[{"volume":34,"day":"01","page":"2150-2173","type":"journal_article","article_processing_charge":"No","publication":"Plant Cell","issue":"6","publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"_id":"10841","pmid":1,"intvolume":"        34","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","citation":{"mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>"},"oa":1,"quality_controlled":"1","article_type":"original","date_created":"2022-03-08T13:47:51Z","year":"2022","oa_version":"Preprint","scopus_import":"1","month":"06","external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"date_updated":"2025-05-14T11:06:15Z","project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"author":[{"last_name":"Dahhan","full_name":"Dahhan, DA","first_name":"DA"},{"first_name":"GD","full_name":"Reynolds, GD","last_name":"Reynolds"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"first_name":"D","full_name":"Eeckhout, D","last_name":"Eeckhout"},{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"last_name":"Vang","full_name":"Vang, N","first_name":"N"},{"first_name":"X","last_name":"Yan","full_name":"Yan, X"},{"full_name":"Hwang, I","last_name":"Hwang","first_name":"I"},{"first_name":"A","last_name":"Heese","full_name":"Heese, A"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Van Damme","full_name":"Van Damme, D","first_name":"D"},{"first_name":"J","last_name":"Pan","full_name":"Pan, J"},{"last_name":"Bednarek","full_name":"Bednarek, SY","first_name":"SY"}],"date_published":"2022-06-01T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"isi":1,"acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"doi":"10.1093/plcell/koac071"},{"date_published":"2022-07-01T00:00:00Z","author":[{"full_name":"Köse, Seyda","last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","first_name":"Seyda"},{"last_name":"Özbudak","full_name":"Özbudak, Ferruh","first_name":"Ferruh"}],"date_updated":"2023-09-05T15:35:55Z","language":[{"iso":"eng"}],"external_id":{"isi":["000766422000002"]},"month":"07","oa_version":"None","scopus_import":"1","doi":"10.1007/s12095-022-00557-8","publication_identifier":{"issn":["1936-2447"],"eissn":["1936-2455"]},"acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","isi":1,"department":[{"_id":"GradSch"}],"publication_status":"published","status":"public","_id":"10842","abstract":[{"lang":"eng","text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory."}],"intvolume":"        14","publisher":"Springer Nature","publication":"Cryptography and Communications","issue":"4","article_processing_charge":"No","type":"journal_article","page":"933-948","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"day":"01","volume":14,"year":"2022","date_created":"2022-03-10T12:16:19Z","article_type":"original","quality_controlled":"1","citation":{"ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948.","ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. 2022;14(4):933-948. doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>.","apa":"Köse, S., &#38; Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>","mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>.","short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.","ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” <i>Cryptography and Communications</i>, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022."},"title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"02","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000758859600001"],"pmid":["35188063"]},"date_updated":"2023-10-03T10:54:54Z","date_published":"2022-02-19T00:00:00Z","author":[{"orcid":"0000-0001-8945-6992","first_name":"Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat"},{"first_name":"Jooyeon","last_name":"Sohn","full_name":"Sohn, Jooyeon"},{"last_name":"Lee","full_name":"Lee, Cheolju","first_name":"Cheolju"},{"first_name":"Seung Yeol","last_name":"Park","full_name":"Park, Seung Yeol"},{"full_name":"Lee, Seung Jae V.","last_name":"Lee","first_name":"Seung Jae V."}],"department":[{"_id":"MaDe"}],"isi":1,"publication_identifier":{"eissn":["1554-8635"],"issn":["1554-8627"]},"acknowledgement":"This work is funded by National Research Foundation of Korea (NRF) grants NRF-2019R1A3B2067745 from the Korean Government (Ministry of Science and Information and Communications Technology (S-J.V.L.). NRF-2017R1A5A1015366 (S.Y.P, S-J.V.L). Korea Institute of Science and Technology (KIST) intramural grant (C.L).","doi":"10.1080/15548627.2022.2039523","type":"journal_article","page":"1208-1210","day":"19","volume":18,"publisher":"Taylor & Francis","issue":"5","publication":"Autophagy","article_processing_charge":"No","status":"public","intvolume":"        18","_id":"10846","abstract":[{"lang":"eng","text":"The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of the Golgi apparatus in organismal longevity remained largely unknown. By employing a quantitative proteomic approach, we demonstrated that MON-2, an evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking, promotes longevity via upregulating macroautophagy/autophagy in C. elegans. Our data using cultured mammalian cells indicate that MON2 translocates from the Golgi to the endosome under starvation conditions, subsequently increasing autophagic flux by binding LGG-1/GABARAPL2. Thus, Golgi-to-endosome trafficking appears to be an evolutionarily conserved process for the upregulation of autophagy, which contributes to organismal longevity."}],"pmid":1,"main_file_link":[{"url":"https://doi.org/10.1080/15548627.2022.2039523","open_access":"1"}],"publication_status":"published","title":"MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"citation":{"short":"M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 1208–1210.","mla":"Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>, vol. 18, no. 5, Taylor &#38; Francis, 2022, pp. 1208–10, doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>.","ieee":"M. Artan, J. Sohn, C. Lee, S. Y. Park, and S. J. V. Lee, “MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications,” <i>Autophagy</i>, vol. 18, no. 5. Taylor &#38; Francis, pp. 1208–1210, 2022.","ama":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. 2022;18(5):1208-1210. doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>","ista":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. 2022. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. Autophagy. 18(5), 1208–1210.","apa":"Artan, M., Sohn, J., Lee, C., Park, S. Y., &#38; Lee, S. J. V. (2022). MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>","chicago":"Artan, Murat, Jooyeon Sohn, Cheolju Lee, Seung Yeol Park, and Seung Jae V. Lee. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>."},"year":"2022","date_created":"2022-03-13T23:01:47Z","article_type":"original","quality_controlled":"1"},{"publication":"Physical Review B","publisher":"American Physical Society","article_processing_charge":"No","type":"journal_article","volume":105,"day":"17","arxiv":1,"publication_status":"published","_id":"10863","intvolume":"       105","abstract":[{"text":"Nonlinear optical responses are commonly used as a probe for studying the electronic properties of materials. For topological materials, studies thus far focused on photogalvanic electric currents, which are forbidden in centrosymmetric materials because they require broken inversion symmetry. In this Letter, we propose a class of symmetry-allowed responses for inversion-symmetric topological insulators with two doubly degenerate bands. We consider a specific example of such a response, the orbital current, and show that the sign of the response reflects the Z2 topological index, i.e., the orbital current changes sign at the transition between trivial and topological insulator phases. This is illustrated in two models of topological insulators: the Bernevig-Hughes-Zhang model and the 1T′ phase of transition metal dichalcogenides.","lang":"eng"}],"status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2101.08277","open_access":"1"}],"title":"Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-03-18T10:20:46Z","year":"2022","quality_controlled":"1","article_type":"letter_note","oa":1,"citation":{"mla":"Davydova, Margarita, et al. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>, vol. 105, L121407, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>.","ieee":"M. Davydova, M. Serbyn, and H. Ishizuka, “Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials,” <i>Physical Review B</i>, vol. 105. American Physical Society, 2022.","short":"M. Davydova, M. Serbyn, H. Ishizuka, Physical Review B 105 (2022).","ama":"Davydova M, Serbyn M, Ishizuka H. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. 2022;105. doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>","ista":"Davydova M, Serbyn M, Ishizuka H. 2022. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. Physical Review B. 105, L121407.","apa":"Davydova, M., Serbyn, M., &#38; Ishizuka, H. (2022). Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>","chicago":"Davydova, Margarita, Maksym Serbyn, and Hiroaki Ishizuka. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>."},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2101.08277"],"isi":["000800752500001"]},"month":"03","oa_version":"Preprint","scopus_import":"1","date_published":"2022-03-17T00:00:00Z","author":[{"first_name":"Margarita","full_name":"Davydova, Margarita","last_name":"Davydova"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"last_name":"Ishizuka","full_name":"Ishizuka, Hiroaki","first_name":"Hiroaki"}],"date_updated":"2023-08-03T06:09:56Z","article_number":"L121407","department":[{"_id":"MaSe"}],"isi":1,"doi":"10.1103/PhysRevB.105.L121407","publication_identifier":{"issn":["2469-9969"]},"acknowledgement":"We are grateful to Takahiro Morimoto and Zhanybek Alpichshev for fruitful discussions. MD was supported by Austrian Agency for International Cooperation in Education and Research (OeAD-GmbH) and by the John Seo Fellowship at MIT. HI was supported by JSPS KAKENHI Grant Numbers JP19K14649 and JP18H03676, and by UTokyo Global Activity Support Program for\r\nYoung Researchers."},{"month":"06","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"arxiv":["2006.09934"],"isi":["000781371300008"]},"date_updated":"2024-10-09T21:01:51Z","ddc":["510"],"date_published":"2022-06-01T00:00:00Z","author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"},{"first_name":"Márton","full_name":"Naszódi, Márton","last_name":"Naszódi"}],"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"UlWa"}],"article_number":"109441","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"acknowledgement":"G.I. was supported by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and KKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI. ","doi":"10.1016/j.jfa.2022.109441","type":"journal_article","day":"01","volume":282,"publisher":"Elsevier","issue":"11","publication":"Journal of Functional Analysis","article_processing_charge":"Yes (via OA deal)","status":"public","_id":"10887","intvolume":"       282","abstract":[{"text":"We introduce a new way of representing logarithmically concave functions on Rd. It allows us to extend the notion of the largest volume ellipsoid contained in a convex body to the setting of logarithmically concave functions as follows. For every s>0, we define a class of non-negative functions on Rd derived from ellipsoids in Rd+1. For any log-concave function f on Rd , and any fixed s>0, we consider functions belonging to this class, and find the one with the largest integral under the condition that it is pointwise less than or equal to f, and we call it the John s-function of f. After establishing existence and uniqueness, we give a characterization of this function similar to the one given by John in his fundamental theorem. We find that John s-functions converge to characteristic functions of ellipsoids as s tends to zero and to Gaussian densities as s tends to infinity.\r\nAs an application, we prove a quantitative Helly type result: the integral of the pointwise minimum of any family of log-concave functions is at least a constant cd multiple of the integral of the pointwise minimum of a properly chosen subfamily of size 3d+2, where cd depends only on d.","lang":"eng"}],"arxiv":1,"file":[{"file_size":734482,"checksum":"1cf185e264e04c87cb1ce67a00db88ab","access_level":"open_access","file_id":"11721","date_created":"2022-08-02T10:40:48Z","file_name":"2022_JourFunctionalAnalysis_Ivanov.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2022-08-02T10:40:48Z","success":1,"creator":"dernst"}],"publication_status":"published","title":"Functional John ellipsoids","file_date_updated":"2022-08-02T10:40:48Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"citation":{"short":"G. Ivanov, M. Naszódi, Journal of Functional Analysis 282 (2022).","ieee":"G. Ivanov and M. Naszódi, “Functional John ellipsoids,” <i>Journal of Functional Analysis</i>, vol. 282, no. 11. Elsevier, 2022.","mla":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>, vol. 282, no. 11, 109441, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>.","chicago":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>.","apa":"Ivanov, G., &#38; Naszódi, M. (2022). Functional John ellipsoids. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>","ista":"Ivanov G, Naszódi M. 2022. Functional John ellipsoids. Journal of Functional Analysis. 282(11), 109441.","ama":"Ivanov G, Naszódi M. Functional John ellipsoids. <i>Journal of Functional Analysis</i>. 2022;282(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>"},"year":"2022","date_created":"2022-03-20T23:01:38Z","article_type":"original","quality_controlled":"1","corr_author":"1"},{"external_id":{"pmid":["35254915"],"isi":["000771756300008"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","month":"03","author":[{"first_name":"Qing","full_name":"Lu, Qing","last_name":"Lu"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"first_name":"Joakim","last_name":"Hellner","full_name":"Hellner, Joakim"},{"full_name":"Giannini, Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina"},{"first_name":"Xiangyu","last_name":"Xu","full_name":"Xu, Xiangyu"},{"first_name":"Jarne","full_name":"Pauwels, Jarne","last_name":"Pauwels"},{"full_name":"Ma, Qian","last_name":"Ma","first_name":"Qian"},{"last_name":"Dejonghe","full_name":"Dejonghe, Wim","first_name":"Wim"},{"full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"full_name":"Impens, Francis","last_name":"Impens","first_name":"Francis"},{"first_name":"Kris","full_name":"Gevaert, Kris","last_name":"Gevaert"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel Martinez","full_name":"Molina, Daniel Martinez","last_name":"Molina"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"ddc":["580"],"date_published":"2022-03-07T00:00:00Z","date_updated":"2025-05-14T11:01:45Z","article_number":"e2118220119","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"isi":1,"department":[{"_id":"JiFr"}],"doi":"10.1073/pnas.2118220119","acknowledgement":"We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\u0003nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.).","publication_identifier":{"eissn":["1091-6490"]},"article_processing_charge":"No","publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"11","day":"07","volume":119,"type":"journal_article","file":[{"date_updated":"2022-03-21T09:19:47Z","success":1,"creator":"dernst","file_name":"2022_PNAS_Lu.pdf","date_created":"2022-03-21T09:19:47Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"10910","checksum":"83e0fea7919570d0b519b41193342571","file_size":2169534}],"publication_status":"published","status":"public","pmid":1,"_id":"10888","abstract":[{"text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling.","lang":"eng"}],"intvolume":"       119","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","file_date_updated":"2022-03-21T09:19:47Z","article_type":"original","quality_controlled":"1","year":"2022","date_created":"2022-03-20T23:01:39Z","citation":{"ieee":"Q. Lu <i>et al.</i>, “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11. National Academy of Sciences, 2022.","mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11, e2118220119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>.","short":"Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>","chicago":"Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>.","ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(11). doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>","ista":"Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119."},"oa":1},{"month":"03","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["35275179"],"isi":["000768384100011"]},"date_updated":"2025-05-14T11:05:40Z","project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}],"date_published":"2022-03-01T00:00:00Z","author":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"department":[{"_id":"RySh"}],"isi":1,"publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"acknowledgement":"European Research Council Advanced Grant (694539 to R.S.).","doi":"10.1093/jmicro/dfab048","type":"journal_article","volume":71,"day":"01","page":"i72-i80","issue":"Supplement_1","publication":"Microscopy","publisher":"Oxford University Press","article_processing_charge":"No","pmid":1,"_id":"10889","intvolume":"        71","abstract":[{"lang":"eng","text":"Genetically encoded tags have introduced extensive lines of application from purification of tagged proteins to their visualization at the single molecular, cellular, histological and whole-body levels. Combined with other rapidly developing technologies such as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, proteomics, super-resolution microscopy and proximity labeling, a large variety of genetically encoded tags have been developed in the last two decades. In this review, I focus on the current status of tag development for electron microscopic (EM) visualization of proteins with metal particle labeling. Compared with conventional immunoelectron microscopy using gold particles, tag-mediated metal particle labeling has several advantages that could potentially improve the sensitivity, spatial and temporal resolution, and applicability to a wide range of proteins of interest (POIs). It may enable researchers to detect single molecules in situ, allowing the quantitative measurement of absolute numbers and exact localization patterns of POI in the ultrastructural context. Thus, genetically encoded tags for EM could revolutionize the field as green fluorescence protein did for light microscopy, although we still have many challenges to overcome before reaching this goal."}],"status":"public","main_file_link":[{"url":"https://doi.org/10.1093/jmicro/dfab048","open_access":"1"}],"publication_status":"published","ec_funded":1,"title":"Electron microscopic visualization of single molecules by tag-mediated metal particle labeling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"citation":{"ista":"Shigemoto R. 2022. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. Microscopy. 71(Supplement_1), i72–i80.","ama":"Shigemoto R. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. 2022;71(Supplement_1):i72-i80. doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>","chicago":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>.","apa":"Shigemoto, R. (2022). Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>","short":"R. Shigemoto, Microscopy 71 (2022) i72–i80.","ieee":"R. Shigemoto, “Electron microscopic visualization of single molecules by tag-mediated metal particle labeling,” <i>Microscopy</i>, vol. 71, no. Supplement_1. Oxford University Press, pp. i72–i80, 2022.","mla":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>, vol. 71, no. Supplement_1, Oxford University Press, 2022, pp. i72–80, doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>."},"date_created":"2022-03-20T23:01:39Z","year":"2022","corr_author":"1","quality_controlled":"1","article_type":"original"},{"publication_status":"published","_id":"10891","abstract":[{"lang":"eng","text":"We present a formal framework for the online black-box monitoring of software using monitors with quantitative verdict functions. Quantitative verdict functions have several advantages. First, quantitative monitors can be approximate, i.e., the value of the verdict function does not need to correspond exactly to the value of the property under observation. Second, quantitative monitors can be quantified universally, i.e., for every possible observed behavior, the monitor tries to make the best effort to estimate the value of the property under observation. Third, quantitative monitors can watch boolean as well as quantitative properties, such as average response time. Fourth, quantitative monitors can use non-finite-state resources, such as counters. As a consequence, quantitative monitors can be compared according to how many resources they use (e.g., the number of counters) and how precisely they approximate the property under observation. This allows for a rich spectrum of cost-precision trade-offs in monitoring software."}],"intvolume":"     13124","status":"public","article_processing_charge":"No","publication":"Software Verification","publisher":"Springer Nature","volume":13124,"day":"22","page":"3-6","series_title":"LNCS","type":"conference","corr_author":"1","quality_controlled":"1","date_created":"2022-03-20T23:01:40Z","year":"2022","citation":{"mla":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” <i>Software Verification</i>, vol. 13124, Springer Nature, 2022, pp. 3–6, doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>.","ieee":"T. A. Henzinger, “Quantitative monitoring of software,” in <i>Software Verification</i>, New Haven, CT, United States, 2022, vol. 13124, pp. 3–6.","short":"T.A. Henzinger, in:, Software Verification, Springer Nature, 2022, pp. 3–6.","apa":"Henzinger, T. A. (2022). Quantitative monitoring of software. In <i>Software Verification</i> (Vol. 13124, pp. 3–6). New Haven, CT, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>","chicago":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” In <i>Software Verification</i>, 13124:3–6. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>.","ama":"Henzinger TA. Quantitative monitoring of software. In: <i>Software Verification</i>. Vol 13124. LNCS. Springer Nature; 2022:3-6. doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>","ista":"Henzinger TA. 2022. Quantitative monitoring of software. Software Verification. NSV: Numerical Software VerificationLNCS vol. 13124, 3–6."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Quantitative monitoring of software","author":[{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-02-22T00:00:00Z","project":[{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"date_updated":"2025-04-15T06:25:58Z","external_id":{"isi":["000771713200001"]},"language":[{"iso":"eng"}],"conference":{"location":"New Haven, CT, United States","name":"NSV: Numerical Software Verification","end_date":"2021-10-19","start_date":"2021-10-18"},"scopus_import":"1","oa_version":"None","month":"02","doi":"10.1007/978-3-030-95561-8_1","acknowledgement":"The formal framework for quantitative monitoring which is presented in this invited talk was defined jointly with N. Ege Saraç at LICS 2021. This work was supported in part by the Wittgenstein Award Z211-N23 of the Austrian Science Fund.","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030955601"],"issn":["0302-9743"]},"department":[{"_id":"ToHe"}],"isi":1},{"publication_status":"published","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosopila.pdf","date_created":"2022-03-24T13:22:41Z","creator":"siekhaus","date_updated":"2022-03-24T13:22:41Z","checksum":"dba48580fe0fefaa4c63078d1d2a35df","file_size":4344585,"file_id":"10919","access_level":"open_access"}],"pmid":1,"_id":"10918","abstract":[{"lang":"eng","text":"Cellular metabolism must adapt to changing demands to enable homeostasis. During immune responses or cancer metastasis, cells leading migration into challenging environments require an energy boost, but what controls this capacity is unclear. Here, we study a previously uncharacterized nuclear protein, Atossa (encoded by CG9005), which supports macrophage invasion into the germband of Drosophila by controlling cellular metabolism. First, nuclear Atossa increases mRNA levels of Porthos, a DEAD-box protein, and of two metabolic enzymes, lysine-α-ketoglutarate reductase (LKR/SDH) and NADPH glyoxylate reductase (GR/HPR), thus enhancing mitochondrial bioenergetics. Then Porthos supports ribosome assembly and thereby raises the translational efficiency of a subset of mRNAs, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Mitochondrial respiration measurements, metabolomics, and live imaging indicate that Atossa and Porthos power up OxPhos and energy production to promote the forging of a path into tissues by leading macrophages. Since many crucial physiological responses require increases in mitochondrial energy output, this previously undescribed genetic program may modulate a wide range of cellular behaviors."}],"intvolume":"        41","status":"public","article_processing_charge":"Yes (via OA deal)","publication":"The Embo Journal","publisher":"Embo Press","volume":41,"day":"23","type":"journal_article","corr_author":"1","quality_controlled":"1","article_type":"original","date_created":"2022-03-24T13:23:09Z","year":"2022","citation":{"ama":"Emtenani S, Martin ET, György A, et al. Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. <i>The Embo Journal</i>. 2022;41. doi:<a href=\"https://doi.org/10.15252/embj.2021109049\">10.15252/embj.2021109049</a>","ista":"Emtenani S, Martin ET, György A, Bicher J, Genger J-W, Köcher T, Akhmanova M, Pereira Guarda M, Roblek M, Bergthaler A, Hurd TR, Rangan P, Siekhaus DE. 2022. Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. The Embo Journal. 41, e109049.","apa":"Emtenani, S., Martin, E. T., György, A., Bicher, J., Genger, J.-W., Köcher, T., … Siekhaus, D. E. (2022). Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. <i>The Embo Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021109049\">https://doi.org/10.15252/embj.2021109049</a>","chicago":"Emtenani, Shamsi, Elliot T Martin, Attila György, Julia Bicher, Jakob-Wendelin Genger, Thomas Köcher, Maria Akhmanova, et al. “Macrophage Mitochondrial Bioenergetics and Tissue Invasion Are Boosted by an Atossa-Porthos Axis in Drosophila.” <i>The Embo Journal</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/embj.2021109049\">https://doi.org/10.15252/embj.2021109049</a>.","ieee":"S. Emtenani <i>et al.</i>, “Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila,” <i>The Embo Journal</i>, vol. 41. Embo Press, 2022.","short":"S. Emtenani, E.T. Martin, A. György, J. Bicher, J.-W. Genger, T. Köcher, M. Akhmanova, M. Pereira Guarda, M. Roblek, A. Bergthaler, T.R. Hurd, P. Rangan, D.E. Siekhaus, The Embo Journal 41 (2022).","mla":"Emtenani, Shamsi, et al. “Macrophage Mitochondrial Bioenergetics and Tissue Invasion Are Boosted by an Atossa-Porthos Axis in Drosophila.” <i>The Embo Journal</i>, vol. 41, e109049, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/embj.2021109049\">10.15252/embj.2021109049</a>."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-03-24T13:22:41Z","ec_funded":1,"title":"Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila","author":[{"first_name":"Shamsi","orcid":"0000-0001-6981-6938","last_name":"Emtenani","full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elliot T","last_name":"Martin","full_name":"Martin, Elliot T"},{"orcid":"0000-0002-1819-198X","first_name":"Attila","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Bicher, Julia","last_name":"Bicher","first_name":"Julia"},{"first_name":"Jakob-Wendelin","last_name":"Genger","full_name":"Genger, Jakob-Wendelin"},{"first_name":"Thomas","full_name":"Köcher, Thomas","last_name":"Köcher"},{"first_name":"Maria","orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova"},{"first_name":"Mariana","orcid":"0000-0001-8238-480X","last_name":"Pereira Guarda","id":"6de81d9d-e2f2-11eb-945a-af8bc2a60b26","full_name":"Pereira Guarda, Mariana"},{"last_name":"Roblek","full_name":"Roblek, Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","first_name":"Marko"},{"last_name":"Bergthaler","full_name":"Bergthaler, Andreas","first_name":"Andreas"},{"first_name":"Thomas R","full_name":"Hurd, Thomas R","last_name":"Hurd"},{"first_name":"Prashanth","last_name":"Rangan","full_name":"Rangan, Prashanth"},{"first_name":"Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-03-23T00:00:00Z","ddc":["570"],"project":[{"name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077"},{"_id":"264CBBAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion","grant_number":"M02379"},{"name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"}],"date_updated":"2025-06-12T06:20:16Z","external_id":{"isi":["000771957000001"],"pmid":["35319107"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"03","doi":"10.15252/embj.2021109049","acknowledgement":"We thank the DGRC (NIH grant 2P40OD010949-10A1) for plasmids, the BDSC (NIH grant P40OD018537) and the VDRC for fly stocks, FlyBase for essential genomic information, the BDGP in situ database for data (Tomancak et al, 2007), the IST Austria Bioimaging facility for support, the VBC Core Facilities for RNA sequencing and analysis, and C. Guet, C. Navarro, C. Desplan, T. Lecuit, I. Miguel-Aliaga, and Siekhaus group members for comments on the manuscript. The VBCF Metabolomics Facility is funded by the City of Vienna through the Vienna Business Agency. This work was supported by the Marie Curie CIG 334077/IRTIM (DES), Austrian Science Fund (FWF) Lise Meitner Fellowship M2379-B28 (MA and DES), Austrian Science Fund (FWF) grant ASI_FWF01_P29638S (DES), NIH/NIGMS (R01GM111779-06 (PR), RO1GM135628-01 (PR), European Research Council (ERC) grant no. 677006 “CMIL” (AB), and Natural Sciences and Engineering Research Council of Canada\r\n(RGPIN-2019-06766) (TRH). ","publication_identifier":{"eissn":["1460-2075"]},"article_number":"e109049","department":[{"_id":"DaSi"},{"_id":"LoSw"}],"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"},"isi":1},{"date_created":"2022-03-24T15:51:11Z","year":"2022","quality_controlled":"1","corr_author":"1","article_type":"original","oa":1,"citation":{"ama":"Jirovec D, Mutter PM, Hofmann AC, et al. Dynamics of hole singlet-triplet qubits with large g-factor differences. <i>Physical Review Letters</i>. 2022;128(12). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">10.1103/PhysRevLett.128.126803</a>","ista":"Jirovec D, Mutter PM, Hofmann AC, Crippa A, Rychetsky M, Craig DL, Kukucka J, Martins F, Ballabio A, Ares N, Chrastina D, Isella G, Burkard G, Katsaros G. 2022. Dynamics of hole singlet-triplet qubits with large g-factor differences. Physical Review Letters. 128(12), 126803.","apa":"Jirovec, D., Mutter, P. M., Hofmann, A. C., Crippa, A., Rychetsky, M., Craig, D. L., … Katsaros, G. (2022). Dynamics of hole singlet-triplet qubits with large g-factor differences. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">https://doi.org/10.1103/PhysRevLett.128.126803</a>","chicago":"Jirovec, Daniel, Philipp M. Mutter, Andrea C Hofmann, Alessandro Crippa, Marek Rychetsky, David L. Craig, Josip Kukucka, et al. “Dynamics of Hole Singlet-Triplet Qubits with Large g-Factor Differences.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">https://doi.org/10.1103/PhysRevLett.128.126803</a>.","mla":"Jirovec, Daniel, et al. “Dynamics of Hole Singlet-Triplet Qubits with Large g-Factor Differences.” <i>Physical Review Letters</i>, vol. 128, no. 12, 126803, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">10.1103/PhysRevLett.128.126803</a>.","ieee":"D. Jirovec <i>et al.</i>, “Dynamics of hole singlet-triplet qubits with large g-factor differences,” <i>Physical Review Letters</i>, vol. 128, no. 12. American Physical Society, 2022.","short":"D. Jirovec, P.M. Mutter, A.C. Hofmann, A. Crippa, M. Rychetsky, D.L. Craig, J. Kukucka, F. Martins, A. Ballabio, N. Ares, D. Chrastina, G. Isella, G. Burkard, G. Katsaros, Physical Review Letters 128 (2022)."},"file_date_updated":"2022-03-28T06:53:39Z","ec_funded":1,"title":"Dynamics of hole singlet-triplet qubits with large g-factor differences","related_material":{"record":[{"relation":"popular_science","id":"18291","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication_status":"published","file":[{"file_name":"2022_PhysRevLetters_Jirovec.pdf","date_created":"2022-03-28T06:53:39Z","content_type":"application/pdf","relation":"main_file","date_updated":"2022-03-28T06:53:39Z","creator":"dernst","success":1,"checksum":"6e66ad548d18db9c131f304acbd5a1f4","file_size":1266515,"access_level":"open_access","file_id":"10928"}],"intvolume":"       128","_id":"10920","pmid":1,"abstract":[{"lang":"eng","text":"The spin-orbit interaction permits to control the state of a spin qubit via electric fields. For holes it is particularly strong, allowing for fast all electrical qubit manipulation, and yet an in-depth understanding of this interaction in hole systems is missing. Here we investigate, experimentally and theoretically, the effect of the cubic Rashba spin-orbit interaction on the mixing of the spin states by studying singlet-triplet oscillations in a planar Ge hole double quantum dot. Landau-Zener sweeps at different magnetic field directions allow us to disentangle the effects of the spin-orbit induced spin-flip term from those caused by strongly site-dependent and anisotropic quantum dot g tensors. Our work, therefore, provides new insights into the hole spin-orbit interaction, necessary for optimizing future qubit experiments."}],"status":"public","publication":"Physical Review Letters","issue":"12","publisher":"American Physical Society","article_processing_charge":"No","type":"journal_article","volume":128,"day":"24","doi":"10.1103/PhysRevLett.128.126803","publication_identifier":{"eissn":["1079-7114"]},"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 844511, No. 75441, and by the FWF-P 30207, I05060, and M3032-N projects. A. B. acknowledges support from the EU Horizon-2020 FET project microSPIRE, ID: 766955. P.M. M. and G. B. acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG—German Research Foundation) under Project No. 450396347. This work was supported by the Royal Society (URF\\R1\\191150) and the European Research Council (Grant Agreement No. 948932), N. A. acknowledges the use of the University of Oxford Advanced Research Computing (ARC) facility.","article_number":"126803","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"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"},"isi":1,"date_published":"2022-03-24T00:00:00Z","ddc":["530"],"author":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801"},{"first_name":"Philipp M.","last_name":"Mutter","full_name":"Mutter, Philipp M."},{"first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"orcid":"0000-0002-2968-611X","first_name":"Alessandro","last_name":"Crippa","full_name":"Crippa, Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"first_name":"Marek","last_name":"Rychetsky","full_name":"Rychetsky, Marek"},{"first_name":"David L.","full_name":"Craig, David L.","last_name":"Craig"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"full_name":"Martins, Frederico","last_name":"Martins","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","orcid":"0000-0003-2668-2401","first_name":"Frederico"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"full_name":"Ares, Natalia","last_name":"Ares","first_name":"Natalia"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"full_name":"Burkard, Guido ","last_name":"Burkard","first_name":"Guido "},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207"},{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"c08c05c4-5a5b-11eb-8a69-dc6ce49d7973","name":"Long-range spin exchange for 2D qubits architectures","grant_number":"M03032"}],"date_updated":"2025-04-14T07:44:07Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"arxiv":["2111.05130"],"pmid":["35394319"],"isi":["000786542500004"]},"month":"03","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1"},{"citation":{"chicago":"Liu, Zhenyuan, Jingyu Hu, Hao Xu, Peng Song, Ran Zhang, Bernd Bickel, and Chi-Wing Fu. “Worst-Case Rigidity Analysis and Optimization for Assemblies with Mechanical Joints.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14490\">https://doi.org/10.1111/cgf.14490</a>.","apa":"Liu, Z., Hu, J., Xu, H., Song, P., Zhang, R., Bickel, B., &#38; Fu, C.-W. (2022). Worst-case rigidity analysis and optimization for assemblies with mechanical joints. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14490\">https://doi.org/10.1111/cgf.14490</a>","ista":"Liu Z, Hu J, Xu H, Song P, Zhang R, Bickel B, Fu C-W. 2022. Worst-case rigidity analysis and optimization for assemblies with mechanical joints. Computer Graphics Forum. 41(2), 507–519.","ama":"Liu Z, Hu J, Xu H, et al. Worst-case rigidity analysis and optimization for assemblies with mechanical joints. <i>Computer Graphics Forum</i>. 2022;41(2):507-519. doi:<a href=\"https://doi.org/10.1111/cgf.14490\">10.1111/cgf.14490</a>","short":"Z. Liu, J. Hu, H. Xu, P. Song, R. Zhang, B. Bickel, C.-W. Fu, Computer Graphics Forum 41 (2022) 507–519.","ieee":"Z. Liu <i>et al.</i>, “Worst-case rigidity analysis and optimization for assemblies with mechanical joints,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 507–519, 2022.","mla":"Liu, Zhenyuan, et al. “Worst-Case Rigidity Analysis and Optimization for Assemblies with Mechanical Joints.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 507–19, doi:<a href=\"https://doi.org/10.1111/cgf.14490\">10.1111/cgf.14490</a>."},"oa":1,"quality_controlled":"1","article_type":"original","date_created":"2022-03-27T17:34:17Z","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2022-03-27T17:34:11Z","title":"Worst-case rigidity analysis and optimization for assemblies with mechanical joints","ec_funded":1,"_id":"10922","intvolume":"        41","abstract":[{"lang":"eng","text":"We study structural rigidity for assemblies with mechanical joints. Existing methods identify whether an assembly is structurally rigid by assuming parts are perfectly rigid. Yet, an assembly identified as rigid may not be that “rigid” in practice, and existing methods cannot quantify how rigid an assembly is. We address this limitation by developing a new measure, worst-case rigidity, to quantify the rigidity of an assembly as the largest possible deformation that the assembly undergoes for arbitrary external loads of fixed magnitude. Computing worst-case rigidity is non-trivial due to non-rigid parts and different joint types. We thus formulate a new computational approach by encoding parts and their connections into a stiffness matrix, in which parts are modeled as deformable objects and joints as soft constraints. Based on this, we formulate worst-case rigidity analysis as an optimization that seeks the worst-case deformation of an assembly for arbitrary external loads, and solve the optimization problem via an eigenanalysis. Furthermore, we present methods to optimize the geometry and topology of various assemblies to enhance their rigidity, as guided by our rigidity measure. In the end, we validate our method on a variety of assembly structures with physical experiments and demonstrate its effectiveness by designing and fabricating several structurally rigid assemblies."}],"status":"public","publication_status":"published","file":[{"file_name":"paper.pdf","date_created":"2022-03-27T17:34:11Z","content_type":"application/pdf","relation":"main_file","date_updated":"2022-03-27T17:34:11Z","creator":"bbickel","file_size":19601689,"checksum":"b62188b07f5c000f1638c782ec92da41","access_level":"open_access","file_id":"10923"}],"volume":41,"page":"507-519","day":"01","type":"journal_article","article_processing_charge":"No","publication":"Computer Graphics Forum","issue":"2","publisher":"Wiley","acknowledgement":"This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, China [Project No.: CUHK 14201921] and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767 – MATERIALIZABLE). We thank the anonymous reviewers for their insightful feedback; Christian Hafner for proofreading and discussions; Ziqi Wang,\r\nHaisen Zhao, and Martin Hafskjold Thoresen for the helpful discussions; and the Miba Machine Shop at IST Austria for 3D printing the BUNNY and BOOMERANG models.","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"doi":"10.1111/cgf.14490","department":[{"_id":"BeBi"}],"isi":1,"project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"date_updated":"2025-04-14T07:28:57Z","author":[{"first_name":"Zhenyuan","orcid":"0000-0001-9200-5690","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","full_name":"Liu, Zhenyuan","last_name":"Liu"},{"first_name":"Jingyu","last_name":"Hu","full_name":"Hu, Jingyu"},{"last_name":"Xu","full_name":"Xu, Hao","first_name":"Hao"},{"first_name":"Peng","full_name":"Song, Peng","last_name":"Song"},{"first_name":"Ran","last_name":"Zhang","full_name":"Zhang, Ran"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"first_name":"Chi-Wing","last_name":"Fu","full_name":"Fu, Chi-Wing"}],"date_published":"2022-05-01T00:00:00Z","ddc":["000"],"oa_version":"Submitted Version","scopus_import":"1","has_accepted_license":"1","month":"05","external_id":{"isi":["000802723900039"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}]},{"title":"On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"citation":{"short":"B. Yang, Z. Yang, Journal of Fluid Mechanics 937 (2022).","ieee":"B. Yang and Z. Yang, “On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow,” <i>Journal of Fluid Mechanics</i>, vol. 937. Cambridge University Press, 2022.","mla":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” <i>Journal of Fluid Mechanics</i>, vol. 937, A39, Cambridge University Press, 2022, doi:<a href=\"https://doi.org/10.1017/jfm.2022.137\">10.1017/jfm.2022.137</a>.","chicago":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2022. <a href=\"https://doi.org/10.1017/jfm.2022.137\">https://doi.org/10.1017/jfm.2022.137</a>.","apa":"Yang, B., &#38; Yang, Z. (2022). On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2022.137\">https://doi.org/10.1017/jfm.2022.137</a>","ista":"Yang B, Yang Z. 2022. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics. 937, A39.","ama":"Yang B, Yang Z. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. <i>Journal of Fluid Mechanics</i>. 2022;937. doi:<a href=\"https://doi.org/10.1017/jfm.2022.137\">10.1017/jfm.2022.137</a>"},"date_created":"2022-03-27T22:01:45Z","year":"2022","quality_controlled":"1","article_type":"original","type":"journal_article","volume":937,"day":"25","publication":"Journal of Fluid Mechanics","publisher":"Cambridge University Press","article_processing_charge":"No","_id":"10925","intvolume":"       937","abstract":[{"text":"Direct numerical simulations (DNS) of turbulent channel flows up to  Reτ≈1000  are conducted to investigate the three-dimensional (consisting of streamwise wavenumber, spanwise wavenumber and frequency) spectrum of wall pressure fluctuations. To develop a predictive model of the wavenumber–frequency spectrum from the wavenumber spectrum, the time decorrelation mechanisms of wall pressure fluctuations are investigated. It is discovered that the energy-containing part of the wavenumber–frequency spectrum of wall pressure fluctuations can be well predicted using a similar random sweeping model for streamwise velocity fluctuations. To refine the investigation, we further decompose the spectrum of the total wall pressure fluctuations into the autospectra of rapid and slow pressure fluctuations, and the cross-spectrum between them. We focus on evaluating the assumption applied in many predictive models, that is, the magnitude of the cross-spectrum is negligibly small. The present DNS shows that neglecting the cross-spectrum causes a maximum error up to 4.7 dB in the subconvective region for all Reynolds numbers under test. Our analyses indicate that the approximation of neglecting the cross-spectrum needs to be applied carefully in the investigations of acoustics at low Mach numbers, in which the subconvective components of wall pressure fluctuations make important contributions to the radiated acoustic power.","lang":"eng"}],"status":"public","main_file_link":[{"url":"https://doi.org/10.1017/jfm.2022.137","open_access":"1"}],"arxiv":1,"publication_status":"published","department":[{"_id":"GradSch"}],"isi":1,"article_number":"A39","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"acknowledgement":"This research is supported by the NSFC Basic Science Center Program for ‘Multiscale Problems in Nonlinear Mechanics’ (no. 11988102), National Key Project (GJXM92579) and the Strategic Priority Research Program (XDB22040104).","doi":"10.1017/jfm.2022.137","month":"04","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000763547000001"],"arxiv":["2201.04702"]},"date_updated":"2023-08-03T06:20:26Z","date_published":"2022-04-25T00:00:00Z","author":[{"orcid":"0000-0002-4843-6853","first_name":"Bowen","last_name":"Yang","full_name":"Yang, Bowen","id":"71b6ff4b-15b2-11ec-abd3-aef6b028cf7e"},{"full_name":"Yang, Zixuan","last_name":"Yang","first_name":"Zixuan"}]},{"language":[{"iso":"eng"}],"external_id":{"isi":["000759081600002"]},"month":"03","scopus_import":"1","oa_version":"Submitted Version","date_published":"2022-03-01T00:00:00Z","author":[{"first_name":"Samuel","full_name":"Perini, Samuel","last_name":"Perini"},{"first_name":"Rogerk","last_name":"Butlin","full_name":"Butlin, Rogerk"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"}],"date_updated":"2025-05-14T11:05:28Z","article_number":"eyab049","department":[{"_id":"BeVi"}],"isi":1,"doi":"10.1093/mollus/eyab049","publication_identifier":{"eissn":["1464-3766"],"issn":["0260-1230"]},"publisher":"Oxford University Press","publication":"Journal of Molluscan Studies","issue":"1","article_processing_charge":"No","type":"journal_article","day":"01","volume":88,"publication_status":"published","status":"public","_id":"10926","intvolume":"        88","abstract":[{"lang":"eng","text":"Conflict over reproduction between females and males exists because of anisogamy and promiscuity. Together they generate differences in fitness optima between the sexes and result in antagonistic coevolution of female and male reproductive traits. Mounting duration is likely to be a compromise between male and female interests whose outcome depends on the intensity of sexual selection. The timing of sperm transfer during mounting is critical. For example, mountings may be interrupted before sperm is transferred as a consequence of female or male choice, or they may be prolonged to function as mate guarding. In the highly promiscuous intertidal snail Littorina saxatilis, mountings vary substantially in duration, from less than a minute to more than an hour, and it has been assumed that mountings of a few minutes do not result in any sperm being transferred. Here, we examined the timing of sperm transfer, a reproductive trait that is likely affected by sexual conflict. We performed time-controlled mounting trials using L. saxatilis males and virgin females, aiming to examine indirectly when the transfer of sperm starts. We observed the relationship between mounting duration and the proportion of developing embryos out of all eggs and embryos in the brood pouch. Developing embryos were observed in similar proportions in all treatments (i.e. 1, 5 and 10 or more minutes at which mountings were artificially interrupted), suggesting that sperm transfer begins rapidly (within 1 min) in L. saxatilis and very short matings do not result in sperm shortage in the females. We discuss how the observed pattern can be influenced by predation risk, population density, and female status and receptivity."}],"main_file_link":[{"open_access":"1","url":"https://eprints.whiterose.ac.uk/187332/"}],"title":"Very short mountings are enough for sperm transfer in Littorina saxatilis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","date_created":"2022-03-27T22:01:46Z","article_type":"original","quality_controlled":"1","oa":1,"citation":{"short":"S. Perini, R. Butlin, A.M. Westram, K. Johannesson, Journal of Molluscan Studies 88 (2022).","mla":"Perini, Samuel, et al. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1, eyab049, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>.","ieee":"S. Perini, R. Butlin, A. M. Westram, and K. Johannesson, “Very short mountings are enough for sperm transfer in Littorina saxatilis,” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1. Oxford University Press, 2022.","chicago":"Perini, Samuel, Rogerk Butlin, Anja M Westram, and Kerstin Johannesson. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>.","apa":"Perini, S., Butlin, R., Westram, A. M., &#38; Johannesson, K. (2022). Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>","ista":"Perini S, Butlin R, Westram AM, Johannesson K. 2022. Very short mountings are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies. 88(1), eyab049.","ama":"Perini S, Butlin R, Westram AM, Johannesson K. Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. 2022;88(1). doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>"}},{"doi":"10.1093/bioinformatics/btab691","publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"acknowledgement":"The authors thank the 2020 student class of the Bioinformatics Institute, who\r\nused the first versions of the tool and provided many valuable suggestions to\r\nimprove usability. They also thank Louisa Gonzalez Somermeyer for manuscript proofreading\r\nThis work was supported by the National Center for Cognitive Research of\r\nITMO University and JetBrains Research [to A.Z and N.A.]; and the European\r\nUnion’s Horizon 2020 Research and Innovation Programme under the Marie\r\nSkłodowska-Curie [754411 to O.B.].\r\nPaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements.","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"FyKo"}],"ddc":["000"],"date_published":"2022-01-15T00:00:00Z","author":[{"last_name":"Zabelkin","full_name":"Zabelkin, Alexey","first_name":"Alexey"},{"full_name":"Yakovleva, Yulia","last_name":"Yakovleva","first_name":"Yulia"},{"full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639"},{"full_name":"Alexeev, Nikita","last_name":"Alexeev","first_name":"Nikita"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"date_updated":"2025-05-14T11:05:09Z","language":[{"iso":"eng"}],"external_id":{"isi":["000743380100008"]},"month":"01","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","year":"2022","date_created":"2022-03-27T22:01:46Z","article_type":"original","quality_controlled":"1","corr_author":"1","oa":1,"citation":{"short":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022) 357–363.","ieee":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel REarrangements and BReaks identification toolkit,” <i>Bioinformatics</i>, vol. 38, no. 2. Oxford University Press, pp. 357–363, 2022.","mla":"Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>, vol. 38, no. 2, Oxford University Press, 2022, pp. 357–63, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btab691\">10.1093/bioinformatics/btab691</a>.","ista":"Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.","ama":"Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>. 2022;38(2):357-363. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btab691\">10.1093/bioinformatics/btab691</a>","chicago":"Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/bioinformatics/btab691\">https://doi.org/10.1093/bioinformatics/btab691</a>.","apa":"Zabelkin, A., Yakovleva, Y., Bochkareva, O., &#38; Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btab691\">https://doi.org/10.1093/bioinformatics/btab691</a>"},"ec_funded":1,"title":"PaReBrick: PArallel REarrangements and BReaks identification toolkit","file_date_updated":"2022-03-28T08:07:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://github.com/ctlab/parallel-rearrangements","relation":"software"}]},"file":[{"date_updated":"2022-03-28T08:07:46Z","success":1,"creator":"dernst","file_name":"2022_Bioinformatics_Zabelkin.pdf","date_created":"2022-03-28T08:07:46Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"10930","file_size":3425744,"checksum":"4b5688ff9ac86180ccdf7f82fa33d926"}],"publication_status":"published","status":"public","intvolume":"        38","_id":"10927","abstract":[{"lang":"eng","text":"Motivation\r\nHigh plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency.\r\nResults\r\nHere, we define the term ‘parallel rearrangements’ as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes."}],"publisher":"Oxford University Press","publication":"Bioinformatics","issue":"2","article_processing_charge":"No","type":"journal_article","page":"357-363","day":"15","volume":38},{"title":"Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level","file_date_updated":"2022-04-04T10:14:39Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"link":[{"relation":"software","url":"https://gitlab.pasteur.fr/adavidov/inferencelnakf"}]},"year":"2022","date_created":"2022-04-03T22:01:42Z","article_type":"original","quality_controlled":"1","oa":1,"citation":{"ieee":"A. Davidović, R. P. Chait, G. Batt, and J. Ruess, “Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level,” <i>PLoS Computational Biology</i>, vol. 18, no. 3. Public Library of Science, 2022.","short":"A. Davidović, R.P. Chait, G. Batt, J. Ruess, PLoS Computational Biology 18 (2022).","mla":"Davidović, Anđela, et al. “Parameter Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised at the Single Cell Level.” <i>PLoS Computational Biology</i>, vol. 18, no. 3, e1009950, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">10.1371/journal.pcbi.1009950</a>.","apa":"Davidović, A., Chait, R. P., Batt, G., &#38; Ruess, J. (2022). Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">https://doi.org/10.1371/journal.pcbi.1009950</a>","chicago":"Davidović, Anđela, Remy P Chait, Gregory Batt, and Jakob Ruess. “Parameter Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised at the Single Cell Level.” <i>PLoS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">https://doi.org/10.1371/journal.pcbi.1009950</a>.","ama":"Davidović A, Chait RP, Batt G, Ruess J. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. <i>PLoS Computational Biology</i>. 2022;18(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">10.1371/journal.pcbi.1009950</a>","ista":"Davidović A, Chait RP, Batt G, Ruess J. 2022. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Computational Biology. 18(3), e1009950."},"publisher":"Public Library of Science","publication":"PLoS Computational Biology","issue":"3","article_processing_charge":"No","type":"journal_article","day":"18","volume":18,"file":[{"creator":"dernst","success":1,"date_updated":"2022-04-04T10:14:39Z","content_type":"application/pdf","relation":"main_file","date_created":"2022-04-04T10:14:39Z","file_name":"2022_PLoSCompBio_Davidovic.pdf","file_id":"10947","access_level":"open_access","checksum":"458ef542761fb714ced214f240daf6b2","file_size":2958642}],"publication_status":"published","status":"public","_id":"10939","abstract":[{"lang":"eng","text":"Understanding and characterising biochemical processes inside single cells requires experimental platforms that allow one to perturb and observe the dynamics of such processes as well as computational methods to build and parameterise models from the collected data. Recent progress with experimental platforms and optogenetics has made it possible to expose each cell in an experiment to an individualised input and automatically record cellular responses over days with fine time resolution. However, methods to infer parameters of stochastic kinetic models from single-cell longitudinal data have generally been developed under the assumption that experimental data is sparse and that responses of cells to at most a few different input perturbations can be observed. Here, we investigate and compare different approaches for calculating parameter likelihoods of single-cell longitudinal data based on approximations of the chemical master equation (CME) with a particular focus on coupling the linear noise approximation (LNA) or moment closure methods to a Kalman filter. We show that, as long as cells are measured sufficiently frequently, coupling the LNA to a Kalman filter allows one to accurately approximate likelihoods and to infer model parameters from data even in cases where the LNA provides poor approximations of the CME. Furthermore, the computational cost of filtering-based iterative likelihood evaluation scales advantageously in the number of measurement times and different input perturbations and is thus ideally suited for data obtained from modern experimental platforms. To demonstrate the practical usefulness of these results, we perform an experiment in which single cells, equipped with an optogenetic gene expression system, are exposed to various different light-input sequences and measured at several hundred time points and use parameter inference based on iterative likelihood evaluation to parameterise a stochastic model of the system."}],"pmid":1,"intvolume":"        18","article_number":"e1009950","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"},"department":[{"_id":"CaGu"}],"isi":1,"doi":"10.1371/journal.pcbi.1009950","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"acknowledgement":"We thank Virgile Andreani for useful discussions about the model and parameter inference. We thank Johan Paulsson and Jeffrey J Tabor for kind gifts of plasmids. R was supported by the ANR grant CyberCircuits (ANR-18-CE91-0002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","language":[{"iso":"eng"}],"external_id":{"pmid":["35303737"],"isi":["001044208400004"]},"month":"03","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","ddc":["570","000"],"date_published":"2022-03-18T00:00:00Z","author":[{"first_name":"Anđela","full_name":"Davidović, Anđela","last_name":"Davidović"},{"full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","orcid":"0000-0003-0876-3187","first_name":"Remy P"},{"full_name":"Batt, Gregory","last_name":"Batt","first_name":"Gregory"},{"orcid":"0000-0003-1615-3282","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","full_name":"Ruess, Jakob"}],"date_updated":"2025-09-09T14:29:53Z"},{"article_processing_charge":"No","issue":"3","publication":"Physical Review Applied","publisher":"American Physical Society","volume":17,"day":"11","type":"journal_article","publication_status":"published","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.01115","open_access":"1"}],"abstract":[{"text":"Magnetic-field-resilient superconducting circuits enable sensing applications and hybrid quantum computing architectures involving spin or topological qubits and electromechanical elements, as well as studying flux noise and quasiparticle loss. We investigate the effect of in-plane magnetic fields up to 1 T on the spectrum and coherence times of thin-film three-dimensional aluminum transmons. Using a copper cavity, unaffected by strong magnetic fields, we can probe solely the effect of magnetic fields on the transmons. We present data on a single-junction and a superconducting-quantum-interference-device (SQUID) transmon that are cooled down in the same cavity. As expected, the transmon frequencies decrease with increasing field, due to suppression of the superconducting gap and a geometric Fraunhofer-like contribution. Nevertheless, the thin-film transmons show strong magnetic field resilience: both transmons display microsecond coherence up to at least 0.65 T, and T1 remains above 1μs over the entire measurable range. SQUID spectroscopy is feasible up to 1 T, the limit of our magnet. We conclude that thin-film aluminum Josephson junctions are suitable hardware for superconducting circuits in the high-magnetic-field regime.","lang":"eng"}],"_id":"10940","intvolume":"        17","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T","quality_controlled":"1","article_type":"original","date_created":"2022-04-03T22:01:43Z","year":"2022","citation":{"chicago":"Krause, J., C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani, Johannes M Fink, and Yoichi Ando. “Magnetic Field Resilience of Three-Dimensional Transmons with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” <i>Physical Review Applied</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">https://doi.org/10.1103/PhysRevApplied.17.034032</a>.","apa":"Krause, J., Dickel, C., Vaal, E., Vielmetter, M., Feng, J., Bounds, R., … Ando, Y. (2022). Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">https://doi.org/10.1103/PhysRevApplied.17.034032</a>","ista":"Krause J, Dickel C, Vaal E, Vielmetter M, Feng J, Bounds R, Catelani G, Fink JM, Ando Y. 2022. Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. Physical Review Applied. 17(3), 034032.","ama":"Krause J, Dickel C, Vaal E, et al. Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. <i>Physical Review Applied</i>. 2022;17(3). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">10.1103/PhysRevApplied.17.034032</a>","ieee":"J. Krause <i>et al.</i>, “Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T,” <i>Physical Review Applied</i>, vol. 17, no. 3. American Physical Society, 2022.","mla":"Krause, J., et al. “Magnetic Field Resilience of Three-Dimensional Transmons with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” <i>Physical Review Applied</i>, vol. 17, no. 3, 034032, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">10.1103/PhysRevApplied.17.034032</a>.","short":"J. Krause, C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani, J.M. Fink, Y. Ando, Physical Review Applied 17 (2022)."},"oa":1,"external_id":{"arxiv":["2111.01115"],"isi":["000770371400003"]},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Preprint","month":"03","author":[{"last_name":"Krause","full_name":"Krause, J.","first_name":"J."},{"last_name":"Dickel","full_name":"Dickel, C.","first_name":"C."},{"full_name":"Vaal, E.","last_name":"Vaal","first_name":"E."},{"last_name":"Vielmetter","full_name":"Vielmetter, M.","first_name":"M."},{"last_name":"Feng","full_name":"Feng, J.","first_name":"J."},{"first_name":"R.","full_name":"Bounds, R.","last_name":"Bounds"},{"full_name":"Catelani, G.","last_name":"Catelani","first_name":"G."},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"Yoichi","last_name":"Ando","full_name":"Ando, Yoichi"}],"date_published":"2022-03-11T00:00:00Z","date_updated":"2023-08-03T06:23:58Z","article_number":"034032","department":[{"_id":"JoFi"}],"isi":1,"doi":"10.1103/PhysRevApplied.17.034032","acknowledgement":"We would like to thank Ida Milow for her internship in the laboratory and contributions to our code base. We thank T. Zent and L. Hamdan for technical assistance, and D. Fan for help with setting up the aluminum evaporator. We thank A. Salari, M. Rößler, S. Barzanjeh, M. Zemlicka, F. Hassani, and M. Peruzzo for contributions in the early stages of the experiments. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 741121) and was also funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under CRC 1238 – 277146847 (Subproject B01), as well as under Germany’s Excellence Strategy – Cluster of Excellence Matter and Light for Quantum Computing (ML4Q), EXC 2004/1\r\n– 390534769.","publication_identifier":{"eissn":["2331-7019"]}},{"department":[{"_id":"LeSa"}],"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"},"doi":"10.3390/colorants1020010","acknowledgement":"This research was partly funded by Hacettepe University (Bilimsel Ara¸stırma Projeleri\r\nKoordinasyon Birimi), grant number FHD-2015-8094.The authors are indebted to Ahmet Önal for his supports in acquiring the fluorescence spectra and the decision of excitation wavelengths. The authors also acknowledge use of the services and facilities of UNAM-National Nanotechnology Research Center at Bilkent University and mica donation from Sabuncular Mining Co.","publication_identifier":{"issn":["2079-6447"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","month":"04","author":[{"id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh","first_name":"Mehmet Orkun","orcid":"0000-0002-3219-2022"},{"first_name":"Güngör","full_name":"Gündüz, Güngör","last_name":"Gündüz"},{"last_name":"Çolak","full_name":"Çolak, Üner","first_name":"Üner"},{"first_name":"Bora","full_name":"Maviş, Bora","last_name":"Maviş"}],"ddc":["570"],"date_published":"2022-04-01T00:00:00Z","date_updated":"2024-10-14T13:52:09Z","OA_place":"publisher","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","title":"pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra","file_date_updated":"2022-04-04T10:39:24Z","article_type":"original","quality_controlled":"1","year":"2022","date_created":"2022-04-04T09:03:54Z","citation":{"chicago":"Çoruh, Mehmet Orkun, Güngör Gündüz, Üner Çolak, and Bora Maviş. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” <i>Colorants</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/colorants1020010\">https://doi.org/10.3390/colorants1020010</a>.","apa":"Çoruh, M. O., Gündüz, G., Çolak, Ü., &#38; Maviş, B. (2022). pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. <i>Colorants</i>. MDPI. <a href=\"https://doi.org/10.3390/colorants1020010\">https://doi.org/10.3390/colorants1020010</a>","ista":"Çoruh MO, Gündüz G, Çolak Ü, Maviş B. 2022. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. 1(2), 149–164.","ama":"Çoruh MO, Gündüz G, Çolak Ü, Maviş B. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. <i>Colorants</i>. 2022;1(2):149-164. doi:<a href=\"https://doi.org/10.3390/colorants1020010\">10.3390/colorants1020010</a>","short":"M.O. Çoruh, G. Gündüz, Ü. Çolak, B. Maviş, Colorants 1 (2022) 149–164.","mla":"Çoruh, Mehmet Orkun, et al. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” <i>Colorants</i>, vol. 1, no. 2, MDPI, 2022, pp. 149–64, doi:<a href=\"https://doi.org/10.3390/colorants1020010\">10.3390/colorants1020010</a>.","ieee":"M. O. Çoruh, G. Gündüz, Ü. Çolak, and B. Maviş, “pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra,” <i>Colorants</i>, vol. 1, no. 2. MDPI, pp. 149–164, 2022."},"oa":1,"article_processing_charge":"Yes","OA_type":"gold","publisher":"MDPI","publication":"Colorants","issue":"2","day":"01","page":"149-164","volume":1,"DOAJ_listed":"1","type":"journal_article","file":[{"date_updated":"2022-04-04T10:39:24Z","success":1,"creator":"dernst","date_created":"2022-04-04T10:39:24Z","file_name":"2022_Colorants_Coruh.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"10949","file_size":2437988,"checksum":"2c15c8d3041ebc36bc64870247081758"}],"publication_status":"published","status":"public","_id":"10945","intvolume":"         1","abstract":[{"lang":"eng","text":"Mica-titania pearlescent pigments (MTs) were previously coated with organic molecules to obtain combination pigments (CPs) for achieving certain improvements or functionalities. Anthocyanins (ACNs) are molecules that can be extracted from natural resources and exhibit color changes via pH modifications of the enclosing medium. The purpose of the study was to produce a new series of CPs by depositing ACNs on MTs at different pH values, to observe the changes in color, and to associate these changes to thermogravimetrically determined deposition efficiencies in light of spectral differences. The extraction and deposition methods were based on aqueous chemistry and were straightforward. The ACN deposition generally increased with increasing pH and correlated with the consistency between the charges of the MT surfaces and the dominant ACN species at a specific pH value. The fluorescence of the CPs was inversely correlated with the deposition quantities invoking the possibility of a quenching effect."}]},{"publisher":"Elsevier","publication":"Materials Today Energy","article_processing_charge":"No","type":"journal_article","day":"01","volume":25,"publication_status":"published","status":"public","intvolume":"        25","_id":"11142","abstract":[{"lang":"eng","text":"SnTe is a promising Pb-free thermoelectric (TE) material with high electrical conductivity. We discovered the synergistic effect of Bi2O3 on enhancing the average power factor (PF) and overall ZT value of the SnTe-based thermoelectric material. The introduction of Bi2O3 forms plenty of SnO2, Bi2O3, and Bi-rich nanoprecipitates. These interfaces between the SnTe matrix and the nanoprecipitates can enhance the average PF through the energy filtering effect. On the other hand, abundant and diverse nanoprecipitates can significantly diminish the lattice thermal conductivity (κlat) through enhanced phonon scattering. The synergistic effect of Bi2O3 resulted in a maximum ZT (ZTmax) value of 0.9 at SnTe-2% Bi2O3 and an average ZT (ZTave) value of 0.4 for SnTe-4% Bi2O3 from 300 K to 823 K. The work provides an excellent reference to develop non-toxic high-performance TE materials."}],"title":"Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","date_created":"2022-04-10T22:01:39Z","article_type":"original","quality_controlled":"1","corr_author":"1","citation":{"short":"T. Hong, C. Guo, D. Wang, B. Qin, C. Chang, X. Gao, L.D. Zhao, Materials Today Energy 25 (2022).","ieee":"T. Hong <i>et al.</i>, “Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3,” <i>Materials Today Energy</i>, vol. 25. Elsevier, 2022.","mla":"Hong, Tao, et al. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” <i>Materials Today Energy</i>, vol. 25, 100985, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">10.1016/j.mtener.2022.100985</a>.","ista":"Hong T, Guo C, Wang D, Qin B, Chang C, Gao X, Zhao LD. 2022. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. Materials Today Energy. 25, 100985.","ama":"Hong T, Guo C, Wang D, et al. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. <i>Materials Today Energy</i>. 2022;25. doi:<a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">10.1016/j.mtener.2022.100985</a>","chicago":"Hong, Tao, Changrong Guo, Dongyang Wang, Bingchao Qin, Cheng Chang, Xiang Gao, and Li Dong Zhao. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” <i>Materials Today Energy</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">https://doi.org/10.1016/j.mtener.2022.100985</a>.","apa":"Hong, T., Guo, C., Wang, D., Qin, B., Chang, C., Gao, X., &#38; Zhao, L. D. (2022). Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. <i>Materials Today Energy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">https://doi.org/10.1016/j.mtener.2022.100985</a>"},"language":[{"iso":"eng"}],"external_id":{"isi":["000798679100010"]},"month":"04","scopus_import":"1","oa_version":"None","date_published":"2022-04-01T00:00:00Z","author":[{"first_name":"Tao","full_name":"Hong, Tao","last_name":"Hong"},{"first_name":"Changrong","full_name":"Guo, Changrong","last_name":"Guo"},{"first_name":"Dongyang","full_name":"Wang, Dongyang","last_name":"Wang"},{"full_name":"Qin, Bingchao","last_name":"Qin","first_name":"Bingchao"},{"orcid":"0000-0002-9515-4277","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","full_name":"Chang, Cheng"},{"first_name":"Xiang","full_name":"Gao, Xiang","last_name":"Gao"},{"first_name":"Li Dong","full_name":"Zhao, Li Dong","last_name":"Zhao"}],"project":[{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"}],"date_updated":"2025-04-14T09:29:32Z","article_number":"100985","department":[{"_id":"MaIb"}],"isi":1,"doi":"10.1016/j.mtener.2022.100985","publication_identifier":{"eissn":["2468-6069"]},"acknowledgement":"This work was supported by National Natural Science Foundation of China (52002042), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), 111 Project (B17002) and Lise Meitner Project M 2889-N. This work was also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the high-performance computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM and TEM measurements."},{"doi":"10.1016/j.celrep.2022.110580","acknowledgement":"We would like to thank Bernardo Rudy, Joanna Mattis, and Laura Mcgarry for comments on a previous version of the manuscript; Xiaohong Zhang for expert technical support and mouse colony maintenance; Melody Cheng for assistance with generation of the graphical abstract; and Jennifer Kearney for the gift of Scn1a+/− mice. This work was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under F31NS111803 (to K.M.G.) and K08NS097633 and R01NS110869 (to E.M.G.), the Dravet Syndrome Foundation (to A.S.), an ERC Consolidator Grant (SYNAPSEEK) (to T.P.V.), and the NOMIS Foundation through the NOMIS Fellowships program at IST Austria (to C.C.). The graphical abstract was prepared using BioRender software (BioRender.com).","publication_identifier":{"eissn":["2211-1247"]},"article_number":"110580","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"TiVo"}],"isi":1,"author":[{"first_name":"Keisuke","full_name":"Kaneko, Keisuke","last_name":"Kaneko"},{"orcid":"0000-0002-4809-5059","first_name":"Christopher","full_name":"Currin, Christopher","last_name":"Currin","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9"},{"full_name":"Goff, Kevin M.","last_name":"Goff","first_name":"Kevin M."},{"first_name":"Eric R.","last_name":"Wengert","full_name":"Wengert, Eric R."},{"first_name":"Ala","full_name":"Somarowthu, Ala","last_name":"Somarowthu"},{"full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181"},{"first_name":"Ethan M.","last_name":"Goldberg","full_name":"Goldberg, Ethan M."}],"ddc":["570"],"date_published":"2022-03-29T00:00:00Z","project":[{"grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"date_updated":"2025-06-11T14:00:11Z","external_id":{"isi":["000779794000001"],"pmid":["35354025"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","month":"03","article_type":"original","quality_controlled":"1","year":"2022","date_created":"2022-04-10T22:01:39Z","citation":{"apa":"Kaneko, K., Currin, C., Goff, K. M., Wengert, E. R., Somarowthu, A., Vogels, T. P., &#38; Goldberg, E. M. (2022). Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>","chicago":"Kaneko, Keisuke, Christopher Currin, Kevin M. Goff, Eric R. Wengert, Ala Somarowthu, Tim P Vogels, and Ethan M. Goldberg. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>.","ama":"Kaneko K, Currin C, Goff KM, et al. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. 2022;38(13). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>","ista":"Kaneko K, Currin C, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg EM. 2022. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 38(13), 110580.","ieee":"K. Kaneko <i>et al.</i>, “Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome,” <i>Cell Reports</i>, vol. 38, no. 13. Elsevier, 2022.","short":"K. Kaneko, C. Currin, K.M. Goff, E.R. Wengert, A. Somarowthu, T.P. Vogels, E.M. Goldberg, Cell Reports 38 (2022).","mla":"Kaneko, Keisuke, et al. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>, vol. 38, no. 13, 110580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome","ec_funded":1,"file_date_updated":"2022-04-15T11:00:58Z","file":[{"success":1,"creator":"dernst","date_updated":"2022-04-15T11:00:58Z","relation":"main_file","content_type":"application/pdf","file_name":"2022_CellReports_Kaneko.pdf","date_created":"2022-04-15T11:00:58Z","file_id":"11172","access_level":"open_access","checksum":"49105c6c27c9af0f37f50a8bbb4d380d","file_size":4774216}],"publication_status":"published","status":"public","_id":"11143","abstract":[{"text":"Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology.","lang":"eng"}],"pmid":1,"intvolume":"        38","article_processing_charge":"No","publisher":"Elsevier","issue":"13","publication":"Cell Reports","day":"29","volume":38,"type":"journal_article"},{"date_published":"2022-03-25T00:00:00Z","author":[{"first_name":"Lizhong","full_name":"Su, Lizhong","last_name":"Su"},{"last_name":"Wang","full_name":"Wang, Dongyang","first_name":"Dongyang"},{"first_name":"Sining","full_name":"Wang, Sining","last_name":"Wang"},{"last_name":"Qin","full_name":"Qin, Bingchao","first_name":"Bingchao"},{"first_name":"Yuping","full_name":"Wang, Yuping","last_name":"Wang"},{"first_name":"Yongxin","last_name":"Qin","full_name":"Qin, Yongxin"},{"full_name":"Jin, Yang","last_name":"Jin","first_name":"Yang"},{"first_name":"Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","last_name":"Chang"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"project":[{"grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}],"date_updated":"2025-04-14T09:29:32Z","language":[{"iso":"eng"}],"external_id":{"isi":["000778894800038"],"pmid":["35324303"]},"month":"03","scopus_import":"1","oa_version":"None","doi":"10.1126/science.abn8997","publication_identifier":{"eissn":["1095-9203"]},"acknowledgement":"This work was supported by the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Key Research and Development Program of China (2018YFA0702100), the National Science Fund for Distinguished Young Scholars (51925101), the 111 Project (B17002), the Lise Meitner Project (M2889-N), and the National Key Research and Development Program of China (2018YFB0703600). This work is also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.-D.Z. is thankful for the high-performance computing resources at Beihang University.","isi":1,"department":[{"_id":"MaIb"}],"publication_status":"published","status":"public","_id":"11144","intvolume":"       375","pmid":1,"abstract":[{"lang":"eng","text":"Thermoelectric materials allow for direct conversion between heat and electricity, offering the potential for power generation. The average dimensionless figure of merit ZTave determines device efficiency. N-type tin selenide crystals exhibit outstanding three-dimensional charge and two-dimensional phonon transport along the out-of-plane direction, contributing to a high maximum figure of merit Zmax of ~3.6 × 10−3 per kelvin but a moderate ZTave of ~1.1. We found an attractive high Zmax of ~4.1 × 10−3 per kelvin at 748 kelvin and a ZTave of ~1.7 at 300 to 773 kelvin in chlorine-doped and lead-alloyed tin selenide crystals by phonon-electron decoupling. The chlorine-induced low deformation potential improved the carrier mobility. The lead-induced mass and strain fluctuations reduced the lattice thermal conductivity. Phonon-electron decoupling plays a critical role to achieve high-performance thermoelectrics."}],"publisher":"American Association for the Advancement of Science","issue":"6587","publication":"Science","article_processing_charge":"No","type":"journal_article","day":"25","page":"1385-1389","volume":375,"year":"2022","date_created":"2022-04-10T22:01:40Z","article_type":"original","corr_author":"1","quality_controlled":"1","citation":{"mla":"Su, Lizhong, et al. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” <i>Science</i>, vol. 375, no. 6587, American Association for the Advancement of Science, 2022, pp. 1385–89, doi:<a href=\"https://doi.org/10.1126/science.abn8997\">10.1126/science.abn8997</a>.","short":"L. Su, D. Wang, S. Wang, B. Qin, Y. Wang, Y. Qin, Y. Jin, C. Chang, L.D. Zhao, Science 375 (2022) 1385–1389.","ieee":"L. Su <i>et al.</i>, “High thermoelectric performance realized through manipulating layered phonon-electron decoupling,” <i>Science</i>, vol. 375, no. 6587. American Association for the Advancement of Science, pp. 1385–1389, 2022.","ista":"Su L, Wang D, Wang S, Qin B, Wang Y, Qin Y, Jin Y, Chang C, Zhao LD. 2022. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. Science. 375(6587), 1385–1389.","ama":"Su L, Wang D, Wang S, et al. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. <i>Science</i>. 2022;375(6587):1385-1389. doi:<a href=\"https://doi.org/10.1126/science.abn8997\">10.1126/science.abn8997</a>","chicago":"Su, Lizhong, Dongyang Wang, Sining Wang, Bingchao Qin, Yuping Wang, Yongxin Qin, Yang Jin, Cheng Chang, and Li Dong Zhao. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abn8997\">https://doi.org/10.1126/science.abn8997</a>.","apa":"Su, L., Wang, D., Wang, S., Qin, B., Wang, Y., Qin, Y., … Zhao, L. D. (2022). High thermoelectric performance realized through manipulating layered phonon-electron decoupling. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abn8997\">https://doi.org/10.1126/science.abn8997</a>"},"title":"High thermoelectric performance realized through manipulating layered phonon-electron decoupling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]