[{"date_updated":"2026-04-02T14:35:47Z","department":[{"_id":"JiFr"}],"author":[{"full_name":"Moturu, Taraka Ramji","last_name":"Moturu","first_name":"Taraka Ramji"},{"full_name":"Sinha, Sansrity","last_name":"Sinha","first_name":"Sansrity"},{"first_name":"Hymavathi","last_name":"Salava","full_name":"Salava, Hymavathi"},{"first_name":"Sravankumar","last_name":"Thula","full_name":"Thula, Sravankumar"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","full_name":"Simon, Sibu","last_name":"Simon"}],"article_processing_charge":"No","doi":"10.3390/plants9030299","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","external_id":{"isi":["000525315000035"],"pmid":["32121542"]},"file":[{"content_type":"application/pdf","creator":"dernst","date_created":"2020-03-23T13:37:00Z","access_level":"open_access","file_id":"7614","file_size":2373484,"checksum":"6d5af3e17266a48996b4af4e67e88a85","relation":"main_file","file_name":"2020_Plants_Moturu.pdf","date_updated":"2020-07-14T12:48:00Z"}],"publication_identifier":{"eissn":["2223-7747"]},"month":"03","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:48:00Z","corr_author":"1","article_number":"299","has_accepted_license":"1","citation":{"mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” <i>Plants</i>, vol. 9, no. 3, 299, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/plants9030299\">10.3390/plants9030299</a>.","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of proteins involved in miRNA maturation pathway,” <i>Plants</i>, vol. 9, no. 3. MDPI, 2020.","ista":"Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J, Simon S. 2020. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. 9(3), 299.","short":"T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Plants 9 (2020).","ama":"Moturu TR, Sinha S, Salava H, et al. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. <i>Plants</i>. 2020;9(3). doi:<a href=\"https://doi.org/10.3390/plants9030299\">10.3390/plants9030299</a>","chicago":"Moturu, Taraka Ramji, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” <i>Plants</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/plants9030299\">https://doi.org/10.3390/plants9030299</a>.","apa":"Moturu, T. R., Sinha, S., Salava, H., Thula, S., Nodzyński, T., Vařeková, R. S., … Simon, S. (2020). Molecular evolution and diversification of proteins involved in miRNA maturation pathway. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants9030299\">https://doi.org/10.3390/plants9030299</a>"},"language":[{"iso":"eng"}],"date_published":"2020-03-01T00:00:00Z","issue":"3","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"abstract":[{"text":"Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes.","lang":"eng"}],"date_created":"2020-03-15T23:00:52Z","intvolume":"         9","quality_controlled":"1","publication":"Plants","volume":9,"article_type":"original","title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","ec_funded":1,"_id":"7582","day":"01","publisher":"MDPI","ddc":["580"],"pmid":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-08-01T00:00:00Z","issue":"8","year":"2020","abstract":[{"text":"Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of\r\nmutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.","lang":"eng"}],"intvolume":"        43","date_created":"2020-06-14T22:00:49Z","quality_controlled":"1","volume":43,"article_type":"original","title":"Neurodevelopmental disorders: From genetics to functional pathways","ec_funded":1,"publication":"Trends in Neurosciences","ddc":["570"],"pmid":1,"_id":"7957","day":"01","publisher":"Elsevier","article_processing_charge":"No","author":[{"last_name":"Parenti","full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria"},{"id":"33D1B084-F248-11E8-B48F-1D18A9856A87","first_name":"Luis E","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda"},{"first_name":"Hanna","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","full_name":"Schön, Hanna","last_name":"Schön"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"}],"date_updated":"2026-04-02T14:36:06Z","department":[{"_id":"GaNo"}],"isi":1,"status":"public","doi":"10.1016/j.tins.2020.05.004","publication_status":"published","oa_version":"Published Version","type":"journal_article","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"08","external_id":{"isi":["000553090600008"],"pmid":["32507511"]},"acknowledgement":"We wish to thank Jasmin Morandell for generously sharing Figure 2. This work was supported by the European Research Council Starting Grant (grant 715508 ) to G.N.","page":"608-621","file":[{"file_size":1439550,"checksum":"67db0251b1d415ae59005f876fcf9e34","relation":"main_file","date_updated":"2020-11-25T09:43:40Z","file_name":"2020_TrendsNeuroscience_Parenti.pdf","content_type":"application/pdf","creator":"dernst","date_created":"2020-11-25T09:43:40Z","success":1,"access_level":"open_access","file_id":"8805"}],"publication_identifier":{"issn":["0166-2236"],"eissn":["1878-108X"]},"has_accepted_license":"1","citation":{"ama":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders: From genetics to functional pathways. <i>Trends in Neurosciences</i>. 2020;43(8):608-621. doi:<a href=\"https://doi.org/10.1016/j.tins.2020.05.004\">10.1016/j.tins.2020.05.004</a>","apa":"Parenti, I., Garcia Rabaneda, L. E., Schön, H., &#38; Novarino, G. (2020). Neurodevelopmental disorders: From genetics to functional pathways. <i>Trends in Neurosciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tins.2020.05.004\">https://doi.org/10.1016/j.tins.2020.05.004</a>","chicago":"Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” <i>Trends in Neurosciences</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.tins.2020.05.004\">https://doi.org/10.1016/j.tins.2020.05.004</a>.","short":"I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences 43 (2020) 608–621.","ista":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8), 608–621.","ieee":"I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental disorders: From genetics to functional pathways,” <i>Trends in Neurosciences</i>, vol. 43, no. 8. Elsevier, pp. 608–621, 2020.","mla":"Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” <i>Trends in Neurosciences</i>, vol. 43, no. 8, Elsevier, 2020, pp. 608–21, doi:<a href=\"https://doi.org/10.1016/j.tins.2020.05.004\">10.1016/j.tins.2020.05.004</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"}],"file_date_updated":"2020-11-25T09:43:40Z","corr_author":"1"},{"volume":11,"title":"Key role of quinone in the mechanism of respiratory complex I","article_type":"original","publication":"Nature Communications","ddc":["570"],"pmid":1,"_id":"8318","publisher":"Springer Nature","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-08-18T00:00:00Z","year":"2020","issue":"1","intvolume":"        11","date_created":"2020-08-30T22:01:10Z","abstract":[{"text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.","lang":"eng"}],"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"08","related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage","relation":"press_release"}]},"file":[{"checksum":"52b96f41d7d0db9728064c08da00d030","relation":"main_file","file_size":7527373,"date_updated":"2020-08-31T13:40:00Z","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","content_type":"application/pdf","creator":"cziletti","file_id":"8326","date_created":"2020-08-31T13:40:00Z","access_level":"open_access","success":1}],"acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"publication_identifier":{"eissn":["2041-1723"]},"citation":{"ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","ieee":"J. Gutierrez-Fernandez <i>et al.</i>, “Key role of quinone in the mechanism of respiratory complex I,” <i>Nature Communications</i>, vol. 11, no. 1. Springer Nature, 2020.","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” <i>Nature Communications</i>, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>.","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. 2020;11(1). doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., &#38; Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>."},"has_accepted_license":"1","article_number":"4135","language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2020-08-31T13:40:00Z","author":[{"last_name":"Gutierrez-Fernandez","full_name":"Gutierrez-Fernandez, Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier"},{"full_name":"Kaszuba, Karol","last_name":"Kaszuba","first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Minhas, Gurdeep S.","last_name":"Minhas","first_name":"Gurdeep S."},{"full_name":"Baradaran, Rozbeh","last_name":"Baradaran","first_name":"Rozbeh"},{"first_name":"Margherita","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","full_name":"Tambalo, Margherita"},{"first_name":"David T.","full_name":"Gallagher, David T.","last_name":"Gallagher"},{"first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"article_processing_charge":"No","date_updated":"2026-04-02T14:36:31Z","department":[{"_id":"LeSa"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1038/s41467-020-17957-0","type":"journal_article","oa_version":"Published Version"},{"scopus_import":"1","file_date_updated":"2020-07-14T12:48:04Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"article_number":"484","has_accepted_license":"1","citation":{"apa":"Armstrong, J. R., Jensen, A. S., Volosniev, A., &#38; Zinner, N. T. (2020). Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. MDPI. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>","chicago":"Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T. Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>.","ama":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. 2020;8(4). doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>","ieee":"J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in separated tubes of tilted dipoles,” <i>Mathematics</i>, vol. 8, no. 4. MDPI, 2020.","short":"J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).","ista":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484.","mla":"Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>, vol. 8, no. 4, 484, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>."},"language":[{"iso":"eng"}],"external_id":{"isi":["000531824100024"]},"file":[{"checksum":"a05a7df724522203d079673a0d4de4bc","relation":"main_file","file_size":990540,"date_updated":"2020-07-14T12:48:04Z","file_name":"2020_Mathematics_Armstrong.pdf","content_type":"application/pdf","creator":"dernst","file_id":"7887","date_created":"2020-05-25T14:42:22Z","access_level":"open_access"}],"publication_identifier":{"eissn":["2227-7390"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"04","doi":"10.3390/math8040484","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","date_updated":"2026-04-02T14:33:47Z","department":[{"_id":"MiLe"}],"article_processing_charge":"No","author":[{"full_name":"Armstrong, Jeremy R.","last_name":"Armstrong","first_name":"Jeremy R."},{"first_name":"Aksel S.","last_name":"Jensen","full_name":"Jensen, Aksel S."},{"full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zinner","full_name":"Zinner, Nikolaj T.","first_name":"Nikolaj T."}],"_id":"7882","day":"01","publisher":"MDPI","ddc":["510"],"publication":"Mathematics","volume":8,"title":"Clusters in separated tubes of tilted dipoles","article_type":"original","ec_funded":1,"intvolume":"         8","date_created":"2020-05-24T22:01:00Z","abstract":[{"lang":"eng","text":"A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes."}],"quality_controlled":"1","date_published":"2020-04-01T00:00:00Z","issue":"4","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1},{"quality_controlled":"1","date_created":"2020-06-29T07:59:35Z","abstract":[{"text":"When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves.","lang":"eng"}],"intvolume":"         3","year":"2020","date_published":"2020-06-19T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"day":"19","publisher":"Springer Nature","_id":"8036","ddc":["530"],"publication":"Communications Physics","title":"Magnetically powered metachronal waves induce locomotion in self-assemblies","article_type":"original","ec_funded":1,"volume":3,"oa_version":"Published Version","type":"journal_article","doi":"10.1038/s42005-020-0380-9","publication_status":"published","status":"public","isi":1,"department":[{"_id":"ScWa"}],"date_updated":"2026-04-02T14:34:21Z","article_processing_charge":"No","author":[{"full_name":"Collard, Ylona","last_name":"Collard","first_name":"Ylona"},{"full_name":"Grosjean, Galien M","last_name":"Grosjean","first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X"},{"first_name":"Nicolas","full_name":"Vandewalle, Nicolas","last_name":"Vandewalle"}],"file_date_updated":"2020-07-14T12:48:08Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","article_number":"112","citation":{"ama":"Collard Y, Grosjean GM, Vandewalle N. Magnetically powered metachronal waves induce locomotion in self-assemblies. <i>Communications Physics</i>. 2020;3. doi:<a href=\"https://doi.org/10.1038/s42005-020-0380-9\">10.1038/s42005-020-0380-9</a>","apa":"Collard, Y., Grosjean, G. M., &#38; Vandewalle, N. (2020). Magnetically powered metachronal waves induce locomotion in self-assemblies. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-020-0380-9\">https://doi.org/10.1038/s42005-020-0380-9</a>","chicago":"Collard, Ylona, Galien M Grosjean, and Nicolas Vandewalle. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” <i>Communications Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s42005-020-0380-9\">https://doi.org/10.1038/s42005-020-0380-9</a>.","ieee":"Y. Collard, G. M. Grosjean, and N. Vandewalle, “Magnetically powered metachronal waves induce locomotion in self-assemblies,” <i>Communications Physics</i>, vol. 3. Springer Nature, 2020.","ista":"Collard Y, Grosjean GM, Vandewalle N. 2020. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 3, 112.","short":"Y. Collard, G.M. Grosjean, N. Vandewalle, Communications Physics 3 (2020).","mla":"Collard, Ylona, et al. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” <i>Communications Physics</i>, vol. 3, 112, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s42005-020-0380-9\">10.1038/s42005-020-0380-9</a>."},"publication_identifier":{"eissn":["2399-3650"]},"external_id":{"isi":["000543328000002"]},"file":[{"creator":"cziletti","content_type":"application/pdf","access_level":"open_access","date_created":"2020-06-29T13:21:24Z","file_id":"8045","file_size":1907821,"relation":"main_file","checksum":"ed984f7a393f19140b5279a54a3336ad","date_updated":"2020-07-14T12:48:08Z","file_name":"2020_CommunicationsPhysics_Collard.pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"06"},{"volume":11,"article_type":"original","title":"Topological data analysis in information space","publication":"Journal of Computational Geometry","ddc":["510","000"],"_id":"9630","publisher":"Carleton University","day":"14","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"oa":1,"date_published":"2020-12-14T00:00:00Z","year":"2020","issue":"2","abstract":[{"text":"Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms.  Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.","lang":"eng"}],"date_created":"2021-07-04T22:01:26Z","intvolume":"        11","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"12","page":"162-182","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","file":[{"relation":"main_file","checksum":"f02d0b2b3838e7891a6c417fc34ffdcd","file_size":1449234,"date_updated":"2021-08-11T11:55:11Z","file_name":"2020_JournalOfComputationalGeometry_Edelsbrunner.pdf","content_type":"application/pdf","creator":"asandaue","file_id":"9882","access_level":"open_access","success":1,"date_created":"2021-08-11T11:55:11Z"}],"publication_identifier":{"eissn":["1920-180X"]},"citation":{"chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data Analysis in Information Space.” <i>Journal of Computational Geometry</i>. Carleton University, 2020. <a href=\"https://doi.org/10.20382/jocg.v11i2a7\">https://doi.org/10.20382/jocg.v11i2a7</a>.","apa":"Edelsbrunner, H., Virk, Z., &#38; Wagner, H. (2020). Topological data analysis in information space. <i>Journal of Computational Geometry</i>. Carleton University. <a href=\"https://doi.org/10.20382/jocg.v11i2a7\">https://doi.org/10.20382/jocg.v11i2a7</a>","ama":"Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information space. <i>Journal of Computational Geometry</i>. 2020;11(2):162-182. doi:<a href=\"https://doi.org/10.20382/jocg.v11i2a7\">10.20382/jocg.v11i2a7</a>","mla":"Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.” <i>Journal of Computational Geometry</i>, vol. 11, no. 2, Carleton University, 2020, pp. 162–82, doi:<a href=\"https://doi.org/10.20382/jocg.v11i2a7\">10.20382/jocg.v11i2a7</a>.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, Journal of Computational Geometry 11 (2020) 162–182.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2020. Topological data analysis in information space. Journal of Computational Geometry. 11(2), 162–182.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information space,” <i>Journal of Computational Geometry</i>, vol. 11, no. 2. Carleton University, pp. 162–182, 2020."},"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","license":"https://creativecommons.org/licenses/by/3.0/","corr_author":"1","file_date_updated":"2021-08-11T11:55:11Z","project":[{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Persistent Homology, Algorithms and Stochastic Geometry","grant_number":"I4887"}],"author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Virk, Ziga","last_name":"Virk","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","first_name":"Ziga"},{"orcid":"0009-0009-9111-8429","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","full_name":"Wagner, Hubert","last_name":"Wagner"}],"article_processing_charge":"Yes","date_updated":"2026-04-02T14:35:31Z","department":[{"_id":"HeEd"}],"status":"public","publication_status":"published","doi":"10.20382/jocg.v11i2a7","type":"journal_article","oa_version":"Published Version"},{"month":"11","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1937-4151"],"issn":["0278-0070"]},"external_id":{"isi":["000587712700069"]},"page":"3981-3992","acknowledgement":"This work was supported by the Austrian Science Foundation (FWF) under the NFN RiSE/SHiNE under Grant S11405 and Grant S11407. This article was presented in the International Conference on Embedded Software 2020 and appears as part of the ESWEEK-TCAD special issue. ","language":[{"iso":"eng"}],"citation":{"ama":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. Precedence-aware automated competitive analysis of real-time scheduling. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. 2020;39(11):3981-3992. doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">10.1109/TCAD.2020.3012803</a>","chicago":"Pavlogiannis, Andreas, Nico Schaumberger, Ulrich Schmid, and Krishnendu Chatterjee. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">https://doi.org/10.1109/TCAD.2020.3012803</a>.","apa":"Pavlogiannis, A., Schaumberger, N., Schmid, U., &#38; Chatterjee, K. (2020). Precedence-aware automated competitive analysis of real-time scheduling. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE. <a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">https://doi.org/10.1109/TCAD.2020.3012803</a>","mla":"Pavlogiannis, Andreas, et al. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11, IEEE, 2020, pp. 3981–92, doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">10.1109/TCAD.2020.3012803</a>.","ista":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. 2020. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 3981–3992.","short":"A. Pavlogiannis, N. Schaumberger, U. Schmid, K. Chatterjee, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 3981–3992.","ieee":"A. Pavlogiannis, N. Schaumberger, U. Schmid, and K. Chatterjee, “Precedence-aware automated competitive analysis of real-time scheduling,” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11. IEEE, pp. 3981–3992, 2020."},"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"scopus_import":"1","article_processing_charge":"No","author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"first_name":"Nico","last_name":"Schaumberger","full_name":"Schaumberger, Nico"},{"full_name":"Schmid, Ulrich","last_name":"Schmid","first_name":"Ulrich"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"department":[{"_id":"KrCh"}],"date_updated":"2026-04-02T14:37:50Z","status":"public","isi":1,"oa_version":"None","type":"journal_article","doi":"10.1109/TCAD.2020.3012803","publication_status":"published","article_type":"original","title":"Precedence-aware automated competitive analysis of real-time scheduling","volume":39,"publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","day":"01","publisher":"IEEE","_id":"8788","issue":"11","year":"2020","date_published":"2020-11-01T00:00:00Z","quality_controlled":"1","intvolume":"        39","abstract":[{"text":"We consider a real-time setting where an environment releases sequences of firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute on a single processor so as to maximize cumulated utility. The competitive ratio is a well-known performance measure for the scheduler: it gives the worst-case ratio, among all possible choices for the environment, of the cumulated utility of the online scheduler versus an offline scheduler that knows these choices in advance. Traditionally, competitive analysis is performed by hand, while automated techniques are rare and only handle static environments with independent tasks. We present a quantitative-verification framework for precedence-aware competitive analysis, where task releases may depend on preceding scheduling choices, i.e., the environment can respond to scheduling decisions dynamically . We consider two general classes of precedences: 1) follower precedences force the release of a dependent task upon the completion of a set of precursor tasks, while and 2) pairing precedences modify the characteristics of a dependent task provided the completion of a set of precursor tasks. Precedences make competitive analysis challenging, as the online and offline schedulers operate on diverging sequences. We make a formal presentation of our framework, and use a GPU-based implementation to analyze ten well-known schedulers on precedence-based application examples taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching; 3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental results show that precedences and task parameters can vary drastically the best scheduler. Our framework thus supports application designers in choosing the best scheduler among a given set automatically.","lang":"eng"}],"date_created":"2020-11-22T23:01:24Z"},{"author":[{"first_name":"Ioanna","full_name":"Antoniadi, Ioanna","last_name":"Antoniadi"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Gelová","full_name":"Gelová, Zuzana","first_name":"Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"last_name":"Plíhal","full_name":"Plíhal, Ondřej","first_name":"Ondřej"},{"last_name":"Simerský","full_name":"Simerský, Radim","first_name":"Radim"},{"first_name":"Václav","last_name":"Mik","full_name":"Mik, Václav"},{"first_name":"Thomas","full_name":"Vain, Thomas","last_name":"Vain"},{"last_name":"Mateo-Bonmatí","full_name":"Mateo-Bonmatí, Eduardo","first_name":"Eduardo"},{"first_name":"Michal","full_name":"Karady, Michal","last_name":"Karady"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"first_name":"Lenka","full_name":"Plačková, Lenka","last_name":"Plačková"},{"full_name":"Opassathian, Korawit","last_name":"Opassathian","first_name":"Korawit"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"last_name":"Doležal","full_name":"Doležal, Karel","first_name":"Karel"},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"first_name":"Colin","last_name":"Turnbull","full_name":"Turnbull, Colin"}],"article_processing_charge":"No","date_updated":"2026-04-03T09:25:48Z","department":[{"_id":"JiFr"}],"isi":1,"status":"public","doi":"10.1038/s41467-020-17700-9","publication_status":"published","oa_version":"Published Version","type":"journal_article","month":"08","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"pmid":["32855409"],"isi":["000567931000001"]},"acknowledged_ssus":[{"_id":"Bio"}],"file":[{"file_size":3526415,"relation":"main_file","checksum":"5b96f39b598de7510cfefefb819b9a6d","date_updated":"2020-12-10T12:23:56Z","file_name":"2020_NatureComm_Antoniadi.pdf","creator":"dernst","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2020-12-10T12:23:56Z","file_id":"8936"}],"acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","publication_identifier":{"eissn":["2041-1723"]},"article_number":"4284","has_accepted_license":"1","citation":{"short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","ieee":"I. Antoniadi <i>et al.</i>, “Cell-surface receptors enable perception of extracellular cytokinins,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” <i>Nature Communications</i>, vol. 11, 4284, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>.","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"file_date_updated":"2020-12-10T12:23:56Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-08-27T00:00:00Z","year":"2020","intvolume":"        11","abstract":[{"text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.","lang":"eng"}],"date_created":"2020-09-06T22:01:13Z","quality_controlled":"1","volume":11,"article_type":"original","title":"Cell-surface receptors enable perception of extracellular cytokinins","ec_funded":1,"publication":"Nature Communications","ddc":["580"],"pmid":1,"_id":"8337","day":"27","publisher":"Springer Nature"},{"publication":"Scientific Reports","volume":10,"title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","article_type":"original","_id":"8643","publisher":"Springer Nature","day":"01","ddc":["570"],"pmid":1,"date_published":"2020-10-01T00:00:00Z","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"intvolume":"        10","abstract":[{"text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.","lang":"eng"}],"date_created":"2020-10-11T22:01:14Z","quality_controlled":"1","file":[{"file_name":"2020_ScientificReport_Deichler.pdf","date_updated":"2020-10-12T12:39:10Z","file_size":3906744,"checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","relation":"main_file","date_created":"2020-10-12T12:39:10Z","access_level":"open_access","success":1,"file_id":"8651","creator":"dernst","content_type":"application/pdf"}],"acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","external_id":{"pmid":["33004866"],"isi":["000577142600032"]},"publication_identifier":{"eissn":["2045-2322"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"10","scopus_import":"1","file_date_updated":"2020-10-12T12:39:10Z","citation":{"mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” <i>Scientific Reports</i>, vol. 10, 16220, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-72848-0\">10.1038/s41598-020-72848-0</a>.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","ieee":"A. Deichler <i>et al.</i>, “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” <i>Scientific Reports</i>, vol. 10. Springer Nature, 2020.","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-72848-0\">https://doi.org/10.1038/s41598-020-72848-0</a>.","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., &#38; Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-72848-0\">https://doi.org/10.1038/s41598-020-72848-0</a>","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. <i>Scientific Reports</i>. 2020;10. doi:<a href=\"https://doi.org/10.1038/s41598-020-72848-0\">10.1038/s41598-020-72848-0</a>"},"article_number":"16220","has_accepted_license":"1","language":[{"iso":"eng"}],"date_updated":"2026-04-03T09:26:41Z","department":[{"_id":"MaJö"}],"author":[{"full_name":"Deichler, Alfonso","last_name":"Deichler","first_name":"Alfonso"},{"full_name":"Carrasco, Denisse","last_name":"Carrasco","first_name":"Denisse"},{"last_name":"Lopez-Jury","full_name":"Lopez-Jury, Luciana","first_name":"Luciana"},{"first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga"},{"first_name":"Natalia","full_name":"Marquez, Natalia","last_name":"Marquez"},{"first_name":"Jorge","full_name":"Mpodozis, Jorge","last_name":"Mpodozis"},{"first_name":"Gonzalo","last_name":"Marin","full_name":"Marin, Gonzalo"}],"article_processing_charge":"No","publication_status":"published","doi":"10.1038/s41598-020-72848-0","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public"},{"isi":1,"status":"public","doi":"10.1098/rsos.200599","publication_status":"published","oa_version":"Published Version","type":"journal_article","article_processing_charge":"No","author":[{"first_name":"Ann Kristin","full_name":"Klose, Ann Kristin","last_name":"Klose"},{"first_name":"Volker","orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle","full_name":"Karle, Volker"},{"last_name":"Winkelmann","full_name":"Winkelmann, Ricarda","first_name":"Ricarda"},{"last_name":"Donges","full_name":"Donges, Jonathan F.","first_name":"Jonathan F."}],"date_updated":"2026-04-03T09:26:55Z","department":[{"_id":"MiLe"}],"article_number":"200599","has_accepted_license":"1","citation":{"mla":"Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” <i>Royal Society Open Science</i>, vol. 7, no. 6, 200599, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsos.200599\">10.1098/rsos.200599</a>.","short":"A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020).","ista":"Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 7(6), 200599.","ieee":"A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements,” <i>Royal Society Open Science</i>, vol. 7, no. 6. The Royal Society, 2020.","ama":"Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. <i>Royal Society Open Science</i>. 2020;7(6). doi:<a href=\"https://doi.org/10.1098/rsos.200599\">10.1098/rsos.200599</a>","chicago":"Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F. Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” <i>Royal Society Open Science</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsos.200599\">https://doi.org/10.1098/rsos.200599</a>.","apa":"Klose, A. K., Karle, V., Winkelmann, R., &#38; Donges, J. F. (2020). Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. <i>Royal Society Open Science</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsos.200599\">https://doi.org/10.1098/rsos.200599</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2020-11-09T09:07:11Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"06","external_id":{"arxiv":["1910.12042"],"isi":["000545625200001"],"pmid":["32742700"]},"acknowledgement":"V.K. thanks the German National Academic Foundation (Studienstiftung des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork (PB.net), the Earth League’s EarthDoc program and the European Research Council Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements. This work has been performed in the context of the copan collaboration and the FutureLab on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments by N. Wunderling, J. Heitzig and M. Wiedermann.","file":[{"file_id":"8748","date_created":"2020-11-09T09:07:11Z","success":1,"access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2020-11-09T09:07:11Z","file_name":"2020_RoyalSocOpenScience_Klose.pdf","checksum":"5505c445de373bfd836eb4d3b48b1f37","relation":"main_file","file_size":1611485}],"publication_identifier":{"eissn":["2054-5703"]},"abstract":[{"text":"In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions\r\non the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of\r\nthese qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements.","lang":"eng"}],"date_created":"2020-11-08T23:01:25Z","intvolume":"         7","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-06-01T00:00:00Z","issue":"6","year":"2020","ddc":["530","550"],"pmid":1,"_id":"8741","day":"01","arxiv":1,"publisher":"The Royal Society","volume":7,"article_type":"original","title":"Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements","publication":"Royal Society Open Science"},{"publication":"eLife","volume":9,"title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","article_type":"original","_id":"7466","publisher":"eLife Sciences Publications","day":"20","ddc":["570"],"date_published":"2020-01-20T00:00:00Z","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"abstract":[{"text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis.","lang":"eng"}],"date_created":"2020-02-09T23:00:51Z","intvolume":"         9","quality_controlled":"1","file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2020-02-10T08:53:16Z","access_level":"open_access","file_id":"7470","file_size":4959933,"checksum":"3a072be843f416c7a7d532a51dc0addb","relation":"main_file","file_name":"2020_eLife_Kierdorf.pdf","date_updated":"2020-07-14T12:47:59Z"}],"external_id":{"isi":["000512304800001"]},"publication_identifier":{"eissn":["2050-084X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","scopus_import":"1","project":[{"name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"}],"file_date_updated":"2020-07-14T12:47:59Z","citation":{"chicago":"Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>.","apa":"Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>","ama":"Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>","mla":"Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>, vol. 9, e51595, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>.","short":"K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).","ista":"Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.","ieee":"K. Kierdorf <i>et al.</i>, “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"article_number":"e51595","has_accepted_license":"1","language":[{"iso":"eng"}],"date_updated":"2026-04-03T09:24:34Z","department":[{"_id":"DaSi"}],"article_processing_charge":"No","author":[{"full_name":"Kierdorf, Katrin","last_name":"Kierdorf","first_name":"Katrin"},{"first_name":"Fabian","last_name":"Hersperger","full_name":"Hersperger, Fabian"},{"first_name":"Jessica","full_name":"Sharrock, Jessica","last_name":"Sharrock"},{"full_name":"Vincent, Crystal M.","last_name":"Vincent","first_name":"Crystal M."},{"first_name":"Pinar","last_name":"Ustaoglu","full_name":"Ustaoglu, Pinar"},{"first_name":"Jiawen","last_name":"Dou","full_name":"Dou, Jiawen"},{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György"},{"first_name":"Olaf","last_name":"Groß","full_name":"Groß, Olaf"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"full_name":"Dionne, Marc S.","last_name":"Dionne","first_name":"Marc S."}],"publication_status":"published","doi":"10.7554/eLife.51595","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public"},{"publication":"Scientific Reports","volume":10,"article_type":"original","title":"A method for identification of the methylation level of CpG islands from NGS data","_id":"7931","day":"25","publisher":"Springer Nature","ddc":["570"],"pmid":1,"date_published":"2020-05-25T00:00:00Z","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"intvolume":"        10","date_created":"2020-06-07T22:00:51Z","abstract":[{"lang":"eng","text":"In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data."}],"quality_controlled":"1","external_id":{"pmid":["32451390"],"isi":["000560774200007"]},"file":[{"date_updated":"2020-07-14T12:48:05Z","file_name":"2020_ScientificReports_Uroshlev.pdf","file_size":1001724,"relation":"main_file","checksum":"099e51611a5b7ca04244d03b2faddf33","access_level":"open_access","date_created":"2020-06-08T06:27:32Z","file_id":"7947","creator":"dernst","content_type":"application/pdf"}],"publication_identifier":{"eissn":["2045-2322"]},"month":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","file_date_updated":"2020-07-14T12:48:05Z","article_number":"8635","has_accepted_license":"1","citation":{"ieee":"L. A. Uroshlev <i>et al.</i>, “A method for identification of the methylation level of CpG islands from NGS data,” <i>Scientific Reports</i>, vol. 10. Springer Nature, 2020.","short":"L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635.","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>, vol. 10, 8635, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>.","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. 2020;10. doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>","apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>","chicago":"Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>."},"language":[{"iso":"eng"}],"date_updated":"2026-04-03T09:26:06Z","department":[{"_id":"FyKo"}],"author":[{"first_name":"Leonid A.","last_name":"Uroshlev","full_name":"Uroshlev, Leonid A."},{"full_name":"Abdullaev, Eldar T.","last_name":"Abdullaev","first_name":"Eldar T."},{"full_name":"Umarova, Iren R.","last_name":"Umarova","first_name":"Iren R."},{"first_name":"Irina A.","last_name":"Il’Icheva","full_name":"Il’Icheva, Irina A."},{"first_name":"Larisa A.","last_name":"Panchenko","full_name":"Panchenko, Larisa A."},{"last_name":"Polozov","full_name":"Polozov, Robert V.","first_name":"Robert V."},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"first_name":"Yury D.","last_name":"Nechipurenko","full_name":"Nechipurenko, Yury D."},{"first_name":"Sergei L.","last_name":"Grokhovsky","full_name":"Grokhovsky, Sergei L."}],"article_processing_charge":"No","doi":"10.1038/s41598-020-65406-1","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public"},{"month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1022-2588"]},"page":"278-284","file":[{"creator":"kschuh","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2020-10-27T16:27:25Z","file_id":"8714","file_size":960317,"relation":"main_file","checksum":"37443c34d91d5bdbeb38c78b14792537","date_updated":"2020-10-27T16:27:25Z","file_name":"2020_VOEB_Danowski.pdf"}],"language":[{"iso":"ger"}],"has_accepted_license":"1","citation":{"ama":"Danowski P, Ferus A, Hikl A-L, et al. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2020;73(2):278-284. doi:<a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">10.31263/voebm.v73i2.3941</a>","apa":"Danowski, P., Ferus, A., Hikl, A.-L., McNeill, G., Miniberger, C., Reding, S., … Zojer, M. (2020). „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. <a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">https://doi.org/10.31263/voebm.v73i2.3941</a>","chicago":"Danowski, Patrick, Andreas Ferus, Anna-Laetitia Hikl, Gerda McNeill, Clemens Miniberger, Steve Reding, Tobias Zarka, and Michael Zojer. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2020. <a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">https://doi.org/10.31263/voebm.v73i2.3941</a>.","short":"P. Danowski, A. Ferus, A.-L. Hikl, G. McNeill, C. Miniberger, S. Reding, T. Zarka, M. Zojer, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 278–284.","ieee":"P. Danowski <i>et al.</i>, “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 73, no. 2. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 278–284, 2020.","ista":"Danowski P, Ferus A, Hikl A-L, McNeill G, Miniberger C, Reding S, Zarka T, Zojer M. 2020. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(2), 278–284.","mla":"Danowski, Patrick, et al. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 73, no. 2, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 278–84, doi:<a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">10.31263/voebm.v73i2.3941</a>."},"file_date_updated":"2020-10-27T16:27:25Z","corr_author":"1","scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Danowski","full_name":"Danowski, Patrick","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409"},{"full_name":"Ferus, Andreas","last_name":"Ferus","first_name":"Andreas"},{"first_name":"Anna-Laetitia","full_name":"Hikl, Anna-Laetitia","last_name":"Hikl"},{"full_name":"McNeill, Gerda","last_name":"McNeill","first_name":"Gerda"},{"first_name":"Clemens","last_name":"Miniberger","full_name":"Miniberger, Clemens"},{"first_name":"Steve","full_name":"Reding, Steve","last_name":"Reding"},{"first_name":"Tobias","full_name":"Zarka, Tobias","last_name":"Zarka"},{"first_name":"Michael","last_name":"Zojer","full_name":"Zojer, Michael"}],"department":[{"_id":"E-Lib"}],"date_updated":"2026-04-03T09:25:27Z","status":"public","oa_version":"Published Version","type":"journal_article","doi":"10.31263/voebm.v73i2.3941","publication_status":"published","title":"„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B","article_type":"original","volume":73,"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","ddc":["020"],"day":"14","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","_id":"8706","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"2","year":"2020","date_published":"2020-07-14T00:00:00Z","quality_controlled":"1","date_created":"2020-10-25T23:01:19Z","intvolume":"        73","abstract":[{"lang":"eng","text":"As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level."},{"lang":"ger","text":"Als Teil des Hochschulraumstrukturmittel-Projekts Austrian Transition to Open Access (AT2OA) befasst sich das Teilprojekt TP1-B mit der Konzeption einer Monitoring-Lösung für den Open Access-Publikationsoutput in Österreich. Der nun vorliegende Bericht zu einem potentiellen Open Access-Monitoring in Österreich ist eines der Ergebnisse dieser Bemühungen und kann als Grundlage einer Diskussion auf internationaler Ebene dienen."}]},{"pmid":1,"_id":"8132","publisher":"AAAS","day":"10","OA_place":"repository","volume":5,"article_type":"original","title":"The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity","publication":"Science Immunology","date_created":"2020-07-19T22:00:58Z","abstract":[{"lang":"eng","text":"The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity."}],"intvolume":"         5","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116756","open_access":"1"}],"quality_controlled":"1","oa":1,"date_published":"2020-07-10T00:00:00Z","year":"2020","issue":"49","citation":{"ama":"Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. <i>Science Immunology</i>. 2020;5(49). doi:<a href=\"https://doi.org/10.1126/sciimmunol.abc3979\">10.1126/sciimmunol.abc3979</a>","apa":"Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., … Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. <i>Science Immunology</i>. AAAS. <a href=\"https://doi.org/10.1126/sciimmunol.abc3979\">https://doi.org/10.1126/sciimmunol.abc3979</a>","chicago":"Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” <i>Science Immunology</i>. AAAS, 2020. <a href=\"https://doi.org/10.1126/sciimmunol.abc3979\">https://doi.org/10.1126/sciimmunol.abc3979</a>.","ista":"Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A, Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 5(49), eabc3979.","ieee":"E. Salzer <i>et al.</i>, “The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity,” <i>Science Immunology</i>, vol. 5, no. 49. AAAS, 2020.","short":"E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel, R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S. Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B. Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei, K. Boztug, Science Immunology 5 (2020).","mla":"Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” <i>Science Immunology</i>, vol. 5, no. 49, eabc3979, AAAS, 2020, doi:<a href=\"https://doi.org/10.1126/sciimmunol.abc3979\">10.1126/sciimmunol.abc3979</a>."},"article_number":"eabc3979","language":[{"iso":"eng"}],"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"07","OA_type":"green","external_id":{"isi":["000546994600004"],"pmid":["32646852"]},"publication_identifier":{"eissn":["2470-9468"]},"isi":1,"status":"public","publication_status":"published","doi":"10.1126/sciimmunol.abc3979","type":"journal_article","oa_version":"Submitted Version","article_processing_charge":"No","author":[{"first_name":"Elisabeth","full_name":"Salzer, Elisabeth","last_name":"Salzer"},{"last_name":"Zoghi","full_name":"Zoghi, Samaneh","first_name":"Samaneh"},{"last_name":"Kiss","full_name":"Kiss, Máté G.","first_name":"Máté G."},{"last_name":"Kage","full_name":"Kage, Frieda","first_name":"Frieda"},{"first_name":"Christina","full_name":"Rashkova, Christina","last_name":"Rashkova"},{"first_name":"Stephanie","last_name":"Stahnke","full_name":"Stahnke, Stephanie"},{"first_name":"Matthias","full_name":"Haimel, Matthias","last_name":"Haimel"},{"full_name":"Platzer, René","last_name":"Platzer","first_name":"René"},{"last_name":"Caldera","full_name":"Caldera, Michael","first_name":"Michael"},{"first_name":"Rico Chandra","last_name":"Ardy","full_name":"Ardy, Rico Chandra"},{"first_name":"Birgit","full_name":"Hoeger, Birgit","last_name":"Hoeger"},{"first_name":"Jana","full_name":"Block, Jana","last_name":"Block"},{"first_name":"David","last_name":"Medgyesi","full_name":"Medgyesi, David"},{"full_name":"Sin, Celine","last_name":"Sin","first_name":"Celine"},{"first_name":"Sepideh","last_name":"Shahkarami","full_name":"Shahkarami, Sepideh"},{"last_name":"Kain","full_name":"Kain, Renate","first_name":"Renate"},{"full_name":"Ziaee, Vahid","last_name":"Ziaee","first_name":"Vahid"},{"last_name":"Hammerl","full_name":"Hammerl, Peter","first_name":"Peter"},{"first_name":"Christoph","full_name":"Bock, Christoph","last_name":"Bock"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"full_name":"Dupré, Loïc","last_name":"Dupré","first_name":"Loïc"},{"first_name":"Johannes B.","full_name":"Huppa, Johannes B.","last_name":"Huppa"},{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"full_name":"Lomakin, Alexis","last_name":"Lomakin","first_name":"Alexis"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"full_name":"Binder, Christoph J.","last_name":"Binder","first_name":"Christoph J."},{"last_name":"Stradal","full_name":"Stradal, Theresia E.B.","first_name":"Theresia E.B."},{"last_name":"Rezaei","full_name":"Rezaei, Nima","first_name":"Nima"},{"first_name":"Kaan","last_name":"Boztug","full_name":"Boztug, Kaan"}],"date_updated":"2026-04-03T09:25:04Z","department":[{"_id":"MiSi"}]},{"has_accepted_license":"1","article_number":"108463","citation":{"mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>, vol. 33, no. 9, 108463, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","ieee":"S. Tan <i>et al.</i>, “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” <i>Cell Reports</i>, vol. 33, no. 9. Elsevier, 2020.","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. 2020;33(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>.","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2020-12-14T07:33:39Z","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"}],"corr_author":"1","month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"external_id":{"isi":["000595658100018"],"pmid":["33264621"]},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/plants-on-aspirin/","description":"News on IST Homepage","relation":"press_release"}]},"acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","file":[{"checksum":"ed18cba0fb48ed2e789381a54cc21904","relation":"main_file","file_size":8056434,"file_name":"2020_CellReports_Tan.pdf","date_updated":"2020-12-14T07:33:39Z","creator":"dernst","content_type":"application/pdf","file_id":"8948","date_created":"2020-12-14T07:33:39Z","access_level":"open_access","success":1}],"publication_identifier":{"eissn":["2211-1247"]},"isi":1,"status":"public","doi":"10.1016/j.celrep.2020.108463","publication_status":"published","oa_version":"Published Version","type":"journal_article","article_processing_charge":"Yes","author":[{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","full_name":"Tan, Shutang","last_name":"Tan"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"first_name":"Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","last_name":"Glanc"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi"},{"first_name":"Petr","last_name":"Klíma","full_name":"Klíma, Petr"},{"full_name":"Liu, Jie","last_name":"Liu","first_name":"Jie"},{"first_name":"Aurélien","full_name":"Bailly, Aurélien","last_name":"Bailly"},{"first_name":"Noel","last_name":"Ferro","full_name":"Ferro, Noel"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"date_updated":"2026-04-03T09:30:47Z","department":[{"_id":"JiFr"}],"ddc":["580"],"pmid":1,"_id":"8943","day":"01","publisher":"Elsevier","volume":33,"article_type":"original","title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","ec_funded":1,"publication":"Cell Reports","intvolume":"        33","abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"date_created":"2020-12-13T23:01:21Z","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-12-01T00:00:00Z","issue":"9","year":"2020"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-07-21T00:00:00Z","year":"2020","issue":"29","intvolume":"       117","date_created":"2020-08-09T22:00:52Z","abstract":[{"lang":"eng","text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings."}],"quality_controlled":"1","volume":117,"ec_funded":1,"title":"Stem cell lineage survival as a noisy competition for niche access","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","ddc":["570"],"pmid":1,"_id":"8220","publisher":"National Academy of Sciences","day":"21","author":[{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."},{"full_name":"Kishi, Kasumi","last_name":"Kishi","orcid":"0000-0001-6060-4795","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi"},{"last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I.J.","first_name":"Saskia I.J."},{"last_name":"Simons","full_name":"Simons, Benjamin D.","first_name":"Benjamin D."},{"full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen","first_name":"Jacco"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"article_processing_charge":"No","date_updated":"2026-04-03T09:29:04Z","department":[{"_id":"EdHa"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1073/pnas.1921205117","type":"journal_article","oa_version":"Published Version","month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","page":"16969-16975","file":[{"file_id":"8223","date_created":"2020-08-10T06:50:28Z","access_level":"open_access","success":1,"content_type":"application/pdf","creator":"dernst","file_name":"2020_PNAS_Corominas.pdf","date_updated":"2020-08-10T06:50:28Z","relation":"main_file","file_size":1111604}],"external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"publication_identifier":{"eissn":["1091-6490"]},"citation":{"ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(29):16969-16975. doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., &#38; Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>.","ieee":"B. Corominas-Murtra <i>et al.</i>, “Stem cell lineage survival as a noisy competition for niche access,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>."},"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2020-08-10T06:50:28Z","project":[{"grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"}]},{"file_date_updated":"2020-07-14T12:48:03Z","corr_author":"1","scopus_import":"1","language":[{"iso":"eng"}],"article_number":"2099","has_accepted_license":"1","citation":{"ama":"Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-15872-y\">10.1038/s41467-020-15872-y</a>","chicago":"Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-15872-y\">https://doi.org/10.1038/s41467-020-15872-y</a>.","apa":"Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., … de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-15872-y\">https://doi.org/10.1038/s41467-020-15872-y</a>","mla":"Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” <i>Nature Communications</i>, vol. 11, 2099, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-15872-y\">10.1038/s41467-020-15872-y</a>.","ieee":"S. M. Flynn <i>et al.</i>, “MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew, F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).","ista":"Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 11, 2099."},"publication_identifier":{"eissn":["2041-1723"]},"external_id":{"pmid":["32350248"],"isi":["000531855500029"]},"file":[{"relation":"main_file","checksum":"dce367abf2c1a1d15f58fe6f7de82893","file_size":4609120,"date_updated":"2020-07-14T12:48:03Z","file_name":"2020_NatureComm_Flynn.pdf","creator":"dernst","content_type":"application/pdf","file_id":"7817","access_level":"open_access","date_created":"2020-05-11T10:36:33Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"04","oa_version":"Published Version","type":"journal_article","doi":"10.1038/s41467-020-15872-y","publication_status":"published","status":"public","isi":1,"department":[{"_id":"MaDe"}],"date_updated":"2026-04-03T09:27:08Z","article_processing_charge":"No","author":[{"first_name":"Sean M.","last_name":"Flynn","full_name":"Flynn, Sean M."},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","first_name":"Murat","last_name":"Artan","full_name":"Artan, Murat"},{"last_name":"Barratt","full_name":"Barratt, Stephen","first_name":"Stephen"},{"last_name":"Crisp","full_name":"Crisp, Alastair","first_name":"Alastair"},{"full_name":"Nelson, Geoffrey M.","last_name":"Nelson","first_name":"Geoffrey M."},{"full_name":"Peak-Chew, Sew Yeu","last_name":"Peak-Chew","first_name":"Sew Yeu"},{"last_name":"Begum","full_name":"Begum, Farida","first_name":"Farida"},{"full_name":"Skehel, Mark","last_name":"Skehel","first_name":"Mark"},{"full_name":"De Bono, Mario","last_name":"De Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"day":"29","publisher":"Springer Nature","_id":"7804","pmid":1,"ddc":["570"],"publication":"Nature Communications","title":"MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity","article_type":"original","volume":11,"quality_controlled":"1","abstract":[{"text":"Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior.","lang":"eng"}],"intvolume":"        11","date_created":"2020-05-10T22:00:47Z","year":"2020","date_published":"2020-04-29T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"11","publication_identifier":{"eissn":["2155-5435"]},"acknowledgement":"The authors also acknowledge financial support from the University Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","page":"13468-13478","external_id":{"isi":["000592978900031"]},"OA_type":"green","language":[{"iso":"eng"}],"citation":{"apa":"Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez, M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. <i>ACS Catalysis</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acscatal.0c03210\">https://doi.org/10.1021/acscatal.0c03210</a>","chicago":"Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” <i>ACS Catalysis</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acscatal.0c03210\">https://doi.org/10.1021/acscatal.0c03210</a>.","ama":"Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. <i>ACS Catalysis</i>. 2020;10(22):13468-13478. doi:<a href=\"https://doi.org/10.1021/acscatal.0c03210\">10.1021/acscatal.0c03210</a>","ista":"Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S, Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478.","short":"E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez, S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478.","ieee":"E. Irtem <i>et al.</i>, “Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction,” <i>ACS Catalysis</i>, vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020.","mla":"Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” <i>ACS Catalysis</i>, vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:<a href=\"https://doi.org/10.1021/acscatal.0c03210\">10.1021/acscatal.0c03210</a>."},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"scopus_import":"1","article_processing_charge":"No","author":[{"first_name":"Erdem","full_name":"Irtem, Erdem","last_name":"Irtem"},{"full_name":"Arenas Esteban, Daniel","last_name":"Arenas Esteban","first_name":"Daniel"},{"first_name":"Miguel","full_name":"Duarte, Miguel","last_name":"Duarte"},{"full_name":"Choukroun, Daniel","last_name":"Choukroun","first_name":"Daniel"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee","full_name":"Lee, Seungho"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"first_name":"Sara","full_name":"Bals, Sara","last_name":"Bals"},{"first_name":"Tom","last_name":"Breugelmans","full_name":"Breugelmans, Tom"}],"department":[{"_id":"MaIb"}],"date_updated":"2026-04-03T09:31:02Z","status":"public","isi":1,"type":"journal_article","oa_version":"Submitted Version","publication_status":"published","doi":"10.1021/acscatal.0c03210","ec_funded":1,"title":"Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction","article_type":"original","OA_place":"repository","volume":10,"publication":"ACS Catalysis","publisher":"American Chemical Society","day":"20","_id":"8926","oa":1,"year":"2020","issue":"22","date_published":"2020-11-20T00:00:00Z","quality_controlled":"1","date_created":"2020-12-06T23:01:15Z","abstract":[{"lang":"eng","text":"Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application."}],"intvolume":"        10","main_file_link":[{"open_access":"1","url":"https://repository.uantwerpen.be/docman/irua/190103/173803.pdf"}]},{"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41467-020-14535-2","status":"public","isi":1,"department":[{"_id":"FlSc"}],"date_updated":"2026-04-03T09:27:26Z","author":[{"first_name":"Beata","last_name":"Turoňová","full_name":"Turoňová, Beata"},{"first_name":"Wim J.H.","last_name":"Hagen","full_name":"Hagen, Wim J.H."},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","first_name":"Martin","last_name":"Obr","full_name":"Obr, Martin"},{"last_name":"Mosalaganti","full_name":"Mosalaganti, Shyamal","first_name":"Shyamal"},{"first_name":"J. Wouter","full_name":"Beugelink, J. Wouter","last_name":"Beugelink"},{"full_name":"Zimmerli, Christian E.","last_name":"Zimmerli","first_name":"Christian E."},{"full_name":"Kräusslich, Hans Georg","last_name":"Kräusslich","first_name":"Hans Georg"},{"full_name":"Beck, Martin","last_name":"Beck","first_name":"Martin"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:59Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>","apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>","chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>.","ieee":"B. Turoňová <i>et al.</i>, “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876.","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>, vol. 11, 876, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>."},"article_number":"876","has_accepted_license":"1","publication_identifier":{"eissn":["2041-1723"]},"file":[{"relation":"main_file","checksum":"2c8d10475e1b0d397500760e28bdf561","file_size":2027529,"date_updated":"2020-07-14T12:47:59Z","file_name":"2020_NatureComm_Turonova.pdf","content_type":"application/pdf","creator":"dernst","file_id":"7517","access_level":"open_access","date_created":"2020-02-24T14:00:54Z"}],"external_id":{"isi":["000514928000017"],"pmid":["32054835"]},"month":"02","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","date_created":"2020-02-23T23:00:35Z","abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"intvolume":"        11","year":"2020","date_published":"2020-02-13T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publisher":"Springer Nature","day":"13","_id":"7511","pmid":1,"ddc":["570"],"publication":"Nature Communications","title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","article_type":"original","volume":11},{"isi":1,"status":"public","doi":"10.1017/fms.2020.17","publication_status":"published","oa_version":"Published Version","type":"journal_article","author":[{"last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"last_name":"Mayer","full_name":"Mayer, Simon","first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"article_processing_charge":"No","date_updated":"2026-04-03T09:30:21Z","department":[{"_id":"RoSe"}],"has_accepted_license":"1","article_number":"e20","citation":{"ista":"Deuchert A, Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 8, e20.","short":"A. Deuchert, S. Mayer, R. Seiringer, Forum of Mathematics, Sigma 8 (2020).","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” <i>Forum of Mathematics, Sigma</i>, vol. 8. Cambridge University Press, 2020.","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>Forum of Mathematics, Sigma</i>, vol. 8, e20, Cambridge University Press, 2020, doi:<a href=\"https://doi.org/10.1017/fms.2020.17\">10.1017/fms.2020.17</a>.","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>Forum of Mathematics, Sigma</i>. 2020;8. doi:<a href=\"https://doi.org/10.1017/fms.2020.17\">10.1017/fms.2020.17</a>","apa":"Deuchert, A., Mayer, S., &#38; Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2020.17\">https://doi.org/10.1017/fms.2020.17</a>","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2020. <a href=\"https://doi.org/10.1017/fms.2020.17\">https://doi.org/10.1017/fms.2020.17</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"}],"file_date_updated":"2020-07-14T12:48:03Z","corr_author":"1","month":"03","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"arxiv":["1910.03372"],"isi":["000527342000001"]},"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7524"}]},"file":[{"file_name":"2020_ForumMath_Deuchert.pdf","date_updated":"2020-07-14T12:48:03Z","file_size":692530,"checksum":"8a64da99d107686997876d7cad8cfe1e","relation":"main_file","date_created":"2020-05-04T12:02:41Z","access_level":"open_access","file_id":"7797","content_type":"application/pdf","creator":"dernst"}],"publication_identifier":{"eissn":["2050-5094"]},"date_created":"2020-05-03T22:00:48Z","intvolume":"         8","abstract":[{"text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density 𝜌 and inverse temperature 𝛽 differs from the one of the noninteracting system by the correction term 𝜋𝜌𝜌𝛽𝛽 . Here, is the scattering length of the interaction potential, and 𝛽 is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. The result is valid in the dilute limit 𝜌 and if 𝛽𝜌 .","lang":"eng"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2020-03-14T00:00:00Z","year":"2020","ddc":["510"],"_id":"7790","day":"14","arxiv":1,"publisher":"Cambridge University Press","volume":8,"article_type":"original","title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","ec_funded":1,"publication":"Forum of Mathematics, Sigma"}]