[{"oa_version":"Preprint","type":"journal_article","doi":"10.1109/tcomm.2022.3211101","publication_status":"published","status":"public","isi":1,"department":[{"_id":"MaMo"}],"date_updated":"2023-08-04T09:34:43Z","author":[{"first_name":"Nghia","last_name":"Doan","full_name":"Doan, Nghia"},{"first_name":"Seyyed Ali","last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","last_name":"Mondelli","full_name":"Mondelli, Marco"},{"last_name":"Gross","full_name":"Gross, Warren J.","first_name":"Warren J."}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"apa":"Doan, N., Hashemi, S. A., Mondelli, M., &#38; Gross, W. J. (2022). Decoding Reed-Muller codes with successive codeword permutations. <i>IEEE Transactions on Communications</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">https://doi.org/10.1109/tcomm.2022.3211101</a>","chicago":"Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “Decoding Reed-Muller Codes with Successive Codeword Permutations.” <i>IEEE Transactions on Communications</i>. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">https://doi.org/10.1109/tcomm.2022.3211101</a>.","ama":"Doan N, Hashemi SA, Mondelli M, Gross WJ. Decoding Reed-Muller codes with successive codeword permutations. <i>IEEE Transactions on Communications</i>. 2022;70(11):7134-7145. doi:<a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">10.1109/tcomm.2022.3211101</a>","ista":"Doan N, Hashemi SA, Mondelli M, Gross WJ. 2022. Decoding Reed-Muller codes with successive codeword permutations. IEEE Transactions on Communications. 70(11), 7134–7145.","ieee":"N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “Decoding Reed-Muller codes with successive codeword permutations,” <i>IEEE Transactions on Communications</i>, vol. 70, no. 11. Institute of Electrical and Electronics Engineers, pp. 7134–7145, 2022.","short":"N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, IEEE Transactions on Communications 70 (2022) 7134–7145.","mla":"Doan, Nghia, et al. “Decoding Reed-Muller Codes with Successive Codeword Permutations.” <i>IEEE Transactions on Communications</i>, vol. 70, no. 11, Institute of Electrical and Electronics Engineers, 2022, pp. 7134–45, doi:<a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">10.1109/tcomm.2022.3211101</a>."},"publication_identifier":{"eissn":["1558-0857"],"issn":["0090-6778"]},"external_id":{"isi":["000937284600006"],"arxiv":["2109.02122"]},"page":"7134-7145","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.02122"}],"intvolume":"        70","abstract":[{"text":"A novel recursive list decoding (RLD) algorithm for Reed-Muller (RM) codes based on successive permutations (SP) of the codeword is presented. A low-complexity SP scheme applied to a subset of the symmetry group of RM codes is first proposed to carefully select a good codeword permutation on the fly. Then, the proposed SP technique is integrated into an improved RLD algorithm that initializes different decoding paths with random codeword permutations, which are sampled from the full symmetry group of RM codes. Finally, efficient latency and complexity reduction schemes are introduced that virtually preserve the error-correction performance of the proposed decoder. Simulation results demonstrate that at the target frame error rate of 10−3 for the RM code of length 256 with 163 information bits, the proposed decoder reduces 6% of the computational complexity and 22% of the decoding latency of the state-of-the-art semi-parallel simplified successive-cancellation decoder with fast Hadamard transform (SSC-FHT) that uses 96 permutations from the full symmetry group of RM codes, while relatively maintaining the error-correction performance and memory consumption of the semi-parallel permuted SSC-FHT decoder.","lang":"eng"}],"date_created":"2023-01-16T09:50:38Z","issue":"11","year":"2022","date_published":"2022-11-01T00:00:00Z","oa":1,"day":"01","arxiv":1,"publisher":"Institute of Electrical and Electronics Engineers","_id":"12233","publication":"IEEE Transactions on Communications","title":"Decoding Reed-Muller codes with successive codeword permutations","article_type":"original","volume":70},{"file_date_updated":"2023-01-27T11:28:38Z","corr_author":"1","scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” <i>Evolution</i>, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.","short":"S. Stankowski, Evolution 76 (2022) 2784–2785.","ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785.","mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” <i>Evolution</i>, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:<a href=\"https://doi.org/10.1111/evo.14632\">10.1111/evo.14632</a>.","apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14632\">https://doi.org/10.1111/evo.14632</a>","chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14632\">https://doi.org/10.1111/evo.14632</a>.","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. <i>Evolution</i>. 2022;76(11):2784-2785. doi:<a href=\"https://doi.org/10.1111/evo.14632\">10.1111/evo.14632</a>"},"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"external_id":{"isi":["000855751600001"],"pmid":["36112597"]},"file":[{"file_name":"2022_Evolution_Stankowski.pdf","date_updated":"2023-01-27T11:28:38Z","relation":"main_file","checksum":"4c0f05083b414ac0323a1b9ee1abc275","file_size":287282,"file_id":"12425","success":1,"access_level":"open_access","date_created":"2023-01-27T11:28:38Z","content_type":"application/pdf","creator":"dernst"}],"page":"2784-2785","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","oa_version":"Published Version","type":"journal_article","doi":"10.1111/evo.14632","publication_status":"published","status":"public","isi":1,"department":[{"_id":"NiBa"}],"date_updated":"2025-06-11T13:40:40Z","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"article_processing_charge":"Yes (via OA deal)","day":"01","publisher":"Wiley","_id":"12234","pmid":1,"ddc":["570"],"keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"publication":"Evolution","article_type":"original","title":"Digest: On the origin of a possible hybrid species","volume":76,"quality_controlled":"1","date_created":"2023-01-16T09:50:48Z","intvolume":"        76","abstract":[{"lang":"eng","text":"Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents."}],"issue":"11","year":"2022","date_published":"2022-11-01T00:00:00Z","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"publication":"European Journal of Haematology","keyword":["Hematology","General Medicine"],"title":"Haematological changes from conception to childbirth: An indicator of major pregnancy complications","article_type":"original","volume":109,"publisher":"Wiley","day":"01","_id":"12235","pmid":1,"ddc":["570","610"],"year":"2022","issue":"5","date_published":"2022-11-01T00:00:00Z","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","intvolume":"       109","date_created":"2023-01-16T09:50:58Z","abstract":[{"text":"Background: About 800 women die every day worldwide from pregnancy-related complications, including excessive blood loss, infections and high-blood pressure (World Health Organization, 2019). To improve screening for high-risk pregnancies, we set out to identify patterns of maternal hematological changes associated with future pregnancy complications.\r\n\r\nMethods: Using mixed effects models, we established changes in 14 complete blood count (CBC) parameters for 1710 healthy pregnancies and compared them to measurements from 98 pregnancy-induced hypertension, 106 gestational diabetes and 339 postpartum hemorrhage cases.\r\n\r\nResults: Results show interindividual variations, but good individual repeatability in CBC values during physiological pregnancies, allowing the identification of specific alterations in women with obstetric complications. For example, in women with uncomplicated pregnancies, haemoglobin count decreases of 0.12 g/L (95% CI −0.16, −0.09) significantly per gestation week (p value <.001). Interestingly, this decrease is three times more pronounced in women who will develop pregnancy-induced hypertension, with an additional decrease of 0.39 g/L (95% CI −0.51, −0.26). We also confirm that obstetric complications and white CBC predict the likelihood of giving birth earlier during pregnancy.\r\n\r\nConclusion: We provide a comprehensive description of the associations between haematological changes through pregnancy and three major obstetric complications to support strategies for prevention, early-diagnosis and maternal care.","lang":"eng"}],"publication_identifier":{"issn":["0902-4441"],"eissn":["1600-0609"]},"page":"566-575","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the study and all the midwives and doctors involved for the computerized obstetrical data from the CHUV Maternity Hospital. Open access funding provided by Universite de Lausanne.","file":[{"file_name":"2022_EuropJourHaematology_Patxot.pdf","date_updated":"2023-01-27T11:42:43Z","file_size":1225073,"checksum":"a676d732f67c2990197e34f96b219370","relation":"main_file","date_created":"2023-01-27T11:42:43Z","access_level":"open_access","success":1,"file_id":"12426","content_type":"application/pdf","creator":"dernst"}],"external_id":{"isi":["000849690500001"],"pmid":["36059200"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","corr_author":"1","file_date_updated":"2023-01-27T11:42:43Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"chicago":"Patxot, Marion, Miloš Stojanov, Sven Erik Ojavee, Rosanna Pescini Gobert, Zoltán Kutalik, Mathilde Gavillet, David Baud, and Matthew Richard Robinson. “Haematological Changes from Conception to Childbirth: An Indicator of Major Pregnancy Complications.” <i>European Journal of Haematology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/ejh.13844\">https://doi.org/10.1111/ejh.13844</a>.","apa":"Patxot, M., Stojanov, M., Ojavee, S. E., Gobert, R. P., Kutalik, Z., Gavillet, M., … Robinson, M. R. (2022). Haematological changes from conception to childbirth: An indicator of major pregnancy complications. <i>European Journal of Haematology</i>. Wiley. <a href=\"https://doi.org/10.1111/ejh.13844\">https://doi.org/10.1111/ejh.13844</a>","ama":"Patxot M, Stojanov M, Ojavee SE, et al. Haematological changes from conception to childbirth: An indicator of major pregnancy complications. <i>European Journal of Haematology</i>. 2022;109(5):566-575. doi:<a href=\"https://doi.org/10.1111/ejh.13844\">10.1111/ejh.13844</a>","mla":"Patxot, Marion, et al. “Haematological Changes from Conception to Childbirth: An Indicator of Major Pregnancy Complications.” <i>European Journal of Haematology</i>, vol. 109, no. 5, Wiley, 2022, pp. 566–75, doi:<a href=\"https://doi.org/10.1111/ejh.13844\">10.1111/ejh.13844</a>.","short":"M. Patxot, M. Stojanov, S.E. Ojavee, R.P. Gobert, Z. Kutalik, M. Gavillet, D. Baud, M.R. Robinson, European Journal of Haematology 109 (2022) 566–575.","ista":"Patxot M, Stojanov M, Ojavee SE, Gobert RP, Kutalik Z, Gavillet M, Baud D, Robinson MR. 2022. Haematological changes from conception to childbirth: An indicator of major pregnancy complications. European Journal of Haematology. 109(5), 566–575.","ieee":"M. Patxot <i>et al.</i>, “Haematological changes from conception to childbirth: An indicator of major pregnancy complications,” <i>European Journal of Haematology</i>, vol. 109, no. 5. Wiley, pp. 566–575, 2022."},"has_accepted_license":"1","department":[{"_id":"MaRo"}],"date_updated":"2024-10-09T21:03:49Z","article_processing_charge":"No","author":[{"first_name":"Marion","last_name":"Patxot","full_name":"Patxot, Marion"},{"first_name":"Miloš","full_name":"Stojanov, Miloš","last_name":"Stojanov"},{"full_name":"Ojavee, Sven Erik","last_name":"Ojavee","first_name":"Sven Erik"},{"last_name":"Gobert","full_name":"Gobert, Rosanna Pescini","first_name":"Rosanna Pescini"},{"full_name":"Kutalik, Zoltán","last_name":"Kutalik","first_name":"Zoltán"},{"first_name":"Mathilde","full_name":"Gavillet, Mathilde","last_name":"Gavillet"},{"full_name":"Baud, David","last_name":"Baud","first_name":"David"},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1111/ejh.13844","status":"public","isi":1},{"language":[{"iso":"eng"}],"citation":{"mla":"Wang, Xiang, et al. “CoFeNiMnZnB as a High-Entropy Metal Boride to Boost the Oxygen Evolution Reaction.” <i>ACS Applied Materials &#38; Interfaces</i>, vol. 14, no. 42, American Chemical Society, 2022, pp. 48212–19, doi:<a href=\"https://doi.org/10.1021/acsami.2c11627\">10.1021/acsami.2c11627</a>.","short":"X. Wang, Y. Zuo, S. Horta, R. He, L. Yang, A. Ostovari Moghaddam, M. Ibáñez, X. Qi, A. Cabot, ACS Applied Materials &#38; Interfaces 14 (2022) 48212–48219.","ieee":"X. Wang <i>et al.</i>, “CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution reaction,” <i>ACS Applied Materials &#38; Interfaces</i>, vol. 14, no. 42. American Chemical Society, pp. 48212–48219, 2022.","ista":"Wang X, Zuo Y, Horta S, He R, Yang L, Ostovari Moghaddam A, Ibáñez M, Qi X, Cabot A. 2022. CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution reaction. ACS Applied Materials &#38; Interfaces. 14(42), 48212–48219.","ama":"Wang X, Zuo Y, Horta S, et al. CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution reaction. <i>ACS Applied Materials &#38; Interfaces</i>. 2022;14(42):48212-48219. doi:<a href=\"https://doi.org/10.1021/acsami.2c11627\">10.1021/acsami.2c11627</a>","chicago":"Wang, Xiang, Yong Zuo, Sharona Horta, Ren He, Linlin Yang, Ahmad Ostovari Moghaddam, Maria Ibáñez, Xueqiang Qi, and Andreu Cabot. “CoFeNiMnZnB as a High-Entropy Metal Boride to Boost the Oxygen Evolution Reaction.” <i>ACS Applied Materials &#38; Interfaces</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsami.2c11627\">https://doi.org/10.1021/acsami.2c11627</a>.","apa":"Wang, X., Zuo, Y., Horta, S., He, R., Yang, L., Ostovari Moghaddam, A., … Cabot, A. (2022). CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution reaction. <i>ACS Applied Materials &#38; Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.2c11627\">https://doi.org/10.1021/acsami.2c11627</a>"},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"external_id":{"pmid":["36239982"],"isi":["000873782700001"]},"acknowledgement":"This work was supported by the Spanish MCIN project COMBENERGY (PID2019-105490RB-C32). X.W. and L.Y. thank the China Scholarship Council (CSC) for the scholarship support.","page":"48212-48219","status":"public","isi":1,"oa_version":"None","type":"journal_article","doi":"10.1021/acsami.2c11627","publication_status":"published","article_processing_charge":"No","author":[{"first_name":"Xiang","full_name":"Wang, Xiang","last_name":"Wang"},{"first_name":"Yong","full_name":"Zuo, Yong","last_name":"Zuo"},{"last_name":"Horta","full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona"},{"first_name":"Ren","last_name":"He","full_name":"He, Ren"},{"first_name":"Linlin","full_name":"Yang, Linlin","last_name":"Yang"},{"first_name":"Ahmad","full_name":"Ostovari Moghaddam, Ahmad","last_name":"Ostovari Moghaddam"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"first_name":"Xueqiang","last_name":"Qi","full_name":"Qi, Xueqiang"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"department":[{"_id":"MaIb"}],"date_updated":"2023-10-04T08:28:14Z","pmid":1,"day":"14","publisher":"American Chemical Society","_id":"12236","article_type":"original","title":"CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution reaction","volume":14,"keyword":["General Materials Science"],"publication":"ACS Applied Materials & Interfaces","quality_controlled":"1","abstract":[{"text":"High-entropy materials offer numerous advantages as catalysts, including a flexible composition to tune the catalytic activity and selectivity and a large variety of adsorption/reaction sites for multistep or multiple reactions. Herein, we report on the synthesis, properties, and electrocatalytic performance of an amorphous high-entropy boride based on abundant transition metals, CoFeNiMnZnB. This metal boride provides excellent performance toward the oxygen evolution reaction (OER), including a low overpotential of 261 mV at 10 mA cm–2, a reduced Tafel slope of 56.8 mV dec–1, and very high stability. The outstanding OER performance of CoFeNiMnZnB is attributed to the synergistic interactions between the different metals, the leaching of Zn ions, the generation of oxygen vacancies, and the in situ formation of an amorphous oxyhydroxide at the CoFeNiMnZnB surface during the OER.","lang":"eng"}],"intvolume":"        14","date_created":"2023-01-16T09:51:10Z","issue":"42","year":"2022","date_published":"2022-10-14T00:00:00Z"},{"article_processing_charge":"No","author":[{"last_name":"Hino","full_name":"Hino, Naoya","first_name":"Naoya","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"first_name":"Kimiya","last_name":"Matsuda","full_name":"Matsuda, Kimiya"},{"full_name":"Jikko, Yuya","last_name":"Jikko","first_name":"Yuya"},{"last_name":"Maryu","full_name":"Maryu, Gembu","first_name":"Gembu"},{"last_name":"Sakai","full_name":"Sakai, Katsuya","first_name":"Katsuya"},{"first_name":"Ryu","last_name":"Imamura","full_name":"Imamura, Ryu"},{"last_name":"Tsukiji","full_name":"Tsukiji, Shinya","first_name":"Shinya"},{"first_name":"Kazuhiro","last_name":"Aoki","full_name":"Aoki, Kazuhiro"},{"last_name":"Terai","full_name":"Terai, Kenta","first_name":"Kenta"},{"full_name":"Hirashima, Tsuyoshi","last_name":"Hirashima","first_name":"Tsuyoshi"},{"first_name":"Xavier","last_name":"Trepat","full_name":"Trepat, Xavier"},{"first_name":"Michiyuki","full_name":"Matsuda, Michiyuki","last_name":"Matsuda"}],"date_updated":"2025-06-25T07:35:27Z","department":[{"_id":"CaHe"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1016/j.devcel.2022.09.003","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","acknowledgement":"We thank the members of the Matsuda Laboratory for their helpful discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical assistance. This work was supported by the Kyoto University Live Imaging Center. Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107 and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no. JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER (no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739 to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO. This work was partly supported by an Extramural Collaborative Research Grant of Cancer Research Institute, Kanazawa University.","page":"2290-2304.e7","OA_type":"free access","external_id":{"isi":["000898428700006"],"pmid":["36174555"]},"publication_identifier":{"issn":["1534-5807"]},"citation":{"short":"N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji, K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57 (2022) 2290–2304.e7.","ieee":"N. Hino <i>et al.</i>, “A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration,” <i>Developmental Cell</i>, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022.","ista":"Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K, Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. Developmental Cell. 57(19), 2290–2304.e7.","mla":"Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>.","apa":"Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda, M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>","chicago":"Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>.","ama":"Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. 2022;57(19):2290-2304.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","oa":1,"date_published":"2022-10-01T00:00:00Z","year":"2022","issue":"19","abstract":[{"lang":"eng","text":"Upon the initiation of collective cell migration, the cells at the free edge are specified as leader cells; however, the mechanism underlying the leader cell specification remains elusive. Here, we show that lamellipodial extension after the release from mechanical confinement causes sustained extracellular signal-regulated kinase (ERK) activation and underlies the leader cell specification. Live-imaging of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use of Förster resonance energy transfer (FRET)-based biosensors showed that leader cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension at the free edge increases the cellular sensitivity to HGF. The HGF-dependent ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive feedback loop between cell extension and ERK activation and specifying the cells at the free edge as the leader cells. Our findings show that the integration of physical and biochemical cues underlies the leader cell specification during collective cell migration."}],"date_created":"2023-01-16T09:51:39Z","intvolume":"        57","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2022.09.003","open_access":"1"}],"quality_controlled":"1","OA_place":"publisher","volume":57,"article_type":"original","title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"publication":"Developmental Cell","pmid":1,"_id":"12238","publisher":"Elsevier","day":"01"},{"date_updated":"2025-04-15T07:32:09Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"last_name":"Costanzo","full_name":"Costanzo, Tommaso","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815"},{"first_name":"Dana A.","last_name":"Dahhan","full_name":"Dahhan, Dana A."},{"first_name":"Sebastian Y.","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y."},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publication_status":"published","doi":"10.1016/j.molp.2022.09.003","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","file":[{"file_name":"2022_MolecularPlant_Johnson.pdf","date_updated":"2023-01-30T07:46:51Z","relation":"main_file","checksum":"04d5c12490052d03e4dc4412338a43dd","file_size":2307251,"file_id":"12435","access_level":"open_access","success":1,"date_created":"2023-01-30T07:46:51Z","creator":"dernst","content_type":"application/pdf"}],"page":"1533-1542","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"publication_identifier":{"issn":["1674-2052"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","scopus_import":"1","corr_author":"1","file_date_updated":"2023-01-30T07:46:51Z","project":[{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"citation":{"mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>"},"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2022-10-03T00:00:00Z","year":"2022","issue":"10","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"intvolume":"        15","abstract":[{"lang":"eng","text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs."}],"date_created":"2023-01-16T09:51:49Z","quality_controlled":"1","publication":"Molecular Plant","keyword":["Plant Science","Molecular Biology"],"volume":15,"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","article_type":"original","_id":"12239","publisher":"Elsevier","day":"03","ddc":["580"],"pmid":1},{"date_updated":"2025-04-14T07:57:18Z","department":[{"_id":"LaEr"}],"author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","last_name":"Erdös"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"},{"full_name":"Xu, Yuanyuan","last_name":"Xu","first_name":"Yuanyuan","orcid":"0000-0003-1559-1205","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3"}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1063/5.0104290","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","external_id":{"isi":["000869715800001"],"arxiv":["2206.04443"]},"acknowledgement":"The authors are grateful to G. Akemann for bringing Refs. 19 and 24–26 to their attention. Discussions with Guillaume Dubach on a preliminary version of this project are acknowledged.\r\nL.E. and Y.X. were supported by the ERC Advanced Grant “RMTBeyond” under Grant No. 101020331. D.S. was supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","file":[{"success":1,"access_level":"open_access","date_created":"2023-01-30T08:01:10Z","file_id":"12436","content_type":"application/pdf","creator":"dernst","date_updated":"2023-01-30T08:01:10Z","file_name":"2022_JourMathPhysics_Cipolloni2.pdf","file_size":7356807,"relation":"main_file","checksum":"2db278ae5b07f345a7e3fec1f92b5c33"}],"publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","grant_number":"101020331"}],"file_date_updated":"2023-01-30T08:01:10Z","has_accepted_license":"1","article_number":"103303","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. Directional extremal statistics for Ginibre eigenvalues. <i>Journal of Mathematical Physics</i>. 2022;63(10). doi:<a href=\"https://doi.org/10.1063/5.0104290\">10.1063/5.0104290</a>","apa":"Cipolloni, G., Erdös, L., Schröder, D. J., &#38; Xu, Y. (2022). Directional extremal statistics for Ginibre eigenvalues. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0104290\">https://doi.org/10.1063/5.0104290</a>","chicago":"Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu. “Directional Extremal Statistics for Ginibre Eigenvalues.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0104290\">https://doi.org/10.1063/5.0104290</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, Journal of Mathematical Physics 63 (2022).","ieee":"G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “Directional extremal statistics for Ginibre eigenvalues,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 10. AIP Publishing, 2022.","ista":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2022. Directional extremal statistics for Ginibre eigenvalues. Journal of Mathematical Physics. 63(10), 103303.","mla":"Cipolloni, Giorgio, et al. “Directional Extremal Statistics for Ginibre Eigenvalues.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 10, 103303, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0104290\">10.1063/5.0104290</a>."},"language":[{"iso":"eng"}],"date_published":"2022-10-14T00:00:00Z","issue":"10","year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_created":"2023-01-16T09:52:58Z","abstract":[{"lang":"eng","text":"We consider the eigenvalues of a large dimensional real or complex Ginibre matrix in the region of the complex plane where their real parts reach their maximum value. This maximum follows the Gumbel distribution and that these extreme eigenvalues form a Poisson point process as the dimension asymptotically tends to infinity. In the complex case, these facts have already been established by Bender [Probab. Theory Relat. Fields 147, 241 (2010)] and in the real case by Akemann and Phillips [J. Stat. Phys. 155, 421 (2014)] even for the more general elliptic ensemble with a sophisticated saddle point analysis. The purpose of this article is to give a very short direct proof in the Ginibre case with an effective error term. Moreover, our estimates on the correlation kernel in this regime serve as a key input for accurately locating [Formula: see text] for any large matrix X with i.i.d. entries in the companion paper [G. Cipolloni et al., arXiv:2206.04448 (2022)]. "}],"intvolume":"        63","quality_controlled":"1","publication":"Journal of Mathematical Physics","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"volume":63,"title":"Directional extremal statistics for Ginibre eigenvalues","article_type":"original","ec_funded":1,"_id":"12243","day":"14","publisher":"AIP Publishing","arxiv":1,"ddc":["510","530"]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","external_id":{"pmid":["36189829"],"isi":["000918161000003"]},"related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"acknowledgement":"We are grateful to Dr Tom Pettini for the advice on smiFISH technique and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological Services Facility, Bioimaging and Systems Microscopy Facilities of the University of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship in Basic Science (219992/Z/19/Z). Open Access funding provided by The University of Manchester. Deposited in PMC for immediate release.","file":[{"access_level":"open_access","success":1,"date_created":"2023-01-30T08:35:44Z","file_id":"12438","creator":"dernst","content_type":"application/pdf","file_name":"2022_Development_Soto.pdf","date_updated":"2023-01-30T08:35:44Z","file_size":9348839,"relation":"main_file","checksum":"d7c29b74e9e4032308228cc704a30e88"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"has_accepted_license":"1","article_number":"dev200474","citation":{"ama":"Soto X, Burton J, Manning CS, et al. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19). doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>","apa":"Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>","chicago":"Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>.","ieee":"X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. The Company of Biologists, 2022.","ista":"Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development. 149(19), dev200474.","short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022).","mla":"Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2023-01-30T08:35:44Z","author":[{"first_name":"Ximena","last_name":"Soto","full_name":"Soto, Ximena"},{"first_name":"Joshua","full_name":"Burton, Joshua","last_name":"Burton"},{"last_name":"Manning","full_name":"Manning, Cerys S.","first_name":"Cerys S."},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas","last_name":"Minchington","full_name":"Minchington, Thomas"},{"full_name":"Lea, Robert","last_name":"Lea","first_name":"Robert"},{"first_name":"Jessica","full_name":"Lee, Jessica","last_name":"Lee"},{"first_name":"Jochen","last_name":"Kursawe","full_name":"Kursawe, Jochen"},{"last_name":"Rattray","full_name":"Rattray, Magnus","first_name":"Magnus"},{"first_name":"Nancy","full_name":"Papalopulu, Nancy","last_name":"Papalopulu"}],"article_processing_charge":"No","date_updated":"2023-08-04T09:41:08Z","department":[{"_id":"AnKi"}],"isi":1,"status":"public","doi":"10.1242/dev.200474","publication_status":"published","oa_version":"Published Version","type":"journal_article","volume":149,"title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","article_type":"original","keyword":["Developmental Biology","Molecular Biology"],"publication":"Development","ddc":["570"],"pmid":1,"_id":"12245","day":"01","publisher":"The Company of Biologists","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2022-10-01T00:00:00Z","issue":"19","year":"2022","abstract":[{"text":"MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.","lang":"eng"}],"intvolume":"       149","date_created":"2023-01-16T09:53:17Z","quality_controlled":"1"},{"quality_controlled":"1","date_created":"2023-01-16T09:53:54Z","intvolume":"       112","abstract":[{"lang":"eng","text":"The Lieb–Oxford inequality provides a lower bound on the Coulomb energy of a classical system of N identical charges only in terms of their one-particle density. We prove here a new estimate on the best constant in this inequality. Numerical evaluation provides the value 1.58, which is a significant improvement to the previously known value 1.64. The best constant has recently been shown to be larger than 1.44. In a second part, we prove that the constant can be reduced to 1.25 when the inequality is restricted to Hartree–Fock states. This is the first proof that the exchange term is always much lower than the full indirect Coulomb energy."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.12473"}],"year":"2022","issue":"5","date_published":"2022-09-15T00:00:00Z","oa":1,"arxiv":1,"publisher":"Springer Nature","day":"15","_id":"12246","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"publication":"Letters in Mathematical Physics","ec_funded":1,"title":"Improved Lieb–Oxford bound on the indirect and exchange energies","article_type":"original","volume":112,"type":"journal_article","oa_version":"Preprint","publication_status":"published","doi":"10.1007/s11005-022-01584-5","status":"public","isi":1,"department":[{"_id":"RoSe"}],"date_updated":"2025-04-14T07:26:59Z","article_processing_charge":"No","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"full_name":"Lieb, Elliott H.","last_name":"Lieb","first_name":"Elliott H."},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"}],"scopus_import":"1","language":[{"iso":"eng"}],"citation":{"short":"M. Lewin, E.H. Lieb, R. Seiringer, Letters in Mathematical Physics 112 (2022).","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Improved Lieb–Oxford bound on the indirect and exchange energies,” <i>Letters in Mathematical Physics</i>, vol. 112, no. 5. Springer Nature, 2022.","ista":"Lewin M, Lieb EH, Seiringer R. 2022. Improved Lieb–Oxford bound on the indirect and exchange energies. Letters in Mathematical Physics. 112(5), 92.","mla":"Lewin, Mathieu, et al. “Improved Lieb–Oxford Bound on the Indirect and Exchange Energies.” <i>Letters in Mathematical Physics</i>, vol. 112, no. 5, 92, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11005-022-01584-5\">10.1007/s11005-022-01584-5</a>.","apa":"Lewin, M., Lieb, E. H., &#38; Seiringer, R. (2022). Improved Lieb–Oxford bound on the indirect and exchange energies. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-022-01584-5\">https://doi.org/10.1007/s11005-022-01584-5</a>","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Improved Lieb–Oxford Bound on the Indirect and Exchange Energies.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11005-022-01584-5\">https://doi.org/10.1007/s11005-022-01584-5</a>.","ama":"Lewin M, Lieb EH, Seiringer R. Improved Lieb–Oxford bound on the indirect and exchange energies. <i>Letters in Mathematical Physics</i>. 2022;112(5). doi:<a href=\"https://doi.org/10.1007/s11005-022-01584-5\">10.1007/s11005-022-01584-5</a>"},"article_number":"92","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"acknowledgement":"We would like to thank David Gontier for useful advice on the numerical simulations. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreements MDFT No. 725528 of M.L. and AQUAMS No. 694227 of R.S.). We are thankful for the hospitality of the Institut Henri Poincaré in Paris, where part of this work was done.","external_id":{"isi":["000854762600001"],"arxiv":["2203.12473"]},"month":"09","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"file_date_updated":"2023-01-30T08:45:35Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"short":"E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 76 (2022) 2332–2346.","ista":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 76(10), 2332–2346.","ieee":"E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution,” <i>Evolution</i>, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.","mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” <i>Evolution</i>, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>.","apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>","chicago":"Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>.","ama":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. <i>Evolution</i>. 2022;76(10):2332-2346. doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>"},"has_accepted_license":"1","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"file":[{"date_updated":"2023-01-30T08:45:35Z","file_name":"2022_Evolution_Koch.pdf","file_size":2990581,"relation":"main_file","checksum":"defd8a4bea61cf00a3c88d4a30e2728c","success":1,"access_level":"open_access","date_created":"2023-01-30T08:45:35Z","file_id":"12439","creator":"dernst","content_type":"application/pdf"}],"acknowledgement":"We thank everyone who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson for their contributions, with inversions and shell shape respectively. KJ was funded by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B. and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS). R.K.B. was also funded by the Natural Environment Research Council and the Swedish Research Council Vetenskapsrådet.","page":"2332-2346","related_material":{"record":[{"relation":"research_data","status":"public","id":"13066"}]},"external_id":{"isi":["000848449100001"],"pmid":["35994296"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1111/evo.14602","status":"public","isi":1,"department":[{"_id":"NiBa"}],"date_updated":"2023-08-04T09:42:11Z","author":[{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_processing_charge":"No","publisher":"Wiley","day":"01","_id":"12247","pmid":1,"ddc":["570"],"keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"publication":"Evolution","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","article_type":"original","volume":76,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"date_created":"2023-01-16T09:54:15Z","intvolume":"        76","year":"2022","issue":"10","date_published":"2022-10-01T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"date_updated":"2025-06-11T13:41:59Z","department":[{"_id":"BiCh"}],"author":[{"full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"article_processing_charge":"No","publication_status":"published","doi":"10.1063/5.0107059","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","acknowledgement":"I thank Daan Frenkel for providing feedback on an early draft and for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions on the manuscript.","related_material":{"link":[{"url":"https://github.com/ BingqingCheng/S0","relation":"software"}]},"file":[{"file_name":"2022_JourChemPhysics_Cheng.pdf","date_updated":"2023-01-30T09:07:00Z","file_size":4402384,"relation":"main_file","checksum":"b0915b706568a663a9a372fca24adf35","success":1,"access_level":"open_access","date_created":"2023-01-30T09:07:00Z","file_id":"12441","content_type":"application/pdf","creator":"dernst"}],"external_id":{"isi":["000862856000003"],"pmid":["36182422"]},"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","corr_author":"1","file_date_updated":"2023-01-30T09:07:00Z","citation":{"mla":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12, 121101, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>.","ista":"Cheng B. 2022. Computing chemical potentials of solutions from structure factors. The Journal of Chemical Physics. 157(12), 121101.","short":"B. Cheng, The Journal of Chemical Physics 157 (2022).","ieee":"B. Cheng, “Computing chemical potentials of solutions from structure factors,” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12. AIP Publishing, 2022.","chicago":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>.","apa":"Cheng, B. (2022). Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>","ama":"Cheng B. Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. 2022;157(12). doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>"},"article_number":"121101","has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2022-09-30T00:00:00Z","year":"2022","issue":"12","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"intvolume":"       157","date_created":"2023-01-16T09:56:20Z","abstract":[{"text":"The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. ","lang":"eng"}],"quality_controlled":"1","publication":"The Journal of Chemical Physics","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"volume":157,"article_type":"original","title":"Computing chemical potentials of solutions from structure factors","_id":"12249","publisher":"AIP Publishing","day":"30","ddc":["530","540"],"pmid":1},{"date_updated":"2023-08-04T09:48:56Z","department":[{"_id":"AnSa"}],"author":[{"full_name":"Weiffert, Tanja","last_name":"Weiffert","first_name":"Tanja"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"last_name":"Cukalevski","full_name":"Cukalevski, Risto","first_name":"Risto"},{"last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"}],"article_processing_charge":"No","publication_status":"published","doi":"10.3389/fnins.2022.943355","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","acknowledgement":"This work was supported by grants from the Swedish Research Council (grant no. 2015-00143) and the European Research Council (grant no. 340890).","file":[{"content_type":"application/pdf","creator":"dernst","date_created":"2023-01-30T09:15:13Z","access_level":"open_access","success":1,"file_id":"12442","file_size":19798610,"checksum":"e67d16113ffb4fb4fa38a183d169f210","relation":"main_file","date_updated":"2023-01-30T09:15:13Z","file_name":"2022_FrontiersNeuroscience_Weiffert2.pdf"}],"external_id":{"isi":["000866287100001"]},"publication_identifier":{"issn":["1662-453X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","scopus_import":"1","file_date_updated":"2023-01-30T09:15:13Z","citation":{"short":"T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles, S. Linse, Frontiers in Neuroscience 16 (2022).","ieee":"T. Weiffert <i>et al.</i>, “Influence of denaturants on amyloid β42 aggregation kinetics,” <i>Frontiers in Neuroscience</i>, vol. 16. Frontiers Media, 2022.","ista":"Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S. 2022. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. 16, 943355.","mla":"Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” <i>Frontiers in Neuroscience</i>, vol. 16, 943355, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fnins.2022.943355\">10.3389/fnins.2022.943355</a>.","ama":"Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42 aggregation kinetics. <i>Frontiers in Neuroscience</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fnins.2022.943355\">10.3389/fnins.2022.943355</a>","apa":"Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P. J., &#38; Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation kinetics. <i>Frontiers in Neuroscience</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fnins.2022.943355\">https://doi.org/10.3389/fnins.2022.943355</a>","chicago":"Weiffert, Tanja, Georg Meisl, Samo Curk, Risto Cukalevski, Anđela Šarić, Tuomas P. J. Knowles, and Sara Linse. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” <i>Frontiers in Neuroscience</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fnins.2022.943355\">https://doi.org/10.3389/fnins.2022.943355</a>."},"article_number":"943355","has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2022-09-20T00:00:00Z","year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"abstract":[{"text":"Amyloid formation is linked to devastating neurodegenerative diseases, motivating detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated with Alzheimer’s disease, the mechanism and rate of aggregation have been established for a range of variants and conditions <jats:italic>in vitro</jats:italic> and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.","lang":"eng"}],"date_created":"2023-01-16T09:56:43Z","intvolume":"        16","quality_controlled":"1","publication":"Frontiers in Neuroscience","keyword":["General Neuroscience"],"volume":16,"title":"Influence of denaturants on amyloid β42 aggregation kinetics","article_type":"original","_id":"12251","publisher":"Frontiers Media","day":"20","ddc":["570"]},{"year":"2022","date_published":"2022-09-16T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","date_created":"2023-01-16T09:56:57Z","abstract":[{"lang":"eng","text":"The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 10<jats:sup>11</jats:sup> diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\\ml and 9.6 ng\\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants."}],"intvolume":"        13","keyword":["Immunology","Immunology and Allergy","COVID-19","SARS-CoV-2","synthetic library","RBD","neutralization nanobody","VHH"],"publication":"Frontiers in Immunology","article_type":"original","title":"Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library","volume":13,"day":"16","publisher":"Frontiers Media","_id":"12252","pmid":1,"ddc":["570"],"department":[{"_id":"LeSa"}],"date_updated":"2025-06-11T13:42:26Z","author":[{"full_name":"Dormeshkin, Dmitri","last_name":"Dormeshkin","first_name":"Dmitri"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"first_name":"Simon","full_name":"Dubovik, Simon","last_name":"Dubovik"},{"first_name":"Anton","id":"4968f7ad-eb97-11eb-a6c2-8ed382e8912c","orcid":"0000-0003-2091-526X","full_name":"Kavaleuski, Anton","last_name":"Kavaleuski"},{"first_name":"Mikalai","last_name":"Katsin","full_name":"Katsin, Mikalai"},{"first_name":"Alexandr","full_name":"Migas, Alexandr","last_name":"Migas"},{"full_name":"Meleshko, Alexander","last_name":"Meleshko","first_name":"Alexander"},{"last_name":"Semyonov","full_name":"Semyonov, Sergei","first_name":"Sergei"}],"article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","doi":"10.3389/fimmu.2022.965446","publication_status":"published","status":"public","isi":1,"publication_identifier":{"issn":["1664-3224"]},"external_id":{"pmid":["36189235"],"isi":["000862479100001"]},"file":[{"date_created":"2023-01-30T09:22:26Z","success":1,"access_level":"open_access","file_id":"12443","creator":"dernst","content_type":"application/pdf","date_updated":"2023-01-30T09:22:26Z","file_name":"2022_FrontiersImmunology_Dormeshkin.pdf","file_size":5695892,"checksum":"f8f5d8110710033d0532e7e08bf9dad4","relation":"main_file"}],"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","file_date_updated":"2023-01-30T09:22:26Z","scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","article_number":"965446","citation":{"ista":"Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13, 965446.","short":"D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas, A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).","ieee":"D. Dormeshkin <i>et al.</i>, “Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library,” <i>Frontiers in Immunology</i>, vol. 13. Frontiers Media, 2022.","mla":"Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” <i>Frontiers in Immunology</i>, vol. 13, 965446, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fimmu.2022.965446\">10.3389/fimmu.2022.965446</a>.","ama":"Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. <i>Frontiers in Immunology</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fimmu.2022.965446\">10.3389/fimmu.2022.965446</a>","apa":"Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas, A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. <i>Frontiers in Immunology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fimmu.2022.965446\">https://doi.org/10.3389/fimmu.2022.965446</a>","chicago":"Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” <i>Frontiers in Immunology</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fimmu.2022.965446\">https://doi.org/10.3389/fimmu.2022.965446</a>."}},{"publisher":"American Association for the Advancement of Science","day":"14","_id":"12253","pmid":1,"ddc":["570"],"publication":"Science Advances","ec_funded":1,"article_type":"original","title":"A self-generated Toddler gradient guides mesodermal cell migration","volume":8,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor–based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo."}],"intvolume":"         8","date_created":"2023-01-16T09:57:10Z","year":"2022","issue":"37","date_published":"2022-09-14T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-01-30T09:27:49Z","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"scopus_import":"1","language":[{"iso":"eng"}],"citation":{"short":"J. Stock, T. Kazmar, F. Schlumm, E.B. Hannezo, A. Pauli, Science Advances 8 (2022).","ieee":"J. Stock, T. Kazmar, F. Schlumm, E. B. Hannezo, and A. Pauli, “A self-generated Toddler gradient guides mesodermal cell migration,” <i>Science Advances</i>, vol. 8, no. 37. American Association for the Advancement of Science, 2022.","ista":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. 2022. A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. 8(37), eadd2488.","mla":"Stock, Jessica, et al. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” <i>Science Advances</i>, vol. 8, no. 37, eadd2488, American Association for the Advancement of Science, 2022, doi:<a href=\"https://doi.org/10.1126/sciadv.add2488\">10.1126/sciadv.add2488</a>.","apa":"Stock, J., Kazmar, T., Schlumm, F., Hannezo, E. B., &#38; Pauli, A. (2022). A self-generated Toddler gradient guides mesodermal cell migration. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add2488\">https://doi.org/10.1126/sciadv.add2488</a>","chicago":"Stock, Jessica, Tomas Kazmar, Friederike Schlumm, Edouard B Hannezo, and Andrea Pauli. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” <i>Science Advances</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/sciadv.add2488\">https://doi.org/10.1126/sciadv.add2488</a>.","ama":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. A self-generated Toddler gradient guides mesodermal cell migration. <i>Science Advances</i>. 2022;8(37). doi:<a href=\"https://doi.org/10.1126/sciadv.add2488\">10.1126/sciadv.add2488</a>"},"article_number":"eadd2488","has_accepted_license":"1","publication_identifier":{"issn":["2375-2548"]},"acknowledgement":"We thank K. Aumayer and the team of the biooptics facility at the Vienna Biocenter, particularly P. Pasierbek and T. Müller, for support with microscopy; K. Panser, C. Pribitzer, and the animal facility personnel for taking care of zebrafish; M. Binner and A. Bandura for help with genotyping; M. Codina Tobias for help with establishing the conditions for the Toddler overexpression compensation experiment; T. Lubiana Alves for sharing the code for scRNA-Seq analyses; the Heisenberg laboratory, particularly D. Pinheiro, for joint laboratory meetings, discussions on the project, and providing the tg(gsc:CAAX-GFP) fish line; the Raz laboratory for providing the Lifeact-GFP plasmid; A. Andersen, A. Schier, C.-P. Heisenberg, and E. Tanaka for comments on the manuscript; and the entire Pauli laboratory, particularly K. Gert and V. Deneke, for valuable discussions and feedback on the manuscript. Funding: Work in A.P.’s laboratory has been supported by the IMP, which receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936), as well as the FWF START program (Y 1031-B28 to A.P.), the Human Frontier Science Program (HFSP) Career Development Award (CDA00066/2015 to A.P.) and Young Investigator Grant (RGY0079/2020 to A.P.), the SFB RNA-Deco (project number F 80 to A.P.), a Whitman Center Fellowship from the Marine Biological Laboratory (to A.P.), and EMBO-YIP funds (to A.P.). This work was supported by the European Union (European Research Council Starting Grant 851288 to E.H.). For the purpose of Open Access, the authors have applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","file":[{"file_name":"2022_ScienceAdvances_Stock.pdf","date_updated":"2023-01-30T09:27:49Z","relation":"main_file","checksum":"f59cdb824e5d4221045def81f46f6c65","file_size":1636732,"file_id":"12444","success":1,"access_level":"open_access","date_created":"2023-01-30T09:27:49Z","content_type":"application/pdf","creator":"dernst"}],"external_id":{"pmid":["36103529"],"isi":["000888875000009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1126/sciadv.add2488","status":"public","isi":1,"department":[{"_id":"EdHa"}],"date_updated":"2025-04-14T07:52:27Z","author":[{"first_name":"Jessica","full_name":"Stock, Jessica","last_name":"Stock"},{"first_name":"Tomas","last_name":"Kazmar","full_name":"Kazmar, Tomas"},{"first_name":"Friederike","last_name":"Schlumm","full_name":"Schlumm, Friederike"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pauli","full_name":"Pauli, Andrea","first_name":"Andrea"}],"article_processing_charge":"No"},{"external_id":{"arxiv":["2206.01531"],"pmid":["36182399"],"isi":["000861009600005"]},"acknowledgement":"This work was partially funded by the Institute of Science and Technology Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos and Quantum Analogies.”","file":[{"date_updated":"2023-01-30T09:41:12Z","file_name":"2022_Chaos_Choueiri.pdf","checksum":"17881eff8b21969359a2dd64620120ba","relation":"main_file","file_size":3209644,"file_id":"12445","date_created":"2023-01-30T09:41:12Z","access_level":"open_access","success":1,"creator":"dernst","content_type":"application/pdf"}],"publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","scopus_import":"1","file_date_updated":"2023-01-30T09:41:12Z","article_number":"093138","has_accepted_license":"1","citation":{"mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>.","ieee":"G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur, “Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9. AIP Publishing, 2022.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","ista":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 32(9), 093138.","ama":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. 2022;32(9). doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>","chicago":"Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>.","apa":"Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., &#38; Budanur, N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>"},"language":[{"iso":"eng"}],"date_updated":"2025-06-11T13:41:34Z","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"author":[{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","last_name":"Choueiri"},{"last_name":"Suri","full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym"},{"last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B"}],"article_processing_charge":"No","doi":"10.1063/5.0102904","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"volume":32,"title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","article_type":"original","_id":"12259","day":"26","arxiv":1,"publisher":"AIP Publishing","ddc":["530"],"pmid":1,"date_published":"2022-09-26T00:00:00Z","issue":"9","year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"intvolume":"        32","date_created":"2023-01-16T09:58:16Z","abstract":[{"text":"Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. ","lang":"eng"}],"quality_controlled":"1"},{"oa":1,"issue":"1","year":"2022","date_published":"2022-11-16T00:00:00Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2210.01928"}],"abstract":[{"lang":"eng","text":"Rotation is typically assumed to induce strictly symmetric rotational splitting into the rotational multiplets of pure p- and g-modes. However, for evolved stars exhibiting mixed modes, avoided crossings between different multiplet components are known to yield asymmetric rotational splitting, in particular for near-degenerate mixed-mode pairs, where notional pure p-modes are fortuitously in resonance with pure g-modes. These near-degeneracy effects have been described in subgiants, but their consequences for the characterization of internal rotation in red giants have not previously been investigated in detail, in part owing to theoretical intractability. We employ new developments in the analytic theory of mixed-mode coupling to study these near-resonance phenomena. In the vicinity of the most p-dominated mixed modes, the near-degenerate intrinsic asymmetry from pure rotational splitting increases dramatically over the course of stellar evolution, and it depends strongly on the mode-mixing fraction ζ. We also find that a linear treatment of rotation remains viable for describing the underlying p- and g-modes, even when it does not for the resulting mixed modes undergoing these avoided crossings. We explore observational consequences for potential measurements of asymmetric mixed-mode splitting, which has been proposed as a magnetic-field diagnostic. Finally, we propose improved measurement techniques for rotational characterization, exploiting the linearity of rotational effects on the underlying p/g-modes, while still accounting for these mixed-mode coupling effects."}],"date_created":"2023-08-01T14:20:41Z","intvolume":"       940","title":"Mode mixing and rotational splittings. I. Near-degeneracy effects revisited","article_type":"original","volume":940,"publication":"The Astrophysical Journal","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"day":"16","publisher":"American Astronomical Society","arxiv":1,"_id":"13445","article_processing_charge":"No","author":[{"last_name":"Ong","full_name":"Ong, J. M. Joel","first_name":"J. M. Joel"},{"last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle"},{"last_name":"Basu","full_name":"Basu, Sarbani","first_name":"Sarbani"}],"date_updated":"2023-09-06T07:27:45Z","status":"public","oa_version":"Published Version","type":"journal_article","doi":"10.3847/1538-4357/ac97e7","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"external_id":{"arxiv":["2210.01928"]},"language":[{"iso":"eng"}],"article_number":"18","citation":{"chicago":"Ong, J. M. Joel, Lisa Annabelle Bugnet, and Sarbani Basu. “Mode Mixing and Rotational Splittings. I. Near-Degeneracy Effects Revisited.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2022. <a href=\"https://doi.org/10.3847/1538-4357/ac97e7\">https://doi.org/10.3847/1538-4357/ac97e7</a>.","apa":"Ong, J. M. J., Bugnet, L. A., &#38; Basu, S. (2022). Mode mixing and rotational splittings. I. Near-degeneracy effects revisited. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.3847/1538-4357/ac97e7\">https://doi.org/10.3847/1538-4357/ac97e7</a>","ama":"Ong JMJ, Bugnet LA, Basu S. Mode mixing and rotational splittings. I. Near-degeneracy effects revisited. <i>The Astrophysical Journal</i>. 2022;940(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/ac97e7\">10.3847/1538-4357/ac97e7</a>","mla":"Ong, J. M. Joel, et al. “Mode Mixing and Rotational Splittings. I. Near-Degeneracy Effects Revisited.” <i>The Astrophysical Journal</i>, vol. 940, no. 1, 18, American Astronomical Society, 2022, doi:<a href=\"https://doi.org/10.3847/1538-4357/ac97e7\">10.3847/1538-4357/ac97e7</a>.","ista":"Ong JMJ, Bugnet LA, Basu S. 2022. Mode mixing and rotational splittings. I. Near-degeneracy effects revisited. The Astrophysical Journal. 940(1), 18.","short":"J.M.J. Ong, L.A. Bugnet, S. Basu, The Astrophysical Journal 940 (2022).","ieee":"J. M. J. Ong, L. A. Bugnet, and S. Basu, “Mode mixing and rotational splittings. I. Near-degeneracy effects revisited,” <i>The Astrophysical Journal</i>, vol. 940, no. 1. American Astronomical Society, 2022."},"scopus_import":"1","extern":"1"},{"oa":1,"date_published":"2022-12-27T00:00:00Z","issue":"2","year":"2022","main_file_link":[{"url":"https://doi.org/10.3847/1538-4357/aca295","open_access":"1"}],"abstract":[{"lang":"eng","text":"We characterize massive stars (M > 8 M⊙) in the nearby (D ∼ 0.8 Mpc) extremely metal-poor (Z ∼ 5% Z⊙) galaxy Leo A using Hubble Space Telescope ultraviolet (UV), optical, and near-infrared (NIR) imaging along with Keck/Low-Resolution Imaging Spectrograph and MMT/Binospec optical spectroscopy for 18 main-sequence OB stars. We find that: (a) 12 of our 18 stars show emission lines, despite not being associated with an H ii region, suggestive of stellar activity (e.g., mass loss, accretion, binary star interaction), which is consistent with previous predictions of enhanced activity at low metallicity; (b) six are Be stars, which are the first to be spectroscopically studied at such low metallicity—these Be stars have unusual panchromatic SEDs; (c) for stars well fit by the TLUSTY nonlocal thermodynamic equilibrium models, the photometric and spectroscopic values of $\\mathrm{log}({T}_{\\mathrm{eff}})$ and $\\mathrm{log}(g)$ agree to within ∼0.01 dex and ∼0.18 dex, respectively, indicating that near-UV/optical/NIR imaging can be used to reliably characterize massive (M ∼ 8–30 M⊙) main-sequence star properties relative to optical spectroscopy; (d) the properties of the most-massive stars in H II regions are consistent with constraints from previous nebular emission line studies; and (e) 13 stars with M > 8M⊙ are >40 pc from a known star cluster or H II region. Our sample comprises ∼50% of all known massive stars at Z ≲ 10% Z⊙with derived stellar parameters, high-quality optical spectra, and panchromatic photometry."}],"date_created":"2023-08-03T10:10:25Z","intvolume":"       941","quality_controlled":"1","volume":941,"article_type":"original","title":"A panchromatic study of massive stars in the extremely metal-poor local group dwarf galaxy Leo A","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"publication":"The Astrophysical Journal","_id":"13451","day":"27","publisher":"American Astronomical Society","arxiv":1,"article_processing_charge":"No","author":[{"last_name":"Gull","full_name":"Gull, Maude","first_name":"Maude"},{"last_name":"Weisz","full_name":"Weisz, Daniel R.","first_name":"Daniel R."},{"first_name":"Peter","last_name":"Senchyna","full_name":"Senchyna, Peter"},{"last_name":"Sandford","full_name":"Sandford, Nathan R.","first_name":"Nathan R."},{"last_name":"Choi","full_name":"Choi, Yumi","first_name":"Yumi"},{"first_name":"Anna F.","full_name":"McLeod, Anna F.","last_name":"McLeod"},{"full_name":"El-Badry, Kareem","last_name":"El-Badry","first_name":"Kareem"},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter"},{"full_name":"Gilbert, Karoline M.","last_name":"Gilbert","first_name":"Karoline M."},{"full_name":"Boyer, Martha","last_name":"Boyer","first_name":"Martha"},{"first_name":"Julianne J.","full_name":"Dalcanton, Julianne J.","last_name":"Dalcanton"},{"last_name":"GuhaThakurta","full_name":"GuhaThakurta, Puragra","first_name":"Puragra"},{"full_name":"Goldman, Steven","last_name":"Goldman","first_name":"Steven"},{"last_name":"Marigo","full_name":"Marigo, Paola","first_name":"Paola"},{"first_name":"Kristen B. W.","last_name":"McQuinn","full_name":"McQuinn, Kristen B. W."},{"last_name":"Pastorelli","full_name":"Pastorelli, Giada","first_name":"Giada"},{"full_name":"Stark, Daniel P.","last_name":"Stark","first_name":"Daniel P."},{"first_name":"Evan","last_name":"Skillman","full_name":"Skillman, Evan"},{"first_name":"Yuan-sen","last_name":"Ting","full_name":"Ting, Yuan-sen"},{"last_name":"Williams","full_name":"Williams, Benjamin F.","first_name":"Benjamin F."}],"date_updated":"2023-08-21T12:04:58Z","status":"public","doi":"10.3847/1538-4357/aca295","publication_status":"published","oa_version":"Published Version","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","external_id":{"arxiv":["2211.14349"]},"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"article_number":"206","citation":{"mla":"Gull, Maude, et al. “A Panchromatic Study of Massive Stars in the Extremely Metal-Poor Local Group Dwarf Galaxy Leo A.” <i>The Astrophysical Journal</i>, vol. 941, no. 2, 206, American Astronomical Society, 2022, doi:<a href=\"https://doi.org/10.3847/1538-4357/aca295\">10.3847/1538-4357/aca295</a>.","ieee":"M. Gull <i>et al.</i>, “A panchromatic study of massive stars in the extremely metal-poor local group dwarf galaxy Leo A,” <i>The Astrophysical Journal</i>, vol. 941, no. 2. American Astronomical Society, 2022.","ista":"Gull M, Weisz DR, Senchyna P, Sandford NR, Choi Y, McLeod AF, El-Badry K, Götberg YLL, Gilbert KM, Boyer M, Dalcanton JJ, GuhaThakurta P, Goldman S, Marigo P, McQuinn KBW, Pastorelli G, Stark DP, Skillman E, Ting Y, Williams BF. 2022. A panchromatic study of massive stars in the extremely metal-poor local group dwarf galaxy Leo A. The Astrophysical Journal. 941(2), 206.","short":"M. Gull, D.R. Weisz, P. Senchyna, N.R. Sandford, Y. Choi, A.F. McLeod, K. El-Badry, Y.L.L. Götberg, K.M. Gilbert, M. Boyer, J.J. Dalcanton, P. GuhaThakurta, S. Goldman, P. Marigo, K.B.W. McQuinn, G. Pastorelli, D.P. Stark, E. Skillman, Y. Ting, B.F. Williams, The Astrophysical Journal 941 (2022).","ama":"Gull M, Weisz DR, Senchyna P, et al. A panchromatic study of massive stars in the extremely metal-poor local group dwarf galaxy Leo A. <i>The Astrophysical Journal</i>. 2022;941(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/aca295\">10.3847/1538-4357/aca295</a>","chicago":"Gull, Maude, Daniel R. Weisz, Peter Senchyna, Nathan R. Sandford, Yumi Choi, Anna F. McLeod, Kareem El-Badry, et al. “A Panchromatic Study of Massive Stars in the Extremely Metal-Poor Local Group Dwarf Galaxy Leo A.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2022. <a href=\"https://doi.org/10.3847/1538-4357/aca295\">https://doi.org/10.3847/1538-4357/aca295</a>.","apa":"Gull, M., Weisz, D. R., Senchyna, P., Sandford, N. R., Choi, Y., McLeod, A. F., … Williams, B. F. (2022). A panchromatic study of massive stars in the extremely metal-poor local group dwarf galaxy Leo A. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.3847/1538-4357/aca295\">https://doi.org/10.3847/1538-4357/aca295</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","extern":"1"},{"publication":"Monthly Notices of the Royal Astronomical Society","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"volume":517,"article_type":"original","title":"The effects of surface fossil magnetic fields on massive star evolution: IV. Grids of models at Solar, LMC, and SMC metallicities","_id":"13452","day":"01","publisher":"Oxford University Press","arxiv":1,"date_published":"2022-12-01T00:00:00Z","issue":"2","year":"2022","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2209.06350","open_access":"1"}],"intvolume":"       517","date_created":"2023-08-03T10:10:37Z","abstract":[{"lang":"eng","text":"Magnetic fields can drastically change predictions of evolutionary models of massive stars via mass-loss quenching, magnetic braking, and efficient angular momentum transport, which we aim to quantify in this work. We use the MESA software instrument to compute an extensive main-sequence grid of stellar structure and evolution models, as well as isochrones, accounting for the effects attributed to a surface fossil magnetic field. The grid is densely populated in initial mass (3–60 M⊙), surface equatorial magnetic field strength (0–50 kG), and metallicity (representative of the Solar neighbourhood and the Magellanic Clouds). We use two magnetic braking and two chemical mixing schemes and compare the model predictions for slowly rotating, nitrogen-enriched (‘Group 2’) stars with observations in the Large Magellanic Cloud. We quantify a range of initial field strengths that allow for producing Group 2 stars and find that typical values (up to a few kG) lead to solutions. Between the subgrids, we find notable departures in surface abundances and evolutionary paths. In our magnetic models, chemical mixing is always less efficient compared to non-magnetic models due to the rapid spin-down. We identify that quasi-chemically homogeneous main sequence evolution by efficient mixing could be prevented by fossil magnetic fields. We recommend comparing this grid of evolutionary models with spectropolarimetric and spectroscopic observations with the goals of (i) revisiting the derived stellar parameters of known magnetic stars, and (ii) observationally constraining the uncertain magnetic braking and chemical mixing schemes."}],"quality_controlled":"1","external_id":{"arxiv":["2209.06350"]},"page":"2028-2055","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","extern":"1","citation":{"mla":"Keszthelyi, Z., et al. “The Effects of Surface Fossil Magnetic Fields on Massive Star Evolution: IV. Grids of Models at Solar, LMC, and SMC Metallicities.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 517, no. 2, Oxford University Press, 2022, pp. 2028–55, doi:<a href=\"https://doi.org/10.1093/mnras/stac2598\">10.1093/mnras/stac2598</a>.","ista":"Keszthelyi Z, de Koter A, Götberg YLL, Meynet G, Brands SA, Petit V, Carrington M, David-Uraz A, Geen ST, Georgy C, Hirschi R, Puls J, Ramalatswa KJ, Shultz ME, ud-Doula A. 2022. The effects of surface fossil magnetic fields on massive star evolution: IV. Grids of models at Solar, LMC, and SMC metallicities. Monthly Notices of the Royal Astronomical Society. 517(2), 2028–2055.","short":"Z. Keszthelyi, A. de Koter, Y.L.L. Götberg, G. Meynet, S.A. Brands, V. Petit, M. Carrington, A. David-Uraz, S.T. Geen, C. Georgy, R. Hirschi, J. Puls, K.J. Ramalatswa, M.E. Shultz, A. ud-Doula, Monthly Notices of the Royal Astronomical Society 517 (2022) 2028–2055.","ieee":"Z. Keszthelyi <i>et al.</i>, “The effects of surface fossil magnetic fields on massive star evolution: IV. Grids of models at Solar, LMC, and SMC metallicities,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 517, no. 2. Oxford University Press, pp. 2028–2055, 2022.","ama":"Keszthelyi Z, de Koter A, Götberg YLL, et al. The effects of surface fossil magnetic fields on massive star evolution: IV. Grids of models at Solar, LMC, and SMC metallicities. <i>Monthly Notices of the Royal Astronomical Society</i>. 2022;517(2):2028-2055. doi:<a href=\"https://doi.org/10.1093/mnras/stac2598\">10.1093/mnras/stac2598</a>","chicago":"Keszthelyi, Z, A de Koter, Ylva Louise Linsdotter Götberg, G Meynet, S A Brands, V Petit, M Carrington, et al. “The Effects of Surface Fossil Magnetic Fields on Massive Star Evolution: IV. Grids of Models at Solar, LMC, and SMC Metallicities.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/mnras/stac2598\">https://doi.org/10.1093/mnras/stac2598</a>.","apa":"Keszthelyi, Z., de Koter, A., Götberg, Y. L. L., Meynet, G., Brands, S. A., Petit, V., … ud-Doula, A. (2022). The effects of surface fossil magnetic fields on massive star evolution: IV. Grids of models at Solar, LMC, and SMC metallicities. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stac2598\">https://doi.org/10.1093/mnras/stac2598</a>"},"language":[{"iso":"eng"}],"date_updated":"2023-08-21T12:02:17Z","article_processing_charge":"No","author":[{"first_name":"Z","last_name":"Keszthelyi","full_name":"Keszthelyi, Z"},{"last_name":"de Koter","full_name":"de Koter, A","first_name":"A"},{"full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter"},{"full_name":"Meynet, G","last_name":"Meynet","first_name":"G"},{"first_name":"S A","full_name":"Brands, S A","last_name":"Brands"},{"full_name":"Petit, V","last_name":"Petit","first_name":"V"},{"first_name":"M","full_name":"Carrington, M","last_name":"Carrington"},{"last_name":"David-Uraz","full_name":"David-Uraz, A","first_name":"A"},{"first_name":"S T","last_name":"Geen","full_name":"Geen, S T"},{"first_name":"C","full_name":"Georgy, C","last_name":"Georgy"},{"full_name":"Hirschi, R","last_name":"Hirschi","first_name":"R"},{"first_name":"J","full_name":"Puls, J","last_name":"Puls"},{"full_name":"Ramalatswa, K J","last_name":"Ramalatswa","first_name":"K J"},{"full_name":"Shultz, M E","last_name":"Shultz","first_name":"M E"},{"last_name":"ud-Doula","full_name":"ud-Doula, A","first_name":"A"}],"doi":"10.1093/mnras/stac2598","publication_status":"published","oa_version":"Preprint","type":"journal_article","status":"public"},{"status":"public","type":"journal_article","oa_version":"None","publication_status":"published","doi":"10.1038/s41566-022-01050-7","article_processing_charge":"No","author":[{"first_name":"Christian","full_name":"Heide, Christian","last_name":"Heide"},{"last_name":"Kobayashi","full_name":"Kobayashi, Yuki","first_name":"Yuki"},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"last_name":"Jain","full_name":"Jain, Deepti","first_name":"Deepti"},{"last_name":"Sobota","full_name":"Sobota, Jonathan A.","first_name":"Jonathan A."},{"first_name":"Makoto","full_name":"Hashimoto, Makoto","last_name":"Hashimoto"},{"first_name":"Patrick S.","last_name":"Kirchmann","full_name":"Kirchmann, Patrick S."},{"last_name":"Oh","full_name":"Oh, Seongshik","first_name":"Seongshik"},{"first_name":"Tony F.","last_name":"Heinz","full_name":"Heinz, Tony F."},{"first_name":"David A.","last_name":"Reis","full_name":"Reis, David A."},{"full_name":"Ghimire, Shambhu","last_name":"Ghimire","first_name":"Shambhu"}],"date_updated":"2023-08-22T07:20:09Z","language":[{"iso":"eng"}],"citation":{"ama":"Heide C, Kobayashi Y, Baykusheva DR, et al. Probing topological phase transitions using high-harmonic generation. <i>Nature Photonics</i>. 2022;16(9):620-624. doi:<a href=\"https://doi.org/10.1038/s41566-022-01050-7\">10.1038/s41566-022-01050-7</a>","chicago":"Heide, Christian, Yuki Kobayashi, Denitsa Rangelova Baykusheva, Deepti Jain, Jonathan A. Sobota, Makoto Hashimoto, Patrick S. Kirchmann, et al. “Probing Topological Phase Transitions Using High-Harmonic Generation.” <i>Nature Photonics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41566-022-01050-7\">https://doi.org/10.1038/s41566-022-01050-7</a>.","apa":"Heide, C., Kobayashi, Y., Baykusheva, D. R., Jain, D., Sobota, J. A., Hashimoto, M., … Ghimire, S. (2022). Probing topological phase transitions using high-harmonic generation. <i>Nature Photonics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41566-022-01050-7\">https://doi.org/10.1038/s41566-022-01050-7</a>","mla":"Heide, Christian, et al. “Probing Topological Phase Transitions Using High-Harmonic Generation.” <i>Nature Photonics</i>, vol. 16, no. 9, Springer Nature, 2022, pp. 620–24, doi:<a href=\"https://doi.org/10.1038/s41566-022-01050-7\">10.1038/s41566-022-01050-7</a>.","ista":"Heide C, Kobayashi Y, Baykusheva DR, Jain D, Sobota JA, Hashimoto M, Kirchmann PS, Oh S, Heinz TF, Reis DA, Ghimire S. 2022. Probing topological phase transitions using high-harmonic generation. Nature Photonics. 16(9), 620–624.","ieee":"C. Heide <i>et al.</i>, “Probing topological phase transitions using high-harmonic generation,” <i>Nature Photonics</i>, vol. 16, no. 9. Springer Nature, pp. 620–624, 2022.","short":"C. Heide, Y. Kobayashi, D.R. Baykusheva, D. Jain, J.A. Sobota, M. Hashimoto, P.S. Kirchmann, S. Oh, T.F. Heinz, D.A. Reis, S. Ghimire, Nature Photonics 16 (2022) 620–624."},"extern":"1","scopus_import":"1","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1749-4885"],"eissn":["1749-4893"]},"page":"620-624","quality_controlled":"1","abstract":[{"lang":"eng","text":"The prediction and realization of topological insulators have sparked great interest in experimental approaches to the classification of materials1,2,3. The phase transition between non-trivial and trivial topological states is important, not only for basic materials science but also for next-generation technology, such as dissipation-free electronics4. It is therefore crucial to develop advanced probes that are suitable for a wide range of samples and environments. Here we demonstrate that circularly polarized laser-field-driven high-harmonic generation is distinctly sensitive to the non-trivial and trivial topological phases in the prototypical three-dimensional topological insulator bismuth selenide5. The phase transition is chemically initiated by reducing the spin–orbit interaction strength through the substitution of bismuth with indium atoms6,7. We find strikingly different high-harmonic responses of trivial and non-trivial topological surface states that manifest themselves as a conversion efficiency and elliptical dichroism that depend both on the driving laser ellipticity and the crystal orientation. The origins of the anomalous high-harmonic response are corroborated by calculations using the semiconductor optical Bloch equations with pairs of surface and bulk bands. As a purely optical approach, this method offers sensitivity to the electronic structure of the material, including its nonlinear response, and is compatible with a wide range of samples and sample environments."}],"date_created":"2023-08-09T13:07:51Z","intvolume":"        16","year":"2022","issue":"9","date_published":"2022-09-01T00:00:00Z","publisher":"Springer Nature","day":"01","_id":"13991","title":"Probing topological phase transitions using high-harmonic generation","article_type":"original","volume":16,"keyword":["Atomic and Molecular Physics","and Optics","Electronic","Optical and Magnetic Materials"],"publication":"Nature Photonics"},{"language":[{"iso":"eng"}],"citation":{"mla":"Svoboda, Vít, et al. “Femtosecond Photoelectron Circular Dichroism of Chemical Reactions.” <i>Science Advances</i>, vol. 8, no. 28, abq2811, American Association for the Advancement of Science, 2022, doi:<a href=\"https://doi.org/10.1126/sciadv.abq2811\">10.1126/sciadv.abq2811</a>.","ista":"Svoboda V, Ram NB, Baykusheva DR, Zindel D, Waters MDJ, Spenger B, Ochsner M, Herburger H, Stohner J, Wörner HJ. 2022. Femtosecond photoelectron circular dichroism of chemical reactions. Science Advances. 8(28), abq2811.","short":"V. Svoboda, N.B. Ram, D.R. Baykusheva, D. Zindel, M.D.J. Waters, B. Spenger, M. Ochsner, H. Herburger, J. Stohner, H.J. Wörner, Science Advances 8 (2022).","ieee":"V. Svoboda <i>et al.</i>, “Femtosecond photoelectron circular dichroism of chemical reactions,” <i>Science Advances</i>, vol. 8, no. 28. American Association for the Advancement of Science, 2022.","ama":"Svoboda V, Ram NB, Baykusheva DR, et al. Femtosecond photoelectron circular dichroism of chemical reactions. <i>Science Advances</i>. 2022;8(28). doi:<a href=\"https://doi.org/10.1126/sciadv.abq2811\">10.1126/sciadv.abq2811</a>","chicago":"Svoboda, Vít, Niraghatam Bhargava Ram, Denitsa Rangelova Baykusheva, Daniel Zindel, Max D. J. Waters, Benjamin Spenger, Manuel Ochsner, Holger Herburger, Jürgen Stohner, and Hans Jakob Wörner. “Femtosecond Photoelectron Circular Dichroism of Chemical Reactions.” <i>Science Advances</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/sciadv.abq2811\">https://doi.org/10.1126/sciadv.abq2811</a>.","apa":"Svoboda, V., Ram, N. B., Baykusheva, D. R., Zindel, D., Waters, M. D. J., Spenger, B., … Wörner, H. J. (2022). Femtosecond photoelectron circular dichroism of chemical reactions. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abq2811\">https://doi.org/10.1126/sciadv.abq2811</a>"},"article_number":"abq2811","extern":"1","scopus_import":"1","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2375-2548"]},"external_id":{"pmid":["35857523"],"arxiv":["2206.04099"]},"status":"public","type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1126/sciadv.abq2811","author":[{"full_name":"Svoboda, Vít","last_name":"Svoboda","first_name":"Vít"},{"first_name":"Niraghatam Bhargava","full_name":"Ram, Niraghatam Bhargava","last_name":"Ram"},{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Zindel","full_name":"Zindel, Daniel","first_name":"Daniel"},{"last_name":"Waters","full_name":"Waters, Max D. J.","first_name":"Max D. J."},{"last_name":"Spenger","full_name":"Spenger, Benjamin","first_name":"Benjamin"},{"first_name":"Manuel","full_name":"Ochsner, Manuel","last_name":"Ochsner"},{"last_name":"Herburger","full_name":"Herburger, Holger","first_name":"Holger"},{"last_name":"Stohner","full_name":"Stohner, Jürgen","first_name":"Jürgen"},{"full_name":"Wörner, Hans Jakob","last_name":"Wörner","first_name":"Hans Jakob"}],"article_processing_charge":"No","date_updated":"2023-08-22T07:24:01Z","pmid":1,"publisher":"American Association for the Advancement of Science","arxiv":1,"day":"15","_id":"13992","title":"Femtosecond photoelectron circular dichroism of chemical reactions","article_type":"original","volume":8,"keyword":["Multidisciplinary"],"publication":"Science Advances","quality_controlled":"1","abstract":[{"lang":"eng","text":"Understanding the chirality of molecular reaction pathways is essential for a broad range of fundamental and applied sciences. However, the current ability to probe chirality on the time scale of primary processes underlying chemical reactions remains very limited. Here, we demonstrate time-resolved photoelectron circular dichroism (TRPECD) with ultrashort circularly polarized vacuum-ultraviolet (VUV) pulses from a tabletop source. We demonstrate the capabilities of VUV-TRPECD by resolving the chirality changes in time during the photodissociation of atomic iodine from two chiral molecules. We identify several general key features of TRPECD, which include the ability to probe dynamical chirality along the complete photochemical reaction path, the sensitivity to the local chirality of the evolving scattering potential, and the influence of electron scattering off dissociating photofragments. Our results are interpreted by comparison with high-level ab-initio calculations of transient PECDs from molecular photoionization calculations. Our experimental and theoretical techniques define a general approach to femtochirality."}],"intvolume":"         8","date_created":"2023-08-09T13:08:04Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciadv.abq2811"}],"oa":1,"year":"2022","issue":"28","date_published":"2022-07-15T00:00:00Z"}]