full_name":"Errafi, Sanae"},{"full_name":"Bucher, Rahel","last_name":"Bucher","first_name":"Rahel"},{"last_name":"Gupta","first_name":"Shibu","full_name":"Gupta, Shibu"},{"first_name":"Bibek","last_name":"Aryal","full_name":"Aryal, Bibek"},{"full_name":"Dobrev, Petre","last_name":"Dobrev","first_name":"Petre"},{"last_name":"Bigler","first_name":"Laurent","full_name":"Bigler, Laurent"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Ringli, Christoph","first_name":"Christoph","last_name":"Ringli"}],"ddc":["581"],"acknowledgement":"European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S) [JF].","date_created":"2018-12-11T11:50:12Z","year":"2017","external_id":{"isi":["000393367600001"]},"quality_controlled":"1","isi":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","day":"06","title":"Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity","publist_id":"6258","date_updated":"2025-07-10T11:50:06Z","article_number":"41906","abstract":[{"lang":"eng","text":"The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium."}],"file":[{"relation":"main_file","file_size":1654496,"file_id":"5328","creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:18:09Z","date_updated":"2018-12-12T10:18:09Z","file_name":"IST-2017-803-v1+1_srep41906.pdf","access_level":"open_access"}],"intvolume":"         7"},{"pubrep_id":"743","scopus_import":"1","publisher":"Nature Publishing Group","fulldoi":"https://doi.org/10.1038/srep40012","publication_identifier":{"issn":["2045-2322"]},"_id":"1160","publication":"Scientific Reports","has_accepted_license":"1","oa":1,"article_processing_charge":"No","department":[{"_id":"BjHo"}],"citation":{"ama":"Altmeyer S, Do Y, Lai Y. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. <i>Scientific Reports</i>. 2017;7. doi:<a href=\"https://doi.org/10.1038/srep40012\">10.1038/srep40012</a>","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” <i>Scientific Reports</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/srep40012\">https://doi.org/10.1038/srep40012</a>.","mla":"Altmeyer, Sebastian, et al. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” <i>Scientific Reports</i>, vol. 7, 40012, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/srep40012\">10.1038/srep40012</a>.","ista":"Altmeyer S, Do Y, Lai Y. 2017. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. 7, 40012.","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2017). Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep40012\">https://doi.org/10.1038/srep40012</a>","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 7 (2017).","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio,” <i>Scientific Reports</i>, vol. 7. Nature Publishing Group, 2017."},"volume":7,"month":"01","date_published":"2017-01-06T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Altmeyer","orcid":"0000-0001-5964-0203","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","full_name":"Altmeyer, Sebastian"},{"full_name":"Do, Younghae","first_name":"Younghae","last_name":"Do"},{"full_name":"Lai, Ying","first_name":"Ying","last_name":"Lai"}],"ddc":["532"],"date_created":"2018-12-11T11:50:28Z","doi":"10.1038/srep40012","status":"public","file_date_updated":"2020-07-14T12:44:36Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"06","title":"Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio","date_updated":"2025-07-10T11:50:13Z","publist_id":"6198","article_number":"40012","abstract":[{"text":"We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined be-tween two concentric independently rotating cylinders - consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying out systematic bifurcation analysis. Without magnetic field, we find steady flow patterns, previously observed with a simple fluid, such as those containing normal one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states. However, when a symmetry-breaking transverse magnetic field is present, all flow states exhibit stimulated, finite two-fold mode. Various bifurcations between steady and unsteady states can occur, corresponding to the transitions between the two-cell and one-cell states. While unsteady, axially oscillating flow states can arise, we also detect the emergence of new unsteady flow states. In particular, we uncover two new states: one contains only the azimuthally oscillating solution in the configuration of the twin-cell flow state, and an-other a rotating flow state. Topologically, these flow states are a limit cycle and a quasiperiodic solution on a two-torus, respectively. Emergence of new flow states in addition to observed ones with classical fluid, indicates that richer but potentially more controllable dynamics in ferrofluidic flows, as such flow states depend on the external magnetic field.","lang":"eng"}],"file":[{"file_size":4546835,"relation":"main_file","file_name":"IST-2017-743-v1+1_srep40012.pdf","date_updated":"2020-07-14T12:44:36Z","access_level":"open_access","file_id":"4802","creator":"system","content_type":"application/pdf","checksum":"694aa70399444570825099c1a7ec91f2","date_created":"2018-12-12T10:10:16Z"}],"intvolume":"         7","year":"2017","external_id":{"isi":["000391269700001"]},"quality_controlled":"1","isi":1},{"file_date_updated":"2020-07-14T12:46:36Z","status":"public","doi":"10.1038/s41598-017-00107-w","type":"journal_article","issue":"1","date_created":"2018-12-11T11:46:53Z","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"ddc":["004"],"quality_controlled":"1","isi":1,"year":"2017","external_id":{"isi":["000396867800013"]},"abstract":[{"lang":"eng","text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. "}],"article_number":"82","file":[{"file_size":1536783,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z","file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","checksum":"7d05cbdd914e194a019c0f91fb64e9a8","content_type":"application/pdf","creator":"system","file_id":"5357","date_created":"2018-12-12T10:18:35Z"}],"intvolume":"         7","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"06","date_updated":"2025-09-18T09:50:10Z","title":"Amplification on undirected population structures: Comets beat stars","publist_id":"7307","has_accepted_license":"1","oa":1,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"publication_identifier":{"issn":["2045-2322"]},"_id":"512","publication":"Scientific Reports","pubrep_id":"938","publisher":"Nature Publishing Group","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41598-017-00107-w","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5449"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"03","date_published":"2017-03-06T00:00:00Z","publication_status":"published","ec_funded":1,"citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” <i>Scientific Reports</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41598-017-00107-w\">https://doi.org/10.1038/s41598-017-00107-w</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. <i>Scientific Reports</i>. 2017;7(1). doi:<a href=\"https://doi.org/10.1038/s41598-017-00107-w\">10.1038/s41598-017-00107-w</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” <i>Scientific Reports</i>, vol. 7, no. 1. Nature Publishing Group, 2017.","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” <i>Scientific Reports</i>, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41598-017-00107-w\">10.1038/s41598-017-00107-w</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-017-00107-w\">https://doi.org/10.1038/s41598-017-00107-w</a>","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017)."},"volume":7,"department":[{"_id":"KrCh"}],"article_processing_charge":"No"},{"publication_status":"published","date_published":"2017-04-04T00:00:00Z","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"MiLe"}],"volume":7,"citation":{"ieee":"G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional ultracold Fermi gases,” <i>Scientific Reports</i>, vol. 7. Nature Publishing Group, 2017.","apa":"Bighin, G., &#38; Salasnich, L. (2017). Vortices and antivortices in two-dimensional ultracold Fermi gases. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep45702\">https://doi.org/10.1038/srep45702</a>","ista":"Bighin G, Salasnich L. 2017. Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. 7, 45702.","mla":"Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” <i>Scientific Reports</i>, vol. 7, 45702, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/srep45702\">10.1038/srep45702</a>.","short":"G. Bighin, L. Salasnich, Scientific Reports 7 (2017).","chicago":"Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” <i>Scientific Reports</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/srep45702\">https://doi.org/10.1038/srep45702</a>.","ama":"Bighin G, Salasnich L. Vortices and antivortices in two-dimensional ultracold Fermi gases. <i>Scientific Reports</i>. 2017;7. doi:<a href=\"https://doi.org/10.1038/srep45702\">10.1038/srep45702</a>"},"oa":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1038/srep45702","pubrep_id":"809","publisher":"Nature Publishing Group","scopus_import":"1","publication":"Scientific Reports","_id":"1015","publication_identifier":{"issn":["2045-2322"]},"external_id":{"isi":["000398148100001"]},"year":"2017","isi":1,"quality_controlled":"1","day":"04","date_updated":"2025-07-10T11:49:43Z","publist_id":"6380","title":"Vortices and antivortices in two-dimensional ultracold Fermi gases","language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"         7","abstract":[{"lang":"eng","text":"Vortices are commonly observed in the context of classical hydrodynamics: from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon such as a tornado, all classical vortices are characterized by an arbitrary circulation value of the local velocity field. On the other hand the appearance of vortices with quantized circulation represents one of the fundamental signatures of macroscopic quantum phenomena. In two-dimensional superfluids quantized vortices play a key role in determining finite-temperature properties, as the superfluid phase and the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless transition. Very recent experiments with two-dimensional superfluid fermions motivate the present work: we present theoretical results based on the renormalization group showing that the universal jump of the superfluid density and the critical temperature crucially depend on the interaction strength, providing a strong benchmark for forthcoming investigations."}],"article_number":"45702","file":[{"date_updated":"2018-12-12T10:12:32Z","file_name":"IST-2017-809-v1+1_srep45702.pdf","access_level":"open_access","date_created":"2018-12-12T10:12:32Z","file_id":"4950","creator":"system","content_type":"application/pdf","file_size":478289,"relation":"main_file"}],"type":"journal_article","status":"public","doi":"10.1038/srep45702","file_date_updated":"2018-12-12T10:12:32Z","author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"full_name":"Salasnich, Luca","last_name":"Salasnich","first_name":"Luca"}],"ddc":["539"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2018-12-11T11:49:42Z"},{"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","publication_status":"published","date_published":"2017-03-23T00:00:00Z","citation":{"ama":"Roth-Walter F, Bergmayr C, Meitz S, et al. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. <i>Scientific Reports</i>. 2017;7. doi:<a href=\"https://doi.org/10.1038/srep45067\">10.1038/srep45067</a>","chicago":"Roth-Walter, Franziska, Cornelia Bergmayr, Sarah Meitz, Stefan Buchleitner, Caroline Stremnitzer, Judit Singer, Anna Moskovskich, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” <i>Scientific Reports</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/srep45067\">https://doi.org/10.1038/srep45067</a>.","ieee":"F. Roth-Walter <i>et al.</i>, “Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure,” <i>Scientific Reports</i>, vol. 7. Springer Nature, 2017.","short":"F. Roth-Walter, C. Bergmayr, S. Meitz, S. Buchleitner, C. Stremnitzer, J. Singer, A. Moskovskich, M.A. Müller, G.A. Roth, K. Manzano-Szalai, Z. Dvorak, A. Neunkirchner, E. Jensen-Jarolim, Scientific Reports 7 (2017).","apa":"Roth-Walter, F., Bergmayr, C., Meitz, S., Buchleitner, S., Stremnitzer, C., Singer, J., … Jensen-Jarolim, E. (2017). Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/srep45067\">https://doi.org/10.1038/srep45067</a>","ista":"Roth-Walter F, Bergmayr C, Meitz S, Buchleitner S, Stremnitzer C, Singer J, Moskovskich A, Müller MA, Roth GA, Manzano-Szalai K, Dvorak Z, Neunkirchner A, Jensen-Jarolim E. 2017. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. 7, 45067.","mla":"Roth-Walter, Franziska, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” <i>Scientific Reports</i>, vol. 7, 45067, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/srep45067\">10.1038/srep45067</a>."},"volume":7,"article_processing_charge":"No","extern":"1","oa":1,"_id":"8239","publication_identifier":{"issn":["2045-2322"]},"publication":"Scientific Reports","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/srep45067","quality_controlled":"1","year":"2017","article_number":"45067","abstract":[{"lang":"eng","text":"Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts during smoking and is best known for its genotoxic capacity. Here, we aimed to assess whether acrolein at concentrations relevant for smokers may also exert immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c allergy model repeated nasal exposure to acrolein abrogated allergen-specific antibody and cytokine formation, and led to a relative accumulation of regulatory T cells in the lungs. Only the acrolein-treated mice were protected from bronchial hyperreactivity as well as from anaphylactic reactions upon challenge with the specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls. Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which could be antagonized by resveratrol. Our mouse and human data thus revealed that acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells. This provides a novel explanation why smokers have a lower allergy, but higher cancer risk."}],"intvolume":"         7","oa_version":"Published Version","language":[{"iso":"eng"}],"title":"Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure","date_updated":"2021-01-12T08:17:40Z","day":"23","status":"public","doi":"10.1038/srep45067","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/srep45067"}],"date_created":"2020-08-10T11:53:46Z","author":[{"last_name":"Roth-Walter","first_name":"Franziska","full_name":"Roth-Walter, Franziska"},{"first_name":"Cornelia","last_name":"Bergmayr","full_name":"Bergmayr, Cornelia"},{"last_name":"Meitz","first_name":"Sarah","full_name":"Meitz, Sarah"},{"full_name":"Buchleitner, Stefan","last_name":"Buchleitner","first_name":"Stefan"},{"last_name":"Stremnitzer","first_name":"Caroline","full_name":"Stremnitzer, Caroline"},{"full_name":"Fazekas, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","last_name":"Fazekas","orcid":"0000-0002-8777-3502"},{"first_name":"Anna","last_name":"Moskovskich","full_name":"Moskovskich, Anna"},{"full_name":"Müller, Mario A.","last_name":"Müller","first_name":"Mario A."},{"first_name":"Georg A.","last_name":"Roth","full_name":"Roth, Georg A."},{"first_name":"Krisztina","last_name":"Manzano-Szalai","full_name":"Manzano-Szalai, Krisztina"},{"last_name":"Dvorak","first_name":"Zdenek","full_name":"Dvorak, Zdenek"},{"full_name":"Neunkirchner, Alina","last_name":"Neunkirchner","first_name":"Alina"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"}]},{"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","date_published":"2017-05-04T00:00:00Z","publication_status":"published","citation":{"short":"Z. Zhu, R.D. McDonald, A. Shekhter, B.J. Ramshaw, K.A. Modic, F.F. Balakirev, N. Harrison, Scientific Reports 7 (2017).","apa":"Zhu, Z., McDonald, R. D., Shekhter, A., Ramshaw, B. J., Modic, K. A., Balakirev, F. F., &#38; Harrison, N. (2017). Magnetic field tuning of an excitonic insulator between the weak and strong coupling regimes in quantum limit graphite. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-017-01693-5\">https://doi.org/10.1038/s41598-017-01693-5</a>","ista":"Zhu Z, McDonald RD, Shekhter A, Ramshaw BJ, Modic KA, Balakirev FF, Harrison N. 2017. Magnetic field tuning of an excitonic insulator between the weak and strong coupling regimes in quantum limit graphite. Scientific Reports. 7, 1733.","mla":"Zhu, Z., et al. “Magnetic Field Tuning of an Excitonic Insulator between the Weak and Strong Coupling Regimes in Quantum Limit Graphite.” <i>Scientific Reports</i>, vol. 7, 1733, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/s41598-017-01693-5\">10.1038/s41598-017-01693-5</a>.","ieee":"Z. Zhu <i>et al.</i>, “Magnetic field tuning of an excitonic insulator between the weak and strong coupling regimes in quantum limit graphite,” <i>Scientific Reports</i>, vol. 7. Springer Nature, 2017.","ama":"Zhu Z, McDonald RD, Shekhter A, et al. Magnetic field tuning of an excitonic insulator between the weak and strong coupling regimes in quantum limit graphite. <i>Scientific Reports</i>. 2017;7. doi:<a href=\"https://doi.org/10.1038/s41598-017-01693-5\">10.1038/s41598-017-01693-5</a>","chicago":"Zhu, Z., R. D. McDonald, A. Shekhter, B. J. Ramshaw, Kimberly A Modic, F. F. Balakirev, and N. Harrison. “Magnetic Field Tuning of an Excitonic Insulator between the Weak and Strong Coupling Regimes in Quantum Limit Graphite.” <i>Scientific Reports</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41598-017-01693-5\">https://doi.org/10.1038/s41598-017-01693-5</a>."},"volume":7,"article_processing_charge":"No","has_accepted_license":"1","extern":"1","oa":1,"_id":"7066","publication_identifier":{"issn":["2045-2322"]},"publication":"Scientific Reports","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s41598-017-01693-5","quality_controlled":"1","year":"2017","article_number":"1733","abstract":[{"text":"The excitonic insulator phase has long been predicted to form in proximity to a band gap opening in the underlying band structure. The character of the pairing is conjectured to crossover from weak (BCS-like) to strong coupling (BEC-like) as the underlying band structure is tuned from the metallic to the insulating side of the gap opening. Here we report the high-magnetic field phase diagram of graphite to exhibit just such a crossover. By way of comprehensive angle-resolved magnetoresistance measurements, we demonstrate that the underlying band gap opening occurs inside the magnetic field-induced phase, paving the way for a systematic study of the BCS-BEC-like crossover by means of conventional condensed matter probes.","lang":"eng"}],"file":[{"file_size":1571567,"relation":"main_file","date_updated":"2020-07-14T12:47:48Z","file_name":"2017_ScientificReports_Zhu.pdf","access_level":"open_access","file_id":"7111","checksum":"801f80b04ecd1ead95c8ab9827cbe067","content_type":"application/pdf","creator":"dernst","date_created":"2019-11-26T11:58:58Z"}],"intvolume":"         7","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"04","date_updated":"2021-01-12T08:11:40Z","title":"Magnetic field tuning of an excitonic insulator between the weak and strong coupling regimes in quantum limit graphite","doi":"10.1038/s41598-017-01693-5","status":"public","file_date_updated":"2020-07-14T12:47:48Z","type":"journal_article","date_created":"2019-11-19T13:17:46Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Zhu","first_name":"Z.","full_name":"Zhu, Z."},{"full_name":"McDonald, R. D.","last_name":"McDonald","first_name":"R. D."},{"first_name":"A.","last_name":"Shekhter","full_name":"Shekhter, A."},{"last_name":"Ramshaw","first_name":"B. J.","full_name":"Ramshaw, B. J."},{"full_name":"Modic, Kimberly A","last_name":"Modic","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"full_name":"Balakirev, F. F.","last_name":"Balakirev","first_name":"F. F."},{"full_name":"Harrison, N.","first_name":"N.","last_name":"Harrison"}],"ddc":["530"]},{"publication":"Scientific Reports","_id":"10377","pmid":1,"publication_identifier":{"issn":["2045-2322"]},"fulldoi":"https://doi.org/10.1038/srep32825","publisher":"Springer Nature","scopus_import":"1","oa":1,"extern":"1","has_accepted_license":"1","arxiv":1,"volume":6,"citation":{"chicago":"Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich, and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/srep32825\">https://doi.org/10.1038/srep32825</a>.","ama":"van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated attraction between curvature inducing objects. <i>Scientific Reports</i>. 2016;6(1). doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>","ieee":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft, “Lipid membrane-mediated attraction between curvature inducing objects,” <i>Scientific Reports</i>, vol. 6, no. 1. Springer Nature, 2016.","apa":"van der Wel, C., Vahid, A., Šarić, A., Idema, T., Heinrich, D., &#38; Kraft, D. J. (2016). Lipid membrane-mediated attraction between curvature inducing objects. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/srep32825\">https://doi.org/10.1038/srep32825</a>","mla":"van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>, vol. 6, no. 1, 32825, Springer Nature, 2016, doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>.","ista":"van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. 2016. Lipid membrane-mediated attraction between curvature inducing objects. Scientific Reports. 6(1), 32825.","short":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific Reports 6 (2016)."},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/srep37382"}]},"article_type":"original","date_published":"2016-09-13T00:00:00Z","publication_status":"published","month":"09","date_created":"2021-11-29T10:34:08Z","acknowledgement":"This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program and VENI grant 680-47-431. We thank Jeroen Appel and Wim Pomp for advice on the protocol design and Marcel Winter and Ruben Verweij for experimental support.","issue":"1","main_file_link":[{"url":"https://www.nature.com/articles/srep32825","open_access":"1"}],"ddc":["540"],"author":[{"full_name":"van der Wel, Casper","first_name":"Casper","last_name":"van der Wel"},{"first_name":"Afshin","last_name":"Vahid","full_name":"Vahid, Afshin"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"},{"full_name":"Heinrich, Doris","first_name":"Doris","last_name":"Heinrich"},{"full_name":"Kraft, Daniela J.","last_name":"Kraft","first_name":"Daniela J."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","doi":"10.1038/srep32825","file_date_updated":"2021-11-29T10:50:00Z","status":"public","intvolume":"         6","file":[{"relation":"main_file","file_size":1598289,"file_id":"10379","content_type":"application/pdf","success":1,"checksum":"d6cf16dd511e15726b001e7cc287cf1d","creator":"cchlebak","date_created":"2021-11-29T10:50:00Z","date_updated":"2021-11-29T10:50:00Z","file_name":"2016_SciRep_vanderWel.pdf","access_level":"open_access"}],"article_number":"32825","abstract":[{"lang":"eng","text":"The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membrane curvature energy. Here, we present a combined experimental and numerical study in which we quantify these interactions directly for the first time. In our experimental model system we control the deformation of a lipid membrane by adhering colloidal particles. Using confocal microscopy, we establish that these membrane deformations cause an attractive interaction force leading to reversible binding. The attraction extends over 2.5 times the particle diameter and has a strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo simulations of the system are in excellent agreement with the experimental results and prove that the measured interaction is independent of length scale. Our combined experimental and numerical results reveal membrane curvature as a common physical origin for interactions between any membrane-deforming objects, from nanometre-sized proteins to micrometre-sized particles."}],"title":"Lipid membrane-mediated attraction between curvature inducing objects","date_updated":"2021-11-29T11:08:15Z","day":"13","oa_version":"Published Version","language":[{"iso":"eng"}],"keyword":["multidisciplinary"],"quality_controlled":"1","external_id":{"arxiv":["1603.04644"],"pmid":["27618764"]},"year":"2016"}]