[{"_id":"7541","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","month":"04","publication_identifier":{"issn":["0935-9648"]},"date_updated":"2024-02-21T12:42:12Z","external_id":{"isi":["000516660900001"]},"article_type":"original","file":[{"date_updated":"2020-11-20T10:11:35Z","file_size":5242880,"file_id":"8782","creator":"dernst","success":1,"date_created":"2020-11-20T10:11:35Z","access_level":"open_access","relation":"main_file","checksum":"c622737dc295972065782558337124a2","file_name":"2020_AdvancedMaterials_Gao.pdf","content_type":"application/pdf"}],"issue":"16","language":[{"iso":"eng"}],"date_published":"2020-04-23T00:00:00Z","quality_controlled":"1","type":"journal_article","file_date_updated":"2020-11-20T10:11:35Z","author":[{"full_name":"Gao, Fei","first_name":"Fei","last_name":"Gao"},{"first_name":"Jian-Huan","last_name":"Wang","full_name":"Wang, Jian-Huan"},{"full_name":"Watzinger, Hannes","first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hu, Hao","first_name":"Hao","last_name":"Hu"},{"full_name":"Rančić, Marko J.","last_name":"Rančić","first_name":"Marko J."},{"first_name":"Jie-Yin","last_name":"Zhang","full_name":"Zhang, Jie-Yin"},{"first_name":"Ting","last_name":"Wang","full_name":"Wang, Ting"},{"full_name":"Yao, Yuan","last_name":"Yao","first_name":"Yuan"},{"last_name":"Wang","first_name":"Gui-Lei","full_name":"Wang, Gui-Lei"},{"last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lada","last_name":"Vukušić","full_name":"Vukušić, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636"},{"full_name":"Kloeffel, Christoph","last_name":"Kloeffel","first_name":"Christoph"},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"full_name":"Liu, Feng","last_name":"Liu","first_name":"Feng"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"},{"last_name":"Zhang","first_name":"Jian-Jun","full_name":"Zhang, Jian-Jun"}],"status":"public","year":"2020","title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","ddc":["530"],"publisher":"Wiley","doi":"10.1002/adma.201906523","has_accepted_license":"1","oa_version":"Published Version","abstract":[{"text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon.","lang":"eng"}],"publication_status":"published","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046"}],"article_number":"1906523","volume":32,"intvolume":"        32","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-02-28T09:47:00Z","day":"23","scopus_import":"1","isi":1,"license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7996"},{"id":"9222","relation":"research_data","status":"public"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication":"Advanced Materials","department":[{"_id":"GeKa"}],"citation":{"mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” <i>Advanced Materials</i>, vol. 32, no. 16, 1906523, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/adma.201906523\">10.1002/adma.201906523</a>.","chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” <i>Advanced Materials</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/adma.201906523\">https://doi.org/10.1002/adma.201906523</a>.","apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201906523\">https://doi.org/10.1002/adma.201906523</a>","ieee":"F. Gao <i>et al.</i>, “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” <i>Advanced Materials</i>, vol. 32, no. 16. Wiley, 2020.","short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020).","ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523.","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. <i>Advanced Materials</i>. 2020;32(16). doi:<a href=\"https://doi.org/10.1002/adma.201906523\">10.1002/adma.201906523</a>"},"ec_funded":1,"oa":1},{"publication":"Developmental Biology","citation":{"short":"J.A. Cohn, E.R. Cebul, G. Valperga, L. Brose, M. de Bono, M.G. Heiman, J.T. Pierce, Developmental Biology 461 (2020) 66–74.","ista":"Cohn JA, Cebul ER, Valperga G, Brose L, de Bono M, Heiman MG, Pierce JT. 2020. Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron. Developmental Biology. 461(1), 66–74.","ama":"Cohn JA, Cebul ER, Valperga G, et al. Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron. <i>Developmental Biology</i>. 2020;461(1):66-74. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.01.005\">10.1016/j.ydbio.2020.01.005</a>","ieee":"J. A. Cohn <i>et al.</i>, “Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron,” <i>Developmental Biology</i>, vol. 461, no. 1. Elsevier, pp. 66–74, 2020.","apa":"Cohn, J. A., Cebul, E. R., Valperga, G., Brose, L., de Bono, M., Heiman, M. G., &#38; Pierce, J. T. (2020). Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.01.005\">https://doi.org/10.1016/j.ydbio.2020.01.005</a>","mla":"Cohn, Jesse A., et al. “Long-Term Activity Drives Dendritic Branch Elaboration of a C. Elegans Sensory Neuron.” <i>Developmental Biology</i>, vol. 461, no. 1, Elsevier, 2020, pp. 66–74, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.01.005\">10.1016/j.ydbio.2020.01.005</a>.","chicago":"Cohn, Jesse A., Elizabeth R. Cebul, Giulio Valperga, Lotti Brose, Mario de Bono, Maxwell G. Heiman, and Jonathan T. Pierce. “Long-Term Activity Drives Dendritic Branch Elaboration of a C. Elegans Sensory Neuron.” <i>Developmental Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.ydbio.2020.01.005\">https://doi.org/10.1016/j.ydbio.2020.01.005</a>."},"oa":1,"day":"01","extern":"1","intvolume":"       461","volume":461,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-02-28T10:38:32Z","abstract":[{"lang":"eng","text":"Neuronal activity often leads to alterations in gene expression and cellular architecture. The nematode Caenorhabditis elegans, owing to its compact translucent nervous system, is a powerful system in which to study conserved aspects of the development and plasticity of neuronal morphology. Here we focus on one pair of sensory neurons, termed URX, which the worm uses to sense and avoid high levels of environmental oxygen. Previous studies have reported that the URX neuron pair has variable branched endings at its dendritic sensory tip. By controlling oxygen levels and analyzing mutants, we found that these microtubule-rich branched endings grow over time as a consequence of neuronal activity in adulthood. We also find that the growth of these branches correlates with an increase in cellular sensitivity to particular ranges of oxygen that is observable in the behavior of older worms. Given the strengths of C. elegans as a model organism, URX may serve as a potent system for uncovering genes and mechanisms involved in activity-dependent morphological changes in neurons and possible adaptive changes in the aging nervous system."}],"publication_status":"published","status":"public","year":"2020","title":"Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron","publisher":"Elsevier","doi":"10.1016/j.ydbio.2020.01.005","oa_version":"Preprint","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1101/685339","open_access":"1"}],"author":[{"first_name":"Jesse A.","last_name":"Cohn","full_name":"Cohn, Jesse A."},{"full_name":"Cebul, Elizabeth R.","last_name":"Cebul","first_name":"Elizabeth R."},{"full_name":"Valperga, Giulio","first_name":"Giulio","last_name":"Valperga"},{"full_name":"Brose, Lotti","first_name":"Lotti","last_name":"Brose"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"},{"full_name":"Heiman, Maxwell G.","first_name":"Maxwell G.","last_name":"Heiman"},{"full_name":"Pierce, Jonathan T.","last_name":"Pierce","first_name":"Jonathan T."}],"date_updated":"2021-01-12T08:14:06Z","article_type":"original","page":"66-74","issue":"1","language":[{"iso":"eng"}],"date_published":"2020-05-01T00:00:00Z","quality_controlled":"1","_id":"7545","article_processing_charge":"No","month":"05","publication_identifier":{"issn":["0012-1606"]}},{"isi":1,"day":"08","oa":1,"department":[{"_id":"MaDe"}],"citation":{"mla":"Beets, Isabel, et al. “Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.” <i>Neuron</i>, vol. 105, no. 1, Cell Press, 2020, p. 106–121.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">10.1016/j.neuron.2019.10.001</a>.","chicago":"Beets, Isabel, Gaotian Zhang, Lorenz A. Fenk, Changchun Chen, Geoffrey M. Nelson, Marie-Anne Félix, and Mario de Bono. “Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression.” <i>Neuron</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">https://doi.org/10.1016/j.neuron.2019.10.001</a>.","apa":"Beets, I., Zhang, G., Fenk, L. A., Chen, C., Nelson, G. M., Félix, M.-A., &#38; de Bono, M. (2020). Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">https://doi.org/10.1016/j.neuron.2019.10.001</a>","ieee":"I. Beets <i>et al.</i>, “Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression,” <i>Neuron</i>, vol. 105, no. 1. Cell Press, p. 106–121.e10, 2020.","short":"I. Beets, G. Zhang, L.A. Fenk, C. Chen, G.M. Nelson, M.-A. Félix, M. de Bono, Neuron 105 (2020) 106–121.e10.","ama":"Beets I, Zhang G, Fenk LA, et al. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. <i>Neuron</i>. 2020;105(1):106-121.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.10.001\">10.1016/j.neuron.2019.10.001</a>","ista":"Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix M-A, de Bono M. 2020. Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression. Neuron. 105(1), 106–121.e10."},"publication":"Neuron","publication_status":"published","abstract":[{"text":"The extent to which behavior is shaped by experience varies between individuals. Genetic differences contribute to this variation, but the neural mechanisms are not understood. Here, we dissect natural variation in the behavioral flexibility of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal regardless of previous O2 experience. We map that variation to a polymorphic dendritic scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2 at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation, an evolutionary process by which phenotypic flexibility in response to environmental variation is reset by genetic change.","lang":"eng"}],"date_created":"2020-02-28T10:43:39Z","intvolume":"       105","volume":105,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"author":[{"full_name":"Beets, Isabel","last_name":"Beets","first_name":"Isabel"},{"last_name":"Zhang","first_name":"Gaotian","full_name":"Zhang, Gaotian"},{"first_name":"Lorenz A.","last_name":"Fenk","full_name":"Fenk, Lorenz A."},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"last_name":"Nelson","first_name":"Geoffrey M.","full_name":"Nelson, Geoffrey M."},{"full_name":"Félix, Marie-Anne","last_name":"Félix","first_name":"Marie-Anne"},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","has_accepted_license":"1","oa_version":"Published Version","publisher":"Cell Press","ddc":["570"],"doi":"10.1016/j.neuron.2019.10.001","status":"public","year":"2020","title":"Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression","publication_identifier":{"issn":["0896-6273"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","month":"01","_id":"7546","quality_controlled":"1","date_published":"2020-01-08T00:00:00Z","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:00Z","file_size":3294066,"creator":"dernst","file_id":"7558","date_created":"2020-03-02T15:43:57Z","checksum":"799bfd297a008753a688b30d3958fa48","relation":"main_file","access_level":"open_access","file_name":"2020_Neuron_Beets.pdf","content_type":"application/pdf"}],"page":"106-121.e10","issue":"1","date_updated":"2023-08-18T06:46:23Z","external_id":{"pmid":["31757604"],"isi":["000507341300012"]},"article_type":"original"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":64,"intvolume":"        64","date_created":"2020-03-01T23:00:39Z","publication_status":"published","abstract":[{"lang":"eng","text":"Slicing a Voronoi tessellation in ${R}^n$ with a $k$-plane gives a $k$-dimensional weighted Voronoi tessellation, also known as a power diagram or Laguerre tessellation. Mapping every simplex of the dual weighted Delaunay mosaic to the radius of the smallest empty circumscribed sphere whose center lies in the $k$-plane gives a generalized discrete Morse function. Assuming the Voronoi tessellation is generated by a Poisson point process in ${R}^n$, we study the expected number of simplices in the $k$-dimensional weighted Delaunay mosaic as well as the expected number of intervals of the Morse function, both as functions of a radius threshold. As a by-product, we obtain a new proof for the expected number of connected components (clumps) in a line section of a circular Boolean model in ${R}^n$."}],"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"arxiv":1,"publication":"Theory of Probability and its Applications","citation":{"ista":"Edelsbrunner H, Nikitenko A. 2020. Weighted Poisson–Delaunay mosaics. Theory of Probability and its Applications. 64(4), 595–614.","ama":"Edelsbrunner H, Nikitenko A. Weighted Poisson–Delaunay mosaics. <i>Theory of Probability and its Applications</i>. 2020;64(4):595-614. doi:<a href=\"https://doi.org/10.1137/S0040585X97T989726\">10.1137/S0040585X97T989726</a>","short":"H. Edelsbrunner, A. Nikitenko, Theory of Probability and Its Applications 64 (2020) 595–614.","apa":"Edelsbrunner, H., &#38; Nikitenko, A. (2020). Weighted Poisson–Delaunay mosaics. <i>Theory of Probability and Its Applications</i>. SIAM. <a href=\"https://doi.org/10.1137/S0040585X97T989726\">https://doi.org/10.1137/S0040585X97T989726</a>","ieee":"H. Edelsbrunner and A. Nikitenko, “Weighted Poisson–Delaunay mosaics,” <i>Theory of Probability and its Applications</i>, vol. 64, no. 4. SIAM, pp. 595–614, 2020.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” <i>Theory of Probability and Its Applications</i>. SIAM, 2020. <a href=\"https://doi.org/10.1137/S0040585X97T989726\">https://doi.org/10.1137/S0040585X97T989726</a>.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Weighted Poisson–Delaunay Mosaics.” <i>Theory of Probability and Its Applications</i>, vol. 64, no. 4, SIAM, 2020, pp. 595–614, doi:<a href=\"https://doi.org/10.1137/S0040585X97T989726\">10.1137/S0040585X97T989726</a>."},"department":[{"_id":"HeEd"}],"ec_funded":1,"oa":1,"day":"13","scopus_import":"1","isi":1,"article_type":"original","date_updated":"2023-08-18T06:45:48Z","external_id":{"isi":["000551393100007"],"arxiv":["1705.08735"]},"issue":"4","page":"595-614","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-02-13T00:00:00Z","_id":"7554","month":"02","article_processing_charge":"No","publication_identifier":{"issn":["0040585X"],"eissn":["10957219"]},"year":"2020","status":"public","title":"Weighted Poisson–Delaunay mosaics","doi":"10.1137/S0040585X97T989726","publisher":"SIAM","oa_version":"Preprint","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1705.08735","open_access":"1"}],"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","full_name":"Nikitenko, Anton","last_name":"Nikitenko","first_name":"Anton","orcid":"0000-0002-0659-3201"}]},{"article_processing_charge":"No","month":"03","_id":"7563","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"issue":"3","external_id":{"isi":["000519254800002"],"arxiv":["1910.04584"]},"date_updated":"2023-08-18T06:47:16Z","article_type":"original","date_published":"2020-03-03T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","author":[{"last_name":"Yalniz","first_name":"Gökhan","full_name":"Yalniz, Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010"}],"main_file_link":[{"url":"https://doi.org/10.1063/1.5122969","open_access":"1"}],"publisher":"AIP Publishing","doi":"10.1063/1.5122969","year":"2020","title":"Inferring symbolic dynamics of chaotic flows from persistence","status":"public","oa_version":"Published Version","publication_status":"published","abstract":[{"lang":"eng","text":"We introduce “state space persistence analysis” for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional Rössler system and a 30-dimensional discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1) dimensions.\r\nOne way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained” state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as Poincaré maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop “state space persistence analysis” and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings."}],"arxiv":1,"article_number":"033109","date_created":"2020-03-04T08:06:25Z","intvolume":"        30","volume":30,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"scopus_import":"1","day":"03","department":[{"_id":"BjHo"}],"citation":{"ieee":"G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows from persistence,” <i>Chaos</i>, vol. 30, no. 3. AIP Publishing, 2020.","apa":"Yalniz, G., &#38; Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>","mla":"Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>, vol. 30, no. 3, 033109, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>.","chicago":"Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>.","short":"G. Yalniz, N.B. Budanur, Chaos 30 (2020).","ista":"Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109.","ama":"Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. 2020;30(3). doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>"},"publication":"Chaos","oa":1},{"file_date_updated":"2020-11-20T10:18:02Z","author":[{"full_name":"Choudhary, Aruni","last_name":"Choudhary","first_name":"Aruni"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","oa_version":"Published Version","has_accepted_license":"1","status":"public","title":"Coxeter triangulations have good quality","year":"2020","doi":"10.1007/s11786-020-00461-5","ddc":["510"],"publisher":"Springer Nature","publication_identifier":{"issn":["1661-8270"],"eissn":["1661-8289"]},"_id":"7567","month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"date_published":"2020-03-01T00:00:00Z","quality_controlled":"1","article_type":"original","date_updated":"2021-01-12T08:14:13Z","page":"141-176","file":[{"date_updated":"2020-11-20T10:18:02Z","file_size":872275,"file_id":"8783","success":1,"creator":"dernst","date_created":"2020-11-20T10:18:02Z","access_level":"open_access","checksum":"1d145f3ab50ccee735983cb89236e609","relation":"main_file","file_name":"2020_MathCompScie_Choudhary.pdf","content_type":"application/pdf"}],"scopus_import":"1","day":"01","oa":1,"ec_funded":1,"publication":"Mathematics in Computer Science","citation":{"apa":"Choudhary, A., Kachanovich, S., &#38; Wintraecken, M. (2020). Coxeter triangulations have good quality. <i>Mathematics in Computer Science</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11786-020-00461-5\">https://doi.org/10.1007/s11786-020-00461-5</a>","ieee":"A. Choudhary, S. Kachanovich, and M. Wintraecken, “Coxeter triangulations have good quality,” <i>Mathematics in Computer Science</i>, vol. 14. Springer Nature, pp. 141–176, 2020.","chicago":"Choudhary, Aruni, Siargey Kachanovich, and Mathijs Wintraecken. “Coxeter Triangulations Have Good Quality.” <i>Mathematics in Computer Science</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11786-020-00461-5\">https://doi.org/10.1007/s11786-020-00461-5</a>.","mla":"Choudhary, Aruni, et al. “Coxeter Triangulations Have Good Quality.” <i>Mathematics in Computer Science</i>, vol. 14, Springer Nature, 2020, pp. 141–76, doi:<a href=\"https://doi.org/10.1007/s11786-020-00461-5\">10.1007/s11786-020-00461-5</a>.","ista":"Choudhary A, Kachanovich S, Wintraecken M. 2020. Coxeter triangulations have good quality. Mathematics in Computer Science. 14, 141–176.","ama":"Choudhary A, Kachanovich S, Wintraecken M. Coxeter triangulations have good quality. <i>Mathematics in Computer Science</i>. 2020;14:141-176. doi:<a href=\"https://doi.org/10.1007/s11786-020-00461-5\">10.1007/s11786-020-00461-5</a>","short":"A. Choudhary, S. Kachanovich, M. Wintraecken, Mathematics in Computer Science 14 (2020) 141–176."},"department":[{"_id":"HeEd"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Coxeter triangulations are triangulations of Euclidean space based on a single simplex. By this we mean that given an individual simplex we can recover the entire triangulation of Euclidean space by inductively reflecting in the faces of the simplex. In this paper we establish that the quality of the simplices in all Coxeter triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate the Delaunay property for these triangulations. Moreover, we consider an extension of the Delaunay property, namely protection, which is a measure of non-degeneracy of a Delaunay triangulation. In particular, one family of Coxeter triangulations achieves the protection O(1/d2). We conjecture that both bounds are optimal for triangulations in Euclidean space."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":14,"intvolume":"        14","date_created":"2020-03-05T13:30:18Z"},{"external_id":{"isi":["000526725200019"]},"date_updated":"2023-09-12T11:02:24Z","article_type":"original","file":[{"file_name":"2020_PlosCompBio_Grah.pdf","access_level":"open_access","relation":"main_file","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","content_type":"application/pdf","file_size":2209325,"date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-09T15:12:21Z","creator":"dernst","file_id":"7579"}],"issue":"2","language":[{"iso":"eng"}],"date_published":"2020-02-25T00:00:00Z","quality_controlled":"1","_id":"7569","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"02","publication_identifier":{"issn":["1553-7358"]},"year":"2020","title":"The relation between crosstalk and gene regulation form revisited","status":"public","publisher":"Public Library of Science","ddc":["000","570"],"doi":"10.1371/journal.pcbi.1007642","oa_version":"Published Version","has_accepted_license":"1","type":"journal_article","file_date_updated":"2020-07-14T12:48:00Z","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","first_name":"Rok","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"volume":16,"intvolume":"        16","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-03-06T07:39:38Z","publication_status":"published","abstract":[{"lang":"eng","text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models."}],"article_number":"e1007642","publication":"PLOS Computational Biology","citation":{"ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. <i>PLOS Computational Biology</i>. 2020;16(2). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">10.1371/journal.pcbi.1007642</a>","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","apa":"Grah, R., &#38; Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">https://doi.org/10.1371/journal.pcbi.1007642</a>","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” <i>PLOS Computational Biology</i>, vol. 16, no. 2. Public Library of Science, 2020.","chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">https://doi.org/10.1371/journal.pcbi.1007642</a>.","mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” <i>PLOS Computational Biology</i>, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">10.1371/journal.pcbi.1007642</a>."},"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"oa":1,"day":"25","scopus_import":"1","isi":1,"related_material":{"record":[{"relation":"research_data","status":"deleted","id":"9716"},{"status":"public","relation":"research_data","id":"9776"},{"id":"9779","status":"public","relation":"used_in_publication"},{"id":"8155","relation":"dissertation_contains","status":"public"},{"id":"9777","relation":"research_data","status":"public"}]}},{"oa_version":"Published Version","has_accepted_license":"1","doi":"10.1103/physrevx.10.011055","publisher":"American Physical Society","ddc":["530"],"status":"public","year":"2020","title":"Slow quantum thermalization and many-body revivals from mixed phase space","author":[{"orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","first_name":"Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Turner, C. J.","first_name":"C. J.","last_name":"Turner"},{"full_name":"Papić, Z.","first_name":"Z.","last_name":"Papić"},{"first_name":"D. A.","last_name":"Abanin","full_name":"Abanin, D. A."},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","quality_controlled":"1","date_published":"2020-03-04T00:00:00Z","language":[{"iso":"eng"}],"issue":"1","file":[{"content_type":"application/pdf","file_name":"2020_PhysicalReviewX_Michailidis.pdf","relation":"main_file","checksum":"4b3f2c13873d35230173c73d0e11c408","access_level":"open_access","date_created":"2020-03-12T12:13:07Z","creator":"dernst","file_id":"7581","file_size":17828638,"date_updated":"2020-07-14T12:48:00Z"}],"article_type":"original","date_updated":"2023-08-18T07:01:07Z","external_id":{"isi":["000517969300001"],"arxiv":["1905.08564"]},"publication_identifier":{"issn":["2160-3308"]},"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","_id":"7570","oa":1,"citation":{"short":"A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review X 10 (2020).","ama":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. Slow quantum thermalization and many-body revivals from mixed phase space. <i>Physical Review X</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1103/physrevx.10.011055\">10.1103/physrevx.10.011055</a>","ista":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. 2020. Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. 10(1), 011055.","apa":"Michailidis, A., Turner, C. J., Papić, Z., Abanin, D. A., &#38; Serbyn, M. (2020). Slow quantum thermalization and many-body revivals from mixed phase space. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.10.011055\">https://doi.org/10.1103/physrevx.10.011055</a>","ieee":"A. Michailidis, C. J. Turner, Z. Papić, D. A. Abanin, and M. Serbyn, “Slow quantum thermalization and many-body revivals from mixed phase space,” <i>Physical Review X</i>, vol. 10, no. 1. American Physical Society, 2020.","mla":"Michailidis, Alexios, et al. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” <i>Physical Review X</i>, vol. 10, no. 1, 011055, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevx.10.011055\">10.1103/physrevx.10.011055</a>.","chicago":"Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym Serbyn. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” <i>Physical Review X</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevx.10.011055\">https://doi.org/10.1103/physrevx.10.011055</a>."},"department":[{"_id":"MaSe"}],"publication":"Physical Review X","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/classical-physics-helps-predict-fate-of-interacting-quantum-systems/","relation":"press_release"}]},"isi":1,"scopus_import":"1","day":"04","date_created":"2020-03-08T18:02:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        10","volume":10,"arxiv":1,"article_number":"011055","publication_status":"published","abstract":[{"lang":"eng","text":"The relaxation of few-body quantum systems can strongly depend on the initial state when the system’s semiclassical phase space is mixed; i.e., regions of chaotic motion coexist with regular islands. In recent years, there has been much effort to understand the process of thermalization in strongly interacting quantum systems that often lack an obvious semiclassical limit. The time-dependent variational principle (TDVP) allows one to systematically derive an effective classical (nonlinear) dynamical system by projecting unitary many-body dynamics onto a manifold of weakly entangled variational states. We demonstrate that such dynamical systems generally possess mixed phase space. When TDVP errors are small, the mixed phase space leaves a footprint on the exact dynamics of the quantum model. For example, when the system is initialized in a state belonging to a stable periodic orbit or the surrounding regular region, it exhibits persistent many-body quantum revivals. As a proof of principle, we identify new types of “quantum many-body scars,” i.e., initial states that lead to long-time oscillations in a model of interacting Rydberg atoms in one and two dimensions. Intriguingly, the initial states that give rise to most robust revivals are typically entangled states. On the other hand, even when TDVP errors are large, as in the thermalizing tilted-field Ising model, initializing the system in a regular region of phase space leads to a surprising slowdown of thermalization. Our work establishes TDVP as a method for identifying interacting quantum systems with anomalous dynamics in arbitrary dimensions. Moreover, the mixed phase space classical variational equations allow one to find slowly thermalizing initial conditions in interacting models. Our results shed light on a link between classical and quantum chaos, pointing toward possible extensions of the classical Kolmogorov-Arnold-Moser theorem to quantum systems."}]},{"type":"book_chapter","main_file_link":[{"url":"https://doi.org/10.1101/839571","open_access":"1"}],"author":[{"orcid":"0000-0001-6730-4461","first_name":"Paulo R","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer"},{"last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","year":"2020","status":"public","publisher":"Elsevier","doi":"10.1016/bs.mcb.2020.01.006","oa_version":"Preprint","_id":"7572","article_processing_charge":"No","month":"02","publication_identifier":{"issn":["0091679X"]},"date_updated":"2023-10-04T09:50:24Z","external_id":{"isi":["000611826500008"]},"page":"145-161","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-02-27T00:00:00Z","scopus_import":"1","day":"27","alternative_title":["Methods in Cell Biology"],"isi":1,"related_material":{"record":[{"id":"8358","relation":"part_of_dissertation","status":"public"}]},"publication":"Methods in Cell Biology","department":[{"_id":"MaLo"}],"citation":{"ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in <i>Methods in Cell Biology</i>, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., &#38; Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), <i>Methods in Cell Biology</i> (Vol. 158, pp. 145–161). Elsevier. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In <i>Methods in Cell Biology</i>, edited by Phong  Tran, 158:145–61. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>.","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” <i>Methods in Cell Biology</i>, edited by Phong  Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>.","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. <i>Methods in Cell Biology</i>. Vol 158. Elsevier; 2020:145-161. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161."},"ec_funded":1,"oa":1,"publication_status":"published","editor":[{"last_name":"Tran","first_name":"Phong ","full_name":"Tran, Phong "}],"abstract":[{"lang":"eng","text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material."}],"project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"intvolume":"       158","volume":158,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-03-08T23:00:47Z"},{"day":"01","scopus_import":"1","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10030"}]},"publication":"Journal de Mathematiques Pures et Appliquees","citation":{"ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” <i>Journal de Mathematiques Pures et Appliquees</i>, vol. 139, no. 7. Elsevier, pp. 204–234, 2020.","apa":"Gladbach, P., Kopfer, E., Maas, J., &#38; Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. <i>Journal de Mathematiques Pures et Appliquees</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">https://doi.org/10.1016/j.matpur.2020.02.008</a>","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” <i>Journal de Mathematiques Pures et Appliquees</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">https://doi.org/10.1016/j.matpur.2020.02.008</a>.","mla":"Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” <i>Journal de Mathematiques Pures et Appliquees</i>, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:<a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">10.1016/j.matpur.2020.02.008</a>.","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234.","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. <i>Journal de Mathematiques Pures et Appliquees</i>. 2020;139(7):204-234. doi:<a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">10.1016/j.matpur.2020.02.008</a>","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234."},"department":[{"_id":"JaMa"}],"ec_funded":1,"oa":1,"publication_status":"published","abstract":[{"lang":"eng","text":"This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport."}],"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Di erential Systems"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"arxiv":1,"intvolume":"       139","volume":139,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-03-08T23:00:47Z","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1905.05757","open_access":"1"}],"author":[{"full_name":"Gladbach, Peter","first_name":"Peter","last_name":"Gladbach"},{"first_name":"Eva","last_name":"Kopfer","full_name":"Kopfer, Eva"},{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo","first_name":"Lorenzo","last_name":"Portinale"}],"status":"public","year":"2020","title":"Homogenisation of one-dimensional discrete optimal transport","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.","publisher":"Elsevier","doi":"10.1016/j.matpur.2020.02.008","oa_version":"Preprint","_id":"7573","article_processing_charge":"No","month":"07","publication_identifier":{"issn":["00217824"]},"external_id":{"arxiv":["1905.05757"],"isi":["000539439400008"]},"date_updated":"2023-09-07T13:31:05Z","article_type":"original","issue":"7","page":"204-234","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-07-01T00:00:00Z"},{"publication_status":"published","abstract":[{"lang":"eng","text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell."}],"project":[{"grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system","_id":"2599F062-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-03-12T05:32:26Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":117,"intvolume":"       117","isi":1,"scopus_import":"1","day":"24","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"8341","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"MaLo"},{"_id":"CaBe"}],"citation":{"short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(12):6504-6549. doi:<a href=\"https://doi.org/10.1073/pnas.1921027117\">10.1073/pnas.1921027117</a>","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549.","mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:<a href=\"https://doi.org/10.1073/pnas.1921027117\">10.1073/pnas.1921027117</a>.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/10.1073/pnas.1921027117</a>.","apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., &#38; Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/10.1073/pnas.1921027117</a>","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020."},"publication":"Proceedings of the National Academy of Sciences","oa":1,"month":"03","article_processing_charge":"No","_id":"7580","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"page":"6504-6549","issue":"12","article_type":"original","external_id":{"isi":["000521821800040"]},"date_updated":"2023-09-07T13:17:06Z","quality_controlled":"1","date_published":"2020-03-24T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","author":[{"last_name":"Bezeljak","first_name":"Urban","full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1365-5631"},{"full_name":"Loya, Hrushikesh","last_name":"Loya","first_name":"Hrushikesh"},{"id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M","last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M"},{"last_name":"Saunders","first_name":"Timothy E.","full_name":"Saunders, Timothy E."},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose"}],"main_file_link":[{"url":"https://doi.org/10.1101/776567","open_access":"1"}],"doi":"10.1073/pnas.1921027117","publisher":"Proceedings of the National Academy of Sciences","status":"public","year":"2020","title":"Stochastic activation and bistability in a Rab GTPase regulatory network","oa_version":"Preprint"},{"article_type":"original","date_updated":"2025-05-07T11:12:28Z","external_id":{"pmid":["32121542"],"isi":["000525315000035"]},"issue":"3","file":[{"content_type":"application/pdf","file_name":"2020_Plants_Moturu.pdf","checksum":"6d5af3e17266a48996b4af4e67e88a85","relation":"main_file","access_level":"open_access","date_created":"2020-03-23T13:37:00Z","file_id":"7614","creator":"dernst","file_size":2373484,"date_updated":"2020-07-14T12:48:00Z"}],"language":[{"iso":"eng"}],"date_published":"2020-03-01T00:00:00Z","quality_controlled":"1","_id":"7582","month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","publication_identifier":{"eissn":["22237747"]},"status":"public","title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","year":"2020","doi":"10.3390/plants9030299","publisher":"MDPI","ddc":["580"],"oa_version":"Published Version","has_accepted_license":"1","type":"journal_article","file_date_updated":"2020-07-14T12:48:00Z","author":[{"first_name":"Taraka Ramji","last_name":"Moturu","full_name":"Moturu, Taraka Ramji"},{"full_name":"Sinha, Sansrity","first_name":"Sansrity","last_name":"Sinha"},{"first_name":"Hymavathi","last_name":"Salava","full_name":"Salava, Hymavathi"},{"full_name":"Thula, Sravankumar","first_name":"Sravankumar","last_name":"Thula"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Vařeková, Radka Svobodová","first_name":"Radka Svobodová","last_name":"Vařeková"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu","last_name":"Simon","first_name":"Sibu"}],"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"         9","volume":9,"date_created":"2020-03-15T23:00:52Z","abstract":[{"lang":"eng","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."}],"publication_status":"published","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"article_number":"299","publication":"Plants","department":[{"_id":"JiFr"}],"citation":{"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>","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.","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>.","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>","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."},"oa":1,"ec_funded":1,"day":"01","scopus_import":"1","isi":1},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","isi":1,"scopus_import":"1","day":"02","oa":1,"department":[{"_id":"GaNo"}],"citation":{"ieee":"S. Weinert <i>et al.</i>, “Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration,” <i>EMBO Journal</i>, vol. 39. EMBO Press, 2020.","apa":"Weinert, S., Gimber, N., Deuschel, D., Stuhlmann, T., Puchkov, D., Farsi, Z., … Jentsch, T. J. (2020). Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. <i>EMBO Journal</i>. EMBO Press. <a href=\"https://doi.org/10.15252/embj.2019103358\">https://doi.org/10.15252/embj.2019103358</a>","chicago":"Weinert, Stefanie, Niclas Gimber, Dorothea Deuschel, Till Stuhlmann, Dmytro Puchkov, Zohreh Farsi, Carmen F. Ludwig, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” <i>EMBO Journal</i>. EMBO Press, 2020. <a href=\"https://doi.org/10.15252/embj.2019103358\">https://doi.org/10.15252/embj.2019103358</a>.","mla":"Weinert, Stefanie, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” <i>EMBO Journal</i>, vol. 39, e103358, EMBO Press, 2020, doi:<a href=\"https://doi.org/10.15252/embj.2019103358\">10.15252/embj.2019103358</a>.","ama":"Weinert S, Gimber N, Deuschel D, et al. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. <i>EMBO Journal</i>. 2020;39. doi:<a href=\"https://doi.org/10.15252/embj.2019103358\">10.15252/embj.2019103358</a>","ista":"Weinert S, Gimber N, Deuschel D, Stuhlmann T, Puchkov D, Farsi Z, Ludwig CF, Novarino G, López-Cayuqueo KI, Planells-Cases R, Jentsch TJ. 2020. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. 39, e103358.","short":"S. Weinert, N. Gimber, D. Deuschel, T. Stuhlmann, D. Puchkov, Z. Farsi, C.F. Ludwig, G. Novarino, K.I. López-Cayuqueo, R. Planells-Cases, T.J. Jentsch, EMBO Journal 39 (2020)."},"publication":"EMBO Journal","article_number":"e103358","abstract":[{"lang":"eng","text":"CLC chloride/proton exchangers may support acidification of endolysosomes and raise their luminal Cl− concentration. Disruption of endosomal ClC‐3 causes severe neurodegeneration. To assess the importance of ClC‐3 Cl−/H+ exchange, we now generate Clcn3unc/unc mice in which ClC‐3 is converted into a Cl− channel. Unlike Clcn3−/− mice, Clcn3unc/unc mice appear normal owing to compensation by ClC‐4 with which ClC‐3 forms heteromers. ClC‐4 protein levels are strongly reduced in Clcn3−/−, but not in Clcn3unc/unc mice because ClC‐3unc binds and stabilizes ClC‐4 like wild‐type ClC‐3. Although mice lacking ClC‐4 appear healthy, its absence in Clcn3unc/unc/Clcn4−/− mice entails even stronger neurodegeneration than observed in Clcn3−/− mice. A fraction of ClC‐3 is found on synaptic vesicles, but miniature postsynaptic currents and synaptic vesicle acidification are not affected in Clcn3unc/unc or Clcn3−/− mice before neurodegeneration sets in. Both, Cl−/H+‐exchange activity and the stabilizing effect on ClC‐4, are central to the biological function of ClC‐3."}],"publication_status":"published","date_created":"2020-03-15T23:00:55Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        39","volume":39,"pmid":1,"author":[{"full_name":"Weinert, Stefanie","last_name":"Weinert","first_name":"Stefanie"},{"full_name":"Gimber, Niclas","last_name":"Gimber","first_name":"Niclas"},{"first_name":"Dorothea","last_name":"Deuschel","full_name":"Deuschel, Dorothea"},{"full_name":"Stuhlmann, Till","last_name":"Stuhlmann","first_name":"Till"},{"full_name":"Puchkov, Dmytro","first_name":"Dmytro","last_name":"Puchkov"},{"first_name":"Zohreh","last_name":"Farsi","full_name":"Farsi, Zohreh"},{"last_name":"Ludwig","first_name":"Carmen F.","full_name":"Ludwig, Carmen F."},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"last_name":"López-Cayuqueo","first_name":"Karen I.","full_name":"López-Cayuqueo, Karen I."},{"first_name":"Rosa","last_name":"Planells-Cases","full_name":"Planells-Cases, Rosa"},{"first_name":"Thomas J.","last_name":"Jentsch","full_name":"Jentsch, Thomas J."}],"file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","has_accepted_license":"1","oa_version":"Published Version","doi":"10.15252/embj.2019103358","publisher":"EMBO Press","ddc":["570"],"acknowledgement":"We thank T. Stauber and T. Breiderhoff for cloning expression constructs; K. Räbel, S. Hohensee, and C. Backhaus for technical assistance; R. Jahn (MPIbpc, Göttingen) for providing the equipment required for SV purification; and A\r\nWoehler (MDC, Berlin) for assistance with SV imaging. Supported, in part, by grants from the Deutsche Forschungsgemeinschaft (JE164/9-2, SFB740 TP C5, FOR 2625 (JE164/14-1), NeuroCure Cluster of Excellence), the European Research Council Advanced Grant CYTOVOLION (ERC 294435) and the Prix Louis-Jeantet de Médecine to TJJ, and Peter and Traudl Engelhorn fellowship to ZF.","status":"public","title":"Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration","year":"2020","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"month":"03","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_processing_charge":"No","_id":"7586","quality_controlled":"1","date_published":"2020-03-02T00:00:00Z","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","checksum":"82750a7a93e3740decbce8474004111a","access_level":"open_access","relation":"main_file","file_name":"2020_EMBO_Weinert.pdf","file_id":"7615","creator":"dernst","date_created":"2020-03-23T13:51:11Z","date_updated":"2020-07-14T12:48:00Z","file_size":12243278}],"article_type":"original","external_id":{"isi":["000517335000001"],"pmid":["32118314"]},"date_updated":"2023-08-18T07:07:36Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_created":"2020-03-19T15:54:34Z","quality_controlled":"1","date_published":"2020-03-18T00:00:00Z","date_updated":"2021-01-12T08:14:22Z","page":"1-42","extern":"1","publication_identifier":{"eisbn":["9783527610426"],"isbn":["9783527302505"]},"_id":"7591","publication_status":"published","abstract":[{"lang":"eng","text":"Rechargeable Li–O2 batteries have gathered enormous attention in the research community for having amongst the highest theoretical energy storage. Realizing the promise, even in part, in practice could produce a device that stores significantly more energy than other rechargeable batteries. Fundamental understanding of the reaction mechanisms is now realized to be key to overcome many challenges. We give a critical overview of the current understanding of the chemistry underpinning the Li–O2 cell with focus on the cathode and give a perspective on the most important research needs. Since performance and reversibility are often grossly misunderstood, we put emphasis on realistic performances to be achieved by Li–O2 cells and on means to identify reversibility. Parasitic chemistry is the foremost barrier for reversible cycling and now realized to be predominantly caused by singlet oxygen rather than by the previously thought superoxide or peroxide. This finding profoundly affects any other area of research from reaction mechanisms, to electrolytes and catalysts and dominates future research needs."}],"month":"03","article_processing_charge":"No","oa_version":"None","year":"2020","status":"public","publication":"Encyclopedia of Electrochemistry","title":"Lithium–Oxygen batteries","doi":"10.1002/9783527610426.bard110017","citation":{"short":"Y.K. Petit, E. Mourad, S.A. Freunberger, in:, Encyclopedia of Electrochemistry, Wiley, 2020, pp. 1–42.","ista":"Petit YK, Mourad E, Freunberger SA. 2020.Lithium–Oxygen batteries. In: Encyclopedia of Electrochemistry. , 1–42.","ama":"Petit YK, Mourad E, Freunberger SA. Lithium–Oxygen batteries. In: <i>Encyclopedia of Electrochemistry</i>. Wiley; 2020:1-42. doi:<a href=\"https://doi.org/10.1002/9783527610426.bard110017\">10.1002/9783527610426.bard110017</a>","apa":"Petit, Y. K., Mourad, E., &#38; Freunberger, S. A. (2020). Lithium–Oxygen batteries. In <i>Encyclopedia of Electrochemistry</i> (pp. 1–42). Wiley. <a href=\"https://doi.org/10.1002/9783527610426.bard110017\">https://doi.org/10.1002/9783527610426.bard110017</a>","ieee":"Y. K. Petit, E. Mourad, and S. A. Freunberger, “Lithium–Oxygen batteries,” in <i>Encyclopedia of Electrochemistry</i>, Wiley, 2020, pp. 1–42.","mla":"Petit, Yann K., et al. “Lithium–Oxygen Batteries.” <i>Encyclopedia of Electrochemistry</i>, Wiley, 2020, pp. 1–42, doi:<a href=\"https://doi.org/10.1002/9783527610426.bard110017\">10.1002/9783527610426.bard110017</a>.","chicago":"Petit, Yann K., Eléonore Mourad, and Stefan Alexander Freunberger. “Lithium–Oxygen Batteries.” In <i>Encyclopedia of Electrochemistry</i>, 1–42. Wiley, 2020. <a href=\"https://doi.org/10.1002/9783527610426.bard110017\">https://doi.org/10.1002/9783527610426.bard110017</a>."},"publisher":"Wiley","author":[{"full_name":"Petit, Yann K.","last_name":"Petit","first_name":"Yann K."},{"first_name":"Eléonore","last_name":"Mourad","full_name":"Mourad, Eléonore"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"day":"18","type":"book_chapter"},{"day":"11","scopus_import":"1","isi":1,"publication":"eLife","citation":{"ama":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.51512\">10.7554/elife.51512</a>","ista":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. 2020. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 9, 51512.","short":"H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).","chicago":"Moon, Hyang Mi, Simon Hippenmeyer, Liqun Luo, and Anthony Wynshaw-Boris. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.51512\">https://doi.org/10.7554/elife.51512</a>.","mla":"Moon, Hyang Mi, et al. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” <i>ELife</i>, vol. 9, 51512, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.51512\">10.7554/elife.51512</a>.","ieee":"H. M. Moon, S. Hippenmeyer, L. Luo, and A. Wynshaw-Boris, “LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Moon, H. M., Hippenmeyer, S., Luo, L., &#38; Wynshaw-Boris, A. (2020). LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.51512\">https://doi.org/10.7554/elife.51512</a>"},"department":[{"_id":"SiHi"}],"oa":1,"abstract":[{"lang":"eng","text":"Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation."}],"publication_status":"published","article_number":"51512","pmid":1,"intvolume":"         9","volume":9,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-03-20T13:16:41Z","type":"journal_article","file_date_updated":"2020-09-24T07:03:20Z","main_file_link":[{"url":"https://doi.org/10.1101/751958","open_access":"1"}],"author":[{"first_name":"Hyang Mi","last_name":"Moon","full_name":"Moon, Hyang Mi"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"full_name":"Wynshaw-Boris, Anthony","first_name":"Anthony","last_name":"Wynshaw-Boris"}],"year":"2020","status":"public","title":"LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility","ddc":["570"],"publisher":"eLife Sciences Publications","doi":"10.7554/elife.51512","has_accepted_license":"1","oa_version":"Published Version","_id":"7593","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"03","publication_identifier":{"issn":["2050-084X"]},"external_id":{"isi":["000522835800001"],"pmid":["32159512"]},"date_updated":"2023-08-18T07:06:31Z","article_type":"original","file":[{"date_updated":"2020-09-24T07:03:20Z","file_size":15089438,"success":1,"creator":"dernst","file_id":"8567","date_created":"2020-09-24T07:03:20Z","checksum":"396ceb2dd10b102ef4e699666b9342c3","relation":"main_file","access_level":"open_access","file_name":"2020_elife_Moon.pdf","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"date_published":"2020-03-11T00:00:00Z","quality_controlled":"1"},{"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"03","_id":"7594","file":[{"file_size":1436735,"date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-23T10:18:38Z","creator":"dernst","file_id":"7610","file_name":"2020_PhysRevResearch_Gotfryd.pdf","relation":"main_file","access_level":"open_access","checksum":"1be551fd5f5583635076017d7391ffdc","content_type":"application/pdf"}],"issue":"1","date_updated":"2021-01-12T08:14:23Z","article_type":"original","date_published":"2020-03-20T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","author":[{"full_name":"Gotfryd, Dorota","last_name":"Gotfryd","first_name":"Dorota"},{"last_name":"Paerschke","first_name":"Ekaterina","full_name":"Paerschke, Ekaterina","id":"8275014E-6063-11E9-9B7F-6338E6697425","orcid":"0000-0003-0853-8182"},{"last_name":"Chaloupka","first_name":"Jiri","full_name":"Chaloupka, Jiri"},{"full_name":"Oles, Andrzej M.","first_name":"Andrzej M.","last_name":"Oles"},{"last_name":"Wohlfeld","first_name":"Krzysztof","full_name":"Wohlfeld, Krzysztof"}],"file_date_updated":"2020-07-14T12:48:00Z","ddc":["530"],"publisher":"American Physical Society","doi":"10.1103/PhysRevResearch.2.013353","year":"2020","title":"How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator","status":"public","has_accepted_license":"1","oa_version":"Published Version","abstract":[{"text":"The concept of the entanglement between spin and orbital degrees of freedom plays a crucial role in our understanding of various phases and exotic ground states in a broad class of materials, including orbitally ordered materials and spin liquids. We investigate how the spin-orbital entanglement in a Mott insulator depends on the value of the spin-orbit coupling of the relativistic origin. To this end, we numerically diagonalize a one-dimensional spin-orbital model with Kugel-Khomskii exchange interactions between spins and orbitals on different sites supplemented by the on-site spin-orbit coupling. In the regime of small spin-orbit coupling with regard to the spin-orbital exchange, the ground state to a large extent resembles the one obtained in the limit of vanishing spin-orbit coupling. On the other hand, for large spin-orbit coupling the ground state can, depending on the model parameters, either still show negligible spin-orbital entanglement or evolve to a highly spin-orbitally-entangled phase with completely distinct properties that are described by an effective XXZ model. The presented results suggest that (i) the spin-orbital entanglement may be induced by large on-site spin-orbit coupling, as found in the 5d transition metal oxides, such as the iridates; (ii) for Mott insulators with weak spin-orbit coupling of Ising type, such as, e.g., the alkali hyperoxides, the effects of the spin-orbit coupling on the ground state can, in the first order of perturbation theory, be neglected.","lang":"eng"}],"publication_status":"published","article_number":"013353","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-03-20T15:21:10Z","volume":2,"intvolume":"         2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","citation":{"ama":"Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. <i>Physical Review Research</i>. 2020;2(1). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">10.1103/PhysRevResearch.2.013353</a>","ista":"Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. 2020. How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. Physical Review Research. 2(1), 013353.","short":"D. Gotfryd, E. Paerschke, J. Chaloupka, A.M. Oles, K. Wohlfeld, Physical Review Research 2 (2020).","ieee":"D. Gotfryd, E. Paerschke, J. Chaloupka, A. M. Oles, and K. Wohlfeld, “How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator,” <i>Physical Review Research</i>, vol. 2, no. 1. American Physical Society, 2020.","apa":"Gotfryd, D., Paerschke, E., Chaloupka, J., Oles, A. M., &#38; Wohlfeld, K. (2020). How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">https://doi.org/10.1103/PhysRevResearch.2.013353</a>","chicago":"Gotfryd, Dorota, Ekaterina Paerschke, Jiri Chaloupka, Andrzej M. Oles, and Krzysztof Wohlfeld. “How Spin-Orbital Entanglement Depends on the Spin-Orbit Coupling in a Mott Insulator.” <i>Physical Review Research</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">https://doi.org/10.1103/PhysRevResearch.2.013353</a>.","mla":"Gotfryd, Dorota, et al. “How Spin-Orbital Entanglement Depends on the Spin-Orbit Coupling in a Mott Insulator.” <i>Physical Review Research</i>, vol. 2, no. 1, 013353, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">10.1103/PhysRevResearch.2.013353</a>."},"department":[{"_id":"MiLe"}],"publication":"Physical Review Research","ec_funded":1,"oa":1},{"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Long Term Fellowship","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"}],"abstract":[{"text":"Directional intercellular transport of the phytohormone auxin mediated by PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. Multilevel regulations of PIN activity under internal and external cues are complicated; however, the underlying molecular mechanism remains elusive. Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub integrating the upstream lipid signalling and the downstream substrate activity through phosphorylation. Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2 exhibits a plethora of abnormalities in organogenesis and growth, due to the defective PIN-dependent auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade connecting membrane composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes.","lang":"eng"}],"publication_status":"published","date_created":"2020-03-21T16:34:16Z","volume":6,"intvolume":"         6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41477-020-0719-y","relation":"erratum"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"isi":1,"day":"01","scopus_import":"1","ec_funded":1,"oa":1,"citation":{"mla":"Tan, Shutang, et al. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” <i>Nature Plants</i>, vol. 6, Springer Nature, 2020, pp. 556–69, doi:<a href=\"https://doi.org/10.1038/s41477-020-0648-9\">10.1038/s41477-020-0648-9</a>.","chicago":"Tan, Shutang, Xixi Zhang, Wei Kong, Xiao-Li Yang, Gergely Molnar, Zuzana Vondráková, Roberta Filepová, Jan Petrášek, Jiří Friml, and Hong-Wei Xue. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” <i>Nature Plants</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41477-020-0648-9\">https://doi.org/10.1038/s41477-020-0648-9</a>.","ieee":"S. Tan <i>et al.</i>, “The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis,” <i>Nature Plants</i>, vol. 6. Springer Nature, pp. 556–569, 2020.","apa":"Tan, S., Zhang, X., Kong, W., Yang, X.-L., Molnar, G., Vondráková, Z., … Xue, H.-W. (2020). The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-020-0648-9\">https://doi.org/10.1038/s41477-020-0648-9</a>","short":"S. Tan, X. Zhang, W. Kong, X.-L. Yang, G. Molnar, Z. Vondráková, R. Filepová, J. Petrášek, J. Friml, H.-W. Xue, Nature Plants 6 (2020) 556–569.","ista":"Tan S, Zhang X, Kong W, Yang X-L, Molnar G, Vondráková Z, Filepová R, Petrášek J, Friml J, Xue H-W. 2020. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 6, 556–569.","ama":"Tan S, Zhang X, Kong W, et al. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. <i>Nature Plants</i>. 2020;6:556-569. doi:<a href=\"https://doi.org/10.1038/s41477-020-0648-9\">10.1038/s41477-020-0648-9</a>"},"department":[{"_id":"JiFr"}],"publication":"Nature Plants","publication_identifier":{"eissn":["20550278"]},"article_processing_charge":"No","month":"05","_id":"7600","date_published":"2020-05-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"page":"556-569","date_updated":"2023-08-18T07:05:57Z","external_id":{"isi":["000531787500006"],"pmid":["32393881"]},"article_type":"original","author":[{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang"},{"orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi"},{"first_name":"Wei","last_name":"Kong","full_name":"Kong, Wei"},{"full_name":"Yang, Xiao-Li","first_name":"Xiao-Li","last_name":"Yang"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","first_name":"Gergely","full_name":"Molnar, Gergely"},{"last_name":"Vondráková","first_name":"Zuzana","full_name":"Vondráková, Zuzana"},{"last_name":"Filepová","first_name":"Roberta","full_name":"Filepová, Roberta"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xue","first_name":"Hong-Wei","full_name":"Xue, Hong-Wei"}],"main_file_link":[{"url":"https://doi.org/10.1101/755504","open_access":"1"}],"type":"journal_article","oa_version":"Preprint","publisher":"Springer Nature","doi":"10.1038/s41477-020-0648-9","status":"public","year":"2020","title":"The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis"},{"oa_version":"Preprint","oa":1,"publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"JiFr"}],"doi":"10.1101/791137","citation":{"ama":"Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by plant remorin in animal cells. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>","ista":"Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020. Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv, <a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>.","short":"Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K. Liao, BioRxiv (2020).","ieee":"Z. Wei <i>et al.</i>, “Plasmodesmata-like intercellular connections by plant remorin in animal cells,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","apa":"Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020). Plasmodesmata-like intercellular connections by plant remorin in animal cells. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/791137\">https://doi.org/10.1101/791137</a>","chicago":"Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen, Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/791137\">https://doi.org/10.1101/791137</a>.","mla":"Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>."},"title":"Plasmodesmata-like intercellular connections by plant remorin in animal cells","status":"public","publication":"bioRxiv","year":"2020","author":[{"full_name":"Wei, Zhuang","last_name":"Wei","first_name":"Zhuang"},{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang"},{"full_name":"Liu, Tao","last_name":"Liu","first_name":"Tao"},{"last_name":"Wu","first_name":"Yuan","full_name":"Wu, Yuan"},{"last_name":"Lei","first_name":"Ji-Gang","full_name":"Lei, Ji-Gang"},{"last_name":"Chen","first_name":"ZhengJun","full_name":"Chen, ZhengJun"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Xue, Hong-Wei","last_name":"Xue","first_name":"Hong-Wei"},{"last_name":"Liao","first_name":"Kan","full_name":"Liao, Kan"}],"main_file_link":[{"url":"https://doi.org/10.1101/791137","open_access":"1"}],"type":"preprint","day":"19","date_created":"2020-03-21T16:34:42Z","date_published":"2020-02-19T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"22","date_updated":"2021-01-12T08:14:26Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals."}],"month":"02","publication_status":"published","_id":"7601"},{"article_number":"91","publication_status":"published","abstract":[{"text":"Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":11,"intvolume":"        11","date_created":"2020-03-22T23:00:46Z","day":"19","scopus_import":"1","isi":1,"oa":1,"publication":"Frontiers in Plant Science","department":[{"_id":"FyKo"}],"citation":{"ama":"Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","ieee":"B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","apa":"Nimeth, B. A., Riegler, S., &#38; Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>","chicago":"Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>.","mla":"Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>, vol. 11, 91, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>."},"publication_identifier":{"eissn":["1664462X"]},"_id":"7603","month":"02","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-02-19T00:00:00Z","article_type":"original","external_id":{"isi":["000518903600001"]},"date_updated":"2023-08-18T07:05:18Z","file":[{"content_type":"application/pdf","file_name":"2020_FrontiersPlants_Nimeth.pdf","relation":"main_file","access_level":"open_access","checksum":"57c37209f7b6712ced86c0f11b2be74e","date_created":"2020-03-23T09:03:40Z","file_id":"7607","creator":"dernst","file_size":507414,"date_updated":"2020-07-14T12:48:01Z"}],"file_date_updated":"2020-07-14T12:48:01Z","author":[{"full_name":"Nimeth, Barbara Anna","last_name":"Nimeth","first_name":"Barbara Anna"},{"orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler","first_name":"Stefan","full_name":"Riegler, Stefan"},{"full_name":"Kalyna, Maria","last_name":"Kalyna","first_name":"Maria"}],"type":"journal_article","has_accepted_license":"1","oa_version":"Published Version","title":"Alternative splicing and DNA damage response in plants","status":"public","year":"2020","doi":"10.3389/fpls.2020.00091","publisher":"Frontiers","ddc":["580"]},{"date_created":"2020-03-22T23:00:46Z","intvolume":"       153","volume":153,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Union-Find (or Disjoint-Set Union) is one of the fundamental problems in computer science; it has been well-studied from both theoretical and practical perspectives in the sequential case. Recently, there has been mounting interest in analyzing this problem in the concurrent scenario, and several asymptotically-efficient algorithms have been proposed. Yet, to date, there is very little known about the practical performance of concurrent Union-Find. This work addresses this gap. We evaluate and analyze the performance of several concurrent Union-Find algorithms and optimization strategies across a wide range of platforms (Intel, AMD, and ARM) and workloads (social, random, and road networks, as well as integrations into more complex algorithms). We first observe that, due to the limited computational cost, the number of induced cache misses is the critical determining factor for the performance of existing algorithms. We introduce new techniques to reduce this cost by storing node priorities implicitly and by using plain reads and writes in a way that does not affect the correctness of the algorithms. Finally, we show that Union-Find implementations are an interesting application for Transactional Memory (TM): one of the fastest algorithm variants we discovered is a sequential one that uses coarse-grained locking with the lock elision optimization to reduce synchronization cost and increase scalability. ","lang":"eng"}],"publication_status":"published","arxiv":1,"department":[{"_id":"DaAl"}],"citation":{"short":"D.-A. Alistarh, A. Fedorov, N. Koval, in:, 23rd International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16.","ista":"Alistarh D-A, Fedorov A, Koval N. 2020. In search of the fastest concurrent union-find algorithm. 23rd International Conference on Principles of Distributed Systems. OPODIS: International Conference on Principles of Distributed Systems, LIPIcs, vol. 153, 15:1-15:16.","ama":"Alistarh D-A, Fedorov A, Koval N. In search of the fastest concurrent union-find algorithm. In: <i>23rd International Conference on Principles of Distributed Systems</i>. Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020:15:1-15:16. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">10.4230/LIPIcs.OPODIS.2019.15</a>","mla":"Alistarh, Dan-Adrian, et al. “In Search of the Fastest Concurrent Union-Find Algorithm.” <i>23rd International Conference on Principles of Distributed Systems</i>, vol. 153, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">10.4230/LIPIcs.OPODIS.2019.15</a>.","chicago":"Alistarh, Dan-Adrian, Alexander Fedorov, and Nikita Koval. “In Search of the Fastest Concurrent Union-Find Algorithm.” In <i>23rd International Conference on Principles of Distributed Systems</i>, 153:15:1-15:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.15</a>.","ieee":"D.-A. Alistarh, A. Fedorov, and N. Koval, “In search of the fastest concurrent union-find algorithm,” in <i>23rd International Conference on Principles of Distributed Systems</i>, Neuchatal, Switzerland, 2020, vol. 153, p. 15:1-15:16.","apa":"Alistarh, D.-A., Fedorov, A., &#38; Koval, N. (2020). In search of the fastest concurrent union-find algorithm. In <i>23rd International Conference on Principles of Distributed Systems</i> (Vol. 153, p. 15:1-15:16). Neuchatal, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.15</a>"},"publication":"23rd International Conference on Principles of Distributed Systems","oa":1,"license":"https://creativecommons.org/licenses/by/3.0/","alternative_title":["LIPIcs"],"scopus_import":"1","day":"01","file":[{"file_name":"2019_LIPIcs_Alistarh.pdf","checksum":"d66f07ecb609d9f02433e39f80a447e9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":13074131,"date_updated":"2020-07-14T12:48:01Z","date_created":"2020-03-23T09:22:48Z","file_id":"7609","creator":"dernst"}],"page":"15:1-15:16","external_id":{"arxiv":["1911.06347"]},"date_updated":"2023-02-23T13:12:12Z","quality_controlled":"1","date_published":"2020-02-01T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"article_processing_charge":"No","month":"02","_id":"7605","publication_identifier":{"isbn":["9783959771337"],"issn":["18688969"]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"doi":"10.4230/LIPIcs.OPODIS.2019.15","year":"2020","status":"public","title":"In search of the fastest concurrent union-find algorithm","oa_version":"Published Version","has_accepted_license":"1","type":"conference","conference":{"start_date":"2019-12-17","end_date":"2019-12-19","name":"OPODIS: International Conference on Principles of Distributed Systems","location":"Neuchatal, Switzerland"},"author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander"},{"full_name":"Koval, Nikita","first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:48:01Z"}]