[{"article_type":"original","author":[{"last_name":"Peleg","full_name":"Peleg, Nadav","first_name":"Nadav"},{"first_name":"Frank","full_name":"Blumensaat, Frank","last_name":"Blumensaat"},{"last_name":"Molnar","first_name":"Peter","full_name":"Molnar, Peter"},{"first_name":"Simone","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi"},{"last_name":"Burlando","first_name":"Paolo","full_name":"Burlando, Paolo"}],"OA_type":"gold","publication_status":"published","day":"14","abstract":[{"text":"The performance of urban drainage systems is typically examined using hydrological and hydrodynamic models where rainfall input is uniformly distributed, i.e., derived from a single or very few rain gauges. When models are fed with a single uniformly distributed rainfall realization, the response of the urban drainage system to the rainfall variability remains unexplored. The goal of this study was to understand how climate variability and spatial rainfall variability, jointly or individually considered, affect the response of a calibrated hydrodynamic urban drainage model. A stochastic spatially distributed rainfall generator (STREAP – Space-Time Realizations of Areal Precipitation) was used to simulate many realizations of rainfall for a 30-year period, accounting for both climate variability and spatial rainfall variability. The generated rainfall ensemble was used as input into a calibrated hydrodynamic model (EPA SWMM – the US EPA's Storm Water Management Model) to simulate surface runoff and channel flow in a small urban catchment in the city of Lucerne, Switzerland. The variability of peak flows in response to rainfall of different return periods was evaluated at three different locations in the urban drainage network and partitioned among its sources. The main contribution to the total flow variability was found to originate from the natural climate variability (on average over 74 %). In addition, the relative contribution of the spatial rainfall variability to the total flow variability was found to increase with longer return periods. This suggests that while the use of spatially distributed rainfall data can supply valuable information for sewer network design (typically based on rainfall with return periods from 5 to 15 years), there is a more pronounced relevance when conducting flood risk assessments for larger return periods. The results show the importance of using multiple distributed rainfall realizations in urban hydrology studies to capture the total flow variability in the response of the urban drainage systems to heavy rainfall events.","lang":"eng"}],"fulldoi":"https://doi.org/10.5194/hess-21-1559-2017","OA_place":"publisher","citation":{"apa":"Peleg, N., Blumensaat, F., Molnar, P., Fatichi, S., &#38; Burlando, P. (2017). Partitioning the impacts of spatial and climatological rainfall variability in urban drainage modeling. <i>Hydrology and Earth System Sciences</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/hess-21-1559-2017\">https://doi.org/10.5194/hess-21-1559-2017</a>","ieee":"N. Peleg, F. Blumensaat, P. Molnar, S. Fatichi, and P. Burlando, “Partitioning the impacts of spatial and climatological rainfall variability in urban drainage modeling,” <i>Hydrology and Earth System Sciences</i>, vol. 21, no. 3. Copernicus Publications, pp. 1559–1572, 2017.","short":"N. Peleg, F. Blumensaat, P. Molnar, S. Fatichi, P. Burlando, Hydrology and Earth System Sciences 21 (2017) 1559–1572.","ista":"Peleg N, Blumensaat F, Molnar P, Fatichi S, Burlando P. 2017. Partitioning the impacts of spatial and climatological rainfall variability in urban drainage modeling. Hydrology and Earth System Sciences. 21(3), 1559–1572.","mla":"Peleg, Nadav, et al. “Partitioning the Impacts of Spatial and Climatological Rainfall Variability in Urban Drainage Modeling.” <i>Hydrology and Earth System Sciences</i>, vol. 21, no. 3, Copernicus Publications, 2017, pp. 1559–72, doi:<a href=\"https://doi.org/10.5194/hess-21-1559-2017\">10.5194/hess-21-1559-2017</a>.","ama":"Peleg N, Blumensaat F, Molnar P, Fatichi S, Burlando P. Partitioning the impacts of spatial and climatological rainfall variability in urban drainage modeling. <i>Hydrology and Earth System Sciences</i>. 2017;21(3):1559-1572. doi:<a href=\"https://doi.org/10.5194/hess-21-1559-2017\">10.5194/hess-21-1559-2017</a>","chicago":"Peleg, Nadav, Frank Blumensaat, Peter Molnar, Simone Fatichi, and Paolo Burlando. “Partitioning the Impacts of Spatial and Climatological Rainfall Variability in Urban Drainage Modeling.” <i>Hydrology and Earth System Sciences</i>. Copernicus Publications, 2017. <a href=\"https://doi.org/10.5194/hess-21-1559-2017\">https://doi.org/10.5194/hess-21-1559-2017</a>."},"issue":"3","das_tickbox":"1","publication":"Hydrology and Earth System Sciences","volume":21,"DOAJ_listed":"1","type":"journal_article","oa":1,"publisher":"Copernicus Publications","scopus_import":"1","doi":"10.5194/hess-21-1559-2017","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)"},"intvolume":"        21","date_updated":"2026-08-12T13:13:18Z","date_published":"2017-03-14T00:00:00Z","date_created":"2026-07-27T12:30:23Z","oa_version":"Published Version","title":"Partitioning the impacts of spatial and climatological rainfall variability in urban drainage modeling","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","year":"2017","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.5194/hess-21-1559-2017","open_access":"1"}],"page":"1559-1572","license":"https://creativecommons.org/licenses/by/3.0/","month":"03","publication_identifier":{"issn":["1027-5606"],"eissn":["1607-7938"]},"language":[{"iso":"eng"}],"extern":"1","_id":"22489"},{"department":[{"_id":"JiFr"},{"_id":"Bio"}],"ddc":["580"],"file":[{"file_size":57678,"relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:16:31Z","content_type":"application/pdf","file_id":"5219","date_created":"2018-12-12T10:16:31Z","creator":"system","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf"},{"relation":"main_file","file_size":1317820,"file_id":"5220","content_type":"application/pdf","date_updated":"2018-12-12T10:16:32Z","access_level":"open_access","date_created":"2018-12-12T10:16:32Z","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","creator":"system"}],"date_created":"2018-12-11T11:50:01Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"date_published":"2017-01-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","oa_version":"Published Version","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5565"}]},"external_id":{"isi":["000397847200041"]},"isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300"}],"status":"public","year":"2017","ec_funded":1,"_id":"1078","pubrep_id":"808","language":[{"iso":"eng"}],"month":"01","has_accepted_license":"1","publist_id":"6302","author":[{"last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel","first_name":"Daniel","orcid":"0000-0002-6862-1247"},{"first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"file_date_updated":"2018-12-12T10:16:32Z","fulldoi":"https://doi.org/10.3791/55044","abstract":[{"text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. ","lang":"eng"}],"publication_status":"published","day":"18","type":"journal_article","volume":2017,"publication":"Journal of Visualized Experiments","issue":"119","citation":{"apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments</i>. MyJove Corporation. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of Visualized Experiments</i>, vol. 2017, no. 119. MyJove Corporation, 2017.","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of Visualized Experiments. 2017(119), e55044.","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments 2017 (2017).","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments</i>, vol. 2017, no. 119, e55044, MyJove Corporation, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments</i>. MyJove Corporation, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>."},"article_number":"e55044","intvolume":"      2017","date_updated":"2026-08-12T14:11:08Z","doi":"10.3791/55044","scopus_import":"1","publisher":"MyJove Corporation","oa":1},{"citation":{"chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:66\">https://doi.org/10.15479/AT:ISTA:66</a>.","short":"D. von Wangenheim, R. Hauschild, J. Friml, (2017).","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:66\">10.15479/AT:ISTA:66</a>.","mla":"von Wangenheim, Daniel, et al. <i>Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:66\">10.15479/AT:ISTA:66</a>.","ama":"von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:66\">10.15479/AT:ISTA:66</a>","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel.” Institute of Science and Technology Austria, 2017.","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:66\">https://doi.org/10.15479/AT:ISTA:66</a>"},"type":"research_data","oa":1,"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:66","date_updated":"2026-08-12T14:11:07Z","author":[{"orcid":"0000-0002-6862-1247","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publist_id":"6302","day":"10","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. "}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:66","file_date_updated":"2020-07-14T12:47:03Z","year":"2017","status":"public","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"has_accepted_license":"1","month":"04","_id":"5565","ec_funded":1,"date_published":"2017-04-10T00:00:00Z","date_created":"2018-12-12T12:31:34Z","file":[{"date_created":"2018-12-12T13:02:33Z","checksum":"b7552fc23540a85dc5a22fd4484eae71","file_name":"IST-2017-66-v1+1_WangenheimHighResolution55044-NEW_1.mp4","creator":"system","relation":"main_file","file_size":101497758,"date_updated":"2020-07-14T12:47:03Z","content_type":"video/mp4","file_id":"5599","access_level":"open_access"}],"ddc":["580"],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"related_material":{"record":[{"id":"1078","relation":"research_paper","status":"public"}]},"oa_version":"Published Version","datarep_id":"66","title":"Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel","acknowledgement":"fund: FP7-ERC 0101109","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":"1","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","oa":1,"date_updated":"2026-08-12T14:14:50Z","intvolume":"        70","doi":"10.31263/voebm.v70i2.1678","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>.","short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 200–207.","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 200–207.","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>, vol. 70, no. 2, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2017, pp. 200–07, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>.","ama":"Petritsch B. Metadata for research data in practice. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2017;70(2):200-207. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>","ieee":"B. Petritsch, “Metadata for research data in practice,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 70, no. 2. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 200–207, 2017.","apa":"Petritsch, B. (2017). Metadata for research data in practice. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>"},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","volume":70,"type":"journal_article","issue":"2","das_tickbox":"1","day":"01","publication_status":"published","fulldoi":"https://doi.org/10.31263/voebm.v70i2.1678","corr_author":"1","file_date_updated":"2020-07-14T12:48:11Z","abstract":[{"text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.","lang":"eng"}],"publist_id":"6823","author":[{"orcid":"0000-0003-2724-4614","first_name":"Barbara","full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1022-2588"]},"has_accepted_license":"1","month":"08","_id":"825","year":"2017","status":"public","page":"200 - 207","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","title":"Metadata for research data in practice","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file":[{"date_updated":"2020-07-14T12:48:11Z","content_type":"application/pdf","file_id":"5850","access_level":"open_access","relation":"main_file","file_size":7843975,"file_name":"2017_VOEB_Petritsch.pdf","creator":"dernst","date_created":"2019-01-18T13:32:17Z","checksum":"7c4544d07efa2c2add8612b489abb4e2"}],"date_created":"2018-12-11T11:48:42Z","date_published":"2017-08-01T00:00:00Z","department":[{"_id":"E-Lib"}],"ddc":["020"]},{"arxiv":1,"publication_status":"published","day":"13","fulldoi":"https://doi.org/10.1103/PhysRevB.95.024506","abstract":[{"text":"Selected universal experimental properties of high-temperature superconducting (HTS) cuprates have been singled out in the last decade. One of the pivotal challenges in this field is the designation of a consistent interpretation framework within which we can describe quantitatively the universal features of those systems. Here we analyze in a detailed manner the principal experimental data and compare them quantitatively with the approach based on a single-band model of strongly correlated electrons supplemented with strong antiferromagnetic (super)exchange interaction (the so-called t−J−U model). The model rationale is provided by estimating its microscopic parameters on the basis of the three-band approach for the Cu-O plane. We use our original full Gutzwiller wave-function solution by going beyond the renormalized mean-field theory (RMFT) in a systematic manner. Our approach reproduces very well the observed hole doping (δ) dependence of the kinetic-energy gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer features of the cuprates. The calculated Fermi velocity in the nodal direction is practically δ-independent and its universal value agrees very well with that determined experimentally. Also, a weak doping dependence of the Fermi wave vector leads to an almost constant value of the effective mass in a pure superconducting phase which is both observed in experiment and reproduced within our approach. An assessment of the currently used models (t−J, Hubbard) is carried out and the results of the canonical RMFT as a zeroth-order solution are provided for comparison to illustrate the necessity of the introduced higher-order contributions.","lang":"eng"}],"publist_id":"6195","author":[{"first_name":"Jozef","full_name":"Spałek, Jozef","last_name":"Spałek"},{"last_name":"Zegrodnik","first_name":"Michał","full_name":"Zegrodnik, Michał"},{"last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675"}],"publisher":"American Physical Society","scopus_import":"1","oa":1,"date_updated":"2026-08-12T14:23:50Z","intvolume":"        95","doi":"10.1103/PhysRevB.95.024506","article_number":"024506","citation":{"ista":"Spałek J, Zegrodnik M, Kaczmarczyk J. 2017. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B. 95(2), 024506.","short":"J. Spałek, M. Zegrodnik, J. Kaczmarczyk, Physical Review B 95 (2017).","mla":"Spałek, Jozef, et al. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” <i>Physical Review B</i>, vol. 95, no. 2, 024506, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.95.024506\">10.1103/PhysRevB.95.024506</a>.","ama":"Spałek J, Zegrodnik M, Kaczmarczyk J. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. <i>Physical Review B</i>. 2017;95(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.95.024506\">10.1103/PhysRevB.95.024506</a>","chicago":"Spałek, Jozef, Michał Zegrodnik, and Jan Kaczmarczyk. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.95.024506\">https://doi.org/10.1103/PhysRevB.95.024506</a>.","apa":"Spałek, J., Zegrodnik, M., &#38; Kaczmarczyk, J. (2017). Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.95.024506\">https://doi.org/10.1103/PhysRevB.95.024506</a>","ieee":"J. Spałek, M. Zegrodnik, and J. Kaczmarczyk, “Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment,” <i>Physical Review B</i>, vol. 95, no. 2. American Physical Society, 2017."},"volume":95,"publication":"Physical Review B","type":"journal_article","issue":"2","oa_version":"Submitted Version","title":"Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment","isi":1,"external_id":{"isi":["000391852800006"],"arxiv":["1606.03247"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_created":"2018-12-11T11:50:29Z","date_published":"2017-01-13T00:00:00Z","department":[{"_id":"MiLe"}],"publication_identifier":{"issn":["2469-9950"]},"language":[{"iso":"eng"}],"month":"01","ec_funded":1,"_id":"1162","year":"2017","quality_controlled":"1","status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.03247"}]},{"publication":"Physical Review B","volume":96,"type":"journal_article","issue":"8","article_number":"085410","citation":{"ieee":"G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment,” <i>Physical Review B</i>, vol. 96, no. 8. American Physical Society, 2017.","apa":"Bighin, G., &#38; Lemeshko, M. (2017). Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.085410\">https://doi.org/10.1103/PhysRevB.96.085410</a>","chicago":"Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.085410\">https://doi.org/10.1103/PhysRevB.96.085410</a>.","mla":"Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” <i>Physical Review B</i>, vol. 96, no. 8, 085410, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.085410\">10.1103/PhysRevB.96.085410</a>.","ama":"Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. <i>Physical Review B</i>. 2017;96(8). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.085410\">10.1103/PhysRevB.96.085410</a>","short":"G. Bighin, M. Lemeshko, Physical Review B 96 (2017).","ista":"Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B. 96(8), 085410."},"intvolume":"        96","date_updated":"2026-08-12T14:24:11Z","doi":"10.1103/PhysRevB.96.085410","scopus_import":"1","publisher":"American Physical Society","oa":1,"publist_id":"6404","author":[{"last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"fulldoi":"https://doi.org/10.1103/PhysRevB.96.085410","corr_author":"1","abstract":[{"text":"Recently it was shown that an impurity exchanging orbital angular momentum with a surrounding bath can be described in terms of the angulon quasiparticle [Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor dressed by a many-particle field of boson excitations, and can be formed out of, for example, a molecule or a nonspherical atom in superfluid helium, or out of an electron coupled to lattice phonons or a Bose condensate. Here we develop an approach to the angulon based on the path-integral formalism, which sets the ground for a systematic, perturbative treatment of the angulon problem. The resulting perturbation series can be interpreted in terms of Feynman diagrams, from which, in turn, one can derive a set of diagrammatic rules. These rules extend the machinery of the graphical theory of angular momentum - well known from theoretical atomic spectroscopy - to the case where an environment with an infinite number of degrees of freedom is present. In particular, we show that each diagram can be interpreted as a 'skeleton', which enforces angular momentum conservation, dressed by an additional many-body contribution. This connection between the angulon theory and the graphical theory of angular momentum is particularly important as it allows to systematically and substantially simplify the analytical representation of each diagram. In order to exemplify the technique, we calculate the 1- and 2-loop contributions to the angulon self-energy, the spectral function, and the quasiparticle weight. The diagrammatic theory we develop paves the way to investigate next-to-leading order quantities in a more compact way compared to the variational approaches.","lang":"eng"}],"arxiv":1,"day":"07","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.02616"}],"status":"public","year":"2017","quality_controlled":"1","project":[{"name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902"}],"_id":"995","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"]},"month":"08","department":[{"_id":"MiLe"}],"date_created":"2018-12-11T11:49:36Z","date_published":"2017-08-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"Submitted Version","title":"Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment","isi":1,"external_id":{"isi":["000407017100009"],"arxiv":["1704.02616"]}},{"doi":"10.1103/PhysRevB.96.104201","date_updated":"2026-08-12T14:24:27Z","intvolume":"        96","oa":1,"scopus_import":"1","publisher":"American Physical Society","issue":"10","publication":"Physical Review B","volume":96,"type":"journal_article","article_number":"104201","citation":{"ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” <i>Physical Review B</i>, vol. 96, no. 10. American Physical Society, 2017.","apa":"Serbyn, M., Zlatko, P., &#38; Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>.","short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B 96 (2017).","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B. 96(10), 104201.","mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B</i>, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>.","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>"},"abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"fulldoi":"https://doi.org/10.1103/PhysRevB.96.104201","day":"06","publication_status":"published","arxiv":1,"author":[{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Zlatko","first_name":"Papic","full_name":"Zlatko, Papic"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"}],"publist_id":"6814","_id":"834","month":"09","publication_identifier":{"issn":["2469-9950"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1610.02389","open_access":"1"}],"quality_controlled":"1","year":"2017","status":"public","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"external_id":{"isi":["000409429300004"],"arxiv":["1610.02389"]},"oa_version":"Submitted Version","title":"Thouless energy and multifractality across the many-body localization transition","acknowledgement":"We   acknowledge   useful   discussions with V. Kravtsov, T. Grover, and R. Vasseur.  M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307.  M.S. and D.A.  acknowledge  hospitality  of  KITP,  where  parts  of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","department":[{"_id":"MaSe"}],"date_published":"2017-09-06T00:00:00Z","date_created":"2018-12-11T11:48:45Z"},{"_id":"947","ec_funded":1,"month":"07","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-0045"]},"main_file_link":[{"url":"https://arxiv.org/abs/1703.00219","open_access":"1"}],"status":"public","year":"2017","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"external_id":{"arxiv":["1703.00219"],"isi":["000405194200002"]},"oa_version":"Submitted Version","title":"Quantifying the entropic cost of cellular growth control","department":[{"_id":"GaTk"}],"date_published":"2017-07-10T00:00:00Z","date_created":"2018-12-11T11:49:21Z","doi":"10.1103/PhysRevE.96.010401","date_updated":"2026-08-12T14:29:46Z","intvolume":"        96","oa":1,"publisher":"American Physical Society","scopus_import":"1","issue":"1","das_tickbox":"1","publication":"Physical Review E","volume":96,"type":"journal_article","article_number":"010401","citation":{"chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Review E 96 (2017).","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E. 96(1), 010401.","mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” <i>Physical Review E</i>, vol. 96, no. 1, 010401, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>.","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. <i>Physical Review E</i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” <i>Physical Review E</i>, vol. 96, no. 1. American Physical Society, 2017.","apa":"De Martino, D., Capuani, F., &#38; De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>"},"abstract":[{"lang":"eng","text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence."}],"fulldoi":"https://doi.org/10.1103/PhysRevE.96.010401","publication_status":"published","day":"10","arxiv":1,"author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"last_name":"Capuani","full_name":"Capuani, Fabrizio","first_name":"Fabrizio"},{"last_name":"De Martino","full_name":"De Martino, Andrea","first_name":"Andrea"}],"publist_id":"6470"},{"main_file_link":[{"url":"https://arxiv.org/abs/1612.07061","open_access":"1"}],"project":[{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"year":"2017","quality_controlled":"1","status":"public","_id":"700","ec_funded":1,"month":"07","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-0045"]},"department":[{"_id":"JoFi"}],"date_published":"2017-07-12T00:00:00Z","date_created":"2018-12-11T11:48:00Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000405367200012"],"arxiv":["1612.07061"]},"isi":1,"title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","oa_version":"Submitted Version","das_tickbox":"1","issue":"1","type":"journal_article","volume":96,"publication":"Physical Review E","citation":{"mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i>Physical Review E</i>, vol. 96, no. 1, 012404, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>.","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. <i>Physical Review E</i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E 96 (2017).","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E. 96(1), 012404.","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., &#38; Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” <i>Physical Review E</i>, vol. 96, no. 1. American Physical Society, 2017."},"article_number":"012404","doi":"10.1103/PhysRevE.96.012404","intvolume":"        96","date_updated":"2026-08-12T14:29:59Z","oa":1,"publisher":"American Physical Society","scopus_import":"1","author":[{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh"},{"first_name":"Vahid","full_name":"Salari, Vahid","last_name":"Salari"},{"first_name":"Jack","full_name":"Tuszynski, Jack","last_name":"Tuszynski"},{"last_name":"Cifra","first_name":"Michal","full_name":"Cifra, Michal"},{"last_name":"Simon","full_name":"Simon, Christoph","first_name":"Christoph"}],"publist_id":"6997","abstract":[{"lang":"eng","text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs."}],"fulldoi":"https://doi.org/10.1103/PhysRevE.96.012404","arxiv":1,"publication_status":"published","day":"12"},{"_id":"959","ec_funded":1,"month":"06","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-0045"]},"main_file_link":[{"url":"https://arxiv.org/abs/1703.00853","open_access":"1"}],"page":"062419","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"year":"2017","status":"public","quality_controlled":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1703.00853"],"isi":["000404546400004"]},"isi":1,"title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","oa_version":"Submitted Version","department":[{"_id":"GaTk"}],"date_published":"2017-06-28T00:00:00Z","date_created":"2018-12-11T11:49:25Z","doi":"10.1103/PhysRevE.95.062419","date_updated":"2026-08-12T14:29:35Z","intvolume":"        95","oa":1,"scopus_import":"1","publisher":"American Physical Society","das_tickbox":"1","issue":"6","type":"journal_article","publication":"Physical Review E","volume":95,"citation":{"chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>.","short":"D. De Martino, Physical Review E 95 (2017) 062419.","ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E. 95(6), 062419.","mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i>Physical Review E</i>, vol. 95, no. 6, American Physical Society, 2017, p. 062419, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>.","ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i>Physical Review E</i>. 2017;95(6):062419. doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” <i>Physical Review E</i>, vol. 95, no. 6. American Physical Society, p. 062419, 2017.","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>"},"abstract":[{"text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.","lang":"eng"}],"fulldoi":"https://doi.org/10.1103/PhysRevE.95.062419","day":"28","arxiv":1,"publication_status":"published","author":[{"last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"}],"publist_id":"6446"},{"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"ddc":["570"],"date_created":"2018-12-11T11:50:01Z","file":[{"creator":"dernst","file_name":"2017_JRSI_Redondo.pdf","date_created":"2019-01-18T09:14:02Z","success":1,"access_level":"open_access","date_updated":"2019-01-18T09:14:02Z","content_type":"application/pdf","file_id":"5843","file_size":1092015,"relation":"main_file"}],"date_published":"2017-01-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","oa_version":"Published Version","related_material":{"record":[{"id":"9864","status":"public","relation":"research_data"}]},"external_id":{"isi":["000393380400001"]},"isi":1,"project":[{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"quality_controlled":"1","year":"2017","status":"public","ec_funded":1,"_id":"1077","publication_identifier":{"issn":["1742-5689"]},"language":[{"iso":"eng"}],"month":"01","has_accepted_license":"1","publist_id":"6303","author":[{"last_name":"Fernandes Redondo","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793"},{"last_name":"Vladar","full_name":"Vladar, Harold","first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653"},{"last_name":"Włodarski","first_name":"Tomasz","full_name":"Włodarski, Tomasz"},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"file_date_updated":"2019-01-18T09:14:02Z","fulldoi":"https://doi.org/10.1098/rsif.2016.0139","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"day":"04","publication_status":"published","type":"journal_article","publication":"Journal of the Royal Society Interface","volume":14,"issue":"126","citation":{"apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society, 2017.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>."},"article_number":"20160139","date_updated":"2026-08-27T12:09:33Z","intvolume":"        14","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1098/rsif.2016.0139","publisher":"Royal Society","scopus_import":"1","oa":1},{"author":[{"full_name":"Ebner, Florian","first_name":"Florian","last_name":"Ebner"},{"last_name":"Sedlyarov","full_name":"Sedlyarov, Vitaly","first_name":"Vitaly"},{"last_name":"Tasciyan","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"},{"last_name":"Ivin","full_name":"Ivin, Masa","first_name":"Masa"},{"first_name":"Franz","full_name":"Kratochvill, Franz","last_name":"Kratochvill"},{"full_name":"Gratz, Nina","first_name":"Nina","last_name":"Gratz"},{"full_name":"Kenner, Lukas","first_name":"Lukas","last_name":"Kenner"},{"last_name":"Villunger","full_name":"Villunger, Andreas","first_name":"Andreas"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Kovarik","full_name":"Kovarik, Pavel","first_name":"Pavel"}],"publist_id":"7038","abstract":[{"text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections.","lang":"eng"}],"fulldoi":"https://doi.org/10.1172/JCI80631","day":"01","publication_status":"published","issue":"6","type":"journal_article","publication":"The Journal of Clinical Investigation","volume":127,"citation":{"ieee":"F. Ebner <i>et al.</i>, “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” <i>The Journal of Clinical Investigation</i>, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. <i>The Journal of Clinical Investigation</i>. American Society for Clinical Investigation. <a href=\"https://doi.org/10.1172/JCI80631\">https://doi.org/10.1172/JCI80631</a>","chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” <i>The Journal of Clinical Investigation</i>. American Society for Clinical Investigation, 2017. <a href=\"https://doi.org/10.1172/JCI80631\">https://doi.org/10.1172/JCI80631</a>.","ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. <i>The Journal of Clinical Investigation</i>. 2017;127(6):2051-2065. doi:<a href=\"https://doi.org/10.1172/JCI80631\">10.1172/JCI80631</a>","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” <i>The Journal of Clinical Investigation</i>, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:<a href=\"https://doi.org/10.1172/JCI80631\">10.1172/JCI80631</a>.","short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065."},"doi":"10.1172/JCI80631","intvolume":"       127","date_updated":"2026-10-08T22:30:16Z","pmid":1,"oa":1,"publisher":"American Society for Clinical Investigation","scopus_import":"1","department":[{"_id":"MiSi"}],"date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:47:53Z","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000402620800008"],"pmid":["28504646"]},"isi":1,"acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna.","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","related_material":{"record":[{"id":"12401","status":"public","relation":"dissertation_contains"}]},"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"page":"2051 - 2065","project":[{"name":"The biochemical basis of PAR polarization","call_identifier":"FWF","_id":"25985A36-B435-11E9-9278-68D0E5697425","grant_number":"T00817-B21"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"status":"public","year":"2017","quality_controlled":"1","_id":"679","month":"06","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9738"]}},{"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000406183700001"]},"isi":1,"title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5564"},{"status":"public","relation":"dissertation_contains","id":"26"}]},"oa_version":"Published Version","ddc":["576"],"department":[{"_id":"CaGu"}],"date_published":"2017-07-25T00:00:00Z","date_created":"2018-12-11T11:48:01Z","file":[{"checksum":"6b908b5db9f61f6820ebd7f8fa815571","date_created":"2018-12-12T10:12:54Z","creator":"system","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","file_size":2092088,"relation":"main_file","access_level":"open_access","file_id":"4975","date_updated":"2020-07-14T12:47:48Z","content_type":"application/pdf"},{"file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","creator":"system","date_created":"2018-12-12T10:12:55Z","checksum":"ca21530389b720243552678125fdba35","file_id":"4976","date_updated":"2020-07-14T12:47:48Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":3428681}],"pubrep_id":"890","_id":"704","month":"07","has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","year":"2017","abstract":[{"text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:48Z","corr_author":"1","fulldoi":"https://doi.org/10.7554/eLife.25100","day":"25","publication_status":"published","author":[{"last_name":"Steinrück","orcid":"0000-0003-1229-9719","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet"}],"publist_id":"6990","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.7554/eLife.25100","date_updated":"2026-10-08T22:30:19Z","intvolume":"         6","oa":1,"publisher":"eLife Sciences Publications","scopus_import":"1","type":"journal_article","publication":"eLife","volume":6,"citation":{"short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>, vol. 6, e25100, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>.","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>.","apa":"Steinrück, M., &#38; Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017."},"article_number":"e25100"},{"date_published":"2017-03-16T00:00:00Z","file":[{"date_created":"2018-12-12T10:09:47Z","creator":"system","file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","file_size":3429381,"relation":"main_file","access_level":"open_access","file_id":"4772","date_updated":"2018-12-12T10:09:47Z","content_type":"application/pdf"}],"date_created":"2018-12-11T11:49:46Z","ddc":["570"],"department":[{"_id":"ToBo"}],"isi":1,"external_id":{"isi":["000396318300121"]},"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5556"},{"relation":"dissertation_contains","status":"public","id":"6392"}]},"title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","quality_controlled":"1","status":"public","has_accepted_license":"1","month":"03","publication_identifier":{"issn":["1932-6203"]},"language":[{"iso":"eng"}],"_id":"1029","pubrep_id":"800","author":[{"last_name":"Lukacisin","full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-6549-4177"},{"last_name":"Landon","first_name":"Matthieu","full_name":"Landon, Matthieu"},{"first_name":"Rishi","full_name":"Jajoo, Rishi","last_name":"Jajoo"}],"publist_id":"6361","day":"16","publication_status":"published","abstract":[{"lang":"eng","text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking."}],"fulldoi":"https://doi.org/10.1371/journal.pone.0174066","file_date_updated":"2018-12-12T10:09:47Z","article_number":"e0174066","citation":{"apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0174066\">https://doi.org/10.1371/journal.pone.0174066</a>","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” <i>PLoS One</i>, vol. 12, no. 3. Public Library of Science, 2017.","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. <i>PLoS One</i>. 2017;12(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0174066\">10.1371/journal.pone.0174066</a>","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” <i>PLoS One</i>, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pone.0174066\">10.1371/journal.pone.0174066</a>.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” <i>PLoS One</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pone.0174066\">https://doi.org/10.1371/journal.pone.0174066</a>."},"issue":"3","volume":12,"publication":"PLoS One","type":"journal_article","oa":1,"publisher":"Public Library of Science","scopus_import":"1","doi":"10.1371/journal.pone.0174066","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        12","date_updated":"2026-10-08T22:30:34Z"},{"status":"public","year":"2017","quality_controlled":"1","page":"1798 - 1806","has_accepted_license":"1","month":"05","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"]},"_id":"676","date_published":"2017-05-15T00:00:00Z","file":[{"checksum":"bc25125fb664706cdf180e061429f91d","date_created":"2019-09-24T06:56:22Z","creator":"dernst","file_name":"2017_Development_Krens.pdf","relation":"main_file","file_size":8194516,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:39Z","file_id":"6905"}],"date_created":"2018-12-11T11:47:52Z","ddc":["570"],"department":[{"_id":"Bio"},{"_id":"CaHe"}],"isi":1,"external_id":{"isi":["000402275900007"],"pmid":["28512197"]},"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"},{"status":"public","relation":"dissertation_contains","id":"50"}]},"title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. 2017;144(10):1798-1806. doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>","chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., &#38; Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>","ieee":"G. Krens <i>et al.</i>, “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” <i>Development</i>, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017."},"issue":"10","volume":144,"publication":"Development","type":"journal_article","oa":1,"pmid":1,"scopus_import":"1","publisher":"Company of Biologists","doi":"10.1242/dev.144964","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       144","date_updated":"2026-10-08T22:30:40Z","article_type":"original","author":[{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"last_name":"Veldhuis","full_name":"Veldhuis, Jim","first_name":"Jim"},{"last_name":"Barone","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"last_name":"Capek","orcid":"0000-0001-5199-9940","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","full_name":"Capek, Daniel"},{"last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474"},{"last_name":"Brodland","first_name":"Wayne","full_name":"Brodland, Wayne"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"publist_id":"7047","publication_status":"published","day":"15","abstract":[{"text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.","lang":"eng"}],"fulldoi":"https://doi.org/10.1242/dev.144964","file_date_updated":"2020-07-14T12:47:39Z","corr_author":"1"},{"_id":"661","ec_funded":1,"month":"03","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1465-7392"]},"main_file_link":[{"url":"https://europepmc.org/articles/pmc5635970","open_access":"1"}],"page":"306 - 317","project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"},{"call_identifier":"FWF","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","grant_number":"I930-B20","name":"Control of Epithelial Cell Layer Spreading in Zebrafish"}],"status":"public","year":"2017","quality_controlled":"1","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"pmid":["28346437"],"isi":["000397917000009"]},"isi":1,"title":"Friction forces position the neural anlage","oa_version":"Submitted Version","related_material":{"record":[{"id":"8350","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"50"}]},"department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"acknowledged_ssus":[{"_id":"SSU"}],"date_published":"2017-03-27T00:00:00Z","date_created":"2018-12-11T11:47:46Z","doi":"10.1038/ncb3492","date_updated":"2026-10-08T22:30:40Z","intvolume":"        19","pmid":1,"oa":1,"scopus_import":"1","publisher":"Nature Publishing Group","type":"journal_article","volume":19,"publication":"Nature Cell Biology","citation":{"ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. <i>Nature Cell Biology</i>. 2017;19:306-317. doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>.","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>.","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>","ieee":"M. Smutny <i>et al.</i>, “Friction forces position the neural anlage,” <i>Nature Cell Biology</i>, vol. 19. Nature Publishing Group, pp. 306–317, 2017."},"abstract":[{"lang":"eng","text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo."}],"corr_author":"1","fulldoi":"https://doi.org/10.1038/ncb3492","publication_status":"published","day":"27","author":[{"full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny"},{"full_name":"Ákos, Zsuzsa","first_name":"Zsuzsa","last_name":"Ákos"},{"first_name":"Silvia","full_name":"Grigolon, Silvia","last_name":"Grigolon"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ruprecht, Verena","first_name":"Verena","last_name":"Ruprecht"},{"orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek"},{"last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Papusheva","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","full_name":"Papusheva, Ekaterina"},{"first_name":"Masazumi","full_name":"Tada, Masazumi","last_name":"Tada"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn"},{"first_name":"Tamás","full_name":"Vicsek, Tamás","last_name":"Vicsek"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"publist_id":"7074"},{"quality_controlled":"1","year":"2017","status":"public","project":[{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"page":"59 - 66","has_accepted_license":"1","month":"01","publication_identifier":{"issn":["0302-9743"]},"language":[{"iso":"eng"}],"pubrep_id":"845","_id":"949","ec_funded":1,"date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:49:22Z","file":[{"file_size":948514,"relation":"main_file","file_id":"4835","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:10:45Z","checksum":"a0d9f5f94dc594c4e71e78525c9942f1","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","creator":"system"}],"ddc":["005"],"department":[{"_id":"KrCh"}],"editor":[{"last_name":"D'Souza","full_name":"D'Souza, Deepak","first_name":"Deepak"}],"isi":1,"external_id":{"isi":["000723567800004"]},"oa_version":"Submitted Version","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"title":"JTDec: A tool for tree decompositions in soot","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["LNCS"],"citation":{"ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","mla":"Chatterjee, Krishnendu, et al. <i>JTDec: A Tool for Tree Decompositions in Soot</i>. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>.","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:<a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">10.1007/978-3-319-68167-2_4</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. <a href=\"https://doi.org/10.1007/978-3-319-68167-2_4\">https://doi.org/10.1007/978-3-319-68167-2_4</a>","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66."},"volume":10482,"type":"conference","oa":1,"publisher":"Springer","scopus_import":"1","doi":"10.1007/978-3-319-68167-2_4","date_updated":"2026-10-08T22:30:58Z","intvolume":"     10482","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","full_name":"Goharshady, Amir"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6468","conference":{"start_date":"2017-10-03","end_date":"2017-10-06","name":"ATVA: Automated Technology for Verification and Analysis","location":"Pune, India"},"day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs."}],"fulldoi":"https://doi.org/10.1007/978-3-319-68167-2_4","file_date_updated":"2020-07-14T12:48:16Z","corr_author":"1"},{"volume":10427,"type":"conference","alternative_title":["LNCS"],"citation":{"ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 41–63.","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar &#38; V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">https://doi.org/10.1007/978-3-319-63390-9_3</a>","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor Kunčak, 10427:41–63. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">https://doi.org/10.1007/978-3-319-63390-9_3</a>.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">10.1007/978-3-319-63390-9_3</a>","mla":"Chatterjee, Krishnendu, et al. <i>Non-Polynomial Worst Case Analysis of Recursive Programs</i>. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 41–63, doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_3\">10.1007/978-3-319-63390-9_3</a>.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63.","ista":"Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63."},"intvolume":"     10427","date_updated":"2026-10-08T22:30:58Z","doi":"10.1007/978-3-319-63390-9_3","publisher":"Springer","scopus_import":"1","oa":1,"publist_id":"7149","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"fulldoi":"https://doi.org/10.1007/978-3-319-63390-9_3","abstract":[{"text":"We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.","lang":"eng"}],"publication_status":"published","day":"01","conference":{"end_date":"2017-07-28","start_date":"2017-07-24","location":"Heidelberg, Germany","name":"CAV: Computer Aided Verification"},"arxiv":1,"page":"41 - 63","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}],"year":"2017","quality_controlled":"1","status":"public","project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"_id":"639","publication_identifier":{"isbn":["978-331963389-3"]},"language":[{"iso":"eng"}],"month":"01","department":[{"_id":"KrCh"}],"editor":[{"last_name":"Majumdar","first_name":"Rupak","full_name":"Majumdar, Rupak"},{"first_name":"Viktor","full_name":"Kunčak, Viktor","last_name":"Kunčak"}],"date_created":"2018-12-11T11:47:39Z","date_published":"2017-01-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","related_material":{"record":[{"id":"7014","relation":"later_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"oa_version":"Submitted Version","title":"Non-polynomial worst case analysis of recursive programs","isi":1,"external_id":{"isi":["000431900900003"],"arxiv":["1705.00317"]}},{"oa_version":"Published Version","related_material":{"record":[{"id":"9962","relation":"dissertation_contains","status":"public"}]},"title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","isi":1,"external_id":{"isi":["000404486700001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","file":[{"file_size":2153858,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","file_id":"4764","checksum":"dc1f5a475b918d09a0f9f587400b1626","date_created":"2018-12-12T10:09:40Z","creator":"system","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf"}],"date_created":"2018-12-11T11:49:25Z","date_published":"2017-06-28T00:00:00Z","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"ddc":["570"],"publication_identifier":{"issn":["1662-5102"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"06","ec_funded":1,"pubrep_id":"830","_id":"960","quality_controlled":"1","status":"public","year":"2017","project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The biochemical basis of PAR polarization"}],"day":"28","publication_status":"published","fulldoi":"https://doi.org/10.3389/fncel.2017.00176","file_date_updated":"2020-07-14T12:48:16Z","abstract":[{"text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.","lang":"eng"}],"publist_id":"6445","author":[{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen"},{"id":"459064DC-F248-11E8-B48F-1D18A9856A87","full_name":"Düllberg, Christian F","first_name":"Christian F","orcid":"0000-0001-6335-9748","last_name":"Düllberg"},{"last_name":"Mieck","first_name":"Christine","full_name":"Mieck, Christine","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1919-7416"},{"last_name":"Loose","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"publisher":"Frontiers Research Foundation","scopus_import":"1","oa":1,"date_updated":"2026-10-08T22:30:59Z","intvolume":"        11","doi":"10.3389/fncel.2017.00176","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"176","citation":{"ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” <i>Frontiers in Cellular Neuroscience</i>, vol. 11. Frontiers Research Foundation, 2017.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., &#38; Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncel.2017.00176\">https://doi.org/10.3389/fncel.2017.00176</a>","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” <i>Frontiers in Cellular Neuroscience</i>. Frontiers Research Foundation, 2017. <a href=\"https://doi.org/10.3389/fncel.2017.00176\">https://doi.org/10.3389/fncel.2017.00176</a>.","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017).","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. <i>Frontiers in Cellular Neuroscience</i>. 2017;11. doi:<a href=\"https://doi.org/10.3389/fncel.2017.00176\">10.3389/fncel.2017.00176</a>","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” <i>Frontiers in Cellular Neuroscience</i>, vol. 11, 176, Frontiers Research Foundation, 2017, doi:<a href=\"https://doi.org/10.3389/fncel.2017.00176\">10.3389/fncel.2017.00176</a>."},"volume":11,"publication":"Frontiers in Cellular Neuroscience","type":"journal_article"},{"citation":{"apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>."},"article_number":"e1005609","type":"journal_article","publication":"PLoS Computational Biology","volume":13,"issue":"7","scopus_import":"1","publisher":"Public Library of Science","oa":1,"intvolume":"        13","date_updated":"2026-10-08T22:31:01Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1371/journal.pcbi.1005609","article_type":"original","publist_id":"7004","author":[{"last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","first_name":"Marta","orcid":"0000-0002-2519-8004"},{"last_name":"Novak","full_name":"Novak, Sebastian","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"},{"last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"}],"publication_status":"published","day":"18","file_date_updated":"2020-07-14T12:47:46Z","corr_author":"1","fulldoi":"https://doi.org/10.1371/journal.pcbi.1005609","abstract":[{"lang":"eng","text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy."}],"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091"}],"year":"2017","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-734X"]},"month":"07","has_accepted_license":"1","ec_funded":1,"pubrep_id":"894","_id":"696","date_created":"2018-12-11T11:47:58Z","file":[{"access_level":"open_access","file_id":"5117","date_updated":"2020-07-14T12:47:46Z","content_type":"application/pdf","file_size":3775716,"relation":"main_file","creator":"system","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","checksum":"9143c290fa6458ed2563bff4b295554a","date_created":"2018-12-12T10:15:01Z"}],"date_published":"2017-07-18T00:00:00Z","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"ddc":["576"],"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","related_material":{"record":[{"status":"public","relation":"research_data","id":"9849"},{"status":"public","relation":"research_data","id":"9850"},{"status":"public","relation":"research_data","id":"9851"},{"id":"9852","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"6263"}]},"oa_version":"Published Version","external_id":{"isi":["000406619800014"]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No"}]