[{"language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"type":"journal_article","date_created":"2022-06-19T22:01:58Z","publication":"Angewandte Chemie - International Edition","has_accepted_license":"1","related_material":{"record":[{"id":"11695","relation":"research_data","status":"public"}]},"external_id":{"isi":["000811084000001"],"pmid":["35612297"]},"quality_controlled":"1","volume":61,"article_type":"original","article_processing_charge":"No","file":[{"file_size":1303202,"success":1,"content_type":"application/pdf","relation":"main_file","date_created":"2022-07-29T09:29:20Z","file_name":"2022_AngewandteChemieInternat_Parvizian.pdf","date_updated":"2022-07-29T09:29:20Z","access_level":"open_access","creator":"dernst","file_id":"11696","checksum":"2a3ee0bb59e044b808ebe85cd94ac899"}],"author":[{"full_name":"Parvizian, Mahsa","first_name":"Mahsa","last_name":"Parvizian"},{"first_name":"Alejandra","last_name":"Duràn Balsa","full_name":"Duràn Balsa, Alejandra"},{"full_name":"Pokratath, Rohan","first_name":"Rohan","last_name":"Pokratath"},{"full_name":"Kalha, Curran","first_name":"Curran","last_name":"Kalha"},{"first_name":"Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"first_name":"Dietger","last_name":"Van Den Eynden","full_name":"Van Den Eynden, Dietger"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"first_name":"Anna","last_name":"Regoutz","full_name":"Regoutz, Anna"},{"first_name":"Jonathan","last_name":"De Roo","full_name":"De Roo, Jonathan"}],"isi":1,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"acknowledgement":"J.D.R. and M.P. acknowledge the SNF Eccellenza funding scheme (project number: 194172). We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz Association HGF, for the provision of experimental facilities. Parts of this research were carried out at beamline P21.1, PETRA III. We thank Dr. Soham Banerjee for acquiring the PDF data and helpful advice. A.R. acknowledges the support from the Analytical Chemistry Trust Fund for her CAMS-UK Fellowship. C.K. acknowledges the support from the Department of Chemistry, UCL. The authors acknowledge Dr Stephan Lany from NREL for providing the Cu3N DFT calculations. The authors thank Prof. Raymond Schaak and Dr. Robert William Lord for helpful advice and suggestions regarding the purification procedure. Open access funding provided by Universitat Basel.","license":"https://creativecommons.org/licenses/by/4.0/","title":"The chemistry of Cu₃N and Cu₃PdN nanocrystals","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-08-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1002/anie.202207013","citation":{"short":"M. Parvizian, A. Duràn Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van Den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, Angewandte Chemie - International Edition 61 (2022).","ieee":"M. Parvizian <i>et al.</i>, “The chemistry of Cu₃N and Cu₃PdN nanocrystals,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31. Wiley, 2022.","ama":"Parvizian M, Duràn Balsa A, Pokratath R, et al. The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. 2022;61(31). doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>","chicago":"Parvizian, Mahsa, Alejandra Duràn Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van Den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>.","ista":"Parvizian M, Duràn Balsa A, Pokratath R, Kalha C, Lee S, Van Den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. The chemistry of Cu₃N and Cu₃PdN nanocrystals. Angewandte Chemie - International Edition. 61(31), e202207013.","apa":"Parvizian, M., Duràn Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van Den Eynden, D., … De Roo, J. (2022). The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>","mla":"Parvizian, Mahsa, et al. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31, e202207013, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>."},"intvolume":"        61","ddc":["540"],"file_date_updated":"2022-07-29T09:29:20Z","scopus_import":"1","_id":"11451","article_number":"e202207013","year":"2022","date_updated":"2023-08-03T07:19:12Z","issue":"31","abstract":[{"lang":"eng","text":"The precursor conversion chemistry and surface chemistry of Cu3N and Cu3PdN nanocrystals are unknown or contested. Here, we first obtain phase-pure, colloidally stable nanocubes. Second, we elucidate the pathway by which copper(II) nitrate and oleylamine form Cu3N. We find that oleylamine is both a reductant and a nitrogen source. Oleylamine is oxidized by nitrate to a primary aldimine, which reacts further with excess oleylamine to a secondary aldimine, eliminating ammonia. Ammonia reacts with CuI to form Cu3N. Third, we investigated the surface chemistry and find a mixed ligand shell of aliphatic amines and carboxylates (formed in situ). While the carboxylates appear tightly bound, the amines are easily desorbed from the surface. Finally, we show that doping with palladium decreases the band gap and the material becomes semi-metallic. These results bring insight into the chemistry of metal nitrides and might help the development of other metal nitride nanocrystals."}],"month":"08","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"oa":1,"status":"public"},{"article_processing_charge":"No","quality_controlled":"1","volume":181,"editor":[{"first_name":"Daisuke","last_name":"Yamamoto","full_name":"Yamamoto, Daisuke"}],"publication":"Behavioral Neurogenetics","date_created":"2022-06-20T08:10:34Z","page":"277-294","department":[{"_id":"MaDe"}],"language":[{"iso":"eng"}],"type":"book_chapter","title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","series_title":"NM","alternative_title":["Neuromethods"],"day":"04","acknowledgement":"We thank de Bono lab members for the helpful comments on the manuscript. The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J. Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly sent by Dr. Dominique Glauser (University of Fribourg). This work was supported by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","author":[{"full_name":"Artan, Murat","first_name":"Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"}],"project":[{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","intvolume":"       181","citation":{"chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>.","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>.","apa":"Artan, M., &#38; de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), <i>Behavioral Neurogenetics</i> (Vol. 181, pp. 277–294). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>","ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","ieee":"M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling,” in <i>Behavioral Neurogenetics</i>, vol. 181, D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.","ama":"Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Yamamoto D, ed. <i>Behavioral Neurogenetics</i>. Vol 181. NM. New York: Springer Nature; 2022:277-294. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294."},"doi":"10.1007/978-1-0716-2321-3_15","publication_status":"published","date_published":"2022-06-04T00:00:00Z","oa_version":"None","publication_identifier":{"isbn":["9781071623206"],"eissn":["1940-6045"],"eisbn":["9781071623213"],"issn":["0893-2336"]},"status":"public","ec_funded":1,"month":"06","year":"2022","abstract":[{"text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal.","lang":"eng"}],"date_updated":"2023-02-21T09:51:55Z","_id":"11456","place":"New York"},{"_id":"11459","date_updated":"2025-07-14T09:09:54Z","abstract":[{"lang":"eng","text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples."}],"arxiv":1,"year":"2022","month":"06","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"isbn":["9781450392655"]},"oa_version":"Published Version","date_published":"2022-06-09T00:00:00Z","conference":{"location":"San Diego, CA, United States","end_date":"2022-06-17","name":"PLDI: Programming Language Design and Implementation","start_date":"2022-06-13"},"publication_status":"published","doi":"10.1145/3519939.3523435","citation":{"short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457.","ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>.","ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>"},"scopus_import":"1","file_date_updated":"2022-06-27T07:38:21Z","ddc":["000"],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"isi":1,"author":[{"orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","full_name":"Zikelic, Dorde"},{"first_name":"Bor-Yuh Evan","last_name":"Chang","full_name":"Chang, Bor-Yuh Evan"},{"last_name":"Bolignano","first_name":"Pauline","full_name":"Bolignano, Pauline"},{"full_name":"Raimondi, Franco","first_name":"Franco","last_name":"Raimondi"}],"file":[{"file_name":"2022_PLDI_Zikelic.pdf","date_updated":"2022-06-27T07:38:21Z","date_created":"2022-06-27T07:38:21Z","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","creator":"dernst","file_id":"11466","access_level":"open_access","content_type":"application/pdf","relation":"main_file","success":1,"file_size":318697}],"acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt).","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"09","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"Association for Computing Machinery","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Differential cost analysis with simultaneous potentials and anti-potentials","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"has_accepted_license":"1","page":"442-457","date_created":"2022-06-21T09:26:15Z","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","external_id":{"isi":["000850435600030"],"arxiv":["2204.00870"]},"quality_controlled":"1","article_processing_charge":"No"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","isi":1,"author":[{"full_name":"Schaaf, Zachary A.","last_name":"Schaaf","first_name":"Zachary A."},{"first_name":"Lyvin","last_name":"Tat","full_name":"Tat, Lyvin"},{"first_name":"Noemi","last_name":"Cannizzaro","full_name":"Cannizzaro, Noemi"},{"full_name":"Green, Ralph","last_name":"Green","first_name":"Ralph"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Zarbalis, Konstantinos S.","first_name":"Konstantinos S.","last_name":"Zarbalis"}],"file":[{"checksum":"525d2618e855139089bbfc3e3d49d1b2","file_id":"11461","creator":"dernst","access_level":"open_access","date_updated":"2022-06-24T08:22:59Z","file_name":"2022_MolecularAutism_Schaaf.pdf","date_created":"2022-06-24T08:22:59Z","content_type":"application/pdf","relation":"main_file","success":1,"file_size":7552298}],"acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","day":"22","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"volume":13,"external_id":{"isi":["000814641400001"]},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"article_processing_charge":"No","article_type":"original","type":"journal_article","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Molecular Autism","date_created":"2022-06-23T14:28:55Z","month":"06","status":"public","oa":1,"publication_identifier":{"issn":["2040-2392"]},"article_number":"27","_id":"11460","abstract":[{"text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life.","lang":"eng"}],"date_updated":"2023-08-03T07:21:32Z","year":"2022","citation":{"ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>."},"intvolume":"        13","file_date_updated":"2022-06-24T08:22:59Z","ddc":["570"],"oa_version":"Published Version","date_published":"2022-06-22T00:00:00Z","doi":"10.1186/s13229-022-00508-3","publication_status":"published"},{"scopus_import":"1","citation":{"apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>","ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022."},"intvolume":"       106","publication_status":"published","doi":"10.1007/s00253-022-12022-w","date_published":"2022-08-01T00:00:00Z","oa_version":"None","publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"status":"public","month":"08","year":"2022","date_updated":"2023-10-10T07:15:02Z","abstract":[{"lang":"eng","text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens."}],"_id":"11462","article_processing_charge":"No","article_type":"original","external_id":{"pmid":["35723693"],"isi":["000813677500001"]},"quality_controlled":"1","volume":106,"date_created":"2022-06-26T22:01:34Z","page":"5093-5103","publication":"Applied Microbiology and Biotechnology","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"type":"journal_article","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","pmid":1,"author":[{"full_name":"Dormeshkin, Dmitri","first_name":"Dmitri","last_name":"Dormeshkin"},{"full_name":"Shapira, Michail","first_name":"Michail","last_name":"Shapira"},{"first_name":"Alena","last_name":"Karputs","full_name":"Karputs, Alena"},{"full_name":"Kavaleuski, Anton","first_name":"Anton","orcid":"0000-0003-2091-526X","id":"62304f89-eb97-11eb-a6c2-8903dd183976","last_name":"Kavaleuski"},{"full_name":"Kuzminski, Ivan","last_name":"Kuzminski","first_name":"Ivan"},{"first_name":"Elena","last_name":"Stepanova","full_name":"Stepanova, Elena"},{"first_name":"Andrei","last_name":"Gilep","full_name":"Gilep, Andrei"}],"isi":1},{"doi":"10.1103/physrevb.105.224208","publication_status":"published","date_published":"2022-06-27T00:00:00Z","oa_version":"Preprint","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2111.08603 Focus to learn more","open_access":"1"}],"citation":{"chicago":"Brighi, Pietro, Alexios Michailidis, Kristina Kirova, Dmitry A. Abanin, and Maksym Serbyn. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>.","mla":"Brighi, Pietro, et al. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, 224208, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>.","ista":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. 2022. Localization of a mobile impurity interacting with an Anderson insulator. Physical Review B. 105(22), 224208.","apa":"Brighi, P., Michailidis, A., Kirova, K., Abanin, D. A., &#38; Serbyn, M. (2022). Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>","ieee":"P. Brighi, A. Michailidis, K. Kirova, D. A. Abanin, and M. Serbyn, “Localization of a mobile impurity interacting with an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","ama":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>","short":"P. Brighi, A. Michailidis, K. Kirova, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022)."},"intvolume":"       105","year":"2022","issue":"22","abstract":[{"text":"Thermalizing and localized many-body quantum systems present two distinct dynamical phases of matter. Recently the fate of a localized system coupled to a thermalizing system viewed as a quantum bath received significant theoretical and experimental attention. In this work, we study a mobile impurity, representing a small quantum bath, that interacts locally with an Anderson insulator with a finite density of localized particles. Using static Hartree approximation to obtain an effective disorder strength, we formulate an analytic criterion for the perturbative stability of the localization. Next, we use an approximate dynamical Hartree method and the quasi-exact time-evolved block decimation (TEBD) algorithm to study the dynamics of the system. We find that the dynamical Hartree approach which completely ignores entanglement between the impurity and localized particles predicts the delocalization of the system. In contrast, the full numerical simulation of the unitary dynamics with TEBD suggests the stability of localization on numerically accessible timescales. Finally, using an extension of the density matrix renormalization group algorithm to excited states (DMRG-X), we approximate the highly excited eigenstates of the system. We find that the impurity remains localized in the eigenstates and entanglement is enhanced in a finite region around the position of the impurity, confirming the dynamical predictions. Dynamics and the DMRG-X results provide compelling evidence for the stability of localization.","lang":"eng"}],"arxiv":1,"date_updated":"2023-09-05T12:12:52Z","_id":"11469","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"224208","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"oa":1,"status":"public","ec_funded":1,"month":"06","publication":"Physical Review B","date_created":"2022-06-29T20:19:51Z","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","related_material":{"record":[{"id":"12732","relation":"dissertation_contains","status":"public"}]},"volume":105,"quality_controlled":"1","external_id":{"arxiv":["2111.08603"],"isi":["000823050000001"]},"day":"27","acknowledgement":"We thank M. Ljubotina for insightful discussions. P. B., A. M. and M. S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D. A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","isi":1,"author":[{"full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","orcid":"0000-0002-7969-2729"},{"first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","full_name":"Michailidis, Alexios"},{"id":"4aeda2ae-f847-11ec-98e0-c4a66fe174d4","last_name":"Kirova","first_name":"Kristina","full_name":"Kirova, Kristina"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"title":"Localization of a mobile impurity interacting with an Anderson insulator","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Physical Society"},{"author":[{"orcid":"0000-0002-7969-2729","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","full_name":"Brighi, Pietro"},{"full_name":"Michailidis, Alexios A.","last_name":"Michailidis","first_name":"Alexios A."},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"isi":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"acknowledgement":"We acknowledge useful discussions with M. Ljubotina. P. B., A. M., and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","day":"27","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","title":"Propagation of many-body localization in an Anderson insulator","type":"journal_article","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"publication":"Physical Review B","date_created":"2022-06-29T20:20:47Z","volume":105,"quality_controlled":"1","external_id":{"arxiv":["2109.07332"],"isi":["000823050000012"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12732"}]},"article_processing_charge":"No","article_type":"original","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"L220203","_id":"11470","arxiv":1,"issue":"22","abstract":[{"text":"Many-body localization (MBL) is an example of a dynamical phase of matter that avoids thermalization. While the MBL phase is robust to weak local perturbations, the fate of an MBL system coupled to a thermalizing quantum system that represents a “heat bath” is an open question that is actively investigated theoretically and experimentally. In this work, we consider the stability of an Anderson insulator with a finite density of particles interacting with a single mobile impurity—a small quantum bath. We give perturbative arguments that support the stability of localization in the strong interaction regime. Large-scale tensor network simulations of dynamics are employed to corroborate the presence of the localized phase and give quantitative predictions in the thermodynamic limit. We develop a phenomenological description of the dynamics in the strong interaction regime, and we demonstrate that the impurity effectively turns the Anderson insulator into an MBL phase, giving rise to nontrivial entanglement dynamics well captured by our phenomenology.","lang":"eng"}],"date_updated":"2023-08-03T07:23:52Z","year":"2022","month":"06","ec_funded":1,"status":"public","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"oa":1,"oa_version":"Preprint","date_published":"2022-06-27T00:00:00Z","doi":"10.1103/physrevb.105.l220203","publication_status":"published","citation":{"chicago":"Brighi, Pietro, Alexios A. Michailidis, Dmitry A. Abanin, and Maksym Serbyn. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>.","ista":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. 2022. Propagation of many-body localization in an Anderson insulator. Physical Review B. 105(22), L220203.","apa":"Brighi, P., Michailidis, A. A., Abanin, D. A., &#38; Serbyn, M. (2022). Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>","mla":"Brighi, Pietro, et al. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, L220203, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>.","ama":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>","ieee":"P. Brighi, A. A. Michailidis, D. A. Abanin, and M. Serbyn, “Propagation of many-body localization in an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","short":"P. Brighi, A.A. Michailidis, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022)."},"intvolume":"       105","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2109.07332","open_access":"1"}]},{"ddc":["530"],"file_date_updated":"2022-06-30T07:14:48Z","intvolume":"         3","citation":{"short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>","ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>.","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>.","apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., &#38; Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>"},"publication_status":"published","doi":"10.1103/prxquantum.3.020365","date_published":"2022-06-29T00:00:00Z","oa_version":"Published Version","publication_identifier":{"issn":["2691-3399"]},"oa":1,"status":"public","ec_funded":1,"month":"06","year":"2022","date_updated":"2023-12-13T14:47:24Z","arxiv":1,"abstract":[{"text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. ","lang":"eng"}],"issue":"2","_id":"11471","article_number":"020365","article_type":"original","article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14622"}]},"external_id":{"arxiv":["2201.08194"],"isi":["000822564300001"]},"volume":3,"quality_controlled":"1","keyword":["General Medicine"],"date_created":"2022-06-29T20:21:32Z","publication":"PRX Quantum","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"type":"journal_article","title":"Avoiding barren plateaus using classical shadows","publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"29","acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","file":[{"access_level":"open_access","checksum":"a7706b28d24a0e32a55ea04b82a2df43","file_id":"11472","creator":"dernst","date_created":"2022-06-30T07:14:48Z","file_name":"2022_PRXQuantum_Sack.pdf","date_updated":"2022-06-30T07:14:48Z","success":1,"file_size":4231591,"content_type":"application/pdf","relation":"main_file"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"isi":1,"author":[{"full_name":"Sack, Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan"},{"full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","first_name":"Raimel A","orcid":"0000-0002-5383-2869"},{"full_name":"Michailidis, Alexios","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis"},{"full_name":"Kueng, Richard","first_name":"Richard","last_name":"Kueng"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827"}]},{"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"language":[{"iso":"eng"}],"type":"dissertation","page":"138","date_created":"2022-06-30T12:15:03Z","has_accepted_license":"1","related_material":{"record":[{"id":"10564","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8705"}]},"article_processing_charge":"No","file":[{"success":1,"file_size":1830973,"relation":"main_file","content_type":"application/pdf","date_created":"2022-07-05T08:12:56Z","date_updated":"2022-07-05T08:12:56Z","file_name":"thes1_no_isbn_2_1b.pdf","access_level":"open_access","creator":"kmysliwy","checksum":"7970714a20a6052f75fb27a6c3e9976e","file_id":"11486"},{"access_level":"closed","file_id":"11487","checksum":"647a2011fdf56277096c9350fefe1097","creator":"kmysliwy","date_created":"2022-07-05T08:15:52Z","date_updated":"2022-07-05T08:17:12Z","file_name":"thes_source.zip","file_size":5831060,"content_type":"application/zip","relation":"source_file"}],"author":[{"last_name":"Mysliwy","id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"day":"01","supervisor":[{"first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","date_published":"2022-07-01T00:00:00Z","oa_version":"Published Version","doi":"10.15479/at:ista:11473","publication_status":"published","citation":{"ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","mla":"Mysliwy, Krzysztof. <i>Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>.","apa":"Mysliwy, K. (2022). <i>Polarons in Bose gases and polar crystals: Some rigorous energy estimates</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>."},"ddc":["515","539"],"file_date_updated":"2022-07-05T08:17:12Z","_id":"11473","acknowledged_ssus":[{"_id":"SSU"}],"year":"2022","abstract":[{"text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n","lang":"eng"}],"date_updated":"2023-09-07T13:43:52Z","ec_funded":1,"month":"07","oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public"},{"date_published":"2022-05-25T00:00:00Z","oa_version":"Preprint","conference":{"end_date":"2022-06-03","location":"Trondheim, Norway","start_date":"2022-05-30","name":"EUROCRYPT: Annual International Conference on the Theory and Applications of Cryptology and Information Security"},"publication_status":"published","doi":"10.1007/978-3-031-07085-3_28","intvolume":"     13276","citation":{"mla":"Alwen, Joël, et al. “CoCoA: Concurrent Continuous Group Key Agreement.” <i>Advances in Cryptology – EUROCRYPT 2022</i>, vol. 13276, Springer Nature, 2022, pp. 815–844, doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>.","apa":"Alwen, J., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., Pietrzak, K. Z., &#38; Walter, M. (2022). CoCoA: Concurrent continuous group key agreement. In <i>Advances in Cryptology – EUROCRYPT 2022</i> (Vol. 13276, pp. 815–844). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>","ista":"Alwen J, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2022. CoCoA: Concurrent continuous group key agreement. Advances in Cryptology – EUROCRYPT 2022. EUROCRYPT: Annual International Conference on the Theory and Applications of Cryptology and Information Security, LNCS, vol. 13276, 815–844.","chicago":"Alwen, Joël, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “CoCoA: Concurrent Continuous Group Key Agreement.” In <i>Advances in Cryptology – EUROCRYPT 2022</i>, 13276:815–844. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>.","ama":"Alwen J, Auerbach B, Cueto Noval M, et al. CoCoA: Concurrent continuous group key agreement. In: <i>Advances in Cryptology – EUROCRYPT 2022</i>. Vol 13276. Cham: Springer Nature; 2022:815–844. doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>","ieee":"J. Alwen <i>et al.</i>, “CoCoA: Concurrent continuous group key agreement,” in <i>Advances in Cryptology – EUROCRYPT 2022</i>, Trondheim, Norway, 2022, vol. 13276, pp. 815–844.","short":"J. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2022, Springer Nature, Cham, 2022, pp. 815–844."},"main_file_link":[{"url":"https://eprint.iacr.org/2022/251","open_access":"1"}],"scopus_import":"1","_id":"11476","place":"Cham","year":"2022","date_updated":"2023-08-03T07:25:02Z","abstract":[{"text":"Messaging platforms like Signal are widely deployed and provide strong security in an asynchronous setting. It is a challenging problem to construct a protocol with similar security guarantees that can efficiently scale to large groups. A major bottleneck are the frequent key rotations users need to perform to achieve post compromise forward security.\r\n\r\nIn current proposals – most notably in TreeKEM (which is part of the IETF’s Messaging Layer Security (MLS) protocol draft) – for users in a group of size n to rotate their keys, they must each craft a message of size log(n) to be broadcast to the group using an (untrusted) delivery server.\r\n\r\nIn larger groups, having users sequentially rotate their keys requires too much bandwidth (or takes too long), so variants allowing any T≤n users to simultaneously rotate their keys in just 2 communication rounds have been suggested (e.g. “Propose and Commit” by MLS). Unfortunately, 2-round concurrent updates are either damaging or expensive (or both); i.e. they either result in future operations being more costly (e.g. via “blanking” or “tainting”) or are costly themselves requiring Ω(T) communication for each user [Bienstock et al., TCC’20].\r\n\r\nIn this paper we propose CoCoA; a new scheme that allows for T concurrent updates that are neither damaging nor costly. That is, they add no cost to future operations yet they only require Ω(log2(n)) communication per user. To circumvent the [Bienstock et al.] lower bound, CoCoA increases the number of rounds needed to complete all updates from 2 up to (at most) log(n); though typically fewer rounds are needed.\r\n\r\nThe key insight of our protocol is the following: in the (non-concurrent version of) TreeKEM, a delivery server which gets T concurrent update requests will approve one and reject the remaining T−1. In contrast, our server attempts to apply all of them. If more than one user requests to rotate the same key during a round, the server arbitrarily picks a winner. Surprisingly, we prove that regardless of how the server chooses the winners, all previously compromised users will recover after at most log(n) such update rounds.\r\n\r\nTo keep the communication complexity low, CoCoA is a server-aided CGKA. That is, the delivery server no longer blindly forwards packets, but instead actively computes individualized packets tailored to each user. As the server is untrusted, this change requires us to develop new mechanisms ensuring robustness of the protocol.","lang":"eng"}],"ec_funded":1,"month":"05","oa":1,"publication_identifier":{"isbn":["9783031070846"],"eissn":["1611-3349"],"eisbn":["9783031070853"],"issn":["0302-9743"]},"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"KrPi"}],"type":"conference","date_created":"2022-06-30T16:48:00Z","page":"815–844","publication":"Advances in Cryptology – EUROCRYPT 2022","external_id":{"isi":["000832305300028"]},"quality_controlled":"1","volume":13276,"article_processing_charge":"No","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"author":[{"first_name":"Joël","last_name":"Alwen","full_name":"Alwen, Joël"},{"first_name":"Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","full_name":"Auerbach, Benedikt"},{"first_name":"Miguel","last_name":"Cueto Noval","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"},{"first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez","full_name":"Pascual Perez, Guillermo"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Walter, Michael","first_name":"Michael","last_name":"Walter"}],"day":"25","acknowledgement":"We thank Marta Mularczyk and Yiannis Tselekounis for their very helpful feedback on an earlier draft of this paper.","alternative_title":["LNCS"],"title":"CoCoA: Concurrent continuous group key agreement","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"11478","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_number":"104580","year":"2022","abstract":[{"text":"Cerebral organoids differentiated from human-induced pluripotent stem cells (hiPSC) provide a unique opportunity to investigate brain development. However, organoids usually lack microglia, brain-resident immune cells, which are present in the early embryonic brain and participate in neuronal circuit development. Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol. Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented, 3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When we guide the retinal organoid differentiation with low-dosed BMP4, we prevent cup development and enhance microglia and 3D-cysts formation. Mass spectrometry identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed this microglia-preferred environment also within the unguided protocol, providing insight into microglial behavior and migration and offer a model to study how they enter and distribute within the human brain.","lang":"eng"}],"issue":"7","date_updated":"2023-11-02T12:21:33Z","ec_funded":1,"month":"07","publication_identifier":{"eissn":["2589-0042"]},"oa":1,"status":"public","date_published":"2022-07-15T00:00:00Z","oa_version":"Published Version","doi":"10.1016/j.isci.2022.104580","publication_status":"published","intvolume":"        25","citation":{"apa":"Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler, K., … Siegert, S. (2022). A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>","ista":"Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. iScience. 25(7), 104580.","mla":"Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>, vol. 25, no. 7, 104580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>.","chicago":"Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>.","ieee":"K. Bartalska <i>et al.</i>, “A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation,” <i>iScience</i>, vol. 25, no. 7. Elsevier, 2022.","ama":"Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>iScience</i>. 2022;25(7). doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>","short":"K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler, T. Czech, S. Siegert, IScience 25 (2022)."},"ddc":["610"],"scopus_import":"1","file_date_updated":"2022-07-04T08:19:25Z","file":[{"date_created":"2022-07-04T08:19:25Z","file_name":"2022_iScience_Bartalska.pdf","date_updated":"2022-07-04T08:19:25Z","access_level":"open_access","checksum":"a470b74e1b3796c710189c81a4cd4329","file_id":"11480","creator":"cchlebak","file_size":19400048,"success":1,"relation":"main_file","content_type":"application/pdf"}],"isi":1,"author":[{"full_name":"Bartalska, Katarina","id":"4D883232-F248-11E8-B48F-1D18A9856A87","last_name":"Bartalska","first_name":"Katarina"},{"full_name":"Hübschmann, Verena","last_name":"Hübschmann","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"first_name":"Medina","orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","last_name":"Korkut","full_name":"Korkut, Medina"},{"last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","first_name":"Ryan J","full_name":"Cubero, Ryan J"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro"},{"full_name":"Rössler, Karl","last_name":"Rössler","first_name":"Karl"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation"}],"day":"15","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank the scientific service units at ISTA, specifically the lab support facility and imaging & optics facility for their support; Nicolas Armel for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner for their help in human brain tissue collection, Rouven Schulz for his insights into the functional assays We thank all members of the Siegert group for constant feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for feedback on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","title":"A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","department":[{"_id":"SaSi"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"iScience","date_created":"2022-07-03T22:01:33Z","has_accepted_license":"1","related_material":{"record":[{"id":"12117","status":"public","relation":"other"}]},"volume":25,"quality_controlled":"1","external_id":{"isi":["000830428500005"]},"article_type":"original","article_processing_charge":"Yes"},{"file":[{"relation":"main_file","content_type":"application/pdf","success":1,"file_size":2324542,"creator":"cchlebak","file_id":"11492","checksum":"e997a57a928ec9d51fad8ce824a05935","access_level":"open_access","file_name":"2022_IntJMolSci_Bilanovicova.pdf","date_updated":"2022-07-06T07:36:59Z","date_created":"2022-07-06T07:36:59Z"}],"author":[{"full_name":"Bilanovičová, V","first_name":"V","last_name":"Bilanovičová"},{"full_name":"Rýdza, N","first_name":"N","last_name":"Rýdza"},{"first_name":"L","last_name":"Koczka","full_name":"Koczka, L"},{"last_name":"Hess","first_name":"M","full_name":"Hess, M"},{"last_name":"Feraru","first_name":"E","full_name":"Feraru, E"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Nodzyński, T","last_name":"Nodzyński","first_name":"T"}],"isi":1,"project":[{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988"}],"day":"06","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","pmid":1,"title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"MDPI","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"International Journal of Molecular Sciences","page":"6352","date_created":"2022-07-05T15:14:34Z","has_accepted_license":"1","quality_controlled":"1","volume":23,"external_id":{"isi":["000808733300001"],"pmid":["35683031"]},"article_processing_charge":"Yes","article_type":"original","_id":"11489","year":"2022","issue":"11","abstract":[{"lang":"eng","text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors."}],"date_updated":"2023-08-09T10:13:57Z","month":"06","oa":1,"publication_identifier":{"issn":["1422-0067"]},"status":"public","date_published":"2022-06-06T00:00:00Z","oa_version":"Published Version","doi":"10.3390/ijms23116352","publication_status":"published","citation":{"ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022."},"intvolume":"        23","ddc":["570"],"file_date_updated":"2022-07-06T07:36:59Z"},{"has_accepted_license":"1","doi":"10.15479/AT:ISTA:11542","date_created":"2022-07-08T11:03:02Z","oa_version":"None","type":"research_data","date_published":"2022-01-01T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"file_date_updated":"2022-07-08T10:56:52Z","article_processing_charge":"No","citation":{"ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","short":"R. Schulz, (2022).","apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>."},"related_material":{"link":[{"relation":"contains","url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1"}],"record":[{"status":"public","relation":"used_in_publication","id":"11995"}]},"date_updated":"2024-02-21T12:34:51Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","author":[{"full_name":"Schulz, Rouven","last_name":"Schulz","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X","first_name":"Rouven"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","file_size":135784571,"success":1,"file_id":"11543","creator":"rschulz","checksum":"71e8186583f3adbb6c69a88ac9e6e49b","access_level":"open_access","date_updated":"2022-07-08T10:56:52Z","file_name":"Source Data.xlsx","date_created":"2022-07-08T10:56:52Z"}],"_id":"11542","publisher":"Institute of Science and Technology Austria","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","oa":1,"contributor":[{"first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","contributor_type":"contact_person"}]},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"author":[{"first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","last_name":"Brown","full_name":"Brown, Adam"},{"full_name":"Romanov, Anna","first_name":"Anna","last_name":"Romanov"}],"file":[{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":582962,"creator":"dernst","file_id":"12473","checksum":"82abaee3d7837f703e499a9ecbb25b7c","access_level":"open_access","date_updated":"2023-02-02T07:32:48Z","file_name":"2022_JournalAlgebra_Brown.pdf","date_created":"2023-02-02T07:32:48Z"}],"acknowledgement":"We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting discussions. The first author acknowledges the support of the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The second author is supported by the National Science Foundation Award No. 1803059 and the Australian Research Council grant DP170101579.","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Contravariant pairings between standard Whittaker modules and Verma modules","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"has_accepted_license":"1","date_created":"2022-07-08T11:40:07Z","page":"145-179","publication":"Journal of Algebra","external_id":{"isi":["000861841100004"]},"volume":609,"keyword":["Algebra and Number Theory"],"quality_controlled":"1","article_type":"original","article_processing_charge":"Yes (via OA deal)","_id":"11545","date_updated":"2023-08-03T11:56:30Z","issue":"11","abstract":[{"lang":"eng","text":"We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings.\r\nWe show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category\r\nN have the structure of highest weight categories and we establish a BGG reciprocity theorem for N ."}],"year":"2022","month":"11","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"issn":["0021-8693"]},"oa_version":"Published Version","date_published":"2022-11-01T00:00:00Z","publication_status":"published","doi":"10.1016/j.jalgebra.2022.06.017","intvolume":"       609","citation":{"short":"A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.","ieee":"A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker modules and Verma modules,” <i>Journal of Algebra</i>, vol. 609, no. 11. Elsevier, pp. 145–179, 2022.","ama":"Brown A, Romanov A. Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. 2022;609(11):145-179. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>","ista":"Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker modules and Verma modules. Journal of Algebra. 609(11), 145–179.","apa":"Brown, A., &#38; Romanov, A. (2022). Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>","mla":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>, vol. 609, no. 11, Elsevier, 2022, pp. 145–79, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>.","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>."},"file_date_updated":"2023-02-02T07:32:48Z","scopus_import":"1","ddc":["510"]},{"article_number":"20210203","_id":"11546","issue":"1856","abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"date_updated":"2023-08-03T11:55:42Z","year":"2022","month":"08","status":"public","oa":1,"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"oa_version":"Published Version","date_published":"2022-08-01T00:00:00Z","doi":"10.1098/rstb.2021.0203","publication_status":"published","intvolume":"       377","citation":{"short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203."},"file_date_updated":"2023-02-02T08:20:29Z","scopus_import":"1","ddc":["570"],"author":[{"first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"isi":1,"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"file":[{"access_level":"open_access","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_id":"12479","creator":"dernst","date_created":"2023-02-02T08:20:29Z","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","date_updated":"2023-02-02T08:20:29Z","file_size":920304,"success":1,"relation":"main_file","content_type":"application/pdf"}],"acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Royal Society of London","title":"Inversions and parallel evolution","type":"journal_article","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","date_created":"2022-07-08T11:41:56Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"quality_controlled":"1","volume":377,"external_id":{"isi":["000812317300005"]},"article_type":"original","article_processing_charge":"Yes (via OA deal)"},{"publication":"Communications Biology","date_created":"2022-07-10T22:01:52Z","has_accepted_license":"1","department":[{"_id":"LeSa"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","volume":5,"quality_controlled":"1","external_id":{"isi":["000815098500002"],"pmid":[" 35739187"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"23","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","pmid":1,"file":[{"success":1,"file_size":2335369,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"11571","creator":"kschuh","checksum":"965f88bbcef3fd0c3e121340555c4467","date_created":"2022-07-13T07:44:58Z","file_name":"2022_communicationsbiology_Molina-Granada.pdf","date_updated":"2022-07-13T07:44:58Z"}],"author":[{"last_name":"Molina-Granada","first_name":"David","full_name":"Molina-Granada, David"},{"first_name":"Emiliano","last_name":"González-Vioque","full_name":"González-Vioque, Emiliano"},{"full_name":"Dibley, Marris G.","first_name":"Marris G.","last_name":"Dibley"},{"full_name":"Cabrera-Pérez, Raquel","last_name":"Cabrera-Pérez","first_name":"Raquel"},{"full_name":"Vallbona-Garcia, Antoni","first_name":"Antoni","last_name":"Vallbona-Garcia"},{"full_name":"Torres-Torronteras, Javier","first_name":"Javier","last_name":"Torres-Torronteras"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A"},{"full_name":"Ryan, Michael T.","first_name":"Michael T.","last_name":"Ryan"},{"full_name":"Cámara, Yolanda","last_name":"Cámara","first_name":"Yolanda"},{"full_name":"Martí, Ramon","last_name":"Martí","first_name":"Ramon"}],"isi":1,"title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","doi":"10.1038/s42003-022-03568-6","publication_status":"published","date_published":"2022-06-23T00:00:00Z","oa_version":"Published Version","ddc":["570"],"scopus_import":"1","file_date_updated":"2022-07-13T07:44:58Z","intvolume":"         5","citation":{"mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>, vol. 5, no. 1, 620, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>.","apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620.","chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>.","ieee":"D. Molina-Granada <i>et al.</i>, “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” <i>Communications Biology</i>, vol. 5, no. 1. Springer Nature, 2022.","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. 2022;5(1). doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>","short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022)."},"year":"2022","abstract":[{"text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.","lang":"eng"}],"issue":"1","date_updated":"2023-08-03T11:51:58Z","_id":"11551","article_number":"620","oa":1,"publication_identifier":{"eissn":["23993642"]},"status":"public","month":"06"},{"year":"2022","issue":"24","abstract":[{"text":"Rotational dynamics of D2 molecules inside helium nanodroplets is induced by a moderately intense femtosecond pump pulse and measured as a function of time by recording the yield of HeD+ ions, created through strong-field dissociative ionization with a delayed femtosecond probe pulse. The yield oscillates with a period of 185 fs, reflecting field-free rotational wave packet dynamics, and the oscillation persists for more than 500 periods. Within the experimental uncertainty, the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier analysis, is the same as Bgas for an isolated D2 molecule. Our observations show that the D2 molecules inside helium nanodroplets essentially rotate as free D2 molecules.","lang":"eng"}],"arxiv":1,"date_updated":"2023-08-03T11:54:14Z","_id":"11552","article_number":"243201","oa":1,"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"status":"public","ec_funded":1,"month":"06","doi":"10.1103/PhysRevLett.128.243201","publication_status":"published","date_published":"2022-06-16T00:00:00Z","oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.09281","open_access":"1"}],"intvolume":"       128","citation":{"chicago":"Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>.","ista":"Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W, Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I, Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201.","apa":"Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>","mla":"Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>, vol. 128, no. 24, 243201, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>.","ama":"Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. 2022;128(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>","ieee":"J. Qiang <i>et al.</i>, “Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets,” <i>Physical Review Letters</i>, vol. 128, no. 24. American Physical Society, 2022.","short":"J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun, W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt, I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022)."},"day":"16","author":[{"first_name":"Junjie","last_name":"Qiang","full_name":"Qiang, Junjie"},{"full_name":"Zhou, Lianrong","first_name":"Lianrong","last_name":"Zhou"},{"full_name":"Lu, Peifen","first_name":"Peifen","last_name":"Lu"},{"full_name":"Lin, Kang","first_name":"Kang","last_name":"Lin"},{"first_name":"Yongzhe","last_name":"Ma","full_name":"Ma, Yongzhe"},{"first_name":"Shengzhe","last_name":"Pan","full_name":"Pan, Shengzhe"},{"full_name":"Lu, Chenxu","first_name":"Chenxu","last_name":"Lu"},{"first_name":"Wenyu","last_name":"Jiang","full_name":"Jiang, Wenyu"},{"first_name":"Fenghao","last_name":"Sun","full_name":"Sun, Fenghao"},{"first_name":"Wenbin","last_name":"Zhang","full_name":"Zhang, Wenbin"},{"full_name":"Li, Hui","first_name":"Hui","last_name":"Li"},{"first_name":"Xiaochun","last_name":"Gong","full_name":"Gong, Xiaochun"},{"last_name":"Averbukh","first_name":"Ilya Sh","full_name":"Averbukh, Ilya Sh"},{"full_name":"Prior, Yehiam","last_name":"Prior","first_name":"Yehiam"},{"full_name":"Schouder, Constant A.","last_name":"Schouder","first_name":"Constant A."},{"last_name":"Stapelfeldt","first_name":"Henrik","full_name":"Stapelfeldt, Henrik"},{"first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","full_name":"Cherepanov, Igor"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"full_name":"Jäger, Wolfgang","first_name":"Wolfgang","last_name":"Jäger"},{"first_name":"Jian","last_name":"Wu","full_name":"Wu, Jian"}],"isi":1,"project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"title":"Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","publication":"Physical Review Letters","date_created":"2022-07-10T22:01:52Z","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","volume":128,"quality_controlled":"1","external_id":{"isi":["000820659700002"],"arxiv":["2201.09281"]}},{"file":[{"access_level":"open_access","checksum":"16e7c659dee9073c6c8aeb87316ef201","creator":"kschuh","file_id":"11559","date_created":"2022-07-12T10:04:55Z","date_updated":"2022-07-12T10:04:55Z","file_name":"2022_ArnoldMathematicalJournal_Clark.pdf","success":1,"file_size":2509915,"content_type":"application/pdf","relation":"main_file"}],"project":[{"call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","grant_number":"885707"}],"author":[{"last_name":"Clark","first_name":"Trevor","full_name":"Clark, Trevor"},{"full_name":"Drach, Kostiantyn","first_name":"Kostiantyn","orcid":"0000-0002-9156-8616","last_name":"Drach","id":"fe8209e2-906f-11eb-847d-950f8fc09115"},{"last_name":"Kozlovski","first_name":"Oleg","full_name":"Kozlovski, Oleg"},{"full_name":"Strien, Sebastian Van","last_name":"Strien","first_name":"Sebastian Van"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We would also like to thank Dzmitry Dudko and Dierk Schleicher for many stimulating discussions and encouragement during our work on this project, and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are grateful to Leon Staresinic who carefully read the revised version of the manuscript and provided many helpful suggestions.","title":"The dynamics of complex box mappings","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"VaKa"}],"type":"journal_article","page":"319-410","date_created":"2022-07-10T22:01:53Z","publication":"Arnold Mathematical Journal","has_accepted_license":"1","related_material":{"link":[{"url":"https://doi.org/10.1007/s40598-022-00209-y","relation":"erratum"},{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00218-x"}]},"volume":8,"quality_controlled":"1","article_processing_charge":"No","article_type":"original","_id":"11553","year":"2022","date_updated":"2023-02-16T10:02:12Z","abstract":[{"text":"In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:\r\n• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.\r\n• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:\r\n  • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;\r\n  • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n   • the QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.\r\n• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:\r\n   • puzzle pieces shrink to points,\r\n   • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings\r\nare the analogues of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.","lang":"eng"}],"issue":"2","ec_funded":1,"month":"06","oa":1,"publication_identifier":{"eissn":["2199-6806"],"issn":["2199-6792"]},"status":"public","date_published":"2022-06-01T00:00:00Z","oa_version":"None","publication_status":"published","doi":"10.1007/s40598-022-00200-7","intvolume":"         8","citation":{"ista":"Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box mappings. Arnold Mathematical Journal. 8(2), 319–410.","apa":"Clark, T., Drach, K., Kozlovski, O., &#38; Strien, S. V. (2022). The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>","mla":"Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>.","chicago":"Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>.","ieee":"T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex box mappings,” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2. Springer Nature, pp. 319–410, 2022.","ama":"Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. 2022;8(2):319-410. doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>","short":"T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal 8 (2022) 319–410."},"ddc":["500"],"scopus_import":"1","file_date_updated":"2022-07-12T10:04:55Z"},{"oa_version":"Preprint","date_published":"2022-10-15T00:00:00Z","publication_status":"published","doi":"10.1016/j.jcp.2022.111439","citation":{"chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022)."},"intvolume":"       467","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"ddc":["518"],"article_number":"111439","_id":"11556","date_updated":"2023-08-03T11:55:06Z","arxiv":1,"abstract":[{"lang":"eng","text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise."}],"year":"2022","month":"10","status":"public","publication_identifier":{"issn":["0021-9991"]},"oa":1,"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_created":"2022-07-11T12:19:59Z","publication":"Journal of Computational Physics","external_id":{"arxiv":["2103.09481"],"isi":["000917225500013"]},"keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"quality_controlled":"1","volume":467,"article_type":"original","article_processing_charge":"No","author":[{"id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","orcid":"0000-0003-2189-3904","first_name":"Aleksei","full_name":"Kalinov, Aleksei"},{"last_name":"Osinskiy","first_name":"A.I.","full_name":"Osinskiy, A.I."},{"full_name":"Matveev, S.A.","first_name":"S.A.","last_name":"Matveev"},{"full_name":"Otieno, W.","first_name":"W.","last_name":"Otieno"},{"full_name":"Brilliantov, N.V.","first_name":"N.V.","last_name":"Brilliantov"}],"isi":1,"acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","day":"15","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics"},{"has_accepted_license":"1","publication":"Genome Biology","date_created":"2022-07-17T22:01:53Z","type":"journal_article","department":[{"_id":"FyKo"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":23,"external_id":{"isi":["000821915500002"]},"acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","day":"07","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Runxuan","last_name":"Zhang","full_name":"Zhang, Runxuan"},{"full_name":"Kuo, Richard","first_name":"Richard","last_name":"Kuo"},{"last_name":"Coulter","first_name":"Max","full_name":"Coulter, Max"},{"full_name":"Calixto, Cristiane P.G.","first_name":"Cristiane P.G.","last_name":"Calixto"},{"full_name":"Entizne, Juan Carlos","last_name":"Entizne","first_name":"Juan Carlos"},{"first_name":"Wenbin","last_name":"Guo","full_name":"Guo, Wenbin"},{"last_name":"Marquez","first_name":"Yamile","full_name":"Marquez, Yamile"},{"first_name":"Linda","last_name":"Milne","full_name":"Milne, Linda"},{"full_name":"Riegler, Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler","first_name":"Stefan","orcid":"0000-0003-3413-1343"},{"first_name":"Akihiro","last_name":"Matsui","full_name":"Matsui, Akihiro"},{"full_name":"Tanaka, Maho","last_name":"Tanaka","first_name":"Maho"},{"last_name":"Harvey","first_name":"Sarah","full_name":"Harvey, Sarah"},{"first_name":"Yubang","last_name":"Gao","full_name":"Gao, Yubang"},{"last_name":"Wießner-Kroh","first_name":"Theresa","full_name":"Wießner-Kroh, Theresa"},{"full_name":"Paniagua, Alejandro","last_name":"Paniagua","first_name":"Alejandro"},{"first_name":"Martin","last_name":"Crespi","full_name":"Crespi, Martin"},{"full_name":"Denby, Katherine","last_name":"Denby","first_name":"Katherine"},{"last_name":"Hur","first_name":"Asa Ben","full_name":"Hur, Asa Ben"},{"last_name":"Huq","first_name":"Enamul","full_name":"Huq, Enamul"},{"last_name":"Jantsch","first_name":"Michael","full_name":"Jantsch, Michael"},{"full_name":"Jarmolowski, Artur","first_name":"Artur","last_name":"Jarmolowski"},{"first_name":"Tino","last_name":"Koester","full_name":"Koester, Tino"},{"last_name":"Laubinger","first_name":"Sascha","full_name":"Laubinger, Sascha"},{"first_name":"Qingshun Quinn","last_name":"Li","full_name":"Li, Qingshun Quinn"},{"full_name":"Gu, Lianfeng","last_name":"Gu","first_name":"Lianfeng"},{"full_name":"Seki, Motoaki","last_name":"Seki","first_name":"Motoaki"},{"full_name":"Staiger, Dorothee","last_name":"Staiger","first_name":"Dorothee"},{"last_name":"Sunkar","first_name":"Ramanjulu","full_name":"Sunkar, Ramanjulu"},{"last_name":"Szweykowska-Kulinska","first_name":"Zofia","full_name":"Szweykowska-Kulinska, Zofia"},{"last_name":"Tu","first_name":"Shih Long","full_name":"Tu, Shih Long"},{"full_name":"Wachter, Andreas","last_name":"Wachter","first_name":"Andreas"},{"full_name":"Waugh, Robbie","first_name":"Robbie","last_name":"Waugh"},{"full_name":"Xiong, Liming","first_name":"Liming","last_name":"Xiong"},{"full_name":"Zhang, Xiao Ning","first_name":"Xiao Ning","last_name":"Zhang"},{"full_name":"Conesa, Ana","first_name":"Ana","last_name":"Conesa"},{"first_name":"Anireddy S.N.","last_name":"Reddy","full_name":"Reddy, Anireddy S.N."},{"full_name":"Barta, Andrea","last_name":"Barta","first_name":"Andrea"},{"full_name":"Kalyna, Maria","first_name":"Maria","last_name":"Kalyna"},{"full_name":"Brown, John W.S.","first_name":"John W.S.","last_name":"Brown"}],"isi":1,"file":[{"file_size":3146207,"success":1,"content_type":"application/pdf","relation":"main_file","date_created":"2022-07-18T08:15:24Z","file_name":"2022_GenomeBiology_Zhang.pdf","date_updated":"2022-07-18T08:15:24Z","access_level":"open_access","checksum":"2c30ef84151d257a6b835b4e069b70ac","file_id":"11597","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"BioMed Central","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","doi":"10.1186/s13059-022-02711-0","publication_status":"published","oa_version":"Published Version","date_published":"2022-07-07T00:00:00Z","scopus_import":"1","file_date_updated":"2022-07-18T08:15:24Z","ddc":["570"],"intvolume":"        23","citation":{"chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>.","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.","mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>.","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022.","ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>"},"abstract":[{"text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.","lang":"eng"}],"date_updated":"2023-08-03T12:04:18Z","year":"2022","article_number":"149","_id":"11587","status":"public","oa":1,"publication_identifier":{"eissn":["1474-760X"]},"month":"07"}]