[{"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"author":[{"last_name":"Henheik","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X"},{"full_name":"Teufel, Stefan","first_name":"Stefan","last_name":"Teufel"}],"month":"01","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2012.15238","open_access":"1"}],"article_type":"original","issue":"1","_id":"10600","publication_status":"published","quality_controlled":"1","isi":1,"year":"2022","title":"Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1063/5.0051632","publisher":"AIP Publishing","keyword":["mathematical physics","statistical and nonlinear physics"],"date_published":"2022-01-03T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"language":[{"iso":"eng"}],"volume":63,"ec_funded":1,"intvolume":" 63","day":"03","publication":"Journal of Mathematical Physics","external_id":{"isi":["000739446000009"],"arxiv":["2012.15238"]},"abstract":[{"lang":"eng","text":"We show that recent results on adiabatic theory for interacting gapped many-body systems on finite lattices remain valid in the thermodynamic limit. More precisely, we prove a generalized super-adiabatic theorem for the automorphism group describing the infinite volume dynamics on the quasi-local algebra of observables. The key assumption is the existence of a sequence of gapped finite volume Hamiltonians, which generates the same infinite volume dynamics in the thermodynamic limit. Our adiabatic theorem also holds for certain perturbations of gapped ground states that close the spectral gap (so it is also an adiabatic theorem for resonances and, in this sense, “generalized”), and it provides an adiabatic approximation to all orders in the adiabatic parameter (a property often called “super-adiabatic”). In addition to the existing results for finite lattices, we also perform a resummation of the adiabatic expansion and allow for observables that are not strictly local. Finally, as an application, we prove the validity of linear and higher order response theory for our class of perturbations for infinite systems. While we consider the result and its proof as new and interesting in itself, we also lay the foundation for the proof of an adiabatic theorem for systems with a gap only in the bulk, which will be presented in a follow-up article."}],"date_created":"2022-01-03T12:19:48Z","type":"journal_article","citation":{"short":"S.J. Henheik, S. Teufel, Journal of Mathematical Physics 63 (2022).","ista":"Henheik SJ, Teufel S. 2022. Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap. Journal of Mathematical Physics. 63(1), 011901.","ama":"Henheik SJ, Teufel S. Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap. Journal of Mathematical Physics. 2022;63(1). doi:10.1063/5.0051632","chicago":"Henheik, Sven Joscha, and Stefan Teufel. “Adiabatic Theorem in the Thermodynamic Limit: Systems with a Uniform Gap.” Journal of Mathematical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0051632.","apa":"Henheik, S. J., & Teufel, S. (2022). Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0051632","mla":"Henheik, Sven Joscha, and Stefan Teufel. “Adiabatic Theorem in the Thermodynamic Limit: Systems with a Uniform Gap.” Journal of Mathematical Physics, vol. 63, no. 1, 011901, AIP Publishing, 2022, doi:10.1063/5.0051632.","ieee":"S. J. Henheik and S. Teufel, “Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap,” Journal of Mathematical Physics, vol. 63, no. 1. AIP Publishing, 2022."},"arxiv":1,"oa":1,"date_updated":"2025-04-14T07:57:17Z","acknowledgement":"J.H. acknowledges partial financial support from ERC Advanced Grant “RMTBeyond” No. 101020331.","article_number":"011901","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","doi":"10.1007/s00236-021-00412-y","year":"2022","isi":1,"title":"Index appearance record with preorders","corr_author":"1","page":"585-618","file":[{"creator":"cchlebak","checksum":"bf1c195b6aaf59e8530cf9e3a9d731f7","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2021_ActaInfor_Křetínský.pdf","date_created":"2022-01-07T07:50:31Z","success":1,"date_updated":"2022-01-07T07:50:31Z","file_id":"10603","file_size":1066082}],"license":"https://creativecommons.org/licenses/by/4.0/","_id":"10602","file_date_updated":"2022-01-07T07:50:31Z","article_type":"original","quality_controlled":"1","publication_status":"published","author":[{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881"},{"last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"last_name":"Waldmann","full_name":"Waldmann, Clara","first_name":"Clara"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"month":"10","status":"public","publication_identifier":{"eissn":["1432-0525"],"issn":["0001-5903"]},"scopus_import":"1","oa_version":"Published Version","oa":1,"citation":{"ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record with preorders,” Acta Informatica, vol. 59. Springer Nature, pp. 585–618, 2022.","mla":"Kretinsky, Jan, et al. “Index Appearance Record with Preorders.” Acta Informatica, vol. 59, Springer Nature, 2022, pp. 585–618, doi:10.1007/s00236-021-00412-y.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2022). Index appearance record with preorders. Acta Informatica. Springer Nature. https://doi.org/10.1007/s00236-021-00412-y","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record with Preorders.” Acta Informatica. Springer Nature, 2022. https://doi.org/10.1007/s00236-021-00412-y.","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, Acta Informatica 59 (2022) 585–618.","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2022. Index appearance record with preorders. Acta Informatica. 59, 585–618.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record with preorders. Acta Informatica. 2022;59:585-618. doi:10.1007/s00236-021-00412-y"},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-04-15T06:53:08Z","abstract":[{"text":"Transforming ω-automata into parity automata is traditionally done using appearance records. We present an efficient variant of this idea, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and show that our method produces significantly smaller automata than previous approaches.","lang":"eng"}],"date_created":"2022-01-06T12:37:27Z","type":"journal_article","article_processing_charge":"Yes (via OA deal)","acknowledgement":"This work is partially funded by the German Research Foundation (DFG) projects Verified Model Checkers (No. 317422601) and Statistical Unbounded Verification (No. 383882557), and the Alexander von Humboldt Foundation with funds from the German Federal Ministry of Education and Research. It is an extended version of [21], including all proofs together with further explanations and examples. Moreover, we provide a new, more efficient construction based on (total) preorders, unifying previous optimizations. Experiments are performed with a new, performant implementation, comparing our approach to the current state of the art.","intvolume":" 59","day":"01","external_id":{"isi":["000735765500001"]},"has_accepted_license":"1","publication":"Acta Informatica","date_published":"2022-10-01T00:00:00Z","keyword":["computer networks and communications","information systems","software"],"ddc":["000"],"volume":59,"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}]},{"author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11686","status":"public","relation":"research_data"}]},"month":"02","status":"public","_id":"10604","file_date_updated":"2022-07-29T06:59:10Z","issue":"1","article_type":"original","publication_status":"published","quality_controlled":"1","year":"2022","isi":1,"title":"Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control","page":"92-105","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"7e9a37e3b65b480cd7014a6a4a7e460a","creator":"dernst","access_level":"open_access","file_size":2435185,"date_created":"2022-07-29T06:59:10Z","file_name":"2022_EvolutionLetters_Turelli.pdf","file_id":"11689","date_updated":"2022-07-29T06:59:10Z","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","doi":"10.1002/evl3.270","date_published":"2022-02-01T00:00:00Z","keyword":["genetics","ecology","evolution","behavior and systematics"],"ddc":["570"],"language":[{"iso":"eng"}],"volume":6,"department":[{"_id":"NiBa"}],"intvolume":" 6","day":"01","external_id":{"pmid":["35127140"],"isi":["000754412600008"]},"has_accepted_license":"1","publication":"Evolution Letters","citation":{"ama":"Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 2022;6(1):92-105. doi:10.1002/evl3.270","short":"M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.","ista":"Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1), 92–105.","apa":"Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.270","chicago":"Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270.","ieee":"M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control,” Evolution Letters, vol. 6, no. 1. Wiley, pp. 92–105, 2022.","mla":"Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270."},"oa":1,"date_updated":"2025-06-11T13:45:56Z","date_created":"2022-01-09T09:45:17Z","abstract":[{"lang":"eng","text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly—but systematically—aids area-wide transformation of disease-vector populations in heterogeneous landscapes."}],"type":"journal_article","article_processing_charge":"No","acknowledgement":"We thank S. O'Neill, C. Simmons, and the World Mosquito Project for providing access to unpublished data. S. Ritchie provided valuable insights into Aedes aegypti biology and the literature describing A. aegypti populations near Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill, S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on an earlier draft. Comments from three reviewers greatly improved our presentation.","pmid":1,"publication_identifier":{"eissn":["2056-3744"]},"oa_version":"Published Version","scopus_import":"1"},{"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We would like to thank the referees for their careful reading and the comments that improved our work. The third named author would like to thank the Division of Mathematics, Physics and Earth Sciences of the Graduate School of Science and Engineering of Ehime University and the second named author for hosting his visit in June 2018. Open access funding provided by Institute of Science and Technology (IST Austria).","citation":{"apa":"Weighill, T., Yamauchi, T., & Zava, N. (2022). Coarse infinite-dimensionality of hyperspaces of finite subsets. European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-021-00515-3","chicago":"Weighill, Thomas, Takamitsu Yamauchi, and Nicolò Zava. “Coarse Infinite-Dimensionality of Hyperspaces of Finite Subsets.” European Journal of Mathematics. Springer Nature, 2022. https://doi.org/10.1007/s40879-021-00515-3.","ieee":"T. Weighill, T. Yamauchi, and N. Zava, “Coarse infinite-dimensionality of hyperspaces of finite subsets,” European Journal of Mathematics, vol. 8, no. 1. Springer Nature, pp. 335–355, 2022.","mla":"Weighill, Thomas, et al. “Coarse Infinite-Dimensionality of Hyperspaces of Finite Subsets.” European Journal of Mathematics, vol. 8, no. 1, Springer Nature, 2022, pp. 335–55, doi:10.1007/s40879-021-00515-3.","ista":"Weighill T, Yamauchi T, Zava N. 2022. Coarse infinite-dimensionality of hyperspaces of finite subsets. European Journal of Mathematics. 8(1), 335–355.","short":"T. Weighill, T. Yamauchi, N. Zava, European Journal of Mathematics 8 (2022) 335–355.","ama":"Weighill T, Yamauchi T, Zava N. Coarse infinite-dimensionality of hyperspaces of finite subsets. European Journal of Mathematics. 2022;8(1):335-355. doi:10.1007/s40879-021-00515-3"},"oa":1,"date_updated":"2024-05-22T11:10:22Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"We consider infinite-dimensional properties in coarse geometry for hyperspaces consisting of finite subsets of metric spaces with the Hausdorff metric. We see that several infinite-dimensional properties are preserved by taking the hyperspace of subsets with at most n points. On the other hand, we prove that, if a metric space contains a sequence of long intervals coarsely, then its hyperspace of finite subsets is not coarsely embeddable into any uniformly convex Banach space. As a corollary, the hyperspace of finite subsets of the real line is not coarsely embeddable into any uniformly convex Banach space. It is also shown that every (not necessarily bounded geometry) metric space with straight finite decomposition complexity has metric sparsification property.","lang":"eng"}],"date_created":"2022-01-09T23:01:27Z","type":"journal_article","publication_identifier":{"issn":["2199-675X"],"eissn":["2199-6768"]},"scopus_import":"1","oa_version":"Published Version","ddc":["500"],"language":[{"iso":"eng"}],"volume":8,"department":[{"_id":"HeEd"}],"date_published":"2022-03-01T00:00:00Z","has_accepted_license":"1","publication":"European Journal of Mathematics","intvolume":" 8","day":"01","page":"335-355","file":[{"success":1,"date_updated":"2024-05-22T11:10:10Z","file_id":"17036","file_name":"2022_EuJournalMath_Weighill.pdf","date_created":"2024-05-22T11:10:10Z","file_size":371515,"access_level":"open_access","creator":"kschuh","checksum":"ce35cbb2d8c889dc7750719972634ed4","content_type":"application/pdf","relation":"main_file"}],"title":"Coarse infinite-dimensionality of hyperspaces of finite subsets","year":"2022","publisher":"Springer Nature","doi":"10.1007/s40879-021-00515-3","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"03","status":"public","author":[{"last_name":"Weighill","full_name":"Weighill, Thomas","first_name":"Thomas"},{"first_name":"Takamitsu","full_name":"Yamauchi, Takamitsu","last_name":"Yamauchi"},{"orcid":"0000-0001-8686-1888","last_name":"Zava","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","full_name":"Zava, Nicolò","first_name":"Nicolò"}],"publication_status":"published","quality_controlled":"1","_id":"10608","file_date_updated":"2024-05-22T11:10:10Z","article_type":"original","issue":"1"},{"oa_version":"Published Version","scopus_import":"1","publication_identifier":{"issn":["0022-538X"],"eissn":["1098-5514"]},"pmid":1,"article_number":"e02146-21","acknowledgement":"This work was supported by INRAE starter funds, Project IDEXLYON (University of Lyon) within the Programme Investissements d’Avenir (ANR-16-IDEX-0005), and FINOVIAO14 (Fondation pour l’Université de Lyon), all to P.Y.L. This work was also supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (grant numbers LO-2338/1-1 and LO-2338/3-1) awarded to P.Y.L., Austrian Science Fund (FWF) grant P31445 to F.K.M.S., a Chinese Scholarship Council (CSC;no. 201904910701) fellowship to Q.X., and a ministére de l’enseignement supérieur, de la recherche et de l’innovation (MESRI) doctoral thesis grant to M.D.","article_processing_charge":"No","date_created":"2022-01-18T10:04:18Z","abstract":[{"text":"With more than 80 members worldwide, the Orthobunyavirus genus in the Peribunyaviridae family is a large genus of enveloped RNA viruses, many of which are emerging pathogens in humans and livestock. How orthobunyaviruses (OBVs) penetrate and infect mammalian host cells remains poorly characterized. Here, we investigated the entry mechanisms of the OBV Germiston (GERV). Viral particles were visualized by cryo-electron microscopy and appeared roughly spherical with an average diameter of 98 nm. Labeling of the virus with fluorescent dyes did not adversely affect its infectivity and allowed the monitoring of single particles in fixed and live cells. Using this approach, we found that endocytic internalization of bound viruses was asynchronous and occurred within 30-40 min. The virus entered Rab5a+ early endosomes and, subsequently, late endosomal vacuoles containing Rab7a but not LAMP-1. Infectious entry did not require proteolytic cleavage, and endosomal acidification was sufficient and necessary for viral fusion. Acid-activated penetration began 15-25 min after initiation of virus internalization and relied on maturation of early endosomes to late endosomes. The optimal pH for viral membrane fusion was slightly below 6.0, and penetration was hampered when the potassium influx was abolished. Overall, our study provides real-time visualization of GERV entry into host cells and demonstrates the importance of late endosomal maturation in facilitating OBV penetration.","lang":"eng"}],"type":"journal_article","oa":1,"citation":{"ama":"Windhaber S, Xin Q, Uckeley ZM, et al. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 2022;96(5). doi:10.1128/jvi.02146-21","ista":"Windhaber S, Xin Q, Uckeley ZM, Koch J, Obr M, Garnier C, Luengo-Guyonnot C, Duboeuf M, Schur FK, Lozach P-Y. 2022. The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. 96(5), e02146-21.","short":"S. Windhaber, Q. Xin, Z.M. Uckeley, J. Koch, M. Obr, C. Garnier, C. Luengo-Guyonnot, M. Duboeuf, F.K. Schur, P.-Y. Lozach, Journal of Virology 96 (2022).","chicago":"Windhaber, Stefan, Qilin Xin, Zina M. Uckeley, Jana Koch, Martin Obr, Céline Garnier, Catherine Luengo-Guyonnot, Maëva Duboeuf, Florian KM Schur, and Pierre-Yves Lozach. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” Journal of Virology. American Society for Microbiology, 2022. https://doi.org/10.1128/jvi.02146-21.","apa":"Windhaber, S., Xin, Q., Uckeley, Z. M., Koch, J., Obr, M., Garnier, C., … Lozach, P.-Y. (2022). The Orthobunyavirus Germiston enters host cells from late endosomes. Journal of Virology. American Society for Microbiology. https://doi.org/10.1128/jvi.02146-21","mla":"Windhaber, Stefan, et al. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.” Journal of Virology, vol. 96, no. 5, e02146-21, American Society for Microbiology, 2022, doi:10.1128/jvi.02146-21.","ieee":"S. Windhaber et al., “The Orthobunyavirus Germiston enters host cells from late endosomes,” Journal of Virology, vol. 96, no. 5. American Society for Microbiology, 2022."},"date_updated":"2025-04-15T08:24:49Z","publication":"Journal of Virology","external_id":{"pmid":["35019710"],"isi":["000779305000033"]},"intvolume":" 96","day":"01","department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"volume":96,"date_published":"2022-03-01T00:00:00Z","keyword":["virology","insect science","immunology","microbiology"],"doi":"10.1128/jvi.02146-21","publisher":"American Society for Microbiology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"EM-Fac"}],"title":"The Orthobunyavirus Germiston enters host cells from late endosomes","isi":1,"year":"2022","quality_controlled":"1","publication_status":"published","article_type":"original","issue":"5","_id":"10639","month":"03","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410","open_access":"1"}],"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"author":[{"full_name":"Windhaber, Stefan","first_name":"Stefan","last_name":"Windhaber"},{"last_name":"Xin","first_name":"Qilin","full_name":"Xin, Qilin"},{"last_name":"Uckeley","full_name":"Uckeley, Zina M.","first_name":"Zina M."},{"full_name":"Koch, Jana","first_name":"Jana","last_name":"Koch"},{"last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","first_name":"Martin","orcid":"0000-0003-1756-6564"},{"first_name":"Céline","full_name":"Garnier, Céline","last_name":"Garnier"},{"last_name":"Luengo-Guyonnot","full_name":"Luengo-Guyonnot, Catherine","first_name":"Catherine"},{"full_name":"Duboeuf, Maëva","first_name":"Maëva","last_name":"Duboeuf"},{"last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"},{"full_name":"Lozach, Pierre-Yves","first_name":"Pierre-Yves","last_name":"Lozach"}]},{"intvolume":" 10","ec_funded":1,"day":"18","external_id":{"isi":["000743615000001"],"arxiv":["2012.15239"]},"has_accepted_license":"1","publication":"Forum of Mathematics, Sigma","date_published":"2022-01-18T00:00:00Z","keyword":["computational mathematics","discrete mathematics and combinatorics","geometry and topology","mathematical physics","statistics and probability","algebra and number theory","theoretical computer science","analysis"],"ddc":["510"],"language":[{"iso":"eng"}],"volume":10,"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"publication_identifier":{"eissn":["2050-5094"]},"scopus_import":"1","oa_version":"Published Version","arxiv":1,"citation":{"short":"S.J. Henheik, S. Teufel, Forum of Mathematics, Sigma 10 (2022).","ista":"Henheik SJ, Teufel S. 2022. Adiabatic theorem in the thermodynamic limit: Systems with a gap in the bulk. Forum of Mathematics, Sigma. 10, e4.","ama":"Henheik SJ, Teufel S. Adiabatic theorem in the thermodynamic limit: Systems with a gap in the bulk. Forum of Mathematics, Sigma. 2022;10. doi:10.1017/fms.2021.80","chicago":"Henheik, Sven Joscha, and Stefan Teufel. “Adiabatic Theorem in the Thermodynamic Limit: Systems with a Gap in the Bulk.” Forum of Mathematics, Sigma. Cambridge University Press, 2022. https://doi.org/10.1017/fms.2021.80.","apa":"Henheik, S. J., & Teufel, S. (2022). Adiabatic theorem in the thermodynamic limit: Systems with a gap in the bulk. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.80","mla":"Henheik, Sven Joscha, and Stefan Teufel. “Adiabatic Theorem in the Thermodynamic Limit: Systems with a Gap in the Bulk.” Forum of Mathematics, Sigma, vol. 10, e4, Cambridge University Press, 2022, doi:10.1017/fms.2021.80.","ieee":"S. J. Henheik and S. Teufel, “Adiabatic theorem in the thermodynamic limit: Systems with a gap in the bulk,” Forum of Mathematics, Sigma, vol. 10. Cambridge University Press, 2022."},"oa":1,"date_updated":"2025-04-14T07:57:17Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2022-01-18T16:18:51Z","abstract":[{"lang":"eng","text":"We prove a generalised super-adiabatic theorem for extended fermionic systems assuming a spectral gap only in the bulk. More precisely, we assume that the infinite system has a unique ground state and that the corresponding Gelfand–Naimark–Segal Hamiltonian has a spectral gap above its eigenvalue zero. Moreover, we show that a similar adiabatic theorem also holds in the bulk of finite systems up to errors that vanish faster than any inverse power of the system size, although the corresponding finite-volume Hamiltonians need not have a spectral gap.\r\n\r\n"}],"type":"journal_article","article_processing_charge":"Yes","acknowledgement":"J.H. acknowledges partial financial support by the ERC Advanced Grant ‘RMTBeyond’ No. 101020331. Support for publication costs from the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of the University of Tübingen is gratefully acknowledged.","article_number":"e4","_id":"10643","file_date_updated":"2022-01-19T09:27:43Z","article_type":"original","quality_controlled":"1","publication_status":"published","author":[{"orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha","last_name":"Henheik"},{"last_name":"Teufel","full_name":"Teufel, Stefan","first_name":"Stefan"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"month":"01","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cambridge University Press","doi":"10.1017/fms.2021.80","corr_author":"1","isi":1,"title":"Adiabatic theorem in the thermodynamic limit: Systems with a gap in the bulk","year":"2022","file":[{"file_size":705323,"file_name":"2022_ForumMathSigma_Henheik.pdf","date_created":"2022-01-19T09:27:43Z","date_updated":"2022-01-19T09:27:43Z","success":1,"file_id":"10646","relation":"main_file","content_type":"application/pdf","creator":"cchlebak","checksum":"87592a755adcef22ea590a99dc728dd3","access_level":"open_access"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevResearch.4.013023","publisher":"American Physical Society","corr_author":"1","year":"2022","title":"Constraints on probing quantum coherence to infer gravitational entanglement","file":[{"file_id":"10660","date_updated":"2022-01-24T11:12:44Z","success":1,"date_created":"2022-01-24T11:12:44Z","file_name":"2022_PhysRevResearch_Hosten.pdf","file_size":236329,"access_level":"open_access","checksum":"7254d267a0633ca5d63131d345e58686","creator":"cchlebak","relation":"main_file","content_type":"application/pdf"}],"article_type":"original","issue":"1","file_date_updated":"2022-01-24T11:12:44Z","_id":"10652","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Hosten","first_name":"Onur","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"}],"status":"public","month":"01","oa_version":"Published Version","scopus_import":"1","publication_identifier":{"issn":["2643-1564"]},"type":"journal_article","date_created":"2022-01-23T23:01:27Z","abstract":[{"lang":"eng","text":"Finding a feasible scheme for testing the quantum mechanical nature of the gravitational interaction has been attracting an increasing level of attention. Gravity mediated entanglement generation so far appears to be the key ingredient for a potential experiment. In a recent proposal [D. Carney et al., PRX Quantum 2, 030330 (2021)] combining an atom interferometer with a low-frequency mechanical oscillator, a coherence revival test is proposed for verifying this entanglement generation. With measurements performed only on the atoms, this protocol bypasses the need for correlation measurements. Here, we explore formulations of such a protocol, and specifically find that in the envisioned regime of operation with high thermal excitation, semiclassical models, where there is no concept of entanglement, also give the same experimental signatures. We elucidate in a fully quantum mechanical calculation that entanglement is not the source of the revivals in the relevant parameter regime. We argue that, in its current form, the suggested test is only relevant if the oscillator is nearly in a pure quantum state, and in this regime the effects are too small to be measurable. We further discuss potential open ends. The results highlight the importance and subtleties of explicitly considering how the quantum case differs from the classical expectations when testing for the quantum mechanical nature of a physical system."}],"date_updated":"2024-10-09T21:01:26Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"citation":{"short":"O. Hosten, Physical Review Research 4 (2022).","ista":"Hosten O. 2022. Constraints on probing quantum coherence to infer gravitational entanglement. Physical Review Research. 4(1), 013023.","ama":"Hosten O. Constraints on probing quantum coherence to infer gravitational entanglement. Physical Review Research. 2022;4(1). doi:10.1103/PhysRevResearch.4.013023","apa":"Hosten, O. (2022). Constraints on probing quantum coherence to infer gravitational entanglement. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.4.013023","chicago":"Hosten, Onur. “Constraints on Probing Quantum Coherence to Infer Gravitational Entanglement.” Physical Review Research. American Physical Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.013023.","mla":"Hosten, Onur. “Constraints on Probing Quantum Coherence to Infer Gravitational Entanglement.” Physical Review Research, vol. 4, no. 1, 013023, American Physical Society, 2022, doi:10.1103/PhysRevResearch.4.013023.","ieee":"O. Hosten, “Constraints on probing quantum coherence to infer gravitational entanglement,” Physical Review Research, vol. 4, no. 1. American Physical Society, 2022."},"acknowledgement":"O.H. is supported by Institute of Science and Technology Austria. The author thanks Jess Riedel for discussions.","article_number":"013023","article_processing_charge":"Yes (via OA deal)","day":"10","intvolume":" 4","publication":"Physical Review Research","has_accepted_license":"1","date_published":"2022-01-10T00:00:00Z","department":[{"_id":"OnHo"}],"language":[{"iso":"eng"}],"volume":4,"ddc":["530"]},{"pmid":1,"publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"oa_version":"Published Version","scopus_import":"1","date_updated":"2025-04-14T07:58:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"citation":{"chicago":"Abramian, Sophie, Caroline J Muller, and Camille Risi. “Shear-Convection Interactions and Orientation of Tropical Squall Lines.” Geophysical Research Letters. Wiley, 2022. https://doi.org/10.1029/2021GL095184.","apa":"Abramian, S., Muller, C. J., & Risi, C. (2022). Shear-convection interactions and orientation of tropical squall lines. Geophysical Research Letters. Wiley. https://doi.org/10.1029/2021GL095184","ieee":"S. Abramian, C. J. Muller, and C. Risi, “Shear-convection interactions and orientation of tropical squall lines,” Geophysical Research Letters, vol. 49, no. 1. Wiley, 2022.","mla":"Abramian, Sophie, et al. “Shear-Convection Interactions and Orientation of Tropical Squall Lines.” Geophysical Research Letters, vol. 49, no. 1, e2021GL095184, Wiley, 2022, doi:10.1029/2021GL095184.","ista":"Abramian S, Muller CJ, Risi C. 2022. Shear-convection interactions and orientation of tropical squall lines. Geophysical Research Letters. 49(1), e2021GL095184.","short":"S. Abramian, C.J. Muller, C. Risi, Geophysical Research Letters 49 (2022).","ama":"Abramian S, Muller CJ, Risi C. Shear-convection interactions and orientation of tropical squall lines. Geophysical Research Letters. 2022;49(1). doi:10.1029/2021GL095184"},"type":"journal_article","abstract":[{"text":"Squall lines are known to be the consequence of the interaction of low-level shear with cold pools associated with convective downdrafts. Also, as the magnitude of the shear increases beyond a critical shear, squall lines tend to orient themselves. The existing literature suggests that this orientation reduces incoming wind shear to the squall line, and maintains equilibrium between wind shear and cold pool spreading. Although this theory is widely accepted, very few quantitative studies have been conducted on supercritical regime especially. Here, we test this hypothesis with tropical squall lines obtained by imposing a vertical wind shear in cloud resolving simulations in radiative convective equilibrium. In the sub-critical regime, squall lines are perpendicular to the shear. In the super-critical regime, their orientation maintain the equilibrium, supporting existing theories. We also find that as shear increases, cold pools become more intense. However, this intensification has little impact on squall line orientation.","lang":"eng"}],"date_created":"2022-01-23T23:01:27Z","article_processing_charge":"No","acknowledgement":"The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041), and from the PhD fellowship of Ecole Normale Supérieure de Paris-Saclay. Two supplementary movies are also provided showing the angle detection method and the squall line of the Usfc = 10 m s−1 simulation.","article_number":"e2021GL095184","day":"16","intvolume":" 49","ec_funded":1,"has_accepted_license":"1","external_id":{"isi":["000743989800040"],"pmid":["35865077"]},"publication":"Geophysical Research Letters","date_published":"2022-01-16T00:00:00Z","language":[{"iso":"eng"}],"volume":49,"ddc":["550"],"department":[{"_id":"CaMu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","doi":"10.1029/2021GL095184","year":"2022","title":"Shear-convection interactions and orientation of tropical squall lines","isi":1,"file":[{"date_created":"2022-01-24T12:14:41Z","file_name":"2022_GeophysResearchLet_Abramian.pdf","file_id":"10662","date_updated":"2022-01-24T12:14:41Z","success":1,"file_size":1117408,"checksum":"08f88b57b8e409b42e382452cd5f297b","creator":"cchlebak","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"_id":"10653","issue":"1","article_type":"original","file_date_updated":"2022-01-24T12:14:41Z","publication_status":"published","quality_controlled":"1","author":[{"last_name":"Abramian","full_name":"Abramian, Sophie","first_name":"Sophie"},{"last_name":"Muller","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350"},{"last_name":"Risi","first_name":"Camille","full_name":"Risi, Camille"}],"project":[{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"related_material":{"link":[{"url":"https://doi.org/10.1002/essoar.10507697.1","relation":"earlier_version"}]},"status":"public","month":"01"},{"external_id":{"arxiv":["2111.14894"],"pmid":["35061458"],"isi":["000748271700010"]},"publication":"Physical Review Letters","day":"05","intvolume":" 128","ec_funded":1,"volume":128,"language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"date_published":"2022-01-05T00:00:00Z","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"oa_version":"Preprint","scopus_import":"1","pmid":1,"article_processing_charge":"No","acknowledgement":"We thank T.Menner, T.Asenov, P. Maier and the Miba machine shop of IST Austria for their valuable support in all technical aspects. We thank Marc Avila for comments on the manuscript. This work was supported by a grant from the Simons Foundation (662960, B.H.). We acknowledge the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. K.A.\r\nacknowledges funding from the Central Research Development Fund of the University of Bremen, grant number ZF04B /2019/FB04 Avila Kerstin (”Independent Project for Postdocs”). L.K. was supported by the European Union’s Horizon 2020 Research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754411.\r\n","article_number":"014502","date_updated":"2024-10-22T11:08:41Z","citation":{"ama":"Klotz L, Lemoult GM, Avila K, Hof B. Phase transition to turbulence in spatially extended shear flows. Physical Review Letters. 2022;128(1). doi:10.1103/PhysRevLett.128.014502","ista":"Klotz L, Lemoult GM, Avila K, Hof B. 2022. Phase transition to turbulence in spatially extended shear flows. Physical Review Letters. 128(1), 014502.","short":"L. Klotz, G.M. Lemoult, K. Avila, B. Hof, Physical Review Letters 128 (2022).","chicago":"Klotz, Lukasz, Grégoire M Lemoult, Kerstin Avila, and Björn Hof. “Phase Transition to Turbulence in Spatially Extended Shear Flows.” Physical Review Letters. American Physical Society, 2022. https://doi.org/10.1103/PhysRevLett.128.014502.","apa":"Klotz, L., Lemoult, G. M., Avila, K., & Hof, B. (2022). Phase transition to turbulence in spatially extended shear flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.128.014502","mla":"Klotz, Lukasz, et al. “Phase Transition to Turbulence in Spatially Extended Shear Flows.” Physical Review Letters, vol. 128, no. 1, 014502, American Physical Society, 2022, doi:10.1103/PhysRevLett.128.014502.","ieee":"L. Klotz, G. M. Lemoult, K. Avila, and B. Hof, “Phase transition to turbulence in spatially extended shear flows,” Physical Review Letters, vol. 128, no. 1. American Physical Society, 2022."},"oa":1,"arxiv":1,"type":"journal_article","date_created":"2022-01-23T23:01:28Z","abstract":[{"lang":"eng","text":"Directed percolation (DP) has recently emerged as a possible solution to the century old puzzle surrounding the transition to turbulence. Multiple model studies reported DP exponents, however, experimental evidence is limited since the largest possible observation times are orders of magnitude shorter than the flows’ characteristic timescales. An exception is cylindrical Couette flow where the limit is not temporal, but rather the realizable system size. We present experiments in a Couette setup of unprecedented azimuthal and axial aspect ratios. Approaching the critical point to within less than 0.1% we determine five critical exponents, all of which are in excellent agreement with the 2+1D DP universality class. The complex dynamics encountered at \r\nthe onset of turbulence can hence be fully rationalized within the framework of statistical mechanics."}],"quality_controlled":"1","publication_status":"published","_id":"10654","issue":"1","article_type":"original","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.14894"}],"month":"01","author":[{"orcid":"0000-0003-1740-7635","last_name":"Klotz","full_name":"Klotz, Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","first_name":"Lukasz"},{"id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M","first_name":"Grégoire M","last_name":"Lemoult"},{"full_name":"Avila, Kerstin","first_name":"Kerstin","last_name":"Avila"},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960"}],"publisher":"American Physical Society","doi":"10.1103/PhysRevLett.128.014502","acknowledged_ssus":[{"_id":"M-Shop"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Phase transition to turbulence in spatially extended shear flows","year":"2022","corr_author":"1","isi":1},{"intvolume":" 54","ec_funded":1,"day":"01","publication":"Annual Review of Fluid Mechanics","external_id":{"isi":["000794152800006"]},"date_published":"2022-01-01T00:00:00Z","department":[{"_id":"CaMu"}],"language":[{"iso":"eng"}],"volume":54,"oa_version":"Published Version","scopus_import":"1","publication_identifier":{"issn":["0066-4189"],"eissn":["1545-4479"]},"date_created":"2022-01-23T23:01:29Z","abstract":[{"text":"Idealized simulations of the tropical atmosphere have predicted that clouds can spontaneously clump together in space, despite perfectly homogeneous settings. This phenomenon has been called self-aggregation, and it results in a state where a moist cloudy region with intense deep convective storms is surrounded by extremely dry subsiding air devoid of deep clouds. We review here the main findings from theoretical work and idealized models of this phenomenon, highlighting the physical processes believed to play a key role in convective self-aggregation. We also review the growing literature on the importance and implications of this phenomenon for the tropical atmosphere, notably, for the hydrological cycle and for precipitation extremes, in our current and in a warming climate.","lang":"eng"}],"type":"journal_article","citation":{"short":"C.J. Muller, D. Yang, G. Craig, T. Cronin, B. Fildier, J.O. Haerter, C. Hohenegger, B. Mapes, D. Randall, S. Shamekh, S.C. Sherwood, Annual Review of Fluid Mechanics 54 (2022) 133–157.","ista":"Muller CJ, Yang D, Craig G, Cronin T, Fildier B, Haerter JO, Hohenegger C, Mapes B, Randall D, Shamekh S, Sherwood SC. 2022. Spontaneous aggregation of convective storms. Annual Review of Fluid Mechanics. 54, 133–157.","ama":"Muller CJ, Yang D, Craig G, et al. Spontaneous aggregation of convective storms. Annual Review of Fluid Mechanics. 2022;54:133-157. doi:10.1146/annurev-fluid-022421-011319","apa":"Muller, C. J., Yang, D., Craig, G., Cronin, T., Fildier, B., Haerter, J. O., … Sherwood, S. C. (2022). Spontaneous aggregation of convective storms. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-022421-011319","chicago":"Muller, Caroline J, Da Yang, George Craig, Timothy Cronin, Benjamin Fildier, Jan O. Haerter, Cathy Hohenegger, et al. “Spontaneous Aggregation of Convective Storms.” Annual Review of Fluid Mechanics. Annual Reviews, 2022. https://doi.org/10.1146/annurev-fluid-022421-011319.","ieee":"C. J. Muller et al., “Spontaneous aggregation of convective storms,” Annual Review of Fluid Mechanics, vol. 54. Annual Reviews, pp. 133–157, 2022.","mla":"Muller, Caroline J., et al. “Spontaneous Aggregation of Convective Storms.” Annual Review of Fluid Mechanics, vol. 54, Annual Reviews, 2022, pp. 133–57, doi:10.1146/annurev-fluid-022421-011319."},"oa":1,"date_updated":"2024-11-05T09:00:40Z","acknowledgement":"C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, grant agreement 805041). She also thanks Grand Équipement National de Calcul Intensif (GENCI), France, for providing access to their computing platforms at Très Grand Centre de Calcul (TGCC). J.O.H. gratefully acknowledges funding from the Villum Foundation (grant 13168), the ERC under the Horizon 2020 research and innovation program (grant 771859), and the Novo Nordisk Foundation's Interdisciplinary Synergy Program (grant NNF19OC0057374). G.C. gratefully acknowledges the support of the transregional collaborative research center (SFB/TRR 165) “Waves to Weather” (http://www.wavestoweather.de) funded by the German Research Foundation (DFG). D.Y. is supported by a Packard Fellowship in Science and Engineering, the France–Berkeley Fund, Laboratory Directed Research and Development (LDRD) funding from the Lawrence Berkeley National Laboratory, and the US Department of Energy, Office of Science, Office of Biological and Environmental Research, Climate and Environmental Sciences Division, Regional and Global Climate Modeling Program under award DE-AC02-05CH11231.","article_processing_charge":"No","article_type":"original","_id":"10656","quality_controlled":"1","publication_status":"published","project":[{"name":"Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"author":[{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350"},{"last_name":"Yang","full_name":"Yang, Da","first_name":"Da"},{"last_name":"Craig","first_name":"George","full_name":"Craig, George"},{"first_name":"Timothy","full_name":"Cronin, Timothy","last_name":"Cronin"},{"full_name":"Fildier, Benjamin","first_name":"Benjamin","last_name":"Fildier"},{"first_name":"Jan O.","full_name":"Haerter, Jan O.","last_name":"Haerter"},{"last_name":"Hohenegger","full_name":"Hohenegger, Cathy","first_name":"Cathy"},{"last_name":"Mapes","first_name":"Brian","full_name":"Mapes, Brian"},{"last_name":"Randall","first_name":"David","full_name":"Randall, David"},{"first_name":"Sara","full_name":"Shamekh, Sara","last_name":"Shamekh"},{"full_name":"Sherwood, Steven C.","first_name":"Steven C.","last_name":"Sherwood"}],"month":"01","status":"public","main_file_link":[{"url":"https://doi.org/10.1146/annurev-fluid-022421-011319","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1146/annurev-fluid-022421-011319","publisher":"Annual Reviews","isi":1,"title":"Spontaneous aggregation of convective storms","year":"2022","corr_author":"1","page":"133-157"},{"intvolume":" 23","day":"17","external_id":{"pmid":["35039062"],"isi":["000744358300002"]},"has_accepted_license":"1","publication":"Genome Biology","date_published":"2022-01-17T00:00:00Z","ddc":["570"],"language":[{"iso":"eng"}],"volume":23,"department":[{"_id":"MaRo"}],"pmid":1,"publication_identifier":{"eissn":["1474-760X"],"issn":["1474-7596"]},"oa_version":"Published Version","scopus_import":"1","oa":1,"citation":{"mla":"McCartney, Daniel L., et al. “Blood-Based Epigenome-Wide Analyses of Cognitive Abilities.” Genome Biology, vol. 23, no. 1, 26, Springer Nature, 2022, doi:10.1186/s13059-021-02596-5.","ieee":"D. L. McCartney et al., “Blood-based epigenome-wide analyses of cognitive abilities,” Genome Biology, vol. 23, no. 1. Springer Nature, 2022.","apa":"McCartney, D. L., Hillary, R. F., Conole, E. L. S., Banos, D. T., Gadd, D. A., Walker, R. M., … Marioni, R. E. (2022). Blood-based epigenome-wide analyses of cognitive abilities. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-021-02596-5","chicago":"McCartney, Daniel L., Robert F. Hillary, Eleanor L.S. Conole, Daniel Trejo Banos, Danni A. Gadd, Rosie M. Walker, Cliff Nangle, et al. “Blood-Based Epigenome-Wide Analyses of Cognitive Abilities.” Genome Biology. Springer Nature, 2022. https://doi.org/10.1186/s13059-021-02596-5.","ama":"McCartney DL, Hillary RF, Conole ELS, et al. Blood-based epigenome-wide analyses of cognitive abilities. Genome Biology. 2022;23(1). doi:10.1186/s13059-021-02596-5","ista":"McCartney DL, Hillary RF, Conole ELS, Banos DT, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Maniega SM, Valdés-Hernández MDC, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. 2022. Blood-based epigenome-wide analyses of cognitive abilities. Genome Biology. 23(1), 26.","short":"D.L. McCartney, R.F. Hillary, E.L.S. Conole, D.T. Banos, D.A. Gadd, R.M. Walker, C. Nangle, R. Flaig, A. Campbell, A.D. Murray, S.M. Maniega, M.D.C. Valdés-Hernández, M.A. Harris, M.E. Bastin, J.M. Wardlaw, S.E. Harris, D.J. Porteous, E.M. Tucker-Drob, A.M. McIntosh, K.L. Evans, I.J. Deary, S.R. Cox, M.R. Robinson, R.E. Marioni, Genome Biology 23 (2022)."},"date_updated":"2025-06-11T13:54:53Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Background: Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation of cognitive impairment and dementia. Results: Using blood-based epigenome-wide analyses of general cognitive function, we show that individual differences in DNA methylation (DNAm) explain 35.0% of the variance in general cognitive function (g). A DNAm predictor explains ~4% of the variance, independently of a polygenic score, in two external cohorts. It also associates with circulating levels of neurology- and inflammation-related proteins, global brain imaging metrics, and regional cortical volumes. Conclusions: As sample sizes increase, the ability to assess cognitive function from DNAm data may be informative in settings where cognitive testing is unreliable or unavailable."}],"date_created":"2022-01-30T23:01:33Z","type":"journal_article","article_processing_charge":"No","article_number":"26","acknowledgement":"GS received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and DNA methylation profiling of the GS samples was carried out by the Genetics Core Laboratory at the Edinburgh Clinical Research Facility, Edinburgh, Scotland, and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award STratifying Resilience and Depression Longitudinally (STRADL; Reference 104036/Z/14/Z). The DNA methylation data assayed for Generation Scotland was partially funded by a 2018 NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation (Ref: 27404; awardee: Dr David M Howard) and by a JMAS SIM fellowship from the Royal College of Physicians of Edinburgh (Awardee: Dr Heather C Whalley). LBC1936 MRI brain imaging was supported by Medical Research Council (MRC) grants [G0701120], [G1001245], [MR/M013111/1] and [MR/R024065/1]. Magnetic resonance image acquisition and analyses were conducted at the Brain Research Imaging Centre, Neuroimaging Sciences, University of Edinburgh (www.bric.ed.ac.uk) which is part of SINAPSE (Scottish Imaging Network: A Platform for Scientific Excellence) collaboration (www.sinapse.ac.uk) funded by the Scottish Funding Council and the Chief Scientist Office. This work was supported by the European Union Horizon 2020 (PHC.03.15, project No 666881), SVDs@Target, the Fondation Leducq Transatlantic Network of Excellence for the Study of Perivascular Spaces in Small Vessel Disease [ref no. 16 CVD 05]. We thank the LBC1936 participants and team members who contributed to these studies. The LBC1936 is supported by Age UK (Disconnected Mind project, which supports S.E.H.), the Medical Research Council (G0701120, G1001245, MR/M013111/1, MR/R024065/1) and the University of Edinburgh. Methylation typing of LBC1936 was supported by the Centre for Cognitive Ageing and Cognitive Epidemiology (Pilot Fund award), Age UK, The Wellcome Trust Institutional Strategic Support Fund, The University of Edinburgh, and The University of Queensland. Genotyping was funded by the Biotechnology and Biological Sciences Research Council (BB/F019394/1). Proteomic analyses in LBC1936 were supported by the Age UK grant and NIH Grants R01AG054628 and R01AG05462802S1. M.V.H. is funded by the Row Fogo Charitable Trust (Grant no. BROD.FID3668413). J.M.W is supported by the UK Dementia Research Institute which receives its funding from DRI Ltd, funded by the UK Medical Research Council, Alzheimers Society and Alzheimers Research UK. R.F.H., E.L.S.C and D.A.G. are supported by funding from the Wellcome Trust 4 year PhD in Translational Neuroscience: training the next generation of basic neuroscientists to embrace clinical research [108890/Z/15/Z]. E.M.T.D. was supported by the National Institutes of Health (NIH) grants R01AG054628, R01MH120219, R01HD083613, P2CHD042849 and P30AG066614. S.R.C. was also supported by a National Institutes of Health (NIH) research grant R01AG054628 and is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant Number 221890/Z/20/Z). D.L.Mc.C. and R.E.M. are supported by Alzheimers Research UK major project grant ARUK/PG2017B/10. R.E.M. is supported by Alzheimer’s Society major project grant AS-PG-19b-010. This research was funded in whole, or in part, by Wellcome [104036/Z/14/Z and 108890/Z/15/Z]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","_id":"10702","file_date_updated":"2022-01-31T13:16:05Z","article_type":"original","issue":"1","publication_status":"published","quality_controlled":"1","author":[{"first_name":"Daniel L.","full_name":"McCartney, Daniel L.","last_name":"McCartney"},{"full_name":"Hillary, Robert F.","first_name":"Robert F.","last_name":"Hillary"},{"last_name":"Conole","full_name":"Conole, Eleanor L.S.","first_name":"Eleanor L.S."},{"last_name":"Banos","first_name":"Daniel Trejo","full_name":"Banos, Daniel Trejo"},{"last_name":"Gadd","full_name":"Gadd, Danni A.","first_name":"Danni A."},{"full_name":"Walker, Rosie M.","first_name":"Rosie M.","last_name":"Walker"},{"first_name":"Cliff","full_name":"Nangle, Cliff","last_name":"Nangle"},{"first_name":"Robin","full_name":"Flaig, Robin","last_name":"Flaig"},{"last_name":"Campbell","first_name":"Archie","full_name":"Campbell, Archie"},{"last_name":"Murray","full_name":"Murray, Alison D.","first_name":"Alison D."},{"last_name":"Maniega","first_name":"Susana Muñoz","full_name":"Maniega, Susana Muñoz"},{"first_name":"María Del C.","full_name":"Valdés-Hernández, María Del C.","last_name":"Valdés-Hernández"},{"full_name":"Harris, Mathew A.","first_name":"Mathew A.","last_name":"Harris"},{"first_name":"Mark E.","full_name":"Bastin, Mark E.","last_name":"Bastin"},{"full_name":"Wardlaw, Joanna M.","first_name":"Joanna M.","last_name":"Wardlaw"},{"last_name":"Harris","first_name":"Sarah E.","full_name":"Harris, Sarah E."},{"last_name":"Porteous","first_name":"David J.","full_name":"Porteous, David J."},{"first_name":"Elliot M.","full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob"},{"first_name":"Andrew M.","full_name":"McIntosh, Andrew M.","last_name":"McIntosh"},{"full_name":"Evans, Kathryn L.","first_name":"Kathryn L.","last_name":"Evans"},{"first_name":"Ian J.","full_name":"Deary, Ian J.","last_name":"Deary"},{"last_name":"Cox","full_name":"Cox, Simon R.","first_name":"Simon R."},{"orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"last_name":"Marioni","full_name":"Marioni, Riccardo E.","first_name":"Riccardo E."}],"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"}],"related_material":{"record":[{"id":"13072","relation":"research_data","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.05.24.21257698"}]},"month":"01","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","doi":"10.1186/s13059-021-02596-5","title":"Blood-based epigenome-wide analyses of cognitive abilities","corr_author":"1","year":"2022","isi":1,"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"34f10bb2b0594189dcac24d13b691d52","creator":"cchlebak","access_level":"open_access","file_size":1540606,"date_created":"2022-01-31T13:16:05Z","file_name":"2022_GenomeBio_McCartney.pdf","file_id":"10708","date_updated":"2022-01-31T13:16:05Z","success":1}]},{"author":[{"orcid":"0000-0002-9582-2634","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamás","last_name":"Hausel"},{"first_name":"Nigel","full_name":"Hitchin, Nigel","last_name":"Hitchin"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-tip-of-the-mathematical-iceberg/","relation":"press_release","description":"News on the ISTA Website"}]},"month":"05","status":"public","_id":"10704","file_date_updated":"2023-02-27T07:30:47Z","article_type":"original","publication_status":"published","quality_controlled":"1","year":"2022","title":"Very stable Higgs bundles, equivariant multiplicity and mirror symmetry","corr_author":"1","isi":1,"page":"893-989","file":[{"checksum":"a382ba75acebc9adfb8fe56247cb410e","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-02-27T07:30:47Z","file_name":"2022_InventionesMahtematicae_Hausel.pdf","file_id":"12687","date_updated":"2023-02-27T07:30:47Z","success":1,"file_size":1069538}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","doi":"10.1007/s00222-021-01093-7","date_published":"2022-05-01T00:00:00Z","ddc":["510"],"volume":228,"language":[{"iso":"eng"}],"department":[{"_id":"TaHa"}],"intvolume":" 228","day":"01","external_id":{"isi":["000745495400001"],"arxiv":["2101.08583"]},"has_accepted_license":"1","publication":"Inventiones Mathematicae","citation":{"ama":"Hausel T, Hitchin N. Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. Inventiones Mathematicae. 2022;228:893-989. doi:10.1007/s00222-021-01093-7","ista":"Hausel T, Hitchin N. 2022. Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. Inventiones Mathematicae. 228, 893–989.","short":"T. Hausel, N. Hitchin, Inventiones Mathematicae 228 (2022) 893–989.","ieee":"T. Hausel and N. Hitchin, “Very stable Higgs bundles, equivariant multiplicity and mirror symmetry,” Inventiones Mathematicae, vol. 228. Springer Nature, pp. 893–989, 2022.","mla":"Hausel, Tamás, and Nigel Hitchin. “Very Stable Higgs Bundles, Equivariant Multiplicity and Mirror Symmetry.” Inventiones Mathematicae, vol. 228, Springer Nature, 2022, pp. 893–989, doi:10.1007/s00222-021-01093-7.","chicago":"Hausel, Tamás, and Nigel Hitchin. “Very Stable Higgs Bundles, Equivariant Multiplicity and Mirror Symmetry.” Inventiones Mathematicae. Springer Nature, 2022. https://doi.org/10.1007/s00222-021-01093-7.","apa":"Hausel, T., & Hitchin, N. (2022). Very stable Higgs bundles, equivariant multiplicity and mirror symmetry. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-021-01093-7"},"arxiv":1,"oa":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-04-15T06:53:08Z","abstract":[{"lang":"eng","text":"We define and study the existence of very stable Higgs bundles on Riemann surfaces, how it implies a precise formula for the multiplicity of the very stable components of the global nilpotent cone and its relationship to mirror symmetry. The main ingredients are the Bialynicki-Birula theory of C∗-actions on semiprojective varieties, C∗ characters of indices of C∗-equivariant coherent sheaves, Hecke transformation for Higgs bundles, relative Fourier–Mukai transform along the Hitchin fibration, hyperholomorphic structures on universal bundles and cominuscule Higgs bundles."}],"date_created":"2022-01-30T23:01:34Z","type":"journal_article","article_processing_charge":"Yes (via OA deal)","acknowledgement":"We would like to thank Brian Collier, Davide Gaiotto, Peter Gothen, Jochen Heinloth, Daniel Huybrechts, Quoc Ho, Joel Kamnitzer, Gérard Laumon, Luca Migliorini, Alexander Minets, Brent Pym, Peng Shan, Carlos Simpson, András Szenes, Fernando R. Villegas, Richard Wentworth, Edward Witten and Kōta Yoshioka for interesting comments and discussions. Most of all we are grateful for a long list of very helpful comments by the referee. We would also like to thank the organizers of the Summer School on Higgs bundles in Hamburg in September 2018, where the authors and Richard Wentworth were giving lectures and where the work in this paper started by considering the mirror of the Lagrangian upward flows W+E investigated in [17]. The second author wishes to thank EPSRC and ICMAT for support. Open access funding provided by Institute of Science and Technology (IST Austria).","publication_identifier":{"eissn":["1432-1297"],"issn":["0020-9910"]},"oa_version":"Published Version","scopus_import":"1"},{"_id":"10705","issue":"5","article_type":"original","quality_controlled":"1","publication_status":"published","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"status":"public","month":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cell Press","doi":"10.1016/j.tcb.2021.12.006","isi":1,"title":"Rigidity transitions in development and disease","corr_author":"1","year":"2022","page":"P433-444","day":"01","intvolume":" 32","external_id":{"isi":["000795773900009"],"pmid":["35058104"]},"publication":"Trends in Cell Biology","date_published":"2022-05-01T00:00:00Z","language":[{"iso":"eng"}],"volume":32,"department":[{"_id":"EdHa"},{"_id":"CaHe"}],"pmid":1,"publication_identifier":{"issn":["0962-8924"],"eissn":["1879-3088"]},"oa_version":"None","scopus_import":"1","date_updated":"2024-10-09T21:01:30Z","citation":{"ama":"Hannezo EB, Heisenberg C-PJ. Rigidity transitions in development and disease. Trends in Cell Biology. 2022;32(5):P433-444. doi:10.1016/j.tcb.2021.12.006","ista":"Hannezo EB, Heisenberg C-PJ. 2022. Rigidity transitions in development and disease. Trends in Cell Biology. 32(5), P433-444.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Trends in Cell Biology 32 (2022) P433-444.","chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Rigidity Transitions in Development and Disease.” Trends in Cell Biology. Cell Press, 2022. https://doi.org/10.1016/j.tcb.2021.12.006.","apa":"Hannezo, E. B., & Heisenberg, C.-P. J. (2022). Rigidity transitions in development and disease. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2021.12.006","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Rigidity transitions in development and disease,” Trends in Cell Biology, vol. 32, no. 5. Cell Press, pp. P433-444, 2022.","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Rigidity Transitions in Development and Disease.” Trends in Cell Biology, vol. 32, no. 5, Cell Press, 2022, pp. P433-444, doi:10.1016/j.tcb.2021.12.006."},"type":"journal_article","date_created":"2022-01-30T23:01:34Z","abstract":[{"lang":"eng","text":"Although rigidity and jamming transitions have been widely studied in physics and material science, their importance in a number of biological processes, including embryo development, tissue homeostasis, wound healing, and disease progression, has only begun to be recognized in the past few years. The hypothesis that biological systems can undergo rigidity/jamming transitions is attractive, as it would allow these systems to change their material properties rapidly and strongly. However, whether such transitions indeed occur in biological systems, how they are being regulated, and what their physiological relevance might be, is still being debated. Here, we review theoretical and experimental advances from the past few years, focusing on the regulation and role of potential tissue rigidity transitions in different biological processes."}],"article_processing_charge":"No","acknowledgement":"We thank present and former members of the Heisenberg and Hannezo groups, in particular Bernat Corominas-Murtra and Nicoletta Petridou, for helpful discussions, and Claudia Flandoli for the artwork. We apologize for not being able to cite a number of highly relevant studies, to stay within the maximum allowed number of citations."},{"article_type":"original","_id":"10706","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Bialy","first_name":"Misha","full_name":"Bialy, Misha"},{"id":"06619f18-9070-11eb-847d-d1ee780bd88b","full_name":"Fiorebe, Corentin","first_name":"Corentin","last_name":"Fiorebe"},{"last_name":"Glutsyuk","full_name":"Glutsyuk, Alexey","first_name":"Alexey"},{"last_name":"Levi","full_name":"Levi, Mark","first_name":"Mark"},{"last_name":"Plakhov","full_name":"Plakhov, Alexander","first_name":"Alexander"},{"first_name":"Serge","full_name":"Tabachnikov, Serge","last_name":"Tabachnikov"}],"month":"10","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.10750"}],"related_material":{"link":[{"url":"https://conferences.cirm-math.fr/2383.html","relation":"earlier_version"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s40598-022-00198-y","publisher":"Springer Nature","title":"Open problems on billiards and geometric optics","year":"2022","page":"411-422","intvolume":" 8","day":"01","publication":"Arnold Mathematical Journal","external_id":{"arxiv":["2110.10750"]},"date_published":"2022-10-01T00:00:00Z","department":[{"_id":"VaKa"}],"volume":8,"language":[{"iso":"eng"}],"oa_version":"Preprint","scopus_import":"1","publication_identifier":{"issn":["2199-6792"],"eissn":["2199-6806"]},"date_created":"2022-01-30T23:01:34Z","abstract":[{"lang":"eng","text":"This is a collection of problems composed by some participants of the workshop “Differential Geometry, Billiards, and Geometric Optics” that took place at CIRM on October 4–8, 2021."}],"type":"journal_article","oa":1,"citation":{"apa":"Bialy, M., Fiorebe, C., Glutsyuk, A., Levi, M., Plakhov, A., & Tabachnikov, S. (2022). Open problems on billiards and geometric optics. Arnold Mathematical Journal. Hybrid: Springer Nature. https://doi.org/10.1007/s40598-022-00198-y","chicago":"Bialy, Misha, Corentin Fiorebe, Alexey Glutsyuk, Mark Levi, Alexander Plakhov, and Serge Tabachnikov. “Open Problems on Billiards and Geometric Optics.” Arnold Mathematical Journal. Springer Nature, 2022. https://doi.org/10.1007/s40598-022-00198-y.","mla":"Bialy, Misha, et al. “Open Problems on Billiards and Geometric Optics.” Arnold Mathematical Journal, vol. 8, Springer Nature, 2022, pp. 411–22, doi:10.1007/s40598-022-00198-y.","ieee":"M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, and S. Tabachnikov, “Open problems on billiards and geometric optics,” Arnold Mathematical Journal, vol. 8. Springer Nature, pp. 411–422, 2022.","short":"M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, S. Tabachnikov, Arnold Mathematical Journal 8 (2022) 411–422.","ista":"Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. 2022. Open problems on billiards and geometric optics. Arnold Mathematical Journal. 8, 411–422.","ama":"Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. Open problems on billiards and geometric optics. Arnold Mathematical Journal. 2022;8:411-422. doi:10.1007/s40598-022-00198-y"},"arxiv":1,"date_updated":"2023-02-27T07:34:08Z","conference":{"name":"CIRM: Centre International de Rencontres Mathématiques","end_date":"2021-10-08","start_date":"2021-10-04","location":"Hybrid"},"article_processing_charge":"No"},{"file":[{"creator":"cchlebak","checksum":"63dfecf30c5bbf9408b3512bd603f78c","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2022_FrontiersOncol_Roblek.pdf","date_created":"2022-02-08T13:26:40Z","date_updated":"2022-02-08T13:26:40Z","success":1,"file_id":"10751","file_size":6303227}],"year":"2022","isi":1,"title":"The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis","corr_author":"1","publisher":"Frontiers","doi":"10.3389/fonc.2022.777634","acknowledged_ssus":[{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"relation":"confirmation","url":"https://ist.ac.at/en/news/suppressing-the-spread-of-tumors/","description":"News on IST Homepage"}]},"month":"02","status":"public","author":[{"orcid":"0000-0001-9588-1389","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","full_name":"Roblek, Marko","last_name":"Roblek"},{"full_name":"Bicher, Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Bicher"},{"last_name":"van Gogh","full_name":"van Gogh, Merel","first_name":"Merel"},{"orcid":"0000-0002-1819-198X","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","last_name":"György"},{"last_name":"Seeböck","full_name":"Seeböck, Rita","first_name":"Rita"},{"first_name":"Bozena","full_name":"Szulc, Bozena","last_name":"Szulc"},{"first_name":"Markus","full_name":"Damme, Markus","last_name":"Damme"},{"last_name":"Olczak","first_name":"Mariusz","full_name":"Olczak, Mariusz"},{"last_name":"Borsig","first_name":"Lubor","full_name":"Borsig, Lubor"},{"first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","orcid":"0000-0001-8323-8353"}],"project":[{"_id":"2637E9C0-B435-11E9-9278-68D0E5697425","grant_number":"LSC16-021","name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis"}],"quality_controlled":"1","publication_status":"published","_id":"10712","file_date_updated":"2022-02-08T13:26:40Z","article_type":"original","article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank M. Sixt, A. Leithner, and J. Alanko for helpful advice and the BioImaging Facility at IST Austria for technical support and assistance. We thank the Siekhaus Lab for the careful review of the manuscript and their input. MR and DS were funded by the NO Forschungs- und Bildungsges.m.b.H. (LS16-021) and IST core funding. MD was funded by Deutsche Forschungsgemeinschaft (DA 1785-1).","article_number":"777634","oa":1,"citation":{"ista":"Roblek M, Bicher J, van Gogh M, György A, Seeböck R, Szulc B, Damme M, Olczak M, Borsig L, Siekhaus DE. 2022. The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. Frontiers in Oncology. 12, 777634.","short":"M. Roblek, J. Bicher, M. van Gogh, A. György, R. Seeböck, B. Szulc, M. Damme, M. Olczak, L. Borsig, D.E. Siekhaus, Frontiers in Oncology 12 (2022).","ama":"Roblek M, Bicher J, van Gogh M, et al. The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. Frontiers in Oncology. 2022;12. doi:10.3389/fonc.2022.777634","ieee":"M. Roblek et al., “The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis,” Frontiers in Oncology, vol. 12. Frontiers, 2022.","mla":"Roblek, Marko, et al. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor Metastasis.” Frontiers in Oncology, vol. 12, 777634, Frontiers, 2022, doi:10.3389/fonc.2022.777634.","apa":"Roblek, M., Bicher, J., van Gogh, M., György, A., Seeböck, R., Szulc, B., … Siekhaus, D. E. (2022). The solute carrier MFSD1 decreases β1 integrin’s activation status and thus tumor metastasis. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2022.777634","chicago":"Roblek, Marko, Julia Bicher, Merel van Gogh, Attila György, Rita Seeböck, Bozena Szulc, Markus Damme, Mariusz Olczak, Lubor Borsig, and Daria E Siekhaus. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor Metastasis.” Frontiers in Oncology. Frontiers, 2022. https://doi.org/10.3389/fonc.2022.777634."},"date_updated":"2025-06-11T13:56:08Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Solute carriers are increasingly recognized as participating in a plethora of pathologies, including cancer. We describe here the involvement of the orphan solute carrier MFSD1 in the regulation of tumor cell migration. Loss of MFSD1 enabled higher levels of metastasis in a mouse model. We identified an increased migratory potential in MFSD1-/- tumor cells which was mediated by increased focal adhesion turn-over, reduced stability of mature inactive β1 integrin, and the resulting increased integrin activation index. We show that MFSD1 promoted recycling to the cell surface of endocytosed inactive β1 integrin and thereby protected β1 integrin from proteolytic degradation; this led to dampening of the integrin activation index. Furthermore, down-regulation of MFSD1 expression was observed during early steps of tumorigenesis and higher MFSD1 expression levels correlate with a better cancer patient prognosis. In sum, we describe a requirement for endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor spread.","lang":"eng"}],"date_created":"2022-02-01T10:33:50Z","type":"journal_article","publication_identifier":{"issn":["2234-943X"]},"scopus_import":"1","oa_version":"Published Version","pmid":1,"ddc":["570"],"volume":12,"language":[{"iso":"eng"}],"department":[{"_id":"DaSi"}],"date_published":"2022-02-08T00:00:00Z","external_id":{"pmid":["35211397"],"isi":["000760618800001"]},"has_accepted_license":"1","publication":"Frontiers in Oncology","intvolume":" 12","day":"08"},{"scopus_import":"1","oa_version":"Preprint","publication_identifier":{"issn":["0036-8075"]},"pmid":1,"acknowledgement":"We thank J. Friml, C. Guet, T. Hurd, M. Fendrych and members of the laboratory for comments on the manuscript; the Bioimaging Facility of IST Austria for excellent support and T. Lecuit, E. Hafen, R. Levayer and A. Martin for fly strains. This work was supported by a grant from the Austrian Science Fund FWF: Lise Meitner Fellowship M2379-B28 to M.A and D.S., and internal funding from IST Austria to D.S. and EMBL to S.D.R.","article_processing_charge":"No","type":"journal_article","date_created":"2022-02-01T11:23:18Z","abstract":[{"lang":"eng","text":"Cells migrate through crowded microenvironments within tissues during normal development, immune response, and cancer metastasis. Although migration through pores and tracks in the extracellular matrix (ECM) has been well studied, little is known about cellular traversal into confining cell-dense tissues. We find that embryonic tissue invasion by Drosophila macrophages requires division of an epithelial ectodermal cell at the site of entry. Dividing ectodermal cells disassemble ECM attachment formed by integrin-mediated focal adhesions next to mesodermal cells, allowing macrophages to move their nuclei ahead and invade between two immediately adjacent tissues. Invasion efficiency depends on division frequency, but reduction of adhesion strength allows macrophage entry independently of division. This work demonstrates that tissue dynamics can regulate cellular infiltration."}],"date_updated":"2025-04-15T07:25:41Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ista":"Akhmanova M, Emtenani S, Krueger D, György A, Pereira Guarda M, Vlasov M, Vlasov F, Akopian A, Ratheesh A, De Renzis S, Siekhaus DE. 2022. Cell division in tissues enables macrophage infiltration. Science. 376(6591), 394–396.","short":"M. Akhmanova, S. Emtenani, D. Krueger, A. György, M. Pereira Guarda, M. Vlasov, F. Vlasov, A. Akopian, A. Ratheesh, S. De Renzis, D.E. Siekhaus, Science 376 (2022) 394–396.","ama":"Akhmanova M, Emtenani S, Krueger D, et al. Cell division in tissues enables macrophage infiltration. Science. 2022;376(6591):394-396. doi:10.1126/science.abj0425","apa":"Akhmanova, M., Emtenani, S., Krueger, D., György, A., Pereira Guarda, M., Vlasov, M., … Siekhaus, D. E. (2022). Cell division in tissues enables macrophage infiltration. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abj0425","chicago":"Akhmanova, Maria, Shamsi Emtenani, Daniel Krueger, Attila György, Mariana Pereira Guarda, Mikhail Vlasov, Fedor Vlasov, et al. “Cell Division in Tissues Enables Macrophage Infiltration.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abj0425.","ieee":"M. Akhmanova et al., “Cell division in tissues enables macrophage infiltration,” Science, vol. 376, no. 6591. American Association for the Advancement of Science, pp. 394–396, 2022.","mla":"Akhmanova, Maria, et al. “Cell Division in Tissues Enables Macrophage Infiltration.” Science, vol. 376, no. 6591, American Association for the Advancement of Science, 2022, pp. 394–96, doi:10.1126/science.abj0425."},"oa":1,"publication":"Science","external_id":{"isi":["000788553700039"],"pmid":["35446632"]},"day":"22","intvolume":" 376","department":[{"_id":"DaSi"}],"language":[{"iso":"eng"}],"volume":376,"date_published":"2022-04-22T00:00:00Z","doi":"10.1126/science.abj0425","publisher":"American Association for the Advancement of Science","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"394-396","corr_author":"1","year":"2022","title":"Cell division in tissues enables macrophage infiltration","isi":1,"publication_status":"published","quality_controlled":"1","issue":"6591","article_type":"original","_id":"10713","main_file_link":[{"url":"https://doi.org/10.1101/2021.04.19.438995","open_access":"1"}],"status":"public","month":"04","project":[{"name":"Modeling epithelial tissue mechanics during cell invasion","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02379"}],"author":[{"orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Akhmanova"},{"last_name":"Emtenani","first_name":"Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938"},{"last_name":"Krueger","first_name":"Daniel","full_name":"Krueger, Daniel"},{"last_name":"György","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","orcid":"0000-0002-1819-198X"},{"first_name":"Mariana","id":"6de81d9d-e2f2-11eb-945a-af8bc2a60b26","full_name":"Pereira Guarda, Mariana","last_name":"Pereira Guarda","orcid":"0000-0001-8238-480X"},{"last_name":"Vlasov","full_name":"Vlasov, Mikhail","first_name":"Mikhail"},{"first_name":"Fedor","full_name":"Vlasov, Fedor","last_name":"Vlasov"},{"first_name":"Andrei","full_name":"Akopian, Andrei","last_name":"Akopian"},{"last_name":"Ratheesh","first_name":"Aparna","full_name":"Ratheesh, Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7190-0776"},{"last_name":"De Renzis","first_name":"Stefano","full_name":"De Renzis, Stefano"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","orcid":"0000-0001-8323-8353"}]},{"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"oa_version":"Preprint","scopus_import":"1","pmid":1,"article_processing_charge":"No","acknowledgement":"We are grateful to all members of the Rangan and Fuchs labs for their discussion and comments on the manuscript. We also thanks Dr. Sammons, Dr. Marlow, Life Science Editors, for their thoughts and comments the manuscript Additionally, we thank the Bloomington Stock Center, the Vienna Drosophila Resource Center, the BDGP Gene Disruption Project, and Flybase for fly stocks, reagents, and other resources. P.R. is funded by the NIH/NIGMS (R01GM111779-06 and RO1GM135628-01), G.F. is funded by NSF MCB-2047629 and NIH RO3 AI144839, D.E.S. was funded by Marie Curie CIG 334077/IRTIM and the Austrian Science Fund (FWF) grant ASI_FWF01_P29638S, and A.B is funded by NIH R01GM116889 and American Cancer Society RSG-17-197-01-RMC.","oa":1,"citation":{"short":"E.T. Martin, P. Blatt, E. Ngyuen, R. Lahr, S. Selvam, H.A.M. Yoon, T. Pocchiari, S. Emtenani, D.E. Siekhaus, A. Berman, G. Fuchs, P. Rangan, Developmental Cell 57 (2022) 883–900.e10.","ista":"Martin ET, Blatt P, Ngyuen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani S, Siekhaus DE, Berman A, Fuchs G, Rangan P. 2022. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Developmental Cell. 57(7), 883–900.e10.","ama":"Martin ET, Blatt P, Ngyuen E, et al. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Developmental Cell. 2022;57(7):883-900.e10. doi:10.1016/j.devcel.2022.03.005","chicago":"Martin, Elliot T., Patrick Blatt, Elaine Ngyuen, Roni Lahr, Sangeetha Selvam, Hyun Ah M. Yoon, Tyler Pocchiari, et al. “A Translation Control Module Coordinates Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.03.005.","apa":"Martin, E. T., Blatt, P., Ngyuen, E., Lahr, R., Selvam, S., Yoon, H. A. M., … Rangan, P. (2022). A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.03.005","mla":"Martin, Elliot T., et al. “A Translation Control Module Coordinates Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.” Developmental Cell, vol. 57, no. 7, Elsevier, 2022, p. 883–900.e10, doi:10.1016/j.devcel.2022.03.005.","ieee":"E. T. Martin et al., “A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis,” Developmental Cell, vol. 57, no. 7. Elsevier, p. 883–900.e10, 2022."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_updated":"2025-06-12T06:19:50Z","abstract":[{"text":"Ribosomal defects perturb stem cell differentiation, causing diseases called ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discovered three RNA helicases are required for ribosome biogenesis and for Drosophila oogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor, Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP-motif containing RNAs during Drosophila oogenesis. Thus, a previously unappreciated TOP-motif in Drosophila responds to reduced ribosome biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation.","lang":"eng"}],"date_created":"2022-02-01T13:15:05Z","type":"journal_article","external_id":{"isi":["000789021800005"],"pmid":["35413237"]},"publication":"Developmental Cell","ec_funded":1,"intvolume":" 57","day":"11","volume":57,"language":[{"iso":"eng"}],"department":[{"_id":"DaSi"}],"date_published":"2022-04-11T00:00:00Z","publisher":"Elsevier","doi":"10.1016/j.devcel.2022.03.005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"883-900.e10","title":"A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis","year":"2022","isi":1,"publication_status":"published","quality_controlled":"1","_id":"10714","article_type":"original","issue":"7","month":"04","main_file_link":[{"url":"https://doi.org/10.1101/2021.04.04.438367","open_access":"1"}],"status":"public","author":[{"last_name":"Martin","full_name":"Martin, Elliot T.","first_name":"Elliot T."},{"last_name":"Blatt","first_name":"Patrick","full_name":"Blatt, Patrick"},{"first_name":"Elaine","full_name":"Ngyuen, Elaine","last_name":"Ngyuen"},{"last_name":"Lahr","full_name":"Lahr, Roni","first_name":"Roni"},{"first_name":"Sangeetha","full_name":"Selvam, Sangeetha","last_name":"Selvam"},{"first_name":"Hyun Ah M.","full_name":"Yoon, Hyun Ah M.","last_name":"Yoon"},{"last_name":"Pocchiari","full_name":"Pocchiari, Tyler","first_name":"Tyler"},{"orcid":"0000-0001-6981-6938","first_name":"Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","full_name":"Emtenani, Shamsi","last_name":"Emtenani"},{"last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"},{"last_name":"Berman","first_name":"Andrea","full_name":"Berman, Andrea"},{"full_name":"Fuchs, Gabriele","first_name":"Gabriele","last_name":"Fuchs"},{"first_name":"Prashanth","full_name":"Rangan, Prashanth","last_name":"Rangan"}],"project":[{"grant_number":"334077","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions"},{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion"}]},{"publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"article_processing_charge":"No","acknowledgement":"We thank Joerg Kudla (WWU Munster, Germany), Petra Dietrich (F.A. University of Erlangen-Nurnberg, Germany) for sharing published materials, and NASC for providing seeds. We thank Veronique Storme for help with the statistical analyses. Part of the imaging analysis was carried out at NOLIMITS, an advanced imaging facility established by the University of Milan.\r\nThis work was supported by grants of the China Scholarship Council (CSC) to RW and JC; Fonds Wetenschappelijk Onderzoek (FWO) to TB and (G002220N) SV; the special research fund of Ghent University to EH; the Deutsche Forschungsgemeinschaft (DFG) through Grants within FOR964 (MK and KS); Piano di Sviluppo di Ateneo 2019 (University of Milan) to AC; the European Research Council (ERC) T-Rex project 682436 to DVD; the ERC ETAP project 742985 to JF, and by a PhD fellowship from the University of Milan to MG.","article_number":"erac019","oa":1,"citation":{"apa":"Wang, R., Himschoot, E., Grenzi, M., Chen, J., Safi, A., Krebs, M., … Vanneste, S. (2022). Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erac019","chicago":"Wang, R, E Himschoot, M Grenzi, J Chen, A Safi, M Krebs, K Schumacher, et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” Journal of Experimental Botany. Oxford University Press, 2022. https://doi.org/10.1093/jxb/erac019.","mla":"Wang, R., et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” Journal of Experimental Botany, vol. 73, no. 8, erac019, Oxford University Press, 2022, doi:10.1093/jxb/erac019.","ieee":"R. Wang et al., “Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots,” Journal of Experimental Botany, vol. 73, no. 8. Oxford University Press, 2022.","short":"R. Wang, E. Himschoot, M. Grenzi, J. Chen, A. Safi, M. Krebs, K. Schumacher, M. Nowack, W. Moeder, K. Yoshioka, D. Van Damme, I. De Smet, D. Geelen, T. Beeckman, J. Friml, A. Costa, S. Vanneste, Journal of Experimental Botany 73 (2022).","ista":"Wang R, Himschoot E, Grenzi M, Chen J, Safi A, Krebs M, Schumacher K, Nowack M, Moeder W, Yoshioka K, Van Damme D, De Smet I, Geelen D, Beeckman T, Friml J, Costa A, Vanneste S. 2022. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. 73(8), erac019.","ama":"Wang R, Himschoot E, Grenzi M, et al. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. 2022;73(8). doi:10.1093/jxb/erac019"},"date_updated":"2025-05-14T11:06:37Z","date_created":"2022-02-03T09:19:01Z","abstract":[{"lang":"eng","text":"Much of what we know about the role of auxin in plant development derives from exogenous manipulations of auxin distribution and signaling, using inhibitors, auxins and auxin analogs. In this context, synthetic auxin analogs, such as 1-Naphtalene Acetic Acid (1-NAA), are often favored over the endogenous auxin indole-3-acetic acid (IAA), in part due to their higher stability. While such auxin analogs have proven to be instrumental to reveal the various faces of auxin, they display in some cases distinct bioactivities compared to IAA. Here, we focused on the effect of auxin analogs on the accumulation of PIN proteins in Brefeldin A-sensitive endosomal aggregations (BFA bodies), and the correlation with the ability to elicit Ca 2+ responses. For a set of commonly used auxin analogs, we evaluated if auxin-analog induced Ca 2+ signaling inhibits PIN accumulation. Not all auxin analogs elicited a Ca 2+ response, and their differential ability to elicit Ca 2+ responses correlated partially with their ability to inhibit BFA-body formation. However, in tir1/afb and cngc14, 1-NAA-induced Ca 2+ signaling was strongly impaired, yet 1-NAA still could inhibit PIN accumulation in BFA bodies. This demonstrates that TIR1/AFB-CNGC14-dependent Ca 2+ signaling does not inhibit BFA body formation in Arabidopsis roots."}],"type":"journal_article","external_id":{"isi":["000764220900001"],"pmid":["35085386"]},"publication":"Journal of Experimental Botany","intvolume":" 73","ec_funded":1,"day":"18","language":[{"iso":"eng"}],"volume":73,"department":[{"_id":"JiFr"}],"date_published":"2022-04-18T00:00:00Z","publisher":"Oxford University Press","doi":"10.1093/jxb/erac019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots","isi":1,"year":"2022","quality_controlled":"1","publication_status":"published","_id":"10717","issue":"8","article_type":"original","month":"04","status":"public","main_file_link":[{"open_access":"1","url":"https://biblio.ugent.be/publication/8738721"}],"author":[{"full_name":"Wang, R","first_name":"R","last_name":"Wang"},{"last_name":"Himschoot","first_name":"E","full_name":"Himschoot, E"},{"last_name":"Grenzi","first_name":"M","full_name":"Grenzi, M"},{"last_name":"Chen","first_name":"J","full_name":"Chen, J"},{"last_name":"Safi","first_name":"A","full_name":"Safi, A"},{"last_name":"Krebs","first_name":"M","full_name":"Krebs, M"},{"last_name":"Schumacher","full_name":"Schumacher, K","first_name":"K"},{"full_name":"Nowack, MK","first_name":"MK","last_name":"Nowack"},{"first_name":"W","full_name":"Moeder, W","last_name":"Moeder"},{"last_name":"Yoshioka","first_name":"K","full_name":"Yoshioka, K"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"last_name":"De Smet","first_name":"I","full_name":"De Smet, I"},{"last_name":"Geelen","full_name":"Geelen, D","first_name":"D"},{"last_name":"Beeckman","full_name":"Beeckman, T","first_name":"T"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"A","full_name":"Costa, A","last_name":"Costa"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1111/jipb.13225","publisher":"Wiley","corr_author":"1","year":"2022","title":"Auxin signaling: Research advances over the past 30 years","isi":1,"page":"371-392","article_type":"review","issue":"2","_id":"10719","quality_controlled":"1","publication_status":"published","author":[{"first_name":"Z","full_name":"Yu, Z","last_name":"Yu"},{"full_name":"Zhang, F","first_name":"F","last_name":"Zhang"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"Ding, Z","first_name":"Z","last_name":"Ding"}],"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13225"}],"month":"02","pmid":1,"oa_version":"Published Version","scopus_import":"1","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"type":"journal_article","date_created":"2022-02-03T09:52:59Z","abstract":[{"lang":"eng","text":"Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development."}],"date_updated":"2024-10-09T21:01:32Z","citation":{"mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:10.1111/jipb.13225.","ieee":"Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” Journal of Integrative Plant Biology, vol. 64, no. 2. Wiley, pp. 371–392, 2022.","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13225.","apa":"Yu, Z., Zhang, F., Friml, J., & Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13225","ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 2022;64(2):371-392. doi:10.1111/jipb.13225","short":"Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392.","ista":"Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392."},"oa":1,"acknowledgement":"This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n","article_processing_charge":"No","day":"01","intvolume":" 64","publication":"Journal of Integrative Plant Biology","external_id":{"isi":["000761281200011"],"pmid":["35018726"]},"date_published":"2022-02-01T00:00:00Z","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"volume":64},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-04-14T07:52:45Z","arxiv":1,"citation":{"apa":"Svoboda, J., Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2022). Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-05333-5","chicago":"Svoboda, Jakub, Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-05333-5.","mla":"Svoboda, Jakub, et al. “Infection Dynamics of COVID-19 Virus under Lockdown and Reopening.” Scientific Reports, vol. 12, no. 1, 1526, Springer Nature, 2022, doi:10.1038/s41598-022-05333-5.","ieee":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Infection dynamics of COVID-19 virus under lockdown and reopening,” Scientific Reports, vol. 12, no. 1. Springer Nature, 2022.","ista":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2022. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 12(1), 1526.","short":"J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Scientific Reports 12 (2022).","ama":"Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Infection dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 2022;12(1). doi:10.1038/s41598-022-05333-5"},"oa":1,"type":"journal_article","abstract":[{"text":"Motivated by COVID-19, we develop and analyze a simple stochastic model for the spread of disease in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening society and we compare their efficiency in mitigating the spread of the virus from several different points of view. We find that in order to avoid overwhelming of the hospital system, a policy must impose a harsh lockdown or it must react swiftly (or both). While reacting swiftly is universally beneficial, being harsh pays off only when the country is patient about reopening and when the neighboring countries coordinate their mitigation efforts. Our work highlights the importance of acting decisively when closing down and the importance of patience and coordination between neighboring countries when reopening.","lang":"eng"}],"date_created":"2022-02-06T23:01:30Z","article_processing_charge":"No","acknowledgement":"K.C. acknowledges support from ERC Consolidator Grant No. (863818: ForM-SMart). A.P. acknowledges support from FWF Grant No. J-4220. M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","article_number":"1526","publication_identifier":{"eissn":["2045-2322"]},"oa_version":"Published Version","scopus_import":"1","date_published":"2022-01-27T00:00:00Z","volume":12,"language":[{"iso":"eng"}],"ddc":["570"],"department":[{"_id":"KrCh"}],"day":"27","intvolume":" 12","ec_funded":1,"has_accepted_license":"1","external_id":{"arxiv":["2012.15155"],"isi":["000749198000039"]},"publication":"Scientific Reports","title":"Infection dynamics of COVID-19 virus under lockdown and reopening","isi":1,"year":"2022","file":[{"file_name":"2022_ScientificReports_Svoboda.pdf","date_created":"2022-02-07T14:57:59Z","date_updated":"2022-02-07T14:57:59Z","success":1,"file_id":"10744","file_size":2971922,"creator":"alisjak","checksum":"247afd30c173390940f099ead35a28ed","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","doi":"10.1038/s41598-022-05333-5","author":[{"orcid":"0000-0002-1419-3267","last_name":"Svoboda","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub"},{"last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"status":"public","month":"01","_id":"10731","issue":"1","article_type":"original","file_date_updated":"2022-02-07T14:57:59Z","quality_controlled":"1","publication_status":"published"}]