[{"date_updated":"2026-08-12T06:26:09Z","publisher":"Dryad","doi":"10.5061/dryad.85dn7","status":"public","abstract":[{"lang":"eng","text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments."}],"type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.85dn7"}],"date_created":"2021-07-28T08:48:06Z","oa_version":"Published Version","citation":{"chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.","mla":"Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014, doi:10.5061/dryad.85dn7.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","apa":"Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. https://doi.org/10.5061/dryad.85dn7","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, 10.5061/dryad.85dn7.","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:10.5061/dryad.85dn7"},"_id":"9741","date_published":"2014-08-21T00:00:00Z","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014","month":"08","department":[{"_id":"CaGu"}],"day":"21","related_material":{"record":[{"relation":"used_in_publication","id":"2036","status":"public"}]},"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"full_name":"Colegrave, Nick","last_name":"Colegrave","first_name":"Nick"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}],"article_processing_charge":"No"},{"type":"journal_article","corr_author":"1","date_created":"2018-12-11T11:56:34Z","publist_id":"4697","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","scopus_import":"1","oa_version":"Published Version","status":"public","has_accepted_license":"1","external_id":{"pmid":["24366138"],"isi":["000332465300014"]},"abstract":[{"text":"Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"mla":"Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635, 20120528, Royal Society, 2014, doi:10.1098/rstb.2012.0528.","short":"J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 369 (2014).","apa":"Csicsvari, J. L., & Dupret, D. (2014). Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2012.0528","ama":"Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2014;369(1635). doi:10.1098/rstb.2012.0528","ista":"Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 369(1635), 20120528.","ieee":"J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and learning-associated hippocampal maps,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635. Royal Society, 2014.","chicago":"Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2014. https://doi.org/10.1098/rstb.2012.0528."},"intvolume":" 369","pubrep_id":"527","ddc":["570"],"date_updated":"2026-08-12T06:27:15Z","author":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"},{"first_name":"David","last_name":"Dupret","full_name":"Dupret, David"}],"pmid":1,"year":"2014","file_date_updated":"2020-07-14T12:45:34Z","publication_status":"published","volume":369,"issue":"1635","month":"02","das_tickbox":"1","_id":"2251","date_published":"2014-02-05T00:00:00Z","quality_controlled":"1","article_number":"20120528","isi":1,"file":[{"creator":"system","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:13:24Z","content_type":"application/pdf","file_size":771896,"checksum":"51beb33de71c9c19e0c205a20d206f9a","file_id":"5006","file_name":"IST-2016-527-v1+1_20120528.full.pdf","date_updated":"2020-07-14T12:45:34Z"}],"doi":"10.1098/rstb.2012.0528","publisher":"Royal Society","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)"},"publication_identifier":{"issn":["0962-8436"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sharp wave/ripple network oscillations and learning-associated hippocampal maps","oa":1,"day":"05","department":[{"_id":"JoCs"}]},{"language":[{"iso":"eng"}],"citation":{"short":"R. Seiringer, Journal of Mathematical Physics 55 (2014).","mla":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, AIP Publishing, 2014, doi:10.1063/1.4881536.","ieee":"R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. AIP Publishing, 2014.","ama":"Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536","ista":"Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536.","apa":"Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4881536","chicago":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4881536."},"external_id":{"isi":["000341174600010"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end."}],"type":"journal_article","corr_author":"1","publication":"Journal of Mathematical Physics","oa_version":"Submitted Version","publist_id":"5285","scopus_import":"1","date_created":"2018-12-11T11:54:11Z","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"ddc":["510","530"],"pubrep_id":"532","date_updated":"2026-08-12T13:58:01Z","intvolume":" 55","author":[{"first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"month":"06","volume":55,"issue":"7","publication_status":"published","file_date_updated":"2020-07-14T12:45:17Z","year":"2014","article_number":"1.4881536","_id":"1821","date_published":"2014-06-26T00:00:00Z","quality_controlled":"1","publisher":"AIP Publishing","doi":"10.1063/1.4881536","file":[{"checksum":"ed0efc93c10f1341155f0316af617b82","file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","file_id":"5172","date_updated":"2020-07-14T12:45:17Z","file_size":269171,"date_created":"2018-12-12T10:15:49Z","content_type":"application/pdf","creator":"system","relation":"main_file","access_level":"open_access"}],"isi":1,"article_processing_charge":"No","department":[{"_id":"RoSe"}],"day":"26","title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"RoSe"}],"month":"07","day":"01","issue":"7","volume":55,"publication_status":"published","title":"Introduction","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Vojkan","last_name":"Jakšić","full_name":"Jakšić, Vojkan"},{"first_name":"Claude","last_name":"Pillet","full_name":"Pillet, Claude"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"publisher":"AIP Publishing","isi":1,"doi":"10.1063/1.4884877","date_updated":"2026-08-12T13:58:20Z","intvolume":" 55","citation":{"chicago":"Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4884877.","short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).","mla":"Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, AIP Publishing, 2014, doi:10.1063/1.4884877.","ieee":"V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. AIP Publishing, 2014.","ama":"Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101.","apa":"Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4884877"},"article_number":"075101","language":[{"iso":"eng"}],"_id":"1822","quality_controlled":"1","date_published":"2014-07-01T00:00:00Z","status":"public","external_id":{"isi":["000341174600001"]},"publication":"Journal of Mathematical Physics","publist_id":"5284","scopus_import":"1","oa_version":"None","date_created":"2018-12-11T11:54:12Z","type":"journal_article"},{"citation":{"apa":"Caracciolo, D., Noto, L. V., Istanbulluoglu, E., Fatichi, S., & Zhou, X. (2014). Climate change and Ecotone boundaries: Insights from a cellular automata ecohydrology model in a Mediterranean catchment with topography controlled vegetation patterns. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2014.08.001","ieee":"D. Caracciolo, L. V. Noto, E. Istanbulluoglu, S. Fatichi, and X. Zhou, “Climate change and Ecotone boundaries: Insights from a cellular automata ecohydrology model in a Mediterranean catchment with topography controlled vegetation patterns,” Advances in Water Resources, vol. 73. Elsevier, pp. 159–175, 2014.","ama":"Caracciolo D, Noto LV, Istanbulluoglu E, Fatichi S, Zhou X. Climate change and Ecotone boundaries: Insights from a cellular automata ecohydrology model in a Mediterranean catchment with topography controlled vegetation patterns. Advances in Water Resources. 2014;73:159-175. doi:10.1016/j.advwatres.2014.08.001","ista":"Caracciolo D, Noto LV, Istanbulluoglu E, Fatichi S, Zhou X. 2014. Climate change and Ecotone boundaries: Insights from a cellular automata ecohydrology model in a Mediterranean catchment with topography controlled vegetation patterns. Advances in Water Resources. 73, 159–175.","mla":"Caracciolo, Domenico, et al. “Climate Change and Ecotone Boundaries: Insights from a Cellular Automata Ecohydrology Model in a Mediterranean Catchment with Topography Controlled Vegetation Patterns.” Advances in Water Resources, vol. 73, Elsevier, 2014, pp. 159–75, doi:10.1016/j.advwatres.2014.08.001.","short":"D. Caracciolo, L.V. Noto, E. Istanbulluoglu, S. Fatichi, X. Zhou, Advances in Water Resources 73 (2014) 159–175.","chicago":"Caracciolo, Domenico, Leonardo Valerio Noto, Erkan Istanbulluoglu, Simone Fatichi, and Xiaochi Zhou. “Climate Change and Ecotone Boundaries: Insights from a Cellular Automata Ecohydrology Model in a Mediterranean Catchment with Topography Controlled Vegetation Patterns.” Advances in Water Resources. Elsevier, 2014. https://doi.org/10.1016/j.advwatres.2014.08.001."},"article_type":"original","language":[{"iso":"eng"}],"oa_version":"None","publication":"Advances in Water Resources","scopus_import":"1","date_created":"2026-07-27T12:30:23Z","type":"journal_article","abstract":[{"text":"Regions of vegetation transitions (ecotones) are known to be highly sensitive to climate fluctuations. In this study, the Cellular-Automata Tree Grass Shrub Simulator (CATGraSS) has been modified, calibrated and used with downscaled future climate scenarios to examine the role of climate change on vegetation patterns in a steep mountainous catchment (1.3 km2) located in Sicily, Italy. In the catchment, north-facing slopes are mostly covered by trees and grass, and south-facing slopes by Indian Fig opuntia and grass, with grasses dominating as elevation grows. CATGraSS simulates solar radiation, evapotranspiration, and soil moisture in space and time. Each model cell can hold a single plant type or can be bare soil. Plant competition is modeled explicitly through mortality and the establishment of individual plants in open spaces. In this study, CATGraSS is modified to account for heterogeneity in soil thickness and tested in the study catchment using the historical climate of the region. Predicted vegetation patterns are compared with those obtained from satellite images. Results of model under current climate underscore the importance of solar irradiance and soil thickness, especially in the uplands where soil is shallow, in determining vegetation composition over complex terrain. A stochastic weather generator is used to generate future climate change scenarios for the catchment by downscaling GCM realizations in space and time. Future increase in atmospheric CO2 concentration was considered through modifying the vegetation water use efficiency and stomatal resistance for our study site. Model results suggest that vegetation pattern is highly sensitive to temperature and rainfall variations provided by climate scenarios (30% reduction of the annual precipitation and a 2.8 °C increase of the mean annual temperature). Future climate change is predicted to bring a considerable reorganization of the plant composition following topographic patterns, leading to a decrease of trees cover at the expenses of a grass expansion, which will cause loss of landscape vegetation diversity.","lang":"eng"}],"status":"public","OA_type":"closed access","intvolume":" 73","date_updated":"2026-08-12T14:11:56Z","page":"159-175","author":[{"last_name":"Caracciolo","first_name":"Domenico","full_name":"Caracciolo, Domenico"},{"first_name":"Leonardo Valerio","last_name":"Noto","full_name":"Noto, Leonardo Valerio"},{"full_name":"Istanbulluoglu, Erkan","first_name":"Erkan","last_name":"Istanbulluoglu"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone","last_name":"Fatichi"},{"first_name":"Xiaochi","last_name":"Zhou","full_name":"Zhou, Xiaochi"}],"volume":73,"month":"11","year":"2014","publication_status":"published","quality_controlled":"1","_id":"22435","date_published":"2014-11-01T00:00:00Z","das_tickbox":"1","doi":"10.1016/j.advwatres.2014.08.001","publisher":"Elsevier","extern":"1","article_processing_charge":"No","publication_identifier":{"issn":["0309-1708"]},"day":"01","keyword":["CA model","Climate change","Ecohydrology","Topography"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Climate change and Ecotone boundaries: Insights from a cellular automata ecohydrology model in a Mediterranean catchment with topography controlled vegetation patterns"},{"publication_status":"published","year":"2014","month":"09","volume":493,"author":[{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone","last_name":"Fatichi"},{"last_name":"Rimkus","first_name":"S.","full_name":"Rimkus, S."},{"first_name":"P.","last_name":"Burlando","full_name":"Burlando, P."},{"full_name":"Bordoy, R.","last_name":"Bordoy","first_name":"R."}],"page":"1171-1182","pmid":1,"date_updated":"2026-08-12T14:17:26Z","intvolume":" 493","OA_type":"closed access","external_id":{"pmid":["24418218"]},"status":"public","abstract":[{"lang":"eng","text":"Projections of climate change effects in streamflow are increasingly required to plan water management strategies. These projections are however largely uncertain due to the spread among climate model realizations, internal climate variability, and difficulties in transferring climate model results at the spatial and temporal scales required by catchment hydrology. A combination of a stochastic downscaling methodology and distributed hydrological modeling was used in the ACQWA project to provide projections of future streamflow (up to year 2050) for the upper Po and Rhone basins, respectively located in northern Italy and south-western Switzerland. Results suggest that internal (stochastic) climate variability is a fundamental source of uncertainty, typically comparable or larger than the projected climate change signal. Therefore, climate change effects in streamflow mean, frequency, and seasonality can be masked by natural climatic fluctuations in large parts of the analyzed regions. An exception to the overwhelming role of stochastic variability is represented by high elevation catchments fed by glaciers where streamflow is expected to be considerably reduced due to glacier retreat, with consequences appreciable in the main downstream rivers in August and September. Simulations also identify regions (west upper Rhone and Toce, Ticino river basins) where a strong precipitation increase in the February to April period projects streamflow beyond the range of natural climate variability during the melting season. This study emphasizes the importance of including internal climate variability in climate change analyses, especially when compared to the limited uncertainty that would be accounted for by few deterministic projections. The presented results could be useful in guiding more specific impact studies, although design or management decisions should be better based on reliability and vulnerability criteria as suggested by recent literature."}],"type":"journal_article","oa_version":"None","date_created":"2026-07-27T12:30:23Z","publication":"Science of The Total Environment","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"apa":"Fatichi, S., Rimkus, S., Burlando, P., & Bordoy, R. (2014). Does internal climate variability overwhelm climate change signals in streamflow? The upper Po and Rhone basin case studies. Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2013.12.014","ama":"Fatichi S, Rimkus S, Burlando P, Bordoy R. Does internal climate variability overwhelm climate change signals in streamflow? The upper Po and Rhone basin case studies. Science of The Total Environment. 2014;493:1171-1182. doi:10.1016/j.scitotenv.2013.12.014","ista":"Fatichi S, Rimkus S, Burlando P, Bordoy R. 2014. Does internal climate variability overwhelm climate change signals in streamflow? The upper Po and Rhone basin case studies. Science of The Total Environment. 493, 1171–1182.","ieee":"S. Fatichi, S. Rimkus, P. Burlando, and R. Bordoy, “Does internal climate variability overwhelm climate change signals in streamflow? The upper Po and Rhone basin case studies,” Science of The Total Environment, vol. 493. Elsevier, pp. 1171–1182, 2014.","mla":"Fatichi, Simone, et al. “Does Internal Climate Variability Overwhelm Climate Change Signals in Streamflow? The Upper Po and Rhone Basin Case Studies.” Science of The Total Environment, vol. 493, Elsevier, 2014, pp. 1171–82, doi:10.1016/j.scitotenv.2013.12.014.","short":"S. Fatichi, S. Rimkus, P. Burlando, R. Bordoy, Science of The Total Environment 493 (2014) 1171–1182.","chicago":"Fatichi, Simone, S. Rimkus, P. Burlando, and R. Bordoy. “Does Internal Climate Variability Overwhelm Climate Change Signals in Streamflow? The Upper Po and Rhone Basin Case Studies.” Science of The Total Environment. Elsevier, 2014. https://doi.org/10.1016/j.scitotenv.2013.12.014."},"article_type":"original","title":"Does internal climate variability overwhelm climate change signals in streamflow? The upper Po and Rhone basin case studies","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","keyword":["Climate change","Hydrological modeling","Stochastic downscaling","Uncertainty","Water resources","Alps"],"day":"15","publication_identifier":{"issn":["0048-9697"],"eissn":["1879-1026"]},"article_processing_charge":"No","extern":"1","publisher":"Elsevier","doi":"10.1016/j.scitotenv.2013.12.014","das_tickbox":"1","quality_controlled":"1","_id":"22459","date_published":"2014-09-15T00:00:00Z"},{"date_updated":"2026-08-12T14:21:11Z","OA_place":"publisher","intvolume":" 52","OA_type":"free access","abstract":[{"lang":"eng","text":"The biological responses to precipitation within the terrestrial components of Earth system models, or land surface models (LSMs), are mechanistically simple and poorly constrained, leaving projections of terrestrial ecosystem functioning and feedbacks to climate change uncertain. A number of field experiments have been conducted or are underway to test how changing precipitation will affect terrestrial ecosystems. Results from these experiments have the potential to vastly improve modeled processes. However, the transformation of experimental results into model improvements still represents a grand challenge. Here we review the current state of precipitation manipulation experiments and the precipitation responses of biological processes in LSMs to explore how these experiments can help improve model realism. First, we discuss contemporary precipitation projections and then review the structure and function of current-generation LSMs. We then examine different experimental designs and discuss basic variables that, if measured, would increase a field experiment's usefulness in a modeling context. Next, we compare biological processes commonly measured in the field with their model analogs and find that, in many cases, the way these processes are measured in the field is not compatible with the way they are represented in LSMs, an effect that hinders model development. We then discuss the challenge of scaling from the plot to the globe. Finally, we provide a series of recommendations aimed to improve the connectivity between experiments and LSMs and conclude that studies designed from the perspective of researchers in both communities will provide the greatest benefit to the broader global change community."}],"status":"public","scopus_import":"1","oa_version":"Published Version","date_created":"2026-07-27T12:30:23Z","publication":"Reviews of Geophysics","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014RG000458"}],"type":"journal_article","article_type":"original","citation":{"short":"N.G. Smith, V.L. Rodgers, E.R. Brzostek, A. Kulmatiski, M.L. Avolio, D.L. Hoover, S.E. Koerner, K. Grant, A. Jentsch, S. Fatichi, D. Niyogi, Reviews of Geophysics 52 (2014) 412–434.","mla":"Smith, Nicholas G., et al. “Toward a Better Integration of Biological Data from Precipitation Manipulation Experiments into Earth System Models.” Reviews of Geophysics, vol. 52, no. 3, American Geophysical Union, 2014, pp. 412–34, doi:10.1002/2014rg000458.","ieee":"N. G. Smith et al., “Toward a better integration of biological data from precipitation manipulation experiments into Earth system models,” Reviews of Geophysics, vol. 52, no. 3. American Geophysical Union, pp. 412–434, 2014.","ista":"Smith NG, Rodgers VL, Brzostek ER, Kulmatiski A, Avolio ML, Hoover DL, Koerner SE, Grant K, Jentsch A, Fatichi S, Niyogi D. 2014. Toward a better integration of biological data from precipitation manipulation experiments into Earth system models. Reviews of Geophysics. 52(3), 412–434.","ama":"Smith NG, Rodgers VL, Brzostek ER, et al. Toward a better integration of biological data from precipitation manipulation experiments into Earth system models. Reviews of Geophysics. 2014;52(3):412-434. doi:10.1002/2014rg000458","apa":"Smith, N. G., Rodgers, V. L., Brzostek, E. R., Kulmatiski, A., Avolio, M. L., Hoover, D. L., … Niyogi, D. (2014). Toward a better integration of biological data from precipitation manipulation experiments into Earth system models. Reviews of Geophysics. American Geophysical Union. https://doi.org/10.1002/2014rg000458","chicago":"Smith, Nicholas G., Vikki L. Rodgers, Edward R. Brzostek, Andrew Kulmatiski, Meghan L. Avolio, David L. Hoover, Sally E. Koerner, et al. “Toward a Better Integration of Biological Data from Precipitation Manipulation Experiments into Earth System Models.” Reviews of Geophysics. American Geophysical Union, 2014. https://doi.org/10.1002/2014rg000458."},"language":[{"iso":"eng"}],"publication_status":"published","year":"2014","month":"09","issue":"3","volume":52,"author":[{"last_name":"Smith","first_name":"Nicholas G.","full_name":"Smith, Nicholas G."},{"first_name":"Vikki L.","last_name":"Rodgers","full_name":"Rodgers, Vikki L."},{"first_name":"Edward R.","last_name":"Brzostek","full_name":"Brzostek, Edward R."},{"last_name":"Kulmatiski","first_name":"Andrew","full_name":"Kulmatiski, Andrew"},{"full_name":"Avolio, Meghan L.","last_name":"Avolio","first_name":"Meghan L."},{"full_name":"Hoover, David L.","first_name":"David L.","last_name":"Hoover"},{"full_name":"Koerner, Sally E.","last_name":"Koerner","first_name":"Sally E."},{"last_name":"Grant","first_name":"Kerstin","full_name":"Grant, Kerstin"},{"full_name":"Jentsch, Anke","last_name":"Jentsch","first_name":"Anke"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone"},{"first_name":"Dev","last_name":"Niyogi","full_name":"Niyogi, Dev"}],"page":"412-434","extern":"1","publisher":"American Geophysical Union","doi":"10.1002/2014rg000458","das_tickbox":"1","date_published":"2014-09-01T00:00:00Z","_id":"22460","quality_controlled":"1","oa":1,"title":"Toward a better integration of biological data from precipitation manipulation experiments into Earth system models","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","publication_identifier":{"eissn":["1944-9208"],"issn":["8755-1209"]},"article_processing_charge":"No"},{"oa":1,"title":"Mathematical model of alternative mechanism of telomere length maintenance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"day":"04","article_processing_charge":"No","publisher":"American Physical Society","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","doi":"10.1103/PhysRevE.89.032701","isi":1,"article_number":"032701","_id":"1896","date_published":"2014-03-04T00:00:00Z","publication_status":"published","year":"2014","month":"03","issue":"3","volume":89,"author":[{"full_name":"Kollár, Richard","first_name":"Richard","last_name":"Kollár"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína","first_name":"Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'ová"},{"full_name":"Nosek, Jozef","first_name":"Jozef","last_name":"Nosek"},{"first_name":"Ľubomír","last_name":"Tomáška","full_name":"Tomáška, Ľubomír"}],"date_updated":"2026-08-12T14:27:46Z","arxiv":1,"intvolume":" 89","abstract":[{"text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.","lang":"eng"}],"external_id":{"isi":["000332274100002"],"arxiv":["1402.0430"]},"status":"public","date_created":"2018-12-11T11:54:35Z","publist_id":"5198","scopus_import":"1","oa_version":"Submitted Version","publication":"Physical Review E","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0430"}],"type":"journal_article","citation":{"chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/PhysRevE.89.032701.","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E 89 (2014).","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E, vol. 89, no. 3, 032701, American Physical Society, 2014, doi:10.1103/PhysRevE.89.032701.","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E, vol. 89, no. 3. American Physical Society, 2014.","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E. 2014;89(3). doi:10.1103/PhysRevE.89.032701","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E. 89(3), 032701.","apa":"Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.89.032701"},"language":[{"iso":"eng"}]},{"publist_id":"4737","publication":"Physical Review E","date_created":"2018-12-11T11:56:26Z","scopus_import":"1","oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1312.5095","open_access":"1"}],"type":"journal_article","corr_author":"1","abstract":[{"lang":"eng","text":"Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability."}],"status":"public","external_id":{"isi":["000332155800013"],"arxiv":["1312.5095"]},"citation":{"mla":"Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” Physical Review E, vol. 89, no. 1, 013001, American Physical Society, 2014, doi:10.1103/PhysRevE.89.013001.","short":"L. Shi, B. Hof, A. Tilgner, Physical Review E 89 (2014).","apa":"Shi, L., Hof, B., & Tilgner, A. (2014). Transient growth of Ekman-Couette flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.89.013001","ieee":"L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,” Physical Review E, vol. 89, no. 1. American Physical Society, 2014.","ista":"Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical Review E. 89(1), 013001.","ama":"Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. Physical Review E. 2014;89(1). doi:10.1103/PhysRevE.89.013001","chicago":"Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette Flow.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/PhysRevE.89.013001."},"language":[{"iso":"eng"}],"intvolume":" 89","date_updated":"2026-08-12T14:26:10Z","arxiv":1,"project":[{"_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B"}],"author":[{"first_name":"Liang","last_name":"Shi","full_name":"Shi, Liang"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754"},{"last_name":"Tilgner","first_name":"Andreas","full_name":"Tilgner, Andreas"}],"year":"2014","publication_status":"published","issue":"1","volume":89,"month":"01","quality_controlled":"1","_id":"2226","date_published":"2014-01-06T00:00:00Z","article_number":"013001","doi":"10.1103/PhysRevE.89.013001","isi":1,"publisher":"American Physical Society","article_processing_charge":"No","publication_identifier":{"issn":["1539-3755"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Transient growth of Ekman-Couette flow","day":"06","department":[{"_id":"BjHo"}]},{"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Hierarchy and polysynchrony in an adaptive network ","day":"16","department":[{"_id":"GaTk"}],"date_published":"2014-06-16T00:00:00Z","_id":"2183","quality_controlled":"1","article_number":"062809","doi":"10.1103/PhysRevE.89.062809","isi":1,"acknowledgement":"V.B.S. is partially supported by contract MEC (Grant No. AYA2010-22111-C03-02).\r\n","publisher":"American Physical Society","author":[{"last_name":"Botella Soler","orcid":"0000-0002-8790-1914","first_name":"Vicente","full_name":"Botella Soler, Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Glendinning, Paul","last_name":"Glendinning","first_name":"Paul"}],"year":"2014","publication_status":"published","issue":"6","volume":89,"month":"06","oa_version":"Preprint","publist_id":"4798","scopus_import":"1","date_created":"2018-12-11T11:56:11Z","publication":"Physical Review E","corr_author":"1","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1403.3209","open_access":"1"}],"abstract":[{"text":"We describe a simple adaptive network of coupled chaotic maps. The network reaches a stationary state (frozen topology) for all values of the coupling parameter, although the dynamics of the maps at the nodes of the network can be nontrivial. The structure of the network shows interesting hierarchical properties and in certain parameter regions the dynamics is polysynchronous: Nodes can be divided in differently synchronized classes but, contrary to cluster synchronization, nodes in the same class need not be connected to each other. These complicated synchrony patterns have been conjectured to play roles in systems biology and circuits. The adaptive system we study describes ways whereby this behavior can evolve from undifferentiated nodes.","lang":"eng"}],"status":"public","external_id":{"isi":["000337733900007"],"arxiv":["1403.3209"]},"citation":{"chicago":"Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/PhysRevE.89.062809.","ama":"Botella Soler V, Glendinning P. Hierarchy and polysynchrony in an adaptive network . Physical Review E. 2014;89(6). doi:10.1103/PhysRevE.89.062809","ista":"Botella Soler V, Glendinning P. 2014. Hierarchy and polysynchrony in an adaptive network . Physical Review E. 89(6), 062809.","ieee":"V. Botella Soler and P. Glendinning, “Hierarchy and polysynchrony in an adaptive network ,” Physical Review E, vol. 89, no. 6. American Physical Society, 2014.","apa":"Botella Soler, V., & Glendinning, P. (2014). Hierarchy and polysynchrony in an adaptive network . Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.89.062809","short":"V. Botella Soler, P. Glendinning, Physical Review E 89 (2014).","mla":"Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E, vol. 89, no. 6, 062809, American Physical Society, 2014, doi:10.1103/PhysRevE.89.062809."},"ec_funded":1,"language":[{"iso":"eng"}],"intvolume":" 89","date_updated":"2026-08-12T14:27:10Z","arxiv":1,"project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"author":[{"full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie","last_name":"Stroeymeyt"},{"full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"page":"1 - 15","year":"2014","publication_status":"published","volume":5,"related_material":{"record":[{"relation":"dissertation_contains","id":"6383"},{"id":"6435","status":"public","relation":"dissertation_contains"}]},"issue":"1","month":"11","corr_author":"1","type":"journal_article","date_created":"2018-12-11T11:55:08Z","scopus_import":"1","publication":"Current Opinion in Insect Science","oa_version":"None","publist_id":"5080","external_id":{"isi":["000209578900002"]},"status":"public","abstract":[{"text":"Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"ieee":"N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” Current Opinion in Insect Science, vol. 5, no. 1. Elsevier, pp. 1–15, 2014.","ama":"Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. Current Opinion in Insect Science. 2014;5(1):1-15. doi:10.1016/j.cois.2014.09.001","ista":"Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15.","apa":"Stroeymeyt, N., Casillas Perez, B. E., & Cremer, S. (2014). Organisational immunity in social insects. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2014.09.001","short":"N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15.","mla":"Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:10.1016/j.cois.2014.09.001.","chicago":"Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science. Elsevier, 2014. https://doi.org/10.1016/j.cois.2014.09.001."},"ec_funded":1,"intvolume":" 5","date_updated":"2026-09-03T22:30:21Z","project":[{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Organisational immunity in social insects","day":"01","department":[{"_id":"SyCr"}],"_id":"1999","quality_controlled":"1","date_published":"2014-11-01T00:00:00Z","doi":"10.1016/j.cois.2014.09.001","isi":1,"publisher":"Elsevier"},{"year":"2014","publication_status":"published","issue":"5","volume":91,"month":"03","author":[{"first_name":"Adam","last_name":"Heikal","full_name":"Heikal, Adam"},{"full_name":"Nakatani, Yoshio","last_name":"Nakatani","first_name":"Yoshio"},{"last_name":"Dunn","first_name":"Elyse","full_name":"Dunn, Elyse"},{"first_name":"Marion","last_name":"Weimar","full_name":"Weimar, Marion"},{"first_name":"Catherine","last_name":"Day","full_name":"Day, Catherine"},{"last_name":"Baker","first_name":"Edward","full_name":"Baker, Edward"},{"last_name":"Lott","first_name":"Shaun","full_name":"Lott, Shaun"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"},{"last_name":"Cook","first_name":"Gregory","full_name":"Cook, Gregory"}],"pmid":1,"page":"950 - 964","intvolume":" 91","date_updated":"2026-09-04T11:27:46Z","OA_type":"free access","date_created":"2018-12-11T11:55:01Z","publist_id":"5103","publication":"Molecular Microbiology","oa_version":"None","type":"journal_article","abstract":[{"text":"Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors.","lang":"eng"}],"status":"public","external_id":{"pmid":["24444429"]},"citation":{"chicago":"Heikal, Adam, Yoshio Nakatani, Elyse Dunn, Marion Weimar, Catherine Day, Edward Baker, Shaun Lott, Leonid A Sazanov, and Gregory Cook. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mmi.12507.","ieee":"A. Heikal et al., “Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation,” Molecular Microbiology, vol. 91, no. 5. Wiley-Blackwell, pp. 950–964, 2014.","ama":"Heikal A, Nakatani Y, Dunn E, et al. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. 2014;91(5):950-964. doi:10.1111/mmi.12507","ista":"Heikal A, Nakatani Y, Dunn E, Weimar M, Day C, Baker E, Lott S, Sazanov LA, Cook G. 2014. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. 91(5), 950–964.","apa":"Heikal, A., Nakatani, Y., Dunn, E., Weimar, M., Day, C., Baker, E., … Cook, G. (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12507","short":"A. Heikal, Y. Nakatani, E. Dunn, M. Weimar, C. Day, E. Baker, S. Lott, L.A. Sazanov, G. Cook, Molecular Microbiology 91 (2014) 950–964.","mla":"Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507."},"article_type":"original","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["0950-382X"],"eissn":["1365-2958"]},"extern":"1","acknowledgement":"Funded by Health Research Council of New Zealand Royal Society of New Zealand University of Otago New Zealand Synchrotron Group","doi":"10.1111/mmi.12507","publisher":"Wiley-Blackwell","date_published":"2014-03-01T00:00:00Z","_id":"1980"},{"_id":"1791","date_published":"2014-06-18T00:00:00Z","doi":"10.1016/j.neuron.2014.04.036","acknowledgement":"This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation","publisher":"Elsevier","extern":"1","article_processing_charge":"No","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"day":"18","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation","language":[{"iso":"eng"}],"citation":{"short":"S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262.","mla":"Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036.","ista":"Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.","ieee":"S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.","ama":"Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036","apa":"Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036","chicago":"Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036."},"article_type":"original","type":"journal_article","publist_id":"5322","oa_version":"None","publication":"Neuron","date_created":"2018-12-11T11:54:01Z","external_id":{"pmid":["24945770"]},"status":"public","abstract":[{"lang":"eng","text":"Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways."}],"OA_type":"closed access","intvolume":" 82","date_updated":"2026-09-04T11:50:27Z","pmid":1,"page":"1255 - 1262","author":[{"full_name":"Baek, Seungtae","first_name":"Seungtae","last_name":"Baek"},{"full_name":"Kerjan, Géraldine","first_name":"Géraldine","last_name":"Kerjan"},{"last_name":"Bielas","first_name":"Stephanie","full_name":"Bielas, Stephanie"},{"full_name":"Lee, Jieun","first_name":"Jieun","last_name":"Lee"},{"first_name":"Ali","last_name":"Fenstermaker","full_name":"Fenstermaker, Ali"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"},{"full_name":"Gleeson, Joseph","last_name":"Gleeson","first_name":"Joseph"}],"volume":82,"issue":"6","month":"06","year":"2014","publication_status":"published"},{"author":[{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"page":"247 - 253","pmid":1,"publication_status":"published","year":"2014","month":"08","volume":46,"issue":"4","external_id":{"pmid":["24943718"]},"status":"public","abstract":[{"text":"NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine.","lang":"eng"}],"type":"journal_article","publist_id":"5104","publication":"Journal of Bioenergetics and Biomembranes","date_created":"2018-12-11T11:55:01Z","oa_version":"None","language":[{"iso":"eng"}],"citation":{"chicago":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes. Springer Nature, 2014. https://doi.org/10.1007/s10863-014-9554-z.","mla":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4, Springer Nature, 2014, pp. 247–53, doi:10.1007/s10863-014-9554-z.","short":"L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.","apa":"Sazanov, L. A. (2014). The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. Springer Nature. https://doi.org/10.1007/s10863-014-9554-z","ista":"Sazanov LA. 2014. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 46(4), 247–253.","ieee":"L. A. Sazanov, “The mechanism of coupling between electron transfer and proton translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4. Springer Nature, pp. 247–253, 2014.","ama":"Sazanov LA. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 2014;46(4):247-253. doi:10.1007/s10863-014-9554-z"},"article_type":"original","date_updated":"2026-09-04T11:48:14Z","intvolume":" 46","OA_type":"closed access","publication_identifier":{"issn":["0145-479X"],"eissn":["1573-6881"]},"article_processing_charge":"No","title":"The mechanism of coupling between electron transfer and proton translocation in respiratory complex I","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","_id":"1979","date_published":"2014-08-01T00:00:00Z","extern":"1","publisher":"Springer Nature","doi":"10.1007/s10863-014-9554-z"},{"issue":"4","volume":3,"month":"01","year":"2014","publication_status":"published","author":[{"first_name":"Massimo","last_name":"Mongillo","full_name":"Mongillo, Massimo"},{"full_name":"Spathis, Panayotis","first_name":"Panayotis","last_name":"Spathis"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"},{"first_name":"Silvano","last_name":"De Franceschi","full_name":"De Franceschi, Silvano"},{"full_name":"Gentile, Pascal","first_name":"Pascal","last_name":"Gentile"},{"first_name":"Riccardo","last_name":"Rurali","full_name":"Rurali, Riccardo"},{"full_name":"Cartoixà, Xavier","first_name":"Xavier","last_name":"Cartoixà"}],"OA_type":"green","OA_place":"repository","intvolume":" 3","date_updated":"2026-09-04T11:52:28Z","arxiv":1,"article_type":"original","citation":{"apa":"Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali, R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025","ista":"Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 3(4).","ama":"Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025","ieee":"M. Mongillo et al., “PtSi clustering in silicon probed by transport spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society, 2014.","mla":"Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025.","short":"M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali, X. Cartoixà, Physical Review X 3 (2014).","chicago":"Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi, Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X. American Physical Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025."},"language":[{"iso":"eng"}],"publist_id":"5363","oa_version":"None","publication":"Physical Review X","date_created":"2018-12-11T11:53:52Z","main_file_link":[{"url":"http://arxiv.org/abs/1407.5413","open_access":"1"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Metal silicides formed by means of thermal annealing processes are employed as contact materials in microelectronics. Control of the structure of silicide/silicon interfaces becomes a critical issue when the characteristic size of the device is reduced below a few tens of nanometers. Here, we report on silicide clustering occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling spectroscopy. Our results provide evidence for the segregation of a PtSi cluster with a diameter of a few nanometers from the silicide contact. The cluster acts as a metallic quantum dot giving rise to distinct signatures of quantum transport through its discrete energy states."}],"external_id":{"arxiv":["abs/1407.5413"]},"status":"public","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"PtSi clustering in silicon probed by transport spectroscopy","article_processing_charge":"No","publication_identifier":{"eissn":["2160-3308"]},"acknowledgement":"This work was supported by the Agence Nationale de la Recherche and by the EU through the ERC Starting Grant HybridNano","doi":"10.1103/PhysRevX.3.041025","publisher":"American Physical Society","extern":"1","date_published":"2014-01-01T00:00:00Z","_id":"1761"},{"author":[{"orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"page":"771 - 818","article_processing_charge":"No","publication_status":"published","title":"Upper bounds on waiting times for the Thin-film equation: The case of weak slippage","year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"01","day":"01","issue":"3","volume":211,"abstract":[{"text":"We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long.","lang":"eng"}],"status":"public","publication":"Archive for Rational Mechanics and Analysis","oa_version":"None","date_created":"2018-12-11T11:51:18Z","publist_id":"5959","type":"journal_article","article_type":"original","citation":{"chicago":"Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis. Springer Nature, 2014. https://doi.org/10.1007/s00205-013-0690-0.","short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818.","mla":"Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis, vol. 211, no. 3, Springer Nature, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.","ieee":"J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation: The case of weak slippage,” Archive for Rational Mechanics and Analysis, vol. 211, no. 3. Springer Nature, pp. 771–818, 2014.","ista":"Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3), 771–818.","ama":"Fischer JL. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818. doi:10.1007/s00205-013-0690-0","apa":"Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-013-0690-0"},"language":[{"iso":"eng"}],"date_published":"2014-01-01T00:00:00Z","_id":"1312","date_updated":"2026-09-04T11:54:26Z","extern":"1","intvolume":" 211","publisher":"Springer Nature","doi":"10.1007/s00205-013-0690-0","OA_type":"closed access"},{"date_updated":"2026-09-04T11:56:53Z","intvolume":" 21","extern":"1","publisher":"Birkhäuser","OA_type":"closed access","doi":"10.1007/s00030-013-0235-0","status":"public","abstract":[{"text":"We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation.","lang":"eng"}],"type":"journal_article","publication":"Nonlinear Differential Equations and Applications","date_created":"2018-12-11T11:51:17Z","oa_version":"None","publist_id":"5960","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0.","short":"J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014) 27–50.","mla":"Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0.","ieee":"J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models,” Nonlinear Differential Equations and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014.","ista":"Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 21(1), 27–50.","ama":"Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0","apa":"Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0"},"_id":"1309","date_published":"2014-01-01T00:00:00Z","title":"Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","month":"01","volume":21,"day":"01","issue":"1","author":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","first_name":"Julian L","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"page":"27 - 50","publication_identifier":{"issn":["1021-9722"],"eissn":["1420-9004"]},"article_processing_charge":"No"},{"publisher":"Wiley-Blackwell","doi":"10.1002/cphc.201301034","extern":"1","date_published":"2014-03-17T00:00:00Z","_id":"1058","day":"17","title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1439-7641"],"issn":["1439-4235"]},"article_processing_charge":"No","OA_type":"closed access","date_updated":"2026-09-04T12:18:04Z","intvolume":" 15","article_type":"original","citation":{"apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034","ieee":"N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762.","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034","mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034.","short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762.","chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034."},"language":[{"iso":"eng"}],"abstract":[{"text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy.","lang":"eng"}],"status":"public","external_id":{"pmid":["24497300"]},"oa_version":"None","date_created":"2018-12-11T11:49:55Z","publication":"ChemPhysChem","publist_id":"6332","type":"journal_article","month":"03","issue":"4","volume":15,"publication_status":"published","year":"2014","page":"756 - 762","pmid":1,"author":[{"full_name":"Jensen, Nickels","first_name":"Nickels","last_name":"Jensen"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Willig, Katrin","first_name":"Katrin","last_name":"Willig"},{"full_name":"Lavoie Cardinal, Flavie","first_name":"Flavie","last_name":"Lavoie Cardinal"},{"first_name":"Tanja","last_name":"Brakemann","full_name":"Brakemann, Tanja"},{"first_name":"Stefan","last_name":"Hell","full_name":"Hell, Stefan"},{"first_name":"Stefan","last_name":"Jakobs","full_name":"Jakobs, Stefan"}]},{"date_published":"2013-10-21T00:00:00Z","_id":"10895","quality_controlled":"1","publisher":"MDPI","doi":"10.3390/plants2040650","file":[{"file_size":670188,"date_updated":"2022-03-21T12:12:56Z","file_id":"10916","file_name":"2013_Plants_Vanneste.pdf","checksum":"fb4ff2e820e344e253c9197544610be6","success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2022-03-21T12:12:56Z","content_type":"application/pdf"}],"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)"},"publication_identifier":{"issn":["2223-7747"]},"article_processing_charge":"No","title":"Calcium: The missing link in auxin action","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"day":"21","keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"has_accepted_license":"1","status":"public","external_id":{"pmid":["27137397"]},"abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"corr_author":"1","type":"journal_article","date_created":"2022-03-21T07:13:49Z","scopus_import":"1","oa_version":"Published Version","publication":"Plants","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.","apa":"Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action. Plants. MDPI. https://doi.org/10.3390/plants2040650","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants. 2013;2(4):650-675. doi:10.3390/plants2040650","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants, vol. 2, no. 4. MDPI, pp. 650–675, 2013.","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675."},"ddc":["580"],"date_updated":"2024-10-09T21:01:52Z","intvolume":" 2","author":[{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"page":"650-675","pmid":1,"publication_status":"published","file_date_updated":"2022-03-21T12:12:56Z","year":"2013","month":"10","volume":2,"issue":"4"},{"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"date_updated":"2025-04-15T08:37:54Z","intvolume":" 7877","language":[{"iso":"eng"}],"citation":{"chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In Graph-Based Representations in Pattern Recognition, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. https://doi.org/10.1007/978-3-642-38221-5_19.","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” Graph-Based Representations in Pattern Recognition, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:10.1007/978-3-642-38221-5_19.","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.","ama":"Edelsbrunner H. Persistent homology in image processing. In: Graph-Based Representations in Pattern Recognition. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:10.1007/978-3-642-38221-5_19","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In Graph-Based Representations in Pattern Recognition (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-38221-5_19"},"ec_funded":1,"status":"public","abstract":[{"text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.","lang":"eng"}],"corr_author":"1","type":"conference","date_created":"2022-03-21T07:30:33Z","publication":"Graph-Based Representations in Pattern Recognition","scopus_import":"1","oa_version":"None","series_title":"LNCS","month":"06","volume":7877,"publication_status":"published","year":"2013","page":"182-183","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert"}],"publisher":"Springer Nature","acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","doi":"10.1007/978-3-642-38221-5_19","place":"Berlin, Heidelberg","conference":{"location":"Vienna, Austria","start_date":"2013-05-15","end_date":"2013-05-17","name":"GbRPR: Graph-based Representations in Pattern Recognition"},"_id":"10897","date_published":"2013-06-01T00:00:00Z","quality_controlled":"1","department":[{"_id":"HeEd"}],"day":"01","title":"Persistent homology in image processing","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eisbn":["9783642382215"],"issn":["0302-9743"],"isbn":["9783642382208"],"eissn":["1611-3349"]},"article_processing_charge":"No"}]