[{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.","apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796","ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455."},"title":"Existence of positive solutions to stochastic thin-film equations","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"last_name":"Grün","full_name":"Grün, Günther","first_name":"Günther"}],"publist_id":"7425","article_processing_charge":"No","external_id":{"isi":["000426630900015"]},"publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","oa":1,"day":"30","publication":"SIAM Journal on Mathematical Analysis","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-01-30T00:00:00Z","doi":"10.1137/16M1098796","date_created":"2018-12-11T11:46:17Z","page":"411 - 455","_id":"404","status":"public","article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-09-11T13:59:22Z","department":[{"_id":"JuFi"}],"file_date_updated":"2020-07-14T12:46:22Z","oa_version":"Published Version","abstract":[{"text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n","lang":"eng"}],"month":"01","intvolume":" 50","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:46:22Z","file_size":557338,"creator":"dernst","date_created":"2019-11-07T12:20:25Z","file_name":"2018_SIAM_Fischer.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"89a8eae7c52bb356c04f52b44bff4b5a","file_id":"6992"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":50},{"year":"2018","day":"30","date_created":"2021-08-06T13:04:32Z","related_material":{"record":[{"relation":"used_in_publication","id":"316","status":"public"}]},"doi":"10.25386/genetics.6148304.v1","date_published":"2018-04-30T00:00:00Z","abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.25386/genetics.6148304.v1","open_access":"1"}],"oa":1,"publisher":"Genetics Society of America","month":"04","date_updated":"2023-09-11T13:57:42Z","citation":{"apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","last_name":"Bod'ová","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína"},{"first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","full_name":"Priklopil, Tadeas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","last_name":"Pickup"}],"title":"Supplemental material for Bodova et al., 2018","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"_id":"9813","type":"research_data_reference","status":"public"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115.","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732."},"title":"Genetically encodable bioluminescent system from fungi","external_id":{"isi":["000452866000068"]},"article_processing_charge":"No","author":[{"last_name":"Kotlobay","full_name":"Kotlobay, Alexey A.","first_name":"Alexey A."},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan"},{"first_name":"Yuliana A.","last_name":"Mokrushina","full_name":"Mokrushina, Yuliana A."},{"first_name":"Marina","full_name":"Marcet-Houben, Marina","last_name":"Marcet-Houben"},{"first_name":"Ekaterina O.","full_name":"Serebrovskaya, Ekaterina O.","last_name":"Serebrovskaya"},{"last_name":"Markina","full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M."},{"orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrey Y.","last_name":"Gorokhovatsky","full_name":"Gorokhovatsky, Andrey Y."},{"last_name":"Vvedensky","full_name":"Vvedensky, Andrey","first_name":"Andrey"},{"first_name":"Konstantin V.","full_name":"Purtov, Konstantin V.","last_name":"Purtov"},{"full_name":"Petushkov, Valentin N.","last_name":"Petushkov","first_name":"Valentin N."},{"first_name":"Natalja S.","last_name":"Rodionova","full_name":"Rodionova, Natalja S."},{"last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V."},{"full_name":"Fakhranurova, Liliia","last_name":"Fakhranurova","first_name":"Liliia"},{"first_name":"Elena B.","full_name":"Guglya, Elena B.","last_name":"Guglya"},{"first_name":"Rustam","full_name":"Ziganshin, Rustam","last_name":"Ziganshin"},{"first_name":"Aleksandra S.","last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S."},{"last_name":"Kaskova","full_name":"Kaskova, Zinaida M.","first_name":"Zinaida M."},{"first_name":"Victoria","last_name":"Shender","full_name":"Shender, Victoria"},{"first_name":"Maxim","last_name":"Abakumov","full_name":"Abakumov, Maxim"},{"full_name":"Abakumova, Tatiana O.","last_name":"Abakumova","first_name":"Tatiana O."},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"last_name":"Eroshkin","full_name":"Eroshkin, Fedor M.","first_name":"Fedor M."},{"first_name":"Andrey G.","last_name":"Zaraisky","full_name":"Zaraisky, Andrey G."},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"first_name":"Sergey V.","full_name":"Dolgov, Sergey V.","last_name":"Dolgov"},{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana Y.","first_name":"Tatiana Y."},{"first_name":"Eugene P.","full_name":"Kopantzev, Eugene P.","last_name":"Kopantzev"},{"first_name":"Hans E.","full_name":"Waldenmaier, Hans E.","last_name":"Waldenmaier"},{"first_name":"Anderson G.","last_name":"Oliveira","full_name":"Oliveira, Anderson G."},{"last_name":"Oba","full_name":"Oba, Yuichi","first_name":"Yuichi"},{"full_name":"Barsova, Ekaterina","last_name":"Barsova","first_name":"Ekaterina"},{"first_name":"Ekaterina A.","full_name":"Bogdanova, Ekaterina A.","last_name":"Bogdanova"},{"first_name":"Toni","last_name":"Gabaldón","full_name":"Gabaldón, Toni"},{"first_name":"Cassius V.","last_name":"Stevani","full_name":"Stevani, Cassius V."},{"last_name":"Lukyanov","full_name":"Lukyanov, Sergey","first_name":"Sergey"},{"first_name":"Ivan V.","full_name":"Smirnov, Ivan V.","last_name":"Smirnov"},{"first_name":"Josef I.","last_name":"Gitelson","full_name":"Gitelson, Josef I."},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"11","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-23T22:59:18Z","doi":"10.1073/pnas.1803615115","date_published":"2018-12-11T00:00:00Z","page":"12728-12732","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","ddc":["580"],"date_updated":"2023-09-11T14:04:05Z","file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"FyKo"}],"_id":"5780","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1271988,"date_updated":"2020-07-14T12:47:11Z","file_name":"2018_PNAS_Kotlobay.pdf","date_created":"2019-02-05T15:21:40Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","file_id":"5926"}],"publication_status":"published","publication_identifier":{"issn":["00278424"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":115,"issue":"50","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"intvolume":" 115","month":"12","scopus_import":"1"},{"month":"04","intvolume":" 115","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses."}],"volume":115,"issue":"14","ec_funded":1,"file":[{"file_name":"2018_PNAS_Salanenka.pdf","date_created":"2018-12-17T12:30:14Z","file_size":1924101,"date_updated":"2020-07-14T12:46:26Z","creator":"dernst","file_id":"5700","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"428","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-09-11T14:06:34Z","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","doi":"10.1073/pnas.1721760115","date_published":"2018-04-03T00:00:00Z","date_created":"2018-12-11T11:46:25Z","page":" 3716 - 3721","day":"03","publication":"PNAS","has_accepted_license":"1","isi":1,"year":"2018","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","publist_id":"7395","author":[{"id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya","last_name":"Salanenka","full_name":"Salanenka, Yuliya"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"last_name":"Tabata","full_name":"Tabata, Kaori","first_name":"Kaori","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"external_id":{"isi":["000429012500073"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721760115","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 2018;115(14):3716-3721. doi:10.1073/pnas.1721760115","ieee":"Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” PNAS, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721.","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721."}},{"ddc":["570"],"date_updated":"2023-09-11T14:02:55Z","file_date_updated":"2020-07-14T12:47:24Z","department":[{"_id":"MaJö"}],"_id":"62","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"dernst","file_size":4141645,"date_updated":"2020-07-14T12:47:24Z","file_name":"2018_ScientificReports_Shahbazi.pdf","date_created":"2018-12-17T12:22:24Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2","file_id":"5699"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":8,"related_material":{"link":[{"url":"http://doi.org/10.1038/s41598-018-36220-7","relation":"erratum"}]},"issue":"1","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","abstract":[{"text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.","lang":"eng"}],"month":"09","intvolume":" 8","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3","mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3."},"title":"Flexible learning-free segmentation and reconstruction of neural volumes","author":[{"first_name":"Ali","full_name":"Shabazi, Ali","last_name":"Shabazi"},{"full_name":"Kinnison, Jeffery","last_name":"Kinnison","first_name":"Jeffery"},{"last_name":"Vescovi","full_name":"Vescovi, Rafael","first_name":"Rafael"},{"full_name":"Du, Ming","last_name":"Du","first_name":"Ming"},{"full_name":"Hill, Robert","last_name":"Hill","first_name":"Robert"},{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch"},{"first_name":"Marc","full_name":"Takeno, Marc","last_name":"Takeno"},{"first_name":"Hongkui","full_name":"Zeng, Hongkui","last_name":"Zeng"},{"first_name":"Nuno","full_name":"Da Costa, Nuno","last_name":"Da Costa"},{"first_name":"Jaime","last_name":"Grutzendler","full_name":"Grutzendler, Jaime"},{"last_name":"Kasthuri","full_name":"Kasthuri, Narayanan","first_name":"Narayanan"},{"first_name":"Walter","full_name":"Scheirer, Walter","last_name":"Scheirer"}],"publist_id":"7992","external_id":{"isi":["000445336600015"]},"article_processing_charge":"No","article_number":"14247","day":"24","publication":"Scientific Reports","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1038/s41598-018-32628-3","date_published":"2018-09-24T00:00:00Z","date_created":"2018-12-11T11:44:25Z","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1}]