[{"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"872db70bba9b401500abe3c6ae2f1a61","file_id":"5711","creator":"dernst","file_size":799337,"date_updated":"2020-07-14T12:48:01Z","file_name":"2018_DistributedComputing_Lenzen.pdf","date_created":"2018-12-17T14:21:22Z"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"09","date_updated":"2023-09-13T09:01:06Z","ddc":["000"],"department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","_id":"76","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","isi":1,"year":"2018","day":"12","publication":"Distributed Computing","date_published":"2018-09-12T00:00:00Z","doi":"10.1007/s00446-018-0342-6","date_created":"2018-12-11T11:44:30Z","quality_controlled":"1","publisher":"Springer","oa":1,"citation":{"mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Lenzen","full_name":"Lenzen, Christoph","first_name":"Christoph"},{"last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"}],"publist_id":"7978","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000475627800005"]},"title":"Near-optimal self-stabilising counting and firing squads","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018."},"title":"Multiple covers with balls I: Inclusion–exclusion","publist_id":"7289","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"}],"article_processing_charge":"No","external_id":{"isi":["000415778300010"]},"project":[{"name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"01","publication":"Computational Geometry: Theory and Applications","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1016/j.comgeo.2017.06.014","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:59Z","page":"119 - 133","publisher":"Elsevier","quality_controlled":"1","oa":1,"ddc":["000"],"date_updated":"2023-09-13T08:59:00Z","file_date_updated":"2020-07-14T12:46:38Z","department":[{"_id":"HeEd"}],"_id":"530","status":"public","type":"journal_article","file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:38Z","file_size":708357,"date_created":"2019-02-12T06:47:52Z","file_name":"2018_Edelsbrunner.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_id":"5953"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":68,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software."}],"month":"03","intvolume":" 68","scopus_import":"1"},{"article_number":" 043812 ","citation":{"mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812.","ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.","ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000429454000015"],"arxiv":["1712.10127"]},"publist_id":"7572","author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","full_name":"Makarov, Alexander","last_name":"Makarov"},{"last_name":"Yudson","full_name":"Yudson, Vladimir","first_name":"Vladimir"}],"title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2018","isi":1,"publication":" Physical Review A - Atomic, Molecular, and Optical Physics","day":"09","date_created":"2018-12-11T11:45:44Z","doi":"10.1103/PhysRevA.97.043812","date_published":"2018-04-09T00:00:00Z","_id":"307","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-13T09:00:41Z","department":[{"_id":"JoFi"}],"abstract":[{"lang":"eng","text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. "}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10127"}],"scopus_import":"1","intvolume":" 97","month":"04","publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":97},{"scopus_import":"1","month":"05","intvolume":" 19","abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"oa_version":"Published Version","volume":19,"related_material":{"record":[{"status":"public","id":"9811","relation":"research_data"},{"id":"9812","status":"public","relation":"research_data"}]},"ec_funded":1,"publication_status":"published","file":[{"file_id":"5708","checksum":"f3e4922486bd9bf1483271bdbed394a7","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_GenomeBiology_Zapata.pdf","date_created":"2018-12-17T14:05:01Z","file_size":1414722,"date_updated":"2020-07-14T12:45:47Z","creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"279","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:45:47Z","date_updated":"2023-09-13T09:01:32Z","ddc":["570"],"publisher":"BioMed Central","quality_controlled":"1","oa":1,"doi":"10.1186/s13059-018-1434-0","date_published":"2018-05-31T00:00:00Z","date_created":"2018-12-11T11:45:35Z","isi":1,"has_accepted_license":"1","year":"2018","day":"31","publication":"Genome Biology","project":[{"grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution","_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"67","publist_id":"7620","author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"first_name":"Luis","full_name":"Serrano, Luis","last_name":"Serrano"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","full_name":"Schaefer, Martin","first_name":"Martin"}],"external_id":{"isi":["000433986200001"]},"article_processing_charge":"No","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_updated":"2023-09-13T09:02:48Z","ddc":["570"],"department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:44:56Z","_id":"145","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["0261-4189"]},"publication_status":"published","file":[{"date_created":"2018-12-17T14:17:29Z","file_name":"2018_EMBO_Truckenbrodt.pdf","date_updated":"2020-07-14T12:44:56Z","file_size":2846470,"creator":"dernst","checksum":"a540feb6c9af6aefc78de531461a8835","file_id":"5710","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"15","volume":37,"abstract":[{"text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 37","citation":{"ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044.","ieee":"S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7778","author":[{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt"},{"full_name":"Viplav, Abhiyan","last_name":"Viplav","first_name":"Abhiyan"},{"first_name":"Sebsatian","full_name":"Jähne, Sebsatian","last_name":"Jähne"},{"full_name":"Vogts, Angela","last_name":"Vogts","first_name":"Angela"},{"last_name":"Denker","full_name":"Denker, Annette","first_name":"Annette"},{"full_name":"Wildhagen, Hanna","last_name":"Wildhagen","first_name":"Hanna"},{"last_name":"Fornasiero","full_name":"Fornasiero, Eugenio","first_name":"Eugenio"},{"first_name":"Silvio","last_name":"Rizzoli","full_name":"Rizzoli, Silvio"}],"external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"article_processing_charge":"No","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","article_number":"e98044","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"The EMBO Journal","doi":"10.15252/embj.201798044","date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:44:52Z","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","publisher":"Wiley","quality_controlled":"1","oa":1},{"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}],"month":"05","intvolume":" 41","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7042","checksum":"6a20f843565f962cb20281cdf5e40914","creator":"dernst","file_size":1937976,"date_updated":"2020-07-14T12:46:32Z","file_name":"2018_PlantCellEnv_Fan.pdf","date_created":"2019-11-18T16:22:22Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":41,"license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"462","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"ddc":["580"],"date_updated":"2023-09-13T09:03:18Z","file_date_updated":"2020-07-14T12:46:32Z","department":[{"_id":"JiFr"}],"acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"day":"01","publication":"Plant, Cell and Environment","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1111/pce.13153","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:46:36Z","page":"850 - 864","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153.","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153."},"title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","author":[{"full_name":"Fan, Ligang","last_name":"Fan","first_name":"Ligang"},{"last_name":"Zhao","full_name":"Zhao, Lei","first_name":"Lei"},{"first_name":"Wei","last_name":"Hu","full_name":"Hu, Wei"},{"last_name":"Li","full_name":"Li, Weina","first_name":"Weina"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"first_name":"Miroslav","full_name":"Strnad, Miroslav","last_name":"Strnad"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Jinbo","full_name":"Shen, Jinbo","last_name":"Shen"},{"first_name":"Liwen","full_name":"Jiang, Liwen","last_name":"Jiang"},{"last_name":"Qiu","full_name":"Qiu, Quan","first_name":"Quan"}],"publist_id":"7359","external_id":{"isi":["000426870500012"],"pmid":["29360148"]},"article_processing_charge":"No"},{"scopus_import":"1","month":"04","intvolume":" 452","abstract":[{"lang":"eng","text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. 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(2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073.","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_updated":"2023-09-13T09:02:22Z","department":[{"_id":"KrCh"}],"_id":"5679","type":"conference","conference":{"name":"16th Asian Symposium on Programming Languages and Systems, APLAS","location":"Wellington, New Zealand","end_date":"2018-12-06","start_date":"2018-12-02"},"status":"public","publication_identifier":{"issn":["03029743"],"isbn":["9783030027674"]},"language":[{"iso":"eng"}],"volume":11275,"abstract":[{"text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs.","lang":"eng"}],"oa_version":"Preprint","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"month":"12","intvolume":" 11275","citation":{"ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Huang, Mingzhang","last_name":"Huang","first_name":"Mingzhang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"external_id":{"arxiv":["1806.06683"],"isi":["000916310900011"]},"article_processing_charge":"No","editor":[{"full_name":"Ryu, Sukyoung","last_name":"Ryu","first_name":"Sukyoung"}],"title":"New approaches for almost-sure termination of probabilistic programs","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"isi":1,"year":"2018","day":"01","page":"181-201","doi":"10.1007/978-3-030-02768-1_11","date_published":"2018-12-01T00:00:00Z","date_created":"2018-12-16T22:59:20Z","quality_controlled":"1","publisher":"Springer","oa":1},{"issue":"2","volume":48,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 48","month":"02","abstract":[{"lang":"eng","text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies."}],"oa_version":"None","department":[{"_id":"GaNo"}],"date_updated":"2023-09-13T09:01:56Z","type":"journal_article","status":"public","_id":"546","page":"131 - 138","date_created":"2018-12-11T11:47:06Z","date_published":"2018-02-01T00:00:00Z","doi":"10.1016/j.conb.2017.12.005","year":"2018","isi":1,"publication":"Current Opinion in Neurobiology","day":"01","quality_controlled":"1","publisher":"Elsevier","article_processing_charge":"No","external_id":{"isi":["000427101600018"]},"publist_id":"7268","author":[{"first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","last_name":"Sacco","full_name":"Sacco, Roberto"},{"first_name":"Emanuele","full_name":"Cacci, Emanuele","last_name":"Cacci"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"}],"title":"Neural stem cells in neuropsychiatric disorders","citation":{"apa":"Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:01:31Z","citation":{"mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 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