[{"author":[{"first_name":"Naika","full_name":"Meili, Naika","last_name":"Meili"},{"first_name":"Gabriele","last_name":"Manoli","full_name":"Manoli, Gabriele"},{"first_name":"Paolo","full_name":"Burlando, Paolo","last_name":"Burlando"},{"last_name":"Bou-Zeid","full_name":"Bou-Zeid, Elie","first_name":"Elie"},{"full_name":"Chow, Winston T. L.","last_name":"Chow","first_name":"Winston T. L."},{"full_name":"Coutts, Andrew M.","last_name":"Coutts","first_name":"Andrew M."},{"full_name":"Daly, Edoardo","last_name":"Daly","first_name":"Edoardo"},{"last_name":"Nice","full_name":"Nice, Kerry A.","first_name":"Kerry A."},{"last_name":"Roth","full_name":"Roth, Matthias","first_name":"Matthias"},{"full_name":"Tapper, Nigel J.","last_name":"Tapper","first_name":"Nigel J."},{"full_name":"Velasco, Erik","last_name":"Velasco","first_name":"Erik"},{"first_name":"Enrique R.","last_name":"Vivoni","full_name":"Vivoni, Enrique R."},{"last_name":"Fatichi","full_name":"Fatichi, Simone","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"}],"doi":"10.5194/gmd-13-335-2020","oa_version":"Published Version","DOAJ_listed":"1","extern":"1","issue":"1","publication_status":"published","intvolume":"        13","das_tickbox":"1","day":"31","date_updated":"2026-08-07T09:11:10Z","publication_identifier":{"issn":["1991-959X"],"eissn":["1991-9603"]},"type":"journal_article","year":"2020","language":[{"iso":"eng"}],"date_published":"2020-01-31T00:00:00Z","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/gmd-13-335-2020"}],"OA_type":"gold","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"An urban ecohydrological model to quantify the effect of vegetation on urban climate and hydrology (UT&C v1.0)","citation":{"ieee":"N. Meili <i>et al.</i>, “An urban ecohydrological model to quantify the effect of vegetation on urban climate and hydrology (UT&#38;C v1.0),” <i>Geoscientific Model Development</i>, vol. 13, no. 1. Copernicus Publications, pp. 335–362, 2020.","apa":"Meili, N., Manoli, G., Burlando, P., Bou-Zeid, E., Chow, W. T. L., Coutts, A. M., … Fatichi, S. (2020). An urban ecohydrological model to quantify the effect of vegetation on urban climate and hydrology (UT&#38;C v1.0). <i>Geoscientific Model Development</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/gmd-13-335-2020\">https://doi.org/10.5194/gmd-13-335-2020</a>","ama":"Meili N, Manoli G, Burlando P, et al. An urban ecohydrological model to quantify the effect of vegetation on urban climate and hydrology (UT&#38;C v1.0). <i>Geoscientific Model Development</i>. 2020;13(1):335-362. doi:<a href=\"https://doi.org/10.5194/gmd-13-335-2020\">10.5194/gmd-13-335-2020</a>","chicago":"Meili, Naika, Gabriele Manoli, Paolo Burlando, Elie Bou-Zeid, Winston T. L. Chow, Andrew M. Coutts, Edoardo Daly, et al. “An Urban Ecohydrological Model to Quantify the Effect of Vegetation on Urban Climate and Hydrology (UT&#38;C v1.0).” <i>Geoscientific Model Development</i>. Copernicus Publications, 2020. <a href=\"https://doi.org/10.5194/gmd-13-335-2020\">https://doi.org/10.5194/gmd-13-335-2020</a>.","short":"N. Meili, G. Manoli, P. Burlando, E. Bou-Zeid, W.T.L. Chow, A.M. Coutts, E. Daly, K.A. Nice, M. Roth, N.J. Tapper, E. Velasco, E.R. Vivoni, S. Fatichi, Geoscientific Model Development 13 (2020) 335–362.","mla":"Meili, Naika, et al. “An Urban Ecohydrological Model to Quantify the Effect of Vegetation on Urban Climate and Hydrology (UT&#38;C v1.0).” <i>Geoscientific Model Development</i>, vol. 13, no. 1, Copernicus Publications, 2020, pp. 335–62, doi:<a href=\"https://doi.org/10.5194/gmd-13-335-2020\">10.5194/gmd-13-335-2020</a>.","ista":"Meili N, Manoli G, Burlando P, Bou-Zeid E, Chow WTL, Coutts AM, Daly E, Nice KA, Roth M, Tapper NJ, Velasco E, Vivoni ER, Fatichi S. 2020. An urban ecohydrological model to quantify the effect of vegetation on urban climate and hydrology (UT&#38;C v1.0). Geoscientific Model Development. 13(1), 335–362."},"volume":13,"_id":"22520","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","scopus_import":"1","date_created":"2026-07-27T12:30:24Z","page":"335-362","publisher":"Copernicus Publications","article_type":"original","abstract":[{"text":"Increasing urbanization is likely to intensify the urban heat island effect, decrease outdoor thermal comfort, and enhance runoff generation in cities. Urban green spaces are often proposed as a mitigation strategy to counteract these adverse effects, and many recent developments of urban climate models focus on the inclusion of green and blue infrastructure to inform urban planning. However, many models still lack the ability to account for different plant types and oversimplify the interactions between the built environment, vegetation, and hydrology. In this study, we present an urban ecohydrological model, Urban Tethys-Chloris (UT&C), that combines principles of ecosystem modelling with an urban canopy scheme accounting for the biophysical and ecophysiological characteristics of roof vegetation, ground vegetation, and urban trees. UT&C is a fully coupled energy and water balance model that calculates 2 m air temperature, 2 m humidity, and surface temperatures based on the infinite urban canyon approach. It further calculates the urban hydrological fluxes in the absence of snow, including transpiration as a function of plant photosynthesis. Hence, UT&C accounts for the effects of different plant types on the urban climate and hydrology, as well as the effects of the urban environment on plant well-being and performance. UT&C performs well when compared against energy flux measurements of eddy-covariance towers located in three cities in different climates (Singapore, Melbourne, and Phoenix). A sensitivity analysis, performed as a proof of concept for the city of Singapore, shows a mean decrease in 2 m air temperature of 1.1 ∘C for fully grass-covered ground, 0.2 ∘C for high values of leaf area index (LAI), and 0.3 ∘C for high values of Vc,max (an expression of photosynthetic capacity). These reductions in temperature were combined with a simultaneous increase in relative humidity by 6.5 %, 2.1 %, and 1.6 %, for fully grass-covered ground, high values of LAI, and high values of Vc,max, respectively. Furthermore, the increase of pervious vegetated ground is able to significantly reduce surface runoff.","lang":"eng"}],"month":"01","publication":"Geoscientific Model Development","status":"public","oa":1,"quality_controlled":"1"},{"intvolume":"        10","das_tickbox":"1","publication_status":"published","extern":"1","oa_version":"None","doi":"10.1038/s41558-019-0676-5","author":[{"full_name":"Mastrotheodoros, Theodoros","last_name":"Mastrotheodoros","first_name":"Theodoros"},{"full_name":"Pappas, Christoforos","last_name":"Pappas","first_name":"Christoforos"},{"full_name":"Molnar, Peter","last_name":"Molnar","first_name":"Peter"},{"last_name":"Burlando","full_name":"Burlando, Paolo","first_name":"Paolo"},{"last_name":"Manoli","full_name":"Manoli, Gabriele","first_name":"Gabriele"},{"full_name":"Parajka, Juraj","last_name":"Parajka","first_name":"Juraj"},{"full_name":"Rigon, Riccardo","last_name":"Rigon","first_name":"Riccardo"},{"first_name":"Borbala","last_name":"Szeles","full_name":"Szeles, Borbala"},{"full_name":"Bottazzi, Michele","last_name":"Bottazzi","first_name":"Michele"},{"last_name":"Hadjidoukas","full_name":"Hadjidoukas, Panagiotis","first_name":"Panagiotis"},{"last_name":"Fatichi","full_name":"Fatichi, Simone","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"}],"quality_controlled":"1","month":"02","publication":"Nature Climate Change","status":"public","article_type":"original","abstract":[{"text":"Climate change can reduce surface-water supply by enhancing evapotranspiration in forested mountains, especially during heatwaves. We investigate this ‘drought paradox’ for the European Alps using a 1,212-station database and hyper-resolution ecohydrological simulations to quantify blue (runoff) and green (evapotranspiration) water fluxes. During the 2003 heatwave, evapotranspiration in large areas over the Alps was above average despite low precipitation, amplifying the runoff deficit by 32% in the most runoff-productive areas (1,300–3,000 m above sea level). A 3 °C air temperature increase could enhance annual evapotranspiration by up to 100 mm (45 mm on average), which would reduce annual runoff at a rate similar to a 3% precipitation decrease. This suggests that green-water feedbacks—which are often poorly represented in large-scale model simulations—pose an additional threat to water resources, especially in dry summers. Despite uncertainty in the validation of the hyper-resolution ecohydrological modelling with observations, this approach permits more realistic predictions of mountain region water availability.","lang":"eng"}],"publisher":"Springer Nature","_id":"22526","date_created":"2026-07-27T12:30:24Z","page":"155-161","scopus_import":"1","volume":10,"title":"More green and less blue water in the Alps during warmer summers","citation":{"mla":"Mastrotheodoros, Theodoros, et al. “More Green and Less Blue Water in the Alps during Warmer Summers.” <i>Nature Climate Change</i>, vol. 10, Springer Nature, 2020, pp. 155–61, doi:<a href=\"https://doi.org/10.1038/s41558-019-0676-5\">10.1038/s41558-019-0676-5</a>.","ista":"Mastrotheodoros T, Pappas C, Molnar P, Burlando P, Manoli G, Parajka J, Rigon R, Szeles B, Bottazzi M, Hadjidoukas P, Fatichi S. 2020. More green and less blue water in the Alps during warmer summers. Nature Climate Change. 10, 155–161.","short":"T. Mastrotheodoros, C. Pappas, P. Molnar, P. Burlando, G. Manoli, J. Parajka, R. Rigon, B. Szeles, M. Bottazzi, P. Hadjidoukas, S. Fatichi, Nature Climate Change 10 (2020) 155–161.","chicago":"Mastrotheodoros, Theodoros, Christoforos Pappas, Peter Molnar, Paolo Burlando, Gabriele Manoli, Juraj Parajka, Riccardo Rigon, et al. “More Green and Less Blue Water in the Alps during Warmer Summers.” <i>Nature Climate Change</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41558-019-0676-5\">https://doi.org/10.1038/s41558-019-0676-5</a>.","ama":"Mastrotheodoros T, Pappas C, Molnar P, et al. More green and less blue water in the Alps during warmer summers. <i>Nature Climate Change</i>. 2020;10:155-161. doi:<a href=\"https://doi.org/10.1038/s41558-019-0676-5\">10.1038/s41558-019-0676-5</a>","apa":"Mastrotheodoros, T., Pappas, C., Molnar, P., Burlando, P., Manoli, G., Parajka, J., … Fatichi, S. (2020). More green and less blue water in the Alps during warmer summers. <i>Nature Climate Change</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41558-019-0676-5\">https://doi.org/10.1038/s41558-019-0676-5</a>","ieee":"T. Mastrotheodoros <i>et al.</i>, “More green and less blue water in the Alps during warmer summers,” <i>Nature Climate Change</i>, vol. 10. Springer Nature, pp. 155–161, 2020."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_type":"closed access","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2020-02-01T00:00:00Z","type":"journal_article","year":"2020","publication_identifier":{"eissn":["1758-6798"],"issn":["1758-678X"]},"day":"01","date_updated":"2026-08-07T09:15:51Z"},{"volume":117,"title":"Seasonal hysteresis of surface urban heat islands","citation":{"mla":"Manoli, Gabriele, et al. “Seasonal Hysteresis of Surface Urban Heat Islands.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 13, National Academy of Sciences, 2020, pp. 7082–89, doi:<a href=\"https://doi.org/10.1073/pnas.1917554117\">10.1073/pnas.1917554117</a>.","ista":"Manoli G, Fatichi S, Bou-Zeid E, Katul GG. 2020. Seasonal hysteresis of surface urban heat islands. Proceedings of the National Academy of Sciences. 117(13), 7082–7089.","short":"G. Manoli, S. Fatichi, E. Bou-Zeid, G.G. Katul, Proceedings of the National Academy of Sciences 117 (2020) 7082–7089.","chicago":"Manoli, Gabriele, Simone Fatichi, Elie Bou-Zeid, and Gabriel G. Katul. “Seasonal Hysteresis of Surface Urban Heat Islands.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1917554117\">https://doi.org/10.1073/pnas.1917554117</a>.","ieee":"G. Manoli, S. Fatichi, E. Bou-Zeid, and G. G. Katul, “Seasonal hysteresis of surface urban heat islands,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 13. National Academy of Sciences, pp. 7082–7089, 2020.","apa":"Manoli, G., Fatichi, S., Bou-Zeid, E., &#38; Katul, G. G. (2020). Seasonal hysteresis of surface urban heat islands. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1917554117\">https://doi.org/10.1073/pnas.1917554117</a>","ama":"Manoli G, Fatichi S, Bou-Zeid E, Katul GG. Seasonal hysteresis of surface urban heat islands. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(13):7082-7089. doi:<a href=\"https://doi.org/10.1073/pnas.1917554117\">10.1073/pnas.1917554117</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_type":"free access","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1917554117"}],"date_published":"2020-03-31T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"year":"2020","date_updated":"2026-08-07T09:21:58Z","day":"31","quality_controlled":"1","month":"03","publication":"Proceedings of the National Academy of Sciences","oa":1,"status":"public","article_type":"original","abstract":[{"text":"Temporal dynamics of urban warming have been extensivelystudied at the diurnal scale, but the impact of background cli-mate on the observed seasonality of surface urban heat islands(SUHIs) remains largely unexplored. On seasonal time scales, theintensity of urban–rural surface temperature differences (∆Ts)exhibits distinctive hysteretic cycles whose shape and loopingdirection vary across climatic zones. These observations high-light possible delays underlying the dynamics of the coupledurban–biosphere system. However, a general argument explain-ing the observed hysteretic patterns remains elusive. A coarse-grained model of SUHI coupled with a stochastic soil waterbalance is developed to demonstrate that the time lags betweenradiation forcing, air temperature, and rainfall generate a rate-dependent hysteresis, explaining the observed seasonal varia-tions of ∆Ts. If solar radiation is in phase with water availability,summer conditions cause strong SUHI intensities due to highrural evaporative cooling. Conversely, cities in seasonally dryregions where evapotranspiration is out of phase with radia-tion show a summertime oasis effect controlled by backgroundclimate and vegetation properties. These seasonal patterns ofwarming and cooling have significant implications for heat mit-igation strategies as urban green spaces can reduce ∆Ts duringsummertime, while potentially negative effects of albedo man-agement during winter are mitigated by the seasonality of solarradiation.","lang":"eng"}],"publisher":"National Academy of Sciences","keyword":["Cities","Hysteresis","Seasonality","Surface temperature","Urban heat island"],"_id":"22542","OA_place":"publisher","scopus_import":"1","page":"7082-7089","date_created":"2026-07-27T12:30:24Z","pmid":1,"external_id":{"pmid":["32184330 "]},"oa_version":"Published Version","doi":"10.1073/pnas.1917554117","author":[{"first_name":"Gabriele","last_name":"Manoli","full_name":"Manoli, Gabriele"},{"full_name":"Fatichi, Simone","last_name":"Fatichi","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone"},{"full_name":"Bou-Zeid, Elie","last_name":"Bou-Zeid","first_name":"Elie"},{"last_name":"Katul","full_name":"Katul, Gabriel G.","first_name":"Gabriel G."}],"intvolume":"       117","das_tickbox":"1","issue":"13","publication_status":"published","extern":"1"},{"arxiv":1,"intvolume":"         2","issue":"1","publication_status":"published","oa_version":"Preprint","doi":"10.2140/paa.2020.2.35","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"first_name":"Elliott H.","last_name":"Lieb","full_name":"Lieb, Elliott H."},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"external_id":{"arxiv":["1903.04046"]},"article_type":"original","abstract":[{"text":"We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space.","lang":"eng"}],"publisher":"Mathematical Sciences Publishers","_id":"14891","scopus_import":"1","page":"35-73","date_created":"2024-01-28T23:01:44Z","quality_controlled":"1","corr_author":"1","month":"01","publication":"Pure and Applied Analysis","status":"public","oa":1,"department":[{"_id":"RoSe"}],"date_published":"2020-01-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","year":"2020","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"date_updated":"2026-08-12T08:47:14Z","day":"01","volume":2,"title":"The local density approximation in density functional theory","citation":{"short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.","ista":"Lewin M, Lieb EH, Seiringer R. 2020. The local density approximation in density functional theory. Pure and Applied Analysis. 2(1), 35–73.","mla":"Lewin, Mathieu, et al. “The Local Density Approximation in Density Functional Theory.” <i>Pure and Applied Analysis</i>, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:<a href=\"https://doi.org/10.2140/paa.2020.2.35\">10.2140/paa.2020.2.35</a>.","apa":"Lewin, M., Lieb, E. H., &#38; Seiringer, R. (2020). The local density approximation in density functional theory. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2020.2.35\">https://doi.org/10.2140/paa.2020.2.35</a>","ama":"Lewin M, Lieb EH, Seiringer R. The local density approximation in density functional theory. <i>Pure and Applied Analysis</i>. 2020;2(1):35-73. doi:<a href=\"https://doi.org/10.2140/paa.2020.2.35\">10.2140/paa.2020.2.35</a>","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “The Local Density Approximation in Density Functional Theory.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2020. <a href=\"https://doi.org/10.2140/paa.2020.2.35\">https://doi.org/10.2140/paa.2020.2.35</a>.","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “The local density approximation in density functional theory,” <i>Pure and Applied Analysis</i>, vol. 2, no. 1. Mathematical Sciences Publishers, pp. 35–73, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1903.04046","open_access":"1"}],"article_processing_charge":"No"},{"month":"05","publication":"Annales de l'Institut Henri Poincaré C","oa":1,"status":"public","isi":1,"quality_controlled":"1","_id":"7388","scopus_import":"1","date_created":"2020-01-29T09:39:41Z","page":"663-682","publisher":"Elsevier","article_type":"original","abstract":[{"text":"We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general ‘integration by parts’ formula that provides a number of linear identities for the renormalisation constants.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07635"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Nondivergence form quasilinear heat equations driven by space-time white noise","citation":{"mla":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C</i>, vol. 37, no. 3, Elsevier, 2020, pp. 663–82, doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>.","ista":"Gerencser M. 2020. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C. 37(3), 663–682.","short":"M. Gerencser, Annales de l’Institut Henri Poincaré C 37 (2020) 663–682.","chicago":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>.","ieee":"M. Gerencser, “Nondivergence form quasilinear heat equations driven by space-time white noise,” <i>Annales de l’Institut Henri Poincaré C</i>, vol. 37, no. 3. Elsevier, pp. 663–682, 2020.","apa":"Gerencser, M. (2020). Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>","ama":"Gerencser M. Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C</i>. 2020;37(3):663-682. doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>"},"volume":37,"day":"01","date_updated":"2026-08-12T09:16:09Z","publication_identifier":{"issn":["0294-1449"]},"type":"journal_article","year":"2020","date_published":"2020-05-01T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"issue":"3","publication_status":"published","intvolume":"        37","arxiv":1,"external_id":{"arxiv":["1902.07635"],"isi":["000531049800007"]},"author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1016/j.anihpc.2020.01.003","oa_version":"Preprint"},{"author":[{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"},{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"last_name":"Goldsmith","full_name":"Goldsmith, Andrea","first_name":"Andrea"}],"doi":"10.1109/ISIT44484.2020.9174141","oa_version":"Preprint","external_id":{"isi":["000714963400069"],"arxiv":["1909.04892"]},"related_material":{"record":[{"relation":"later_version","status":"public","id":"9047"}]},"arxiv":1,"article_number":"401-406","publication_status":"published","day":"01","date_updated":"2026-08-12T11:12:23Z","publication_identifier":{"issn":["2157-8095"],"isbn":["9781728164328"]},"type":"conference","year":"2020","date_published":"2020-06-01T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"MaMo"}],"article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"conference":{"end_date":"2020-06-26","name":"ISIT: International Symposium on Information Theory","location":"Los Angeles, CA, United States","start_date":"2020-06-21"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Simplified successive cancellation decoding of polar codes has sublinear latency","citation":{"short":"M. Mondelli, S.A. Hashemi, J. Cioffi, A. Goldsmith, in:, IEEE International Symposium on Information Theory, IEEE, 2020.","ista":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. 2020. Simplified successive cancellation decoding of polar codes has sublinear latency. IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2020–June, 401–406.","mla":"Mondelli, Marco, et al. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” <i>IEEE International Symposium on Information Theory</i>, vol. 2020–June, 401–406, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>.","ieee":"M. Mondelli, S. A. Hashemi, J. Cioffi, and A. Goldsmith, “Simplified successive cancellation decoding of polar codes has sublinear latency,” in <i>IEEE International Symposium on Information Theory</i>, Los Angeles, CA, United States, 2020, vol. 2020–June.","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John Cioffi, and Andrea Goldsmith. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” In <i>IEEE International Symposium on Information Theory</i>, Vol. 2020–June. IEEE, 2020. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>.","ama":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. Simplified successive cancellation decoding of polar codes has sublinear latency. In: <i>IEEE International Symposium on Information Theory</i>. Vol 2020-June. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J., &#38; Goldsmith, A. (2020). Simplified successive cancellation decoding of polar codes has sublinear latency. In <i>IEEE International Symposium on Information Theory</i> (Vol. 2020–June). Los Angeles, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>"},"volume":"2020-June","_id":"8536","date_created":"2020-09-20T22:01:37Z","scopus_import":"1","publisher":"IEEE","abstract":[{"lang":"eng","text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1."}],"acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162 and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei.","month":"06","publication":"IEEE International Symposium on Information Theory","oa":1,"status":"public","isi":1,"quality_controlled":"1"},{"oa_version":"Published Version","doi":"10.1098/rsif.2019.0721","author":[{"first_name":"J.","full_name":"Larsson, J.","last_name":"Larsson"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"S.","full_name":"Bengmark, S.","last_name":"Bengmark"},{"full_name":"Lundh, T.","last_name":"Lundh","first_name":"T."},{"first_name":"R. K.","full_name":"Butlin, R. K.","last_name":"Butlin"}],"file":[{"creator":"dernst","file_name":"2020_JournRoyalSociety_Larsson.pdf","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T12:31:16Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":1556190,"file_id":"7660","checksum":"4eb102304402f5c56432516b84df86d6"}],"intvolume":"        17","article_number":"20190721","publication_status":"published","issue":"163","has_accepted_license":"1","department":[{"_id":"NiBa"}],"date_published":"2020-02-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1742-5689"],"eissn":["1742-5662"]},"year":"2020","type":"journal_article","date_updated":"2026-08-12T14:06:19Z","day":"01","file_date_updated":"2020-07-14T12:48:01Z","volume":17,"citation":{"ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of the Royal Society Interface</i>. 2020;17(163). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>","ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 163. Royal Society, 2020.","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., &#38; Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>","chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of the Royal Society Interface 17 (2020).","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 163, 20190721, Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>.","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of the Royal Society Interface. 17(163), 20190721."},"title":"A developmentally descriptive method for quantifying shape in gastropod shells","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","article_type":"original","abstract":[{"text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.","lang":"eng"}],"publisher":"Royal Society","date_created":"2020-04-08T15:19:17Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"7651","quality_controlled":"1","ddc":["570"],"status":"public","oa":1,"month":"02","publication":"Journal of the Royal Society Interface"},{"quality_controlled":"1","publication":"Journal of the Royal Society Interface","month":"01","oa":1,"status":"public","isi":1,"publisher":"Royal Society","abstract":[{"text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.","lang":"eng"}],"article_type":"original","acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","_id":"7431","scopus_import":"1","date_created":"2020-02-02T23:01:03Z","title":"Decomposing information into copying versus transformation","citation":{"short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623.","mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162, 0623, Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>.","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162. Royal Society, 2020.","chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>.","apa":"Kolchinsky, A., &#38; Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. 2020;17(162). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>"},"volume":17,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.10693"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-29T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"date_updated":"2026-08-12T14:08:47Z","day":"29","year":"2020","type":"journal_article","publication_identifier":{"eissn":["1742-5662"]},"intvolume":"        17","issue":"162","article_number":"0623","publication_status":"published","arxiv":1,"pmid":1,"external_id":{"isi":["000538369800002"],"pmid":["31964273"],"arxiv":["1903.10693"]},"oa_version":"Preprint","author":[{"first_name":"Artemy","last_name":"Kolchinsky","full_name":"Kolchinsky, Artemy"},{"last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1098/rsif.2019.0623"},{"citation":{"ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">https://doi.org/10.6084/m9.figshare.5973013.v1</a>","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">https://doi.org/10.6084/m9.figshare.5973013.v1</a>.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>.","mla":"Ibsen-Jensen, Rasmus, et al. <i>Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners</i>. Royal Society, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>."},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"198"}]},"title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","OA_type":"hybrid","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"department":[{"_id":"KrCh"}],"date_published":"2020-10-15T00:00:00Z","oa_version":"Published Version","type":"research_data_reference","year":"2020","doi":"10.6084/m9.figshare.5973013.v1","day":"15","author":[{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"date_updated":"2026-08-12T14:08:28Z","oa":1,"status":"public","month":"10","abstract":[{"text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners","lang":"eng"}],"publisher":"Royal Society","date_created":"2021-08-06T13:09:57Z","OA_place":"publisher","_id":"9814"},{"doi":"10.1063/1.5122969","author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan","full_name":"Yalniz, Gökhan","last_name":"Yalniz","orcid":"0000-0002-8490-9312"},{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B"}],"oa_version":"Published Version","external_id":{"arxiv":["1910.04584"],"isi":["000519254800002"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19684"}]},"arxiv":1,"issue":"3","article_number":"033109","publication_status":"published","intvolume":"        30","year":"2020","type":"journal_article","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"date_updated":"2026-09-02T08:16:31Z","day":"03","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"date_published":"2020-03-03T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1063/1.5122969","open_access":"1"}],"article_processing_charge":"No","volume":30,"title":"Inferring symbolic dynamics of chaotic flows from persistence","citation":{"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>.","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>","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>","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.","short":"G. Yalniz, N.B. Budanur, Chaos 30 (2020).","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>.","ista":"Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109."},"_id":"7563","date_created":"2020-03-04T08:06:25Z","scopus_import":"1","article_type":"original","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."}],"publisher":"AIP Publishing","corr_author":"1","isi":1,"publication":"Chaos","month":"03","status":"public","oa":1,"ddc":["530"],"quality_controlled":"1"},{"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Fäßler, F., Zens, B., Hauschild, R., &#38; Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. 2020;212(3). doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>.","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” <i>Journal of Structural Biology</i>, vol. 212, no. 3. Elsevier, 2020.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>, vol. 212, no. 3, 107633, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>.","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633."},"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","volume":212,"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"date_updated":"2026-09-05T22:30:02Z","day":"01","file_date_updated":"2020-12-10T14:01:10Z","type":"journal_article","publication_identifier":{"issn":["1047-8477"]},"year":"2020","language":[{"iso":"eng"}],"date_published":"2020-12-01T00:00:00Z","department":[{"_id":"FlSc"}],"has_accepted_license":"1","status":"public","oa":1,"month":"12","publication":"Journal of Structural Biology","isi":1,"corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"quality_controlled":"1","ddc":["570"],"scopus_import":"1","date_created":"2020-09-29T13:24:06Z","_id":"8586","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"publisher":"Elsevier","article_type":"original","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"external_id":{"isi":["000600997800008"],"pmid":["32987119"]},"related_material":{"record":[{"id":"14592","status":"public","relation":"used_in_publication"},{"id":"12491","status":"public","relation":"dissertation_contains"}]},"pmid":1,"author":[{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"file":[{"file_name":"2020_JourStrucBiology_Faessler.pdf","creator":"dernst","success":1,"date_updated":"2020-12-10T14:01:10Z","date_created":"2020-12-10T14:01:10Z","checksum":"c48cbf594e84fc2f91966ffaafc0918c","access_level":"open_access","relation":"main_file","file_id":"8937","content_type":"application/pdf","file_size":7076870}],"doi":"10.1016/j.jsb.2020.107633","oa_version":"Published Version","publication_status":"published","article_number":"107633","issue":"3","intvolume":"       212"},{"intvolume":"       105","publication_status":"published","related_material":{"record":[{"id":"11196","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/"}]},"pmid":1,"external_id":{"isi":["000520854700008"],"pmid":["31928842"]},"oa_version":"Published Version","file":[{"file_name":"2020_Neuron_BorgesMerjane.pdf","creator":"dernst","date_updated":"2020-11-20T08:58:53Z","date_created":"2020-11-20T08:58:53Z","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":9712957,"file_id":"8778","checksum":"3582664addf26859e86ac5bec3e01416"}],"author":[{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","full_name":"Kim, Olena","orcid":"0000-0003-2344-1039","last_name":"Kim"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"doi":"10.1016/j.neuron.2019.12.022","quality_controlled":"1","ddc":["570"],"oa":1,"status":"public","month":"03","publication":"Neuron","isi":1,"corr_author":"1","publisher":"Elsevier","article_type":"original","abstract":[{"text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses.","lang":"eng"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","ec_funded":1,"page":"992-1006","scopus_import":"1","date_created":"2020-02-10T15:59:45Z","_id":"7473","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"citation":{"short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>, vol. 105, Elsevier, 2020, pp. 992–1006, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>.","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” <i>Neuron</i>, vol. 105. Elsevier, pp. 992–1006, 2020.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. 2020;105:992-1006. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>","apa":"Borges Merjane, C., Kim, O., &#38; Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>."},"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","volume":105,"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"},{"call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_published":"2020-03-18T00:00:00Z","has_accepted_license":"1","department":[{"_id":"PeJo"}],"date_updated":"2026-09-05T22:30:04Z","day":"18","file_date_updated":"2020-11-20T08:58:53Z","publication_identifier":{"issn":["0896-6273"]},"year":"2020","type":"journal_article"},{"publication_status":"published","intvolume":"         5","external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","description":"News on IST Homepage"}],"record":[{"id":"14280","status":"public","relation":"dissertation_contains"}]},"pmid":1,"author":[{"first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","last_name":"Baranova","full_name":"Baranova, Natalia S."},{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora","first_name":"Víctor M."},{"first_name":"Carlos","full_name":"Alfonso, Carlos","last_name":"Alfonso"},{"full_name":"Lopez Pelegrin, Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D"},{"full_name":"Rivas, Germán","last_name":"Rivas","first_name":"Germán"},{"first_name":"Waldemar","last_name":"Vollmer","full_name":"Vollmer, Waldemar"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"}],"doi":"10.1038/s41564-019-0657-5","oa_version":"Submitted Version","publication":"Nature Microbiology","month":"01","oa":1,"status":"public","corr_author":"1","isi":1,"quality_controlled":"1","_id":"7387","page":"407-417","scopus_import":"1","date_created":"2020-01-28T16:14:41Z","publisher":"Springer Nature","ec_funded":1,"abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}],"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","article_type":"letter_note","main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","citation":{"chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>.","ieee":"N. S. Baranova <i>et al.</i>, “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” <i>Nature Microbiology</i>, vol. 5. Springer Nature, pp. 407–417, 2020.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. 2020;5:407-417. doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>, vol. 5, Springer Nature, 2020, pp. 407–17, doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>.","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417."},"project":[{"call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","name":"Reconstitution of bacterial cell wall synthesis","grant_number":"LT000824/2016"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163"}],"volume":5,"date_updated":"2026-09-05T22:30:11Z","day":"20","year":"2020","type":"journal_article","publication_identifier":{"issn":["2058-5276"]},"date_published":"2020-01-20T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"MaLo"}]},{"intvolume":"         9","article_number":"e55190","publication_status":"published","pmid":1,"related_material":{"record":[{"id":"12891","relation":"dissertation_contains","status":"public"}]},"external_id":{"isi":["000531544400001"],"pmid":["32250246"]},"oa_version":"Published Version","doi":"10.7554/elife.55190","author":[{"last_name":"Schauer","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","last_name":"Nunes Pinheiro","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"file":[{"creator":"dernst","file_name":"2020_eLife_Schauer.pdf","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-25T15:15:43Z","file_size":7744848,"file_id":"7890","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f6aad884cf706846ae9357fcd728f8b5"}],"ddc":["570"],"quality_controlled":"1","corr_author":"1","isi":1,"publication":"eLife","month":"04","status":"public","oa":1,"ec_funded":1,"article_type":"original","abstract":[{"lang":"eng","text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order."}],"publisher":"eLife Sciences Publications","_id":"7888","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_created":"2020-05-25T15:01:40Z","scopus_import":"1","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429"}],"volume":9,"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","citation":{"ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., &#38; Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>, vol. 9, e55190, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"CaHe"},{"_id":"Bio"}],"date_published":"2020-04-06T00:00:00Z","language":[{"iso":"eng"}],"year":"2020","type":"journal_article","publication_identifier":{"issn":["2050-084X"]},"file_date_updated":"2020-07-14T12:48:04Z","date_updated":"2026-09-05T22:30:14Z","day":"06"},{"doi":"10.1038/s41586-020-2283-z","author":[{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat"},{"last_name":"Gärtner","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"},{"last_name":"Aguilera Servin","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6625-3348","last_name":"Hons","full_name":"Hons, Miroslav","first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Piel","full_name":"Piel, Matthieu","first_name":"Matthieu"},{"full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones","first_name":"Andrew"},{"first_name":"Raphael","last_name":"Voituriez","full_name":"Voituriez, Raphael"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"oa_version":"Preprint","external_id":{"pmid":["32581372"],"isi":["000532688300008"]},"pmid":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/","relation":"press_release"}],"record":[{"id":"12401","relation":"dissertation_contains","status":"public"},{"id":"14697","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","intvolume":"       582","year":"2020","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"type":"journal_article","day":"25","date_updated":"2026-09-05T22:30:15Z","department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"language":[{"iso":"eng"}],"date_published":"2020-06-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","main_file_link":[{"url":"https://doi.org/10.1101/793919","open_access":"1"}],"article_processing_charge":"No","volume":582,"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373"},{"grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>, vol. 582, Springer Nature, 2020, pp. 582–585, doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>.","ieee":"A. Reversat <i>et al.</i>, “Cellular locomotion using environmental topography,” <i>Nature</i>, vol. 582. Springer Nature, pp. 582–585, 2020.","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. <i>Nature</i>. 2020;582:582–585. doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>","chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>."},"title":"Cellular locomotion using environmental topography","page":"582–585","date_created":"2020-05-24T22:01:01Z","scopus_import":"1","_id":"7885","OA_place":"repository","acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","article_type":"original","abstract":[{"text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.","lang":"eng"}],"ec_funded":1,"publisher":"Springer Nature","isi":1,"status":"public","oa":1,"publication":"Nature","month":"06","quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}]},{"publisher":"ML Research Press","abstract":[{"text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks.","lang":"eng"}],"acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","date_created":"2021-02-25T09:36:22Z","page":"8773-8784","_id":"9198","ddc":["000"],"quality_controlled":"1","status":"public","oa":1,"publication":"Proceedings of the 37th International Conference on Machine Learning","month":"07","language":[{"iso":"eng"}],"date_published":"2020-07-13T00:00:00Z","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"has_accepted_license":"1","day":"13","date_updated":"2026-09-05T22:30:17Z","file_date_updated":"2021-03-02T15:38:14Z","year":"2020","type":"conference","citation":{"ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","mla":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, ML Research Press, 2020, pp. 8773–84.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, 2020, vol. 119, pp. 8773–8784.","chicago":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:8773–84. ML Research Press, 2020.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ML Research Press; 2020:8773-8784.","apa":"Shevchenko, A., &#38; Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 8773–8784). ML Research Press."},"title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","volume":119,"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","arxiv":1,"intvolume":"       119","publication_status":"published","oa_version":"Published Version","author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko"},{"last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"file":[{"success":1,"date_updated":"2021-03-02T15:38:14Z","date_created":"2021-03-02T15:38:14Z","creator":"dernst","file_name":"2020_PMLR_Shevchenko.pdf","file_size":5336380,"content_type":"application/pdf","file_id":"9217","relation":"main_file","access_level":"open_access","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe"}],"related_material":{"record":[{"id":"17465","relation":"dissertation_contains","status":"public"}]},"external_id":{"arxiv":["1912.10095"]}},{"article_number":"e61147","publication_status":"published","issue":"159","doi":"10.3791/61147","file":[{"content_type":"application/pdf","file_id":"7816","file_size":1352186,"access_level":"open_access","relation":"main_file","checksum":"3154ea7f90b9fb45e084cd1c2770597d","date_created":"2020-05-11T08:28:38Z","date_updated":"2020-07-14T12:48:03Z","creator":"rbeattie","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf"}],"author":[{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","full_name":"Beattie, Robert J","last_name":"Beattie","orcid":"0000-0002-8483-8753"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher"},{"full_name":"Amberg, Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H","last_name":"Hansen"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"oa_version":"Published Version","external_id":{"pmid":["32449730"],"isi":["000546406600043"]},"pmid":1,"related_material":{"record":[{"id":"7902","status":"public","relation":"part_of_dissertation"}]},"scopus_import":"1","date_created":"2020-05-11T08:31:20Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"7815","article_type":"original","abstract":[{"text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.","lang":"eng"}],"ec_funded":1,"publisher":"MyJove Corporation","isi":1,"corr_author":"1","status":"public","oa":1,"month":"05","publication":"Journal of Visual Experiments","quality_controlled":"1","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"type":"journal_article","publication_identifier":{"issn":["1940-087X"]},"year":"2020","day":"08","date_updated":"2026-09-05T22:30:19Z","file_date_updated":"2020-07-14T12:48:03Z","has_accepted_license":"1","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"date_published":"2020-05-08T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T01031","name":"Role of Eed in neural stem cell lineage progression"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Molecular mechanisms of radial neuronal migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"citation":{"short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>, no. 159, e61147, MyJove Corporation, 2020, doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>.","ieee":"R. J. Beattie <i>et al.</i>, “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” <i>Journal of Visual Experiments</i>, no. 159. MyJove Corporation, 2020.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., &#38; Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. MyJove Corporation. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. 2020;(159). doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>","chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>. MyJove Corporation, 2020. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>."},"title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"28"},{"relation":"dissertation_contains","status":"public","id":"7815"},{"relation":"dissertation_contains","status":"public","id":"6830"}]},"oa_version":"Published Version","doi":"10.15479/AT:ISTA:7902","author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"7927","file_size":53134142,"access_level":"closed","relation":"source_file","checksum":"43c172bf006c95b65992d473c7240d13","creator":"xcontreras","file_name":"PhDThesis_Contreras.docx","embargo_to":"open_access","date_created":"2020-06-05T08:18:08Z","date_updated":"2021-06-07T22:30:03Z"},{"date_created":"2020-06-05T08:18:07Z","date_updated":"2021-06-07T22:30:03Z","creator":"xcontreras","file_name":"PhDThesis_Contreras.pdf","checksum":"addfed9128271be05cae3608e03a6ec0","embargo":"2021-06-06","file_id":"7928","file_size":35117191,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"title":"Genetic dissection of neural development in health and disease at single cell resolution","citation":{"ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","apa":"Contreras, X. (2020). <i>Genetic dissection of neural development in health and disease at single cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","mla":"Contreras, Ximena. <i>Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","department":[{"_id":"SiHi"}],"has_accepted_license":"1","date_published":"2020-06-05T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"year":"2020","type":"dissertation","file_date_updated":"2021-06-07T22:30:03Z","day":"05","date_updated":"2026-06-18T19:12:39Z","ddc":["570"],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"corr_author":"1","month":"06","status":"public","oa":1,"ec_funded":1,"abstract":[{"text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"degree_awarded":"PhD","_id":"7902","OA_place":"publisher","date_created":"2020-05-29T08:27:32Z","page":"214"},{"_id":"8190","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"date_created":"2020-08-02T22:00:57Z","scopus_import":"1","publisher":"Rockefeller University Press","article_type":"letter_note","month":"07","publication":"The Journal of Cell Biology","oa":1,"status":"public","isi":1,"ddc":["570"],"file_date_updated":"2021-02-02T23:30:03Z","date_updated":"2025-06-12T07:34:40Z","day":"22","publication_identifier":{"eissn":["1540-8140"]},"type":"journal_article","year":"2020","date_published":"2020-07-22T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"MiSi"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Zena Werb (1945-2020): Cell biology in context","citation":{"ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” <i>The Journal of Cell Biology</i>, vol. 219, no. 8. Rockefeller University Press, 2020.","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>.","apa":"Sixt, M. K., &#38; Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. 2020;219(8). doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>"},"volume":219,"issue":"8","article_number":"e202007029","publication_status":"published","intvolume":"       219","author":[{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","last_name":"Huttenlocher","full_name":"Huttenlocher, Anna"}],"file":[{"relation":"main_file","access_level":"open_access","file_size":830725,"file_id":"8200","content_type":"application/pdf","embargo":"2021-02-01","checksum":"30016d778d266b8e17d01094917873b8","date_created":"2020-08-04T13:11:52Z","date_updated":"2021-02-02T23:30:03Z","file_name":"2020_JCB_Sixt.pdf","creator":"dernst"}],"doi":"10.1083/jcb.202007029","oa_version":"Published Version","external_id":{"isi":["000573631000004"],"pmid":["32699885"]},"pmid":1},{"publication_status":"published","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7001"},{"id":"6508","relation":"part_of_dissertation","status":"public"},{"id":"735","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"661"}]},"doi":"10.15479/AT:ISTA:8350","file":[{"file_name":"Shayan-Thesis-Final.docx","creator":"sshamip","embargo_to":"open_access","date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:27Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8351","file_size":65194814,"access_level":"closed","relation":"source_file","checksum":"6e47871c74f85008b9876112eb3fcfa1"},{"checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","embargo":"2021-09-10","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":23729605,"file_id":"8352","file_name":"Shayan-Thesis-Final.pdf","creator":"sshamip","date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:13Z"}],"author":[{"last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","corr_author":"1","status":"public","oa":1,"month":"09","ddc":["570"],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"degree_awarded":"PhD","page":"107","date_created":"2020-09-09T11:12:10Z","_id":"8350","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","citation":{"short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","mla":"Shamipour, Shayan. <i>Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes </i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>","apa":"Shamipour, S. (2020). <i>Bulk actin dynamics drive phase segregation in zebrafish oocytes </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>."},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","year":"2020","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2025-09-11T07:08:52Z","day":"09","file_date_updated":"2021-09-11T22:30:05Z","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2020-09-09T00:00:00Z"}]