[{"month":"01","day":"01","citation":{"ista":"Liu J, Marensi E, Wu X. 2022.Effects of streaky structures on the instability of supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. vol. 38, 587–598.","short":"J. Liu, E. Marensi, X. Wu, in:, S. Sherwin, P. Schmid, X. Wu (Eds.), IUTAM Laminar-Turbulent Transition, 1st ed., Springer Nature, Cham, 2022, pp. 587–598.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: Sherwin S, Schmid P, Wu X, eds. <i>IUTAM Laminar-Turbulent Transition</i>. Vol 38. 1st ed. IUTAM Bookseries. Cham: Springer Nature; 2022:587-598. doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>","apa":"Liu, J., Marensi, E., &#38; Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In S. Sherwin, P. Schmid, &#38; X. Wu (Eds.), <i>IUTAM Laminar-Turbulent Transition</i> (1st ed., Vol. 38, pp. 587–598). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>","ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in <i>IUTAM Laminar-Turbulent Transition</i>, 1st ed., vol. 38, S. Sherwin, P. Schmid, and X. Wu, Eds. Cham: Springer Nature, 2022, pp. 587–598.","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” <i>IUTAM Laminar-Turbulent Transition</i>, edited by Spencer Sherwin et al., 1st ed., vol. 38, Springer Nature, 2022, pp. 587–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>.","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In <i>IUTAM Laminar-Turbulent Transition</i>, edited by Spencer Sherwin, Peter Schmid, and Xuesong Wu, 1st ed., 38:587–98. IUTAM Bookseries. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>."},"conference":{"name":"IUTAM Symposium","location":"London, United Kingdom","start_date":"2019-09-02","end_date":"2019-09-06"},"oa_version":"None","article_processing_charge":"No","volume":38,"_id":"10820","editor":[{"first_name":"Spencer","last_name":"Sherwin","full_name":"Sherwin, Spencer"},{"last_name":"Schmid","full_name":"Schmid, Peter","first_name":"Peter"},{"first_name":"Xuesong","last_name":"Wu","full_name":"Wu, Xuesong"}],"author":[{"last_name":"Liu","full_name":"Liu, Jianxin","first_name":"Jianxin"},{"last_name":"Marensi","full_name":"Marensi, Elena","first_name":"Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E"},{"first_name":"Xuesong","full_name":"Wu, Xuesong","last_name":"Wu"}],"title":"Effects of streaky structures on the instability of supersonic boundary layers","doi":"10.1007/978-3-030-67902-6_51","abstract":[{"text":"Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating.","lang":"eng"}],"edition":"1","publication_identifier":{"eissn":["1875-3493"],"issn":["1875-3507"],"eisbn":["9783030679026"],"isbn":["9783030679019"]},"place":"Cham","status":"public","acknowledgement":"The work is supported by the National Key Research and Development Program of China (No. 2016YFA0401200), the National Natural Science Foundation of China (Grant Nos. 91952202 and 11402167).","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BjHo"}],"scopus_import":"1","date_created":"2022-03-04T09:14:34Z","external_id":{"isi":["000709087600051"]},"date_published":"2022-01-01T00:00:00Z","intvolume":"        38","publisher":"Springer Nature","series_title":"IUTAM Bookseries","type":"book_chapter","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"year":"2022","date_updated":"2023-08-03T12:54:59Z","publication":"IUTAM Laminar-Turbulent Transition","page":"587-598"},{"publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.03.482657"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"preprint","citation":{"chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2022. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>.","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2022, doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>","ieee":"F. Lombardi <i>et al.</i>, “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2022.","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. 2022. doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. 2022. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022)."},"day":"04","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","date_published":"2022-03-04T00:00:00Z","date_created":"2022-03-04T22:20:59Z","oa_version":"Preprint","publication":"bioRxiv","date_updated":"2022-03-07T07:28:34Z","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"status":"public","publication_status":"published","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and the project E-PASSION of the program VALERE 2019 funded by the University of Campania, Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation, Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.","page":"25","ec_funded":1,"oa":1,"title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","author":[{"last_name":"Lombardi","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249"},{"full_name":"Herrmann, Hans J.","last_name":"Herrmann","first_name":"Hans J."},{"first_name":"Liborio","full_name":"Parrino, Liborio","last_name":"Parrino"},{"first_name":"Dietmar","full_name":"Plenz, Dietmar","last_name":"Plenz"},{"last_name":"Scarpetta","full_name":"Scarpetta, Silvia","first_name":"Silvia"},{"first_name":"Anna Elisabetta","last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"},{"first_name":"Oren","full_name":"Shriki, Oren","last_name":"Shriki"}],"_id":"10821","abstract":[{"text":"Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the \"waxing and waning\" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the \"waxing and waning\" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.","lang":"eng"}],"year":"2022","doi":"10.1101/2022.03.03.482657"},{"oa":1,"year":"2022","date_updated":"2023-08-02T14:43:50Z","publication":"Cell","page":"777-793.e20","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"EdHa"}],"date_created":"2022-03-06T23:01:52Z","scopus_import":"1","date_published":"2022-02-22T00:00:00Z","external_id":{"pmid":["35196500"],"isi":["000796293700007"]},"publisher":"Cell Press","intvolume":"       185","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"_id":"10825","title":"Cell surface fluctuations regulate early embryonic lineage sorting","author":[{"last_name":"Yanagida","full_name":"Yanagida, Ayaka","first_name":"Ayaka"},{"full_name":"Corujo-Simon, Elena","last_name":"Corujo-Simon","first_name":"Elena"},{"last_name":"Revell","full_name":"Revell, Christopher K.","first_name":"Christopher K."},{"full_name":"Sahu, Preeti","last_name":"Sahu","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti"},{"first_name":"Giuliano G.","full_name":"Stirparo, Giuliano G.","last_name":"Stirparo"},{"last_name":"Aspalter","full_name":"Aspalter, Irene M.","first_name":"Irene M."},{"last_name":"Winkel","full_name":"Winkel, Alex K.","first_name":"Alex K."},{"last_name":"Peters","full_name":"Peters, Ruby","first_name":"Ruby"},{"last_name":"De Belly","full_name":"De Belly, Henry","first_name":"Henry"},{"first_name":"Davide A.D.","last_name":"Cassani","full_name":"Cassani, Davide A.D."},{"first_name":"Sarra","last_name":"Achouri","full_name":"Achouri, Sarra"},{"last_name":"Blumenfeld","full_name":"Blumenfeld, Raphael","first_name":"Raphael"},{"first_name":"Kristian","last_name":"Franze","full_name":"Franze, Kristian"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"last_name":"Paluch","full_name":"Paluch, Ewa K.","first_name":"Ewa K."},{"last_name":"Nichols","full_name":"Nichols, Jennifer","first_name":"Jennifer"},{"first_name":"Kevin J.","full_name":"Chalut, Kevin J.","last_name":"Chalut"}],"doi":"10.1016/j.cell.2022.01.022","abstract":[{"lang":"eng","text":"In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages."}],"issue":"5","project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M. Merkel for developing and sharing the original version of the 3D Voronoi code. This work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C. and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637 -MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H., and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation (Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). 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.","pmid":1,"month":"02","file_date_updated":"2022-03-07T07:55:23Z","ddc":["570"],"citation":{"mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>.","chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>.","short":"A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20.","ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. 2022;185(5):777-793.e20. doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>","ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>","ieee":"A. Yanagida <i>et al.</i>, “Cell surface fluctuations regulate early embryonic lineage sorting,” <i>Cell</i>, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022."},"day":"22","oa_version":"Published Version","file":[{"access_level":"open_access","checksum":"ae305060e8031297771b89dae9e36a29","content_type":"application/pdf","success":1,"date_updated":"2022-03-07T07:55:23Z","file_name":"2022_Cell_Yanagida.pdf","file_size":8478995,"creator":"dernst","relation":"main_file","file_id":"10831","date_created":"2022-03-07T07:55:23Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":185,"article_processing_charge":"No","has_accepted_license":"1"},{"year":"2022","oa":1,"article_number":"e68040","article_type":"original","publication":"eLife","date_updated":"2023-08-02T14:42:55Z","date_published":"2022-02-24T00:00:00Z","external_id":{"isi":["000763432300001"],"pmid":["35201977"]},"date_created":"2022-03-06T23:01:52Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"scopus_import":"1","department":[{"_id":"MaDe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","intvolume":"        11","abstract":[{"lang":"eng","text":"Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome."}],"doi":"10.7554/eLife.68040","title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","author":[{"id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E","first_name":"Giulio","full_name":"Valperga, Giulio","last_name":"Valperga"},{"orcid":"0000-0001-8347-0443","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","full_name":"De Bono, Mario"}],"_id":"10826","status":"public","acknowledgement":"We would like to thank Gemma Chandratillake and Merav Cohen for identifying mutants and José David Moñino Sánchez for his help on neurosecretion assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida) for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp, GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets (KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank the CRUK Cambridge Research Institute Genomics Core for next generation sequencing and the Flow Cytometry Facility at LMB for FACS. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing (SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome Investigator Award (209504/Z/17/Z to MdB).","publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"}],"oa_version":"Published Version","citation":{"ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040.","short":"G. Valperga, M. de Bono, ELife 11 (2022).","apa":"Valperga, G., &#38; de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>.","mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>, vol. 11, e68040, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>."},"day":"24","month":"02","file_date_updated":"2022-03-07T07:39:25Z","pmid":1,"ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","volume":11,"file":[{"file_name":"2022_eLife_Valperga.pdf","relation":"main_file","file_size":4095591,"creator":"dernst","success":1,"date_updated":"2022-03-07T07:39:25Z","access_level":"open_access","checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","content_type":"application/pdf","file_id":"10830","date_created":"2022-03-07T07:39:25Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"_id":"10827","author":[{"full_name":"Lee, Jacob G.","last_name":"Lee","first_name":"Jacob G."},{"full_name":"Pickard, Chris J.","last_name":"Pickard","first_name":"Chris J."},{"last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"}],"title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","doi":"10.1063/5.0079844","issue":"7","abstract":[{"lang":"eng","text":"Titanium dioxide has been extensively studied in the rutile or anatase phase, while its high-pressure phases are less well-understood, despite that many are thought to have interesting optical, mechanical, and electrochemical properties. First-principles methods, such as density functional theory (DFT), are often used to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus, impractical for long time scale and large system-size simulations at finite temperatures. On the other hand, cheap empirical potentials fail to capture the relative stabilities of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure phases of TiO2, we design an empirical model as a baseline and then train a machine learning potential based on the difference between the DFT data and the empirical model. This so-called Δ-learning potential contains long-range electrostatic interactions and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range 0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition processes by compressing anatase at different temperatures. At 300 K, we predominantly observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic two-step mechanism with a highly ordered and collective atomic motion. At 2000 K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The pressures computed for these transitions show good agreement with experiments. Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases, and our method is generally applicable to other functional materials with multiple polymorphs."}],"publication_identifier":{"eissn":["10897690"]},"publication_status":"published","acknowledgement":"J.G.L. and B.C. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).","status":"public","month":"02","day":"16","citation":{"mla":"Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 7, 074106, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>.","chicago":"Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>.","ama":"Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of chemical physics</i>. 2022;156(7). doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>","short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","ista":"Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7), 074106.","ieee":"J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential,” <i>The Journal of chemical physics</i>, vol. 156, no. 7. AIP Publishing, 2022.","apa":"Lee, J. G., Pickard, C. J., &#38; Cheng, B. (2022). High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>"},"oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","volume":156,"oa":1,"year":"2022","date_updated":"2023-08-02T14:45:46Z","publication":"The Journal of chemical physics","article_type":"original","article_number":"074106","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BiCh"}],"scopus_import":"1","date_created":"2022-03-06T23:01:53Z","date_published":"2022-02-16T00:00:00Z","external_id":{"isi":["000796704500014"],"arxiv":["2111.12968"]},"intvolume":"       156","main_file_link":[{"url":"https://arxiv.org/abs/2111.12968","open_access":"1"}],"publisher":"AIP Publishing","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1},{"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.05663"}],"external_id":{"arxiv":["2111.05663"],"isi":["000800559503126"]},"date_published":"2022-01-13T00:00:00Z","date_created":"2022-03-06T23:01:53Z","scopus_import":"1","department":[{"_id":"HeEd"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"3824-3834","publication":"2021 IEEE International Conference on Big Data","date_updated":"2023-08-02T14:44:21Z","year":"2022","oa":1,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","conference":{"location":"Orlando, FL, United States; Virtuell","start_date":"2021-12-15","end_date":"2021-12-18","name":"Big Data: International Conference on Big Data"},"citation":{"short":"T. Heiss, S. Tymochko, B. Story, A. Garin, H. Bui, B. Bleile, V. Robins, in:, 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 3824–3834.","ista":"Heiss T, Tymochko S, Story B, Garin A, Bui H, Bleile B, Robins V. 2022. The impact of changes in resolution on the persistent homology of images. 2021 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 3824–3834.","ama":"Heiss T, Tymochko S, Story B, et al. The impact of changes in resolution on the persistent homology of images. In: <i>2021 IEEE International Conference on Big Data</i>. IEEE; 2022:3824-3834. doi:<a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">10.1109/BigData52589.2021.9671483</a>","ieee":"T. Heiss <i>et al.</i>, “The impact of changes in resolution on the persistent homology of images,” in <i>2021 IEEE International Conference on Big Data</i>, Orlando, FL, United States; Virtuell, 2022, pp. 3824–3834.","apa":"Heiss, T., Tymochko, S., Story, B., Garin, A., Bui, H., Bleile, B., &#38; Robins, V. (2022). The impact of changes in resolution on the persistent homology of images. In <i>2021 IEEE International Conference on Big Data</i> (pp. 3824–3834). Orlando, FL, United States; Virtuell: IEEE. <a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">https://doi.org/10.1109/BigData52589.2021.9671483</a>","mla":"Heiss, Teresa, et al. “The Impact of Changes in Resolution on the Persistent Homology of Images.” <i>2021 IEEE International Conference on Big Data</i>, IEEE, 2022, pp. 3824–34, doi:<a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">10.1109/BigData52589.2021.9671483</a>.","chicago":"Heiss, Teresa, Sarah Tymochko, Brittany Story, Adélie Garin, Hoa Bui, Bea Bleile, and Vanessa Robins. “The Impact of Changes in Resolution on the Persistent Homology of Images.” In <i>2021 IEEE International Conference on Big Data</i>, 3824–34. IEEE, 2022. <a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">https://doi.org/10.1109/BigData52589.2021.9671483</a>."},"day":"13","month":"01","publication_status":"published","status":"public","publication_identifier":{"isbn":["9781665439022"]},"abstract":[{"lang":"eng","text":"Digital images enable quantitative analysis of material properties at micro and macro length scales, but choosing an appropriate resolution when acquiring the image is challenging. A high resolution means longer image acquisition and larger data requirements for a given sample, but if the resolution is too low, significant information may be lost. This paper studies the impact of changes in resolution on persistent homology, a tool from topological data analysis that provides a signature of structure in an image across all length scales. Given prior information about a function, the geometry of an object, or its density distribution at a given resolution, we provide methods to select the coarsest resolution yielding results within an acceptable tolerance. We present numerical case studies for an illustrative synthetic example and samples from porous materials where the theoretical bounds are unknown."}],"doi":"10.1109/BigData52589.2021.9671483","title":"The impact of changes in resolution on the persistent homology of images","author":[{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","full_name":"Heiss, Teresa","last_name":"Heiss","orcid":"0000-0002-1780-2689"},{"last_name":"Tymochko","full_name":"Tymochko, Sarah","first_name":"Sarah"},{"full_name":"Story, Brittany","last_name":"Story","first_name":"Brittany"},{"first_name":"Adélie","last_name":"Garin","full_name":"Garin, Adélie"},{"first_name":"Hoa","last_name":"Bui","full_name":"Bui, Hoa"},{"first_name":"Bea","last_name":"Bleile","full_name":"Bleile, Bea"},{"first_name":"Vanessa","last_name":"Robins","full_name":"Robins, Vanessa"}],"_id":"10828"},{"oa":1,"year":"2022","date_updated":"2023-08-02T14:46:17Z","publication":"ACS Sensors","page":"504-512","article_type":"original","related_material":{"record":[{"relation":"research_data","status":"public","id":"10833"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaIb"}],"date_created":"2022-03-06T23:01:54Z","scopus_import":"1","date_published":"2022-02-08T00:00:00Z","external_id":{"isi":["000765113000016"]},"publisher":"American Chemical Society","intvolume":"         7","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"10829","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"first_name":"Stefan","full_name":"Fossati, Stefan","last_name":"Fossati"},{"last_name":"Aspermair","full_name":"Aspermair, Patrik","first_name":"Patrik"},{"last_name":"Dostalek","full_name":"Dostalek, Jakub","first_name":"Jakub"},{"last_name":"Lee","full_name":"Lee, Seungho","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"first_name":"Johannes","full_name":"Bintinger, Johannes","last_name":"Bintinger"},{"first_name":"Wolfgang","last_name":"Knoll","full_name":"Knoll, Wolfgang"}],"doi":"10.1021/acssensors.1c02313","abstract":[{"text":"A novel multivariable system, combining a transistor with fiber optic-based surface plasmon resonance spectroscopy with the gate electrode simultaneously acting as the fiber optic sensor surface, is reported. The dual-mode sensor allows for discrimination of mass and charge contributions for binding assays on the same sensor surface. Furthermore, we optimize the sensor geometry by investigating the influence of the fiber area to transistor channel area ratio and distance. We show that larger fiber optic tip diameters are favorable for electronic and optical signals and demonstrate the reversibility of plasmon resonance wavelength shifts after electric field application. As a proof of principle, a layer-by-layer assembly of polyelectrolytes is performed to benchmark the system against multivariable sensing platforms with planar surface plasmon resonance configurations. Furthermore, the biosensing performance is assessed using a thrombin binding assay with surface-immobilized aptamers as receptors, allowing for the detection of medically relevant thrombin concentrations.","lang":"eng"}],"issue":"2","publication_identifier":{"eissn":["23793694"]},"publication_status":"published","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863-\r\nBORGES. Additionally, we gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 870025 and 873541) for this research. The data that support the findings of this study are openly available in Zenodo (DOI: 10.5281/zenodo.5500360)","status":"public","month":"02","file_date_updated":"2022-03-07T08:15:01Z","ddc":["540"],"citation":{"apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device,” <i>ACS Sensors</i>, vol. 7, no. 2. American Chemical Society, pp. 504–512, 2022.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, ACS Sensors 7 (2022) 504–512.","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. 2022;7(2):504-512. doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>","ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. 7(2), 504–512.","mla":"Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>, vol. 7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>.","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>."},"day":"08","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"success":1,"date_updated":"2022-03-07T08:15:01Z","access_level":"open_access","checksum":"d704af7262cd484da9bb84b7d84e2b09","content_type":"application/pdf","file_name":"2022_ACSSensors_Hasler.pdf","creator":"dernst","file_size":2969415,"relation":"main_file","file_id":"10832","date_created":"2022-03-07T08:15:01Z"}],"volume":7,"article_processing_charge":"No","has_accepted_license":"1"},{"type":"research_data_reference","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5500360"}],"publisher":"Zenodo","date_published":"2022-02-08T00:00:00Z","date_created":"2022-03-07T08:19:11Z","oa_version":"Published Version","day":"08","department":[{"_id":"MaIb"}],"citation":{"ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022).","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 2022.","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>.","mla":"Hasler, Roger, et al. <i>Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"02","ddc":["540"],"status":"public","related_material":{"record":[{"id":"10829","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-08-02T14:46:16Z","year":"2022","abstract":[{"lang":"eng","text":"Detailed information about the data set see \"dataset description.txt\" file."}],"doi":"10.5281/ZENODO.5500360","author":[{"first_name":"Roger","full_name":"Hasler, Roger","last_name":"Hasler"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"full_name":"Fossati, Stefan","last_name":"Fossati","first_name":"Stefan"},{"last_name":"Aspermair","full_name":"Aspermair, Patrik","first_name":"Patrik"},{"first_name":"Jakub","full_name":"Dostalek, Jakub","last_name":"Dostalek"},{"orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0001-5013-2843"},{"full_name":"Bintinger, Johannes","last_name":"Bintinger","first_name":"Johannes"},{"first_name":"Wolfgang","last_name":"Knoll","full_name":"Knoll, Wolfgang"}],"title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","oa":1,"_id":"10833"},{"oa_version":"Preprint","pmid":1,"month":"06","day":"01","citation":{"mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford Academic, pp. 2150–2173, 2022.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173."},"article_processing_charge":"No","volume":34,"doi":"10.1093/plcell/koac071","issue":"6","abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"_id":"10841","author":[{"first_name":"DA","full_name":"Dahhan, DA","last_name":"Dahhan"},{"first_name":"GD","full_name":"Reynolds, GD","last_name":"Reynolds"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"full_name":"Eeckhout, D","last_name":"Eeckhout","first_name":"D"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"first_name":"K","full_name":"Yperman, K","last_name":"Yperman"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"full_name":"Vang, N","last_name":"Vang","first_name":"N"},{"last_name":"Yan","full_name":"Yan, X","first_name":"X"},{"first_name":"I","full_name":"Hwang, I","last_name":"Hwang"},{"full_name":"Heese, A","last_name":"Heese","first_name":"A"},{"first_name":"G","full_name":"De Jaeger, G","last_name":"De Jaeger"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"first_name":"J","full_name":"Pan, J","last_name":"Pan"},{"first_name":"SY","full_name":"Bednarek, SY","last_name":"Bednarek"}],"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","status":"public","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","publication_status":"published","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"scopus_import":"1","date_created":"2022-03-08T13:47:51Z","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"date_published":"2022-06-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"intvolume":"        34","publisher":"Oxford Academic","year":"2022","oa":1,"article_type":"original","page":"2150-2173","date_updated":"2023-08-02T14:46:48Z","publication":"Plant Cell"},{"publication_identifier":{"eissn":["1936-2455"],"issn":["1936-2447"]},"acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","status":"public","publication_status":"published","author":[{"last_name":"Köse","full_name":"Köse, Seyda","first_name":"Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"},{"first_name":"Ferruh","full_name":"Özbudak, Ferruh","last_name":"Özbudak"}],"title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","_id":"10842","issue":"4","abstract":[{"text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory.","lang":"eng"}],"doi":"10.1007/s12095-022-00557-8","volume":14,"article_processing_charge":"No","day":"01","citation":{"short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.","ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948.","ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. 2022;14(4):933-948. doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>","ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” <i>Cryptography and Communications</i>, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022.","apa":"Köse, S., &#38; Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>.","mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>."},"month":"07","oa_version":"None","publication":"Cryptography and Communications","date_updated":"2023-09-05T15:35:55Z","article_type":"original","page":"933-948","year":"2022","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"intvolume":"        14","publisher":"Springer Nature","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000766422000002"]},"date_published":"2022-07-01T00:00:00Z","scopus_import":"1","date_created":"2022-03-10T12:16:19Z"},{"oa":1,"year":"2022","date_updated":"2022-03-14T08:42:24Z","publication":"Physical Review Research","article_type":"original","article_number":"013160","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"scopus_import":"1","date_created":"2022-03-13T23:01:46Z","external_id":{"arxiv":["2111.13570"]},"date_published":"2022-03-01T00:00:00Z","intvolume":"         4","publisher":"American Physical Society","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"10845","author":[{"full_name":"Maslov, Mikhail","last_name":"Maslov","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0003-4074-2570"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"title":"Impurity with a resonance in the vicinity of the Fermi energy","doi":"10.1103/PhysRevResearch.4.013160","abstract":[{"lang":"eng","text":"We study an impurity with a resonance level whose position coincides with the Fermi energy of the surrounding Fermi gas. An impurity causes a rapid variation of the scattering phase shift for fermions at the Fermi surface, introducing a new characteristic length scale into the problem. We investigate manifestations of this length scale in the self-energy of the impurity and in the density of the bath. Our calculations reveal a model-independent deformation of the density of the Fermi gas, which is determined by the width of the resonance. To provide a broader picture, we investigate time evolution of the density in quench dynamics, and study the behavior of the system at finite temperatures. Finally, we briefly discuss implications of our findings for the Fermi-polaron problem."}],"project":[{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"publication_identifier":{"issn":["2643-1564"]},"ec_funded":1,"publication_status":"published","acknowledgement":"M.L. acknowledges support by the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council (ERC) starting Grant No. 801770 (ANGULON). A.G.V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","status":"public","month":"03","file_date_updated":"2022-03-14T08:38:49Z","ddc":["530"],"day":"01","citation":{"chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Artem Volosniev. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>.","mla":"Maslov, Mikhail, et al. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>, vol. 4, 013160, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>.","apa":"Maslov, M., Lemeshko, M., &#38; Volosniev, A. (2022). Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>","ieee":"M. Maslov, M. Lemeshko, and A. Volosniev, “Impurity with a resonance in the vicinity of the Fermi energy,” <i>Physical Review Research</i>, vol. 4. American Physical Society, 2022.","short":"M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022).","ama":"Maslov M, Lemeshko M, Volosniev A. Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. 2022;4. doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>","ista":"Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. 4, 013160."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2022_PhysicalReviewResearch_Maslov.pdf","relation":"main_file","creator":"dernst","file_size":1258324,"success":1,"date_updated":"2022-03-14T08:38:49Z","access_level":"open_access","content_type":"application/pdf","checksum":"62f64b3421a969656ebf52467fa7b6e8","file_id":"10848","date_created":"2022-03-14T08:38:49Z"}],"arxiv":1,"article_processing_charge":"No","volume":4,"has_accepted_license":"1"},{"publisher":"Taylor & Francis","intvolume":"        18","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2022.2039523"}],"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"MaDe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["35188063"],"isi":["000758859600001"]},"date_published":"2022-02-19T00:00:00Z","date_created":"2022-03-13T23:01:47Z","scopus_import":"1","publication":"Autophagy","date_updated":"2023-10-03T10:54:54Z","page":"1208-1210","article_type":"original","oa":1,"year":"2022","volume":18,"article_processing_charge":"No","citation":{"apa":"Artan, M., Sohn, J., Lee, C., Park, S. Y., &#38; Lee, S. J. V. (2022). MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>","ieee":"M. Artan, J. Sohn, C. Lee, S. Y. Park, and S. J. V. Lee, “MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications,” <i>Autophagy</i>, vol. 18, no. 5. Taylor &#38; Francis, pp. 1208–1210, 2022.","short":"M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 1208–1210.","ista":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. 2022. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. Autophagy. 18(5), 1208–1210.","ama":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. 2022;18(5):1208-1210. doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>","chicago":"Artan, Murat, Jooyeon Sohn, Cheolju Lee, Seung Yeol Park, and Seung Jae V. Lee. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>.","mla":"Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>, vol. 18, no. 5, Taylor &#38; Francis, 2022, pp. 1208–10, doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>."},"day":"19","pmid":1,"month":"02","oa_version":"Published Version","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"status":"public","acknowledgement":"This work is funded by National Research Foundation of Korea (NRF) grants NRF-2019R1A3B2067745 from the Korean Government (Ministry of Science and Information and Communications Technology (S-J.V.L.). NRF-2017R1A5A1015366 (S.Y.P, S-J.V.L). Korea Institute of Science and Technology (KIST) intramural grant (C.L).","publication_status":"published","title":"MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications","author":[{"orcid":"0000-0001-8945-6992","first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","last_name":"Artan","full_name":"Artan, Murat"},{"first_name":"Jooyeon","last_name":"Sohn","full_name":"Sohn, Jooyeon"},{"last_name":"Lee","full_name":"Lee, Cheolju","first_name":"Cheolju"},{"first_name":"Seung Yeol","full_name":"Park, Seung Yeol","last_name":"Park"},{"last_name":"Lee","full_name":"Lee, Seung Jae V.","first_name":"Seung Jae V."}],"_id":"10846","abstract":[{"text":"The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of the Golgi apparatus in organismal longevity remained largely unknown. By employing a quantitative proteomic approach, we demonstrated that MON-2, an evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking, promotes longevity via upregulating macroautophagy/autophagy in C. elegans. Our data using cultured mammalian cells indicate that MON2 translocates from the Golgi to the endosome under starvation conditions, subsequently increasing autophagic flux by binding LGG-1/GABARAPL2. Thus, Golgi-to-endosome trafficking appears to be an evolutionarily conserved process for the upregulation of autophagy, which contributes to organismal longevity.","lang":"eng"}],"issue":"5","doi":"10.1080/15548627.2022.2039523"},{"oa":1,"year":"2022","keyword":["Analysis"],"publication":"Journal of Functional Analysis","date_updated":"2023-10-27T10:37:29Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14374"}]},"article_type":"original","article_number":"109455","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2105.04874"],"isi":["000795160200009"]},"date_published":"2022-06-15T00:00:00Z","scopus_import":"1","date_created":"2022-03-16T08:41:53Z","intvolume":"       282","publisher":"Elsevier","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","full_name":"Roos, Barbara","last_name":"Roos"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"title":"Two-particle bound states at interfaces and corners","_id":"10850","issue":"12","abstract":[{"text":"We study two interacting quantum particles forming a bound state in d-dimensional free\r\nspace, and constrain the particles in k directions to (0, ∞)k ×Rd−k, with Neumann boundary\r\nconditions. First, we prove that the ground state energy strictly decreases upon going from k\r\nto k+1. This shows that the particles stick to the corner where all boundary planes intersect.\r\nSecond, we show that for all k the resulting Hamiltonian, after removing the free part of the\r\nkinetic energy, has only finitely many eigenvalues below the essential spectrum. This paper\r\ngeneralizes the work of Egger, Kerner and Pankrashkin (J. Spectr. Theory 10(4):1413–1444,\r\n2020) to dimensions d > 1.","lang":"eng"}],"doi":"10.1016/j.jfa.2022.109455","publication_identifier":{"issn":["0022-1236"]},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"status":"public","publication_status":"published","acknowledgement":"We thank Rupert Frank for contributing Appendix B. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 is gratefully acknowledged.","ec_funded":1,"day":"15","citation":{"apa":"Roos, B., &#38; Seiringer, R. (2022). Two-particle bound states at interfaces and corners. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">https://doi.org/10.1016/j.jfa.2022.109455</a>","ieee":"B. Roos and R. Seiringer, “Two-particle bound states at interfaces and corners,” <i>Journal of Functional Analysis</i>, vol. 282, no. 12. Elsevier, 2022.","ama":"Roos B, Seiringer R. Two-particle bound states at interfaces and corners. <i>Journal of Functional Analysis</i>. 2022;282(12). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">10.1016/j.jfa.2022.109455</a>","short":"B. Roos, R. Seiringer, Journal of Functional Analysis 282 (2022).","ista":"Roos B, Seiringer R. 2022. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 282(12), 109455.","mla":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” <i>Journal of Functional Analysis</i>, vol. 282, no. 12, 109455, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">10.1016/j.jfa.2022.109455</a>.","chicago":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">https://doi.org/10.1016/j.jfa.2022.109455</a>."},"ddc":["510"],"month":"06","file_date_updated":"2022-08-02T10:37:55Z","oa_version":"Published Version","file":[{"file_id":"11720","date_created":"2022-08-02T10:37:55Z","access_level":"open_access","content_type":"application/pdf","checksum":"63efcefaa1f2717244ef5407bd564426","success":1,"date_updated":"2022-08-02T10:37:55Z","file_name":"2022_JourFunctionalAnalysis_Roos.pdf","relation":"main_file","creator":"dernst","file_size":631391}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":282},{"doi":"10.1103/physrevlett.128.107701","issue":"10","abstract":[{"text":"Superconductor-semiconductor hybrid devices are at the heart of several proposed approaches to quantum information processing, but their basic properties remain to be understood. We embed a twodimensional Al-InAs hybrid system in a resonant microwave circuit, probing the breakdown of superconductivity due to an applied magnetic field. We find a fingerprint from the two-component nature of the hybrid system, and quantitatively compare with a theory that includes the contribution of intraband p±ip pairing in the InAs, as well as the emergence of Bogoliubov-Fermi surfaces due to magnetic field. Separately resolving the Al and InAs contributions allows us to determine the carrier density and mobility in the InAs.","lang":"eng"}],"_id":"10851","author":[{"first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan","full_name":"Phan, Duc T"},{"last_name":"Senior","full_name":"Senior, Jorden L","first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","orcid":"0000-0002-0672-9295"},{"orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hatefipour, M.","last_name":"Hatefipour","first_name":"M."},{"full_name":"Strickland, W. M.","last_name":"Strickland","first_name":"W. M."},{"first_name":"J.","full_name":"Shabani, J.","last_name":"Shabani"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827"},{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"}],"title":"Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit","ec_funded":1,"status":"public","acknowledgement":"M. S. acknowledges useful discussions with A. Levchenko and P. A. Lee, and E. Berg. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. J. S. and A. G. acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.W. M. Hatefipour, W. M. Strickland and J. Shabani acknowledge funding from Office of Naval Research Award No. N00014-21-1-2450.","publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"oa_version":"Preprint","month":"03","pmid":1,"day":"11","citation":{"mla":"Phan, Duc T., et al. “Detecting Induced P±ip Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” <i>Physical Review Letters</i>, vol. 128, no. 10, 107701, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevlett.128.107701\">10.1103/physrevlett.128.107701</a>.","chicago":"Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland, J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Detecting Induced P±ip Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevlett.128.107701\">https://doi.org/10.1103/physrevlett.128.107701</a>.","ama":"Phan DT, Senior JL, Ghazaryan A, et al. Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. <i>Physical Review Letters</i>. 2022;128(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.128.107701\">10.1103/physrevlett.128.107701</a>","short":"D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J. Shabani, M. Serbyn, A.P. Higginbotham, Physical Review Letters 128 (2022).","ista":"Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn M, Higginbotham AP. 2022. Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. Physical Review Letters. 128(10), 107701.","ieee":"D. T. Phan <i>et al.</i>, “Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit,” <i>Physical Review Letters</i>, vol. 128, no. 10. American Physical Society, 2022.","apa":"Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M., Shabani, J., … Higginbotham, A. P. (2022). Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.128.107701\">https://doi.org/10.1103/physrevlett.128.107701</a>"},"volume":128,"article_processing_charge":"No","arxiv":1,"keyword":["General Physics and Astronomy"],"year":"2022","oa":1,"article_type":"original","article_number":"107701","related_material":{"record":[{"id":"10029","status":"public","relation":"earlier_version"},{"id":"14547","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/characterizing-super-semi-sandwiches-for-quantum-computing/","relation":"press_release"}]},"date_updated":"2023-11-30T10:56:03Z","publication":"Physical Review Letters","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"scopus_import":"1","date_created":"2022-03-17T11:37:47Z","external_id":{"pmid":[" 35333085"],"arxiv":["2107.03695"],"isi":["000771391100002"]},"date_published":"2022-03-11T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MaSe"},{"_id":"AnHi"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"       128","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.03695","open_access":"1"}],"publisher":"American Physical Society"},{"title":"Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials","author":[{"first_name":"Margarita","full_name":"Davydova, Margarita","last_name":"Davydova"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827"},{"full_name":"Ishizuka, Hiroaki","last_name":"Ishizuka","first_name":"Hiroaki"}],"_id":"10863","abstract":[{"lang":"eng","text":"Nonlinear optical responses are commonly used as a probe for studying the electronic properties of materials. For topological materials, studies thus far focused on photogalvanic electric currents, which are forbidden in centrosymmetric materials because they require broken inversion symmetry. In this Letter, we propose a class of symmetry-allowed responses for inversion-symmetric topological insulators with two doubly degenerate bands. We consider a specific example of such a response, the orbital current, and show that the sign of the response reflects the Z2 topological index, i.e., the orbital current changes sign at the transition between trivial and topological insulator phases. This is illustrated in two models of topological insulators: the Bernevig-Hughes-Zhang model and the 1T′ phase of transition metal dichalcogenides."}],"doi":"10.1103/PhysRevB.105.L121407","publication_identifier":{"issn":["2469-9969"]},"acknowledgement":"We are grateful to Takahiro Morimoto and Zhanybek Alpichshev for fruitful discussions. MD was supported by Austrian Agency for International Cooperation in Education and Research (OeAD-GmbH) and by the John Seo Fellowship at MIT. HI was supported by JSPS KAKENHI Grant Numbers JP19K14649 and JP18H03676, and by UTokyo Global Activity Support Program for\r\nYoung Researchers.","publication_status":"published","status":"public","citation":{"chicago":"Davydova, Margarita, Maksym Serbyn, and Hiroaki Ishizuka. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>.","mla":"Davydova, Margarita, et al. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>, vol. 105, L121407, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>.","apa":"Davydova, M., Serbyn, M., &#38; Ishizuka, H. (2022). Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>","ieee":"M. Davydova, M. Serbyn, and H. Ishizuka, “Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials,” <i>Physical Review B</i>, vol. 105. American Physical Society, 2022.","ista":"Davydova M, Serbyn M, Ishizuka H. 2022. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. Physical Review B. 105, L121407.","ama":"Davydova M, Serbyn M, Ishizuka H. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. 2022;105. doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>","short":"M. Davydova, M. Serbyn, H. Ishizuka, Physical Review B 105 (2022)."},"day":"17","month":"03","oa_version":"Preprint","arxiv":1,"volume":105,"article_processing_charge":"No","oa":1,"year":"2022","publication":"Physical Review B","date_updated":"2023-08-03T06:09:56Z","article_number":"L121407","article_type":"letter_note","department":[{"_id":"MaSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-03-17T00:00:00Z","external_id":{"isi":["000800752500001"],"arxiv":["2101.08277"]},"date_created":"2022-03-18T10:20:46Z","scopus_import":"1","publisher":"American Physical Society","intvolume":"       105","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2101.08277"}],"isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}]},{"publication_status":"published","acknowledgement":"G.I. was supported by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and KKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI. ","status":"public","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"doi":"10.1016/j.jfa.2022.109441","abstract":[{"lang":"eng","text":"We introduce a new way of representing logarithmically concave functions on Rd. It allows us to extend the notion of the largest volume ellipsoid contained in a convex body to the setting of logarithmically concave functions as follows. For every s>0, we define a class of non-negative functions on Rd derived from ellipsoids in Rd+1. For any log-concave function f on Rd , and any fixed s>0, we consider functions belonging to this class, and find the one with the largest integral under the condition that it is pointwise less than or equal to f, and we call it the John s-function of f. After establishing existence and uniqueness, we give a characterization of this function similar to the one given by John in his fundamental theorem. We find that John s-functions converge to characteristic functions of ellipsoids as s tends to zero and to Gaussian densities as s tends to infinity.\r\nAs an application, we prove a quantitative Helly type result: the integral of the pointwise minimum of any family of log-concave functions is at least a constant cd multiple of the integral of the pointwise minimum of a properly chosen subfamily of size 3d+2, where cd depends only on d."}],"issue":"11","_id":"10887","title":"Functional John ellipsoids","author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"},{"last_name":"Naszódi","full_name":"Naszódi, Márton","first_name":"Márton"}],"article_processing_charge":"Yes (via OA deal)","volume":282,"has_accepted_license":"1","file":[{"file_id":"11721","date_created":"2022-08-02T10:40:48Z","file_name":"2022_JourFunctionalAnalysis_Ivanov.pdf","creator":"dernst","file_size":734482,"relation":"main_file","access_level":"open_access","checksum":"1cf185e264e04c87cb1ce67a00db88ab","content_type":"application/pdf","success":1,"date_updated":"2022-08-02T10:40:48Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"oa_version":"Published Version","file_date_updated":"2022-08-02T10:40:48Z","month":"06","ddc":["510"],"citation":{"short":"G. Ivanov, M. Naszódi, Journal of Functional Analysis 282 (2022).","ista":"Ivanov G, Naszódi M. 2022. Functional John ellipsoids. Journal of Functional Analysis. 282(11), 109441.","ama":"Ivanov G, Naszódi M. Functional John ellipsoids. <i>Journal of Functional Analysis</i>. 2022;282(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>","apa":"Ivanov, G., &#38; Naszódi, M. (2022). Functional John ellipsoids. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>","ieee":"G. Ivanov and M. Naszódi, “Functional John ellipsoids,” <i>Journal of Functional Analysis</i>, vol. 282, no. 11. Elsevier, 2022.","chicago":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>.","mla":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>, vol. 282, no. 11, 109441, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>."},"day":"01","article_number":"109441","article_type":"original","date_updated":"2023-08-02T14:51:11Z","publication":"Journal of Functional Analysis","year":"2022","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Elsevier","intvolume":"       282","date_created":"2022-03-20T23:01:38Z","scopus_import":"1","external_id":{"isi":["000781371300008"],"arxiv":["2006.09934"]},"date_published":"2022-06-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"UlWa"}]},{"oa_version":"Published Version","ddc":["580"],"month":"03","pmid":1,"file_date_updated":"2022-03-21T09:19:47Z","day":"07","citation":{"mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11, e2118220119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>.","chicago":"Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>.","ieee":"Q. Lu <i>et al.</i>, “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11. Proceedings of the National Academy of Sciences, 2022.","apa":"Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>","ista":"Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119.","ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(11). doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>","short":"Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"volume":119,"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"10910","date_created":"2022-03-21T09:19:47Z","access_level":"open_access","checksum":"83e0fea7919570d0b519b41193342571","content_type":"application/pdf","success":1,"date_updated":"2022-03-21T09:19:47Z","file_name":"2022_PNAS_Lu.pdf","relation":"main_file","file_size":2169534,"creator":"dernst"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"doi":"10.1073/pnas.2118220119","issue":"11","abstract":[{"text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling.","lang":"eng"}],"_id":"10888","author":[{"last_name":"Lu","full_name":"Lu, Qing","first_name":"Qing"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"first_name":"Joakim","last_name":"Hellner","full_name":"Hellner, Joakim"},{"first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini","full_name":"Giannini, Caterina"},{"first_name":"Xiangyu","full_name":"Xu, Xiangyu","last_name":"Xu"},{"first_name":"Jarne","last_name":"Pauwels","full_name":"Pauwels, Jarne"},{"last_name":"Ma","full_name":"Ma, Qian","first_name":"Qian"},{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"first_name":"Francis","full_name":"Impens, Francis","last_name":"Impens"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"first_name":"Ive","full_name":"De Smet, Ive","last_name":"De Smet"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Daniel Martinez","full_name":"Molina, Daniel Martinez","last_name":"Molina"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"}],"title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","acknowledgement":"We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\u0003nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.).","status":"public","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","date_created":"2022-03-20T23:01:39Z","date_published":"2022-03-07T00:00:00Z","external_id":{"isi":["000771756300008"],"pmid":["35254915"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"intvolume":"       119","publisher":"Proceedings of the National Academy of Sciences","year":"2022","oa":1,"article_type":"original","article_number":"e2118220119","date_updated":"2023-08-03T06:06:27Z","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"article_processing_charge":"No","volume":71,"pmid":1,"month":"03","day":"01","citation":{"chicago":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>.","mla":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>, vol. 71, no. Supplement_1, Oxford Academic, 2022, pp. i72–80, doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>.","apa":"Shigemoto, R. (2022). Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>","ieee":"R. Shigemoto, “Electron microscopic visualization of single molecules by tag-mediated metal particle labeling,” <i>Microscopy</i>, vol. 71, no. Supplement_1. Oxford Academic, pp. i72–i80, 2022.","ista":"Shigemoto R. 2022. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. Microscopy. 71(Supplement_1), i72–i80.","ama":"Shigemoto R. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. 2022;71(Supplement_1):i72-i80. doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>","short":"R. Shigemoto, Microscopy 71 (2022) i72–i80."},"oa_version":"Published Version","project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"ec_funded":1,"acknowledgement":"European Research Council Advanced Grant (694539 to R.S.).","publication_status":"published","status":"public","_id":"10889","author":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"title":"Electron microscopic visualization of single molecules by tag-mediated metal particle labeling","doi":"10.1093/jmicro/dfab048","issue":"Supplement_1","abstract":[{"text":"Genetically encoded tags have introduced extensive lines of application from purification of tagged proteins to their visualization at the single molecular, cellular, histological and whole-body levels. Combined with other rapidly developing technologies such as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, proteomics, super-resolution microscopy and proximity labeling, a large variety of genetically encoded tags have been developed in the last two decades. In this review, I focus on the current status of tag development for electron microscopic (EM) visualization of proteins with metal particle labeling. Compared with conventional immunoelectron microscopy using gold particles, tag-mediated metal particle labeling has several advantages that could potentially improve the sensitivity, spatial and temporal resolution, and applicability to a wide range of proteins of interest (POIs). It may enable researchers to detect single molecules in situ, allowing the quantitative measurement of absolute numbers and exact localization patterns of POI in the ultrastructural context. Thus, genetically encoded tags for EM could revolutionize the field as green fluorescence protein did for light microscopy, although we still have many challenges to overcome before reaching this goal.","lang":"eng"}],"intvolume":"        71","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/jmicro/dfab048"}],"publisher":"Oxford Academic","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"RySh"}],"scopus_import":"1","date_created":"2022-03-20T23:01:39Z","external_id":{"isi":["000768384100011"],"pmid":["35275179"]},"date_published":"2022-03-01T00:00:00Z","date_updated":"2023-08-03T06:08:01Z","publication":"Microscopy","article_type":"original","page":"i72-i80","oa":1,"year":"2022"},{"oa":1,"year":"2022","publication":"Frontiers in Neuroanatomy","date_updated":"2024-10-29T07:57:26Z","article_number":"846615","article_type":"original","department":[{"_id":"RySh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-02-24T00:00:00Z","external_id":{"isi":["000766662700001"],"pmid":["35280978"]},"date_created":"2022-03-20T23:01:39Z","scopus_import":"1","publisher":"Frontiers","intvolume":"        16","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","title":"The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals","author":[{"id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","last_name":"Eguchi","orcid":"0000-0002-6170-2546"},{"first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"last_name":"Le Monnier","full_name":"Le Monnier, Elodie","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"_id":"10890","abstract":[{"text":"Upon the arrival of action potentials at nerve terminals, neurotransmitters are released from synaptic vesicles (SVs) by exocytosis. CaV2.1, 2.2, and 2.3 are the major subunits of the voltage-gated calcium channel (VGCC) responsible for increasing intraterminal calcium levels and triggering SV exocytosis in the central nervous system (CNS) synapses. The two-dimensional analysis of CaV2 distributions using sodium dodecyl sulfate (SDS)-digested freeze-fracture replica labeling (SDS-FRL) has revealed their numbers, densities, and nanoscale clustering patterns in individual presynaptic active zones. The variation in these properties affects the coupling of VGCCs with calcium sensors on SVs, synaptic efficacy, and temporal precision of transmission. In this study, we summarize how the morphological parameters of CaV2 distribution obtained using SDS-FRL differ depending on the different types of synapses and could correspond to functional properties in synaptic transmission.","lang":"eng"}],"doi":"10.3389/fnana.2022.846615","publication_identifier":{"eissn":["16625129"]},"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"_id":"05970B30-7A3F-11EA-A408-12923DDC885E","grant_number":"I04638","name":"LGI1 antibody-induced pathophysiology in synapses"}],"status":"public","publication_status":"published","acknowledgement":"This work was supported by the European Research Council advanced grant No. 694539 and the joint German-Austrian DFG and FWF project SYNABS (FWF: I-4638-B) to RS.\r\nThe authors thank Walter Kaufmann for his critical comments on the manuscript.","ec_funded":1,"citation":{"mla":"Eguchi, Kohgaku, et al. “The Number and Distinct Clustering Patterns of Voltage-Gated Calcium Channels in Nerve Terminals.” <i>Frontiers in Neuroanatomy</i>, vol. 16, 846615, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fnana.2022.846615\">10.3389/fnana.2022.846615</a>.","chicago":"Eguchi, Kohgaku, Jacqueline-Claire Montanaro-Punzengruber, Elodie Le Monnier, and Ryuichi Shigemoto. “The Number and Distinct Clustering Patterns of Voltage-Gated Calcium Channels in Nerve Terminals.” <i>Frontiers in Neuroanatomy</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fnana.2022.846615\">https://doi.org/10.3389/fnana.2022.846615</a>.","ista":"Eguchi K, Montanaro-Punzengruber J-C, Le Monnier E, Shigemoto R. 2022. The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals. Frontiers in Neuroanatomy. 16, 846615.","short":"K. Eguchi, J.-C. Montanaro-Punzengruber, E. Le Monnier, R. Shigemoto, Frontiers in Neuroanatomy 16 (2022).","ama":"Eguchi K, Montanaro-Punzengruber J-C, Le Monnier E, Shigemoto R. The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals. <i>Frontiers in Neuroanatomy</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fnana.2022.846615\">10.3389/fnana.2022.846615</a>","apa":"Eguchi, K., Montanaro-Punzengruber, J.-C., Le Monnier, E., &#38; Shigemoto, R. (2022). The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals. <i>Frontiers in Neuroanatomy</i>. Frontiers. <a href=\"https://doi.org/10.3389/fnana.2022.846615\">https://doi.org/10.3389/fnana.2022.846615</a>","ieee":"K. Eguchi, J.-C. Montanaro-Punzengruber, E. Le Monnier, and R. Shigemoto, “The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals,” <i>Frontiers in Neuroanatomy</i>, vol. 16. Frontiers, 2022."},"day":"24","ddc":["570"],"file_date_updated":"2022-03-21T09:41:19Z","pmid":1,"month":"02","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-03-21T09:41:19Z","file_id":"10911","checksum":"51ec9b90e7da919e22c01a15489eaacd","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-03-21T09:41:19Z","success":1,"relation":"main_file","file_size":2416395,"creator":"dernst","file_name":"2022_FrontiersNeuroanatomy_Eguchi.pdf"}],"has_accepted_license":"1","volume":16,"article_processing_charge":"No"},{"status":"public","publication_status":"published","acknowledgement":"The formal framework for quantitative monitoring which is presented in this invited talk was defined jointly with N. Ege Saraç at LICS 2021. This work was supported in part by the Wittgenstein Award Z211-N23 of the Austrian Science Fund.","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030955601"],"issn":["0302-9743"]},"doi":"10.1007/978-3-030-95561-8_1","abstract":[{"text":"We present a formal framework for the online black-box monitoring of software using monitors with quantitative verdict functions. Quantitative verdict functions have several advantages. First, quantitative monitors can be approximate, i.e., the value of the verdict function does not need to correspond exactly to the value of the property under observation. Second, quantitative monitors can be quantified universally, i.e., for every possible observed behavior, the monitor tries to make the best effort to estimate the value of the property under observation. Third, quantitative monitors can watch boolean as well as quantitative properties, such as average response time. Fourth, quantitative monitors can use non-finite-state resources, such as counters. As a consequence, quantitative monitors can be compared according to how many resources they use (e.g., the number of counters) and how precisely they approximate the property under observation. This allows for a rich spectrum of cost-precision trade-offs in monitoring software.","lang":"eng"}],"_id":"10891","title":"Quantitative monitoring of software","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724"}],"volume":13124,"article_processing_charge":"No","oa_version":"None","conference":{"name":"NSV: Numerical Software Verification","end_date":"2021-10-19","location":"New Haven, CT, United States","start_date":"2021-10-18"},"month":"02","citation":{"chicago":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” In <i>Software Verification</i>, 13124:3–6. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>.","mla":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” <i>Software Verification</i>, vol. 13124, Springer Nature, 2022, pp. 3–6, doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>.","short":"T.A. Henzinger, in:, Software Verification, Springer Nature, 2022, pp. 3–6.","ista":"Henzinger TA. 2022. Quantitative monitoring of software. Software Verification. NSV: Numerical Software VerificationLNCS vol. 13124, 3–6.","ama":"Henzinger TA. Quantitative monitoring of software. In: <i>Software Verification</i>. Vol 13124. LNCS. Springer Nature; 2022:3-6. doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>","apa":"Henzinger, T. A. (2022). Quantitative monitoring of software. In <i>Software Verification</i> (Vol. 13124, pp. 3–6). New Haven, CT, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>","ieee":"T. A. Henzinger, “Quantitative monitoring of software,” in <i>Software Verification</i>, New Haven, CT, United States, 2022, vol. 13124, pp. 3–6."},"day":"22","page":"3-6","date_updated":"2023-08-03T06:11:55Z","publication":"Software Verification","year":"2022","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","isi":1,"publisher":"Springer Nature","intvolume":"     13124","series_title":"LNCS","date_created":"2022-03-20T23:01:40Z","scopus_import":"1","external_id":{"isi":["000771713200001"]},"date_published":"2022-02-22T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToHe"}]}]