[{"_id":"2229","month":"02","oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight &quot;nanodomain&quot; channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose &quot;microdomain&quot; coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity."}],"publication":"Science","publist_id":"4732","date_published":"2014-02-01T00:00:00Z","department":[{"_id":"PeJo"}],"scopus_import":"1","citation":{"apa":"Vyleta, N., &#38; Jonas, P. M. (2014). Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>","ieee":"N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse,” <i>Science</i>, vol. 343, no. 6171. American Association for the Advancement of Science, pp. 665–670, 2014.","ama":"Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. 2014;343(6171):665-670. doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>","chicago":"Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>.","mla":"Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>, vol. 343, no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70, doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>.","ista":"Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.","short":"N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670."},"publication_identifier":{"issn":["0036-8075"]},"doi":"10.1126/science.1244811","intvolume":"       343","day":"01","type":"journal_article","fulldoi":"https://doi.org/10.1126/science.1244811","publication_status":"published","project":[{"grant_number":"P24909-B24","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548"}],"external_id":{"isi":["000330724000044"]},"ec_funded":1,"issue":"6171","oa_version":"Submitted Version","title":"Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse","article_processing_charge":"No","publisher":"American Association for the Advancement of Science","date_created":"2018-12-11T11:56:27Z","corr_author":"1","author":[{"first_name":"Nicholas","full_name":"Vyleta, Nicholas","last_name":"Vyleta","id":"36C4978E-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","isi":1,"volume":343,"date_updated":"2025-09-29T11:24:38Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/"}],"language":[{"iso":"eng"}],"page":"665 - 670"},{"article_processing_charge":"No","title":"Stimfit: Quantifying electrophysiological data with Python","pubrep_id":"425","date_created":"2018-12-11T11:56:27Z","publisher":"Frontiers Research Foundation","external_id":{"isi":["000348105900001"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"oa_version":"Published Version","issue":"FEB","file_date_updated":"2020-07-14T12:45:34Z","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2025-09-29T11:24:02Z","article_number":"16","year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","author":[{"first_name":"José","full_name":"Guzmán, José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"last_name":"Schmidt Hieber","full_name":"Schmidt Hieber, Christoph","first_name":"Christoph"}],"volume":8,"isi":1,"quality_controlled":"1","publist_id":"4731","publication":"Frontiers in Neuroinformatics","abstract":[{"text":"Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.","lang":"eng"}],"oa":1,"month":"02","_id":"2230","publication_status":"published","fulldoi":"https://doi.org/10.3389/fninf.2014.00016","type":"journal_article","day":"21","intvolume":"         8","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"date_published":"2014-02-21T00:00:00Z","doi":"10.3389/fninf.2014.00016","publication_identifier":{"issn":["1662-5196"]},"citation":{"ama":"Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. 2014;8(FEB). doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>","apa":"Guzmán, J., Schlögl, A., &#38; Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>","ieee":"J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB. Frontiers Research Foundation, 2014.","ista":"Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.","short":"J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014).","chicago":"Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>.","mla":"Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>."},"has_accepted_license":"1","file":[{"date_created":"2018-12-12T10:12:17Z","access_level":"open_access","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","file_size":2883372,"file_id":"4935","file_name":"IST-2016-425-v1+1_fninf-08-00016.pdf","checksum":"eeca00bba7232ff7d27db83321f6ea30"}],"scopus_import":"1"},{"isi":1,"volume":106,"corr_author":"1","author":[{"first_name":"Georg","full_name":"Rieckh, Georg","last_name":"Rieckh","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","page":"1194 - 1204","date_updated":"2025-09-29T11:23:30Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/"}],"language":[{"iso":"eng"}],"issue":"5","oa_version":"Submitted Version","external_id":{"pmid":["24606943"],"isi":["000332501300022"]},"publisher":"Biophysical Society","pmid":1,"date_created":"2018-12-11T11:56:28Z","title":"Noise and information transmission in promoters with multiple internal states","article_processing_charge":"No","scopus_import":"1","citation":{"ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. 2014;106(5):1194-1204. doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” <i>Biophysical Journal</i>, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.","apa":"Rieckh, G., &#38; Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>","short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204.","mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>.","chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>. Biophysical Society, 2014. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>."},"publication_identifier":{"issn":["0006-3495"]},"doi":"10.1016/j.bpj.2014.01.014","date_published":"2014-03-04T00:00:00Z","department":[{"_id":"GaTk"}],"intvolume":"       106","day":"04","type":"journal_article","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.bpj.2014.01.014","_id":"2231","month":"03","oa":1,"abstract":[{"lang":"eng","text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail."}],"publication":"Biophysical Journal","publist_id":"4730","quality_controlled":"1"},{"_id":"2232","oa":1,"month":"02","quality_controlled":"1","abstract":[{"lang":"eng","text":"The purpose of this contribution is to summarize and discuss recent advances regarding the onset of turbulence in shear flows. The absence of a clear-cut instability mechanism, the spatio-temporal intermittent character and extremely long lived transients are some of the major difficulties encountered in these flows and have hindered progress towards understanding the transition process. We will show for the case of pipe flow that concepts from nonlinear dynamics and statistical physics can help to explain the onset of turbulence. In particular, the turbulent structures (puffs) observed close to onset are spatially localized chaotic transients and their lifetimes increase super-exponentially with Reynolds number. At the same time fluctuations of individual turbulent puffs can (although very rarely) lead to the nucleation of new puffs. The competition between these two stochastic processes gives rise to a non-equilibrium phase transition where turbulence changes from a super-transient to a sustained state."}],"publist_id":"4729","publication":"Journal of Statistical Mechanics Theory and Experiment","date_published":"2014-02-01T00:00:00Z","article_type":"original","department":[{"_id":"BjHo"}],"scopus_import":"1","citation":{"apa":"Song, B., &#38; Hof, B. (2014). Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>","ieee":"B. Song and B. Hof, “Deterministic and stochastic aspects of the transition to turbulence,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2. IOP Publishing, 2014.","ama":"Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2014;2014(2). doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>","chicago":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>.","mla":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>.","short":"B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014 (2014).","ista":"Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2), P02001."},"doi":"10.1088/1742-5468/2014/02/P02001","publication_identifier":{"issn":["1742-5468"]},"day":"01","intvolume":"      2014","fulldoi":"https://doi.org/10.1088/1742-5468/2014/02/P02001","publication_status":"published","type":"journal_article","external_id":{"isi":["000332098100001"],"arxiv":["1403.4516"]},"arxiv":1,"oa_version":"Submitted Version","issue":"2","title":"Deterministic and stochastic aspects of the transition to turbulence","article_processing_charge":"No","publisher":"IOP Publishing","date_created":"2018-12-11T11:56:28Z","status":"public","corr_author":"1","author":[{"first_name":"Baofang","id":"a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72","full_name":"Song, Baofang","last_name":"Song"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"volume":2014,"date_updated":"2025-09-29T11:22:37Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1403.4516"}],"article_number":"P02001"},{"publication_identifier":{"issn":["0028-0836"]},"doi":"10.1038/nature12977","citation":{"mla":"Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>, vol. 506, no. 7488, Nature Publishing Group, 2014, pp. 364–66, doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>.","chicago":"Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>.","ista":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488), 364–366.","short":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014) 364–366.","ieee":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations between honeybees and bumblebees as a threat to wild pollinators,” <i>Nature</i>, vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014.","apa":"Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., &#38; Brown, M. (2014). Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>","ama":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. 2014;506(7488):364-366. doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>"},"scopus_import":"1","department":[{"_id":"SyCr"}],"date_published":"2014-02-20T00:00:00Z","type":"journal_article","publication_status":"published","fulldoi":"https://doi.org/10.1038/nature12977","intvolume":"       506","day":"20","month":"02","oa":1,"_id":"2235","publication":"Nature","publist_id":"4726","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators."}],"quality_controlled":"1","volume":506,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","author":[{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias"},{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"full_name":"Osborne, Juliet","last_name":"Osborne","first_name":"Juliet"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"}],"corr_author":"1","status":"public","page":"364 - 366","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/","open_access":"1"}],"language":[{"iso":"eng"}],"date_updated":"2025-09-29T11:21:06Z","issue":"7488","oa_version":"Submitted Version","external_id":{"isi":["000331477800040"]},"date_created":"2018-12-11T11:56:29Z","publisher":"Nature Publishing Group","article_processing_charge":"No","title":"Disease associations between honeybees and bumblebees as a threat to wild pollinators"},{"conference":{"end_date":"2014-02-26","name":"TCC: Theory of Cryptography Conference","start_date":"2014-02-24","location":"San Diego, USA"},"_id":"2236","month":"02","oa":1,"quality_controlled":"1","abstract":[{"text":"Consider a joint distribution (X,A) on a set. We show that for any family of distinguishers, there exists a simulator such that 1 no function in can distinguish (X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient than the functions in. For the most interesting settings of the parameters (in particular, the cryptographic case where X has superlogarithmic min-entropy, ε &gt; 0 is negligible and consists of circuits of polynomial size), we can make the simulator h deterministic. As an illustrative application of our theorem, we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09. Our proof is simpler and quantitatively much better than the original proof using the dense model theorem, giving meaningful security guarantees if instantiated with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and Pass gave an interactive variant of our main theorem, and used it to investigate weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version of our theorem using their new uniform min-max theorem.","lang":"eng"}],"publist_id":"4725","date_published":"2014-02-01T00:00:00Z","department":[{"_id":"KrPi"}],"scopus_import":"1","file":[{"content_type":"application/pdf","file_size":313528,"date_updated":"2020-07-14T12:45:34Z","relation":"main_file","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:17:21Z","checksum":"42960325c29dcd8d832edadcc3ce0045","file_name":"IST-2016-681-v1+1_869_1_.pdf","file_id":"5275"}],"has_accepted_license":"1","alternative_title":["LNCS"],"citation":{"ista":"Jetchev D, Pietrzak KZ. 2014. How to fake auxiliary input. TCC: Theory of Cryptography Conference, LNCS, vol. 8349, 566–590.","short":"D. Jetchev, K.Z. Pietrzak, in:, Y. Lindell (Ed.), Springer, 2014, pp. 566–590.","chicago":"Jetchev, Dimitar, and Krzysztof Z Pietrzak. “How to Fake Auxiliary Input.” edited by Yehuda Lindell, 8349:566–90. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">https://doi.org/10.1007/978-3-642-54242-8_24</a>.","mla":"Jetchev, Dimitar, and Krzysztof Z. Pietrzak. <i>How to Fake Auxiliary Input</i>. Edited by Yehuda Lindell, vol. 8349, Springer, 2014, pp. 566–90, doi:<a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">10.1007/978-3-642-54242-8_24</a>.","ama":"Jetchev D, Pietrzak KZ. How to fake auxiliary input. In: Lindell Y, ed. Vol 8349. Springer; 2014:566-590. doi:<a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">10.1007/978-3-642-54242-8_24</a>","apa":"Jetchev, D., &#38; Pietrzak, K. Z. (2014). How to fake auxiliary input. In Y. Lindell (Ed.) (Vol. 8349, pp. 566–590). Presented at the TCC: Theory of Cryptography Conference, San Diego, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">https://doi.org/10.1007/978-3-642-54242-8_24</a>","ieee":"D. Jetchev and K. Z. Pietrzak, “How to fake auxiliary input,” presented at the TCC: Theory of Cryptography Conference, San Diego, USA, 2014, vol. 8349, pp. 566–590."},"doi":"10.1007/978-3-642-54242-8_24","publication_identifier":{"isbn":["978-364254241-1"]},"intvolume":"      8349","day":"01","type":"conference","fulldoi":"https://doi.org/10.1007/978-3-642-54242-8_24","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"editor":[{"last_name":"Lindell","full_name":"Lindell, Yehuda","first_name":"Yehuda"}],"file_date_updated":"2020-07-14T12:45:34Z","ec_funded":1,"oa_version":"Submitted Version","ddc":["004"],"title":"How to fake auxiliary input","pubrep_id":"681","article_processing_charge":"No","publisher":"Springer","date_created":"2018-12-11T11:56:29Z","author":[{"first_name":"Dimitar","last_name":"Jetchev","full_name":"Jetchev, Dimitar"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"corr_author":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","volume":8349,"date_updated":"2025-06-11T08:02:25Z","language":[{"iso":"eng"}],"page":"566 - 590"},{"volume":49,"status":"public","author":[{"first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker","full_name":"Boker, Udi"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"}],"year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"595 - 606","date_updated":"2021-01-12T06:56:13Z","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"None","issue":"1","publisher":"ACM","date_created":"2018-12-11T11:56:30Z","title":"Battery transition systems","scopus_import":1,"publication_identifier":{"isbn":["978-145032544-8"]},"doi":"10.1145/2535838.2535875","citation":{"ieee":"U. Boker, T. A. Henzinger, and A. Radhakrishna, “Battery transition systems,” presented at the POPL: Principles of Programming Languages, San Diego, USA, 2014, vol. 49, no. 1, pp. 595–606.","apa":"Boker, U., Henzinger, T. A., &#38; Radhakrishna, A. (2014). Battery transition systems (Vol. 49, pp. 595–606). Presented at the POPL: Principles of Programming Languages, San Diego, USA: ACM. <a href=\"https://doi.org/10.1145/2535838.2535875\">https://doi.org/10.1145/2535838.2535875</a>","ama":"Boker U, Henzinger TA, Radhakrishna A. Battery transition systems. In: Vol 49. ACM; 2014:595-606. doi:<a href=\"https://doi.org/10.1145/2535838.2535875\">10.1145/2535838.2535875</a>","mla":"Boker, Udi, et al. <i>Battery Transition Systems</i>. Vol. 49, no. 1, ACM, 2014, pp. 595–606, doi:<a href=\"https://doi.org/10.1145/2535838.2535875\">10.1145/2535838.2535875</a>.","chicago":"Boker, Udi, Thomas A Henzinger, and Arjun Radhakrishna. “Battery Transition Systems,” 49:595–606. ACM, 2014. <a href=\"https://doi.org/10.1145/2535838.2535875\">https://doi.org/10.1145/2535838.2535875</a>.","short":"U. Boker, T.A. Henzinger, A. Radhakrishna, in:, ACM, 2014, pp. 595–606.","ista":"Boker U, Henzinger TA, Radhakrishna A. 2014. Battery transition systems. POPL: Principles of Programming Languages vol. 49, 595–606."},"date_published":"2014-01-13T00:00:00Z","department":[{"_id":"ToHe"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"day":"13","intvolume":"        49","fulldoi":"https://doi.org/10.1145/2535838.2535875","publication_status":"published","type":"conference","_id":"2239","month":"01","conference":{"end_date":"2014-01-24","name":"POPL: Principles of Programming Languages","start_date":"2014-01-22","location":"San Diego, USA"},"abstract":[{"lang":"eng","text":"The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce battery transition systems. In this model, a battery is viewed as consisting of two parts-the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank. Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the !-regular modelchecking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots."}],"publist_id":"4722","quality_controlled":"1"},{"title":"The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants","article_processing_charge":"No","publisher":"Cell Press","date_created":"2018-12-11T11:56:31Z","external_id":{"isi":["000331379800009"]},"issue":"4","oa_version":"None","date_updated":"2025-09-29T11:20:21Z","language":[{"iso":"eng"}],"page":"691 - 704","author":[{"first_name":"Astrid","last_name":"Gadeyne","full_name":"Gadeyne, Astrid"},{"first_name":"Clara","last_name":"Sánchez Rodríguez","full_name":"Sánchez Rodríguez, Clara"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Simone","last_name":"Di Rubbo","full_name":"Di Rubbo, Simone"},{"first_name":"Henrik","full_name":"Zauber, Henrik","last_name":"Zauber"},{"first_name":"Kevin","full_name":"Vanneste, Kevin","last_name":"Vanneste"},{"full_name":"Van Leene, Jelle","last_name":"Van Leene","first_name":"Jelle"},{"first_name":"Nancy","full_name":"De Winne, Nancy","last_name":"De Winne"},{"first_name":"Dominique","full_name":"Eeckhout, Dominique","last_name":"Eeckhout"},{"full_name":"Persiau, Geert","last_name":"Persiau","first_name":"Geert"},{"full_name":"Van De Slijke, Eveline","last_name":"Van De Slijke","first_name":"Eveline"},{"first_name":"Bernard","full_name":"Cannoot, Bernard","last_name":"Cannoot"},{"full_name":"Vercruysse, Leen","last_name":"Vercruysse","first_name":"Leen"},{"first_name":"Jonathan","full_name":"Mayers, Jonathan","last_name":"Mayers"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257"},{"first_name":"Urszula","last_name":"Kania","full_name":"Kania, Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Ehrlich","full_name":"Ehrlich, Matthias"},{"first_name":"Alois","full_name":"Schweighofer, Alois","last_name":"Schweighofer"},{"first_name":"Tijs","full_name":"Ketelaar, Tijs","last_name":"Ketelaar"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"first_name":"Sebastian","last_name":"Bednarek","full_name":"Bednarek, Sebastian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Kris","full_name":"Gevaert, Kris","last_name":"Gevaert"},{"first_name":"Erwin","last_name":"Witters","full_name":"Witters, Erwin"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"},{"full_name":"Persson, Staffan","last_name":"Persson","first_name":"Staffan"},{"first_name":"Geert","full_name":"De Jaeger, Geert","last_name":"De Jaeger"},{"first_name":"Daniël","last_name":"Van Damme","full_name":"Van Damme, Daniël"}],"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","isi":1,"volume":156,"quality_controlled":"1","abstract":[{"text":"Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.","lang":"eng"}],"publication":"Cell","publist_id":"4721","_id":"2240","month":"02","intvolume":"       156","day":"13","type":"journal_article","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.cell.2014.01.039","date_published":"2014-02-13T00:00:00Z","department":[{"_id":"JiFr"}],"scopus_import":"1","citation":{"chicago":"Gadeyne, Astrid, Clara Sánchez Rodríguez, Steffen Vanneste, Simone Di Rubbo, Henrik Zauber, Kevin Vanneste, Jelle Van Leene, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” <i>Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">https://doi.org/10.1016/j.cell.2014.01.039</a>.","mla":"Gadeyne, Astrid, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” <i>Cell</i>, vol. 156, no. 4, Cell Press, 2014, pp. 691–704, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">10.1016/j.cell.2014.01.039</a>.","ista":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Mayers J, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar T, Maere S, Bednarek S, Friml J, Gevaert K, Witters E, Russinova E, Persson S, De Jaeger G, Van Damme D. 2014. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. 156(4), 691–704.","short":"A. Gadeyne, C. Sánchez Rodríguez, S. Vanneste, S. Di Rubbo, H. Zauber, K. Vanneste, J. Van Leene, N. De Winne, D. Eeckhout, G. Persiau, E. Van De Slijke, B. Cannoot, L. Vercruysse, J. Mayers, M. Adamowski, U. Kania, M. Ehrlich, A. Schweighofer, T. Ketelaar, S. Maere, S. Bednarek, J. Friml, K. Gevaert, E. Witters, E. Russinova, S. Persson, G. De Jaeger, D. Van Damme, Cell 156 (2014) 691–704.","ieee":"A. Gadeyne <i>et al.</i>, “The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants,” <i>Cell</i>, vol. 156, no. 4. Cell Press, pp. 691–704, 2014.","apa":"Gadeyne, A., Sánchez Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H., Vanneste, K., … Van Damme, D. (2014). The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">https://doi.org/10.1016/j.cell.2014.01.039</a>","ama":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, et al. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. <i>Cell</i>. 2014;156(4):691-704. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">10.1016/j.cell.2014.01.039</a>"},"doi":"10.1016/j.cell.2014.01.039","publication_identifier":{"issn":["0092-8674"]}},{"title":"Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage","article_processing_charge":"No","publisher":"Elsevier","date_created":"2018-12-11T11:56:31Z","external_id":{"isi":["000330420700010"]},"issue":"2","oa_version":"None","date_updated":"2026-04-16T10:07:56Z","language":[{"iso":"eng"}],"page":"314 - 320","author":[{"full_name":"Beppu, Kaoru","last_name":"Beppu","first_name":"Kaoru"},{"first_name":"Takuya","full_name":"Sasaki, Takuya","last_name":"Sasaki"},{"full_name":"Tanaka, Kenji","last_name":"Tanaka","first_name":"Kenji"},{"last_name":"Yamanaka","full_name":"Yamanaka, Akihiro","first_name":"Akihiro"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi"},{"first_name":"Ko","last_name":"Matsui","full_name":"Matsui, Ko"}],"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2014","isi":1,"volume":81,"quality_controlled":"1","abstract":[{"text":"The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage.","lang":"eng"}],"publication":"Neuron","publist_id":"4715","_id":"2241","month":"01","intvolume":"        81","day":"22","type":"journal_article","fulldoi":"https://doi.org/10.1016/j.neuron.2013.11.011","publication_status":"published","date_published":"2014-01-22T00:00:00Z","department":[{"_id":"RySh"}],"scopus_import":"1","doi":"10.1016/j.neuron.2013.11.011","citation":{"ama":"Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. 2014;81(2):314-320. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>","ieee":"K. Beppu <i>et al.</i>, “Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage,” <i>Neuron</i>, vol. 81, no. 2. Elsevier, pp. 314–320, 2014.","apa":"Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R., &#38; Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>","ista":"Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K. 2014. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 81(2), 314–320.","short":"K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K. Matsui, Neuron 81 (2014) 314–320.","chicago":"Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>.","mla":"Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>, vol. 81, no. 2, Elsevier, 2014, pp. 314–20, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>."},"publication_identifier":{"issn":["0896-6273"]}},{"publist_id":"4714","publication":"FEBS Letters","abstract":[{"text":"MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages.","lang":"eng"}],"quality_controlled":"1","month":"02","_id":"2242","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.febslet.2014.01.009","type":"journal_article","day":"14","intvolume":"       588","publication_identifier":{"issn":["0014-5793"]},"citation":{"chicago":"Dueck, Anne, Alexander Eichner, Michael K Sixt, and Gunter Meister. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” <i>FEBS Letters</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">https://doi.org/10.1016/j.febslet.2014.01.009</a>.","mla":"Dueck, Anne, et al. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” <i>FEBS Letters</i>, vol. 588, no. 4, Elsevier, 2014, pp. 632–40, doi:<a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">10.1016/j.febslet.2014.01.009</a>.","ista":"Dueck A, Eichner A, Sixt MK, Meister G. 2014. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. 588(4), 632–640.","short":"A. Dueck, A. Eichner, M.K. Sixt, G. Meister, FEBS Letters 588 (2014) 632–640.","apa":"Dueck, A., Eichner, A., Sixt, M. K., &#38; Meister, G. (2014). A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. <i>FEBS Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">https://doi.org/10.1016/j.febslet.2014.01.009</a>","ieee":"A. Dueck, A. Eichner, M. K. Sixt, and G. Meister, “A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation,” <i>FEBS Letters</i>, vol. 588, no. 4. Elsevier, pp. 632–640, 2014.","ama":"Dueck A, Eichner A, Sixt MK, Meister G. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. <i>FEBS Letters</i>. 2014;588(4):632-640. doi:<a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">10.1016/j.febslet.2014.01.009</a>"},"doi":"10.1016/j.febslet.2014.01.009","scopus_import":"1","department":[{"_id":"MiSi"}],"date_published":"2014-02-14T00:00:00Z","date_created":"2018-12-11T11:56:31Z","publisher":"Elsevier","article_processing_charge":"No","title":"A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation","oa_version":"None","issue":"4","external_id":{"isi":["000331115700016"]},"page":"632 - 640","language":[{"iso":"eng"}],"date_updated":"2025-09-29T11:19:23Z","volume":588,"isi":1,"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","author":[{"first_name":"Anne","last_name":"Dueck","full_name":"Dueck, Anne"},{"full_name":"Eichner, Alexander","last_name":"Eichner","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Gunter","last_name":"Meister","full_name":"Meister, Gunter"}]},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. "}],"publication":"Plant Chemical Genomics","publist_id":"4704","_id":"2245","month":"01","intvolume":"      1056","day":"01","type":"book_chapter","fulldoi":"https://doi.org/10.1007/978-1-62703-592-7_23","publication_status":"published","editor":[{"first_name":"Glenn","last_name":"Hicks","full_name":"Hicks, Glenn"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"}],"date_published":"2014-01-01T00:00:00Z","department":[{"_id":"JiFr"}],"series_title":"Methods in Molecular Biology","scopus_import":"1","doi":"10.1007/978-1-62703-592-7_23","publication_identifier":{"issn":["1064-3745"]},"citation":{"short":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:, G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.","ista":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Plant Chemical Genomics. Methods in Molecular Biology, vol. 1056, 255–264.","chicago":"Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” In <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64. Methods in Molecular Biology. Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>.","mla":"Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, vol. 1056, Springer, 2014, pp. 255–64, doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>.","ama":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds. <i>Plant Chemical Genomics</i>. Vol 1056. Methods in Molecular Biology. Springer; 2014:255-264. doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>","ieee":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml, “Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters,” in <i>Plant Chemical Genomics</i>, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014, pp. 255–264.","apa":"Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., &#38; Friml, J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In G. Hicks &#38; S. Robert (Eds.), <i>Plant Chemical Genomics</i> (Vol. 1056, pp. 255–264). Springer. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>"},"alternative_title":["Methods in Molecular Biology"],"title":"Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters","article_processing_charge":"No","publisher":"Springer","date_created":"2018-12-11T11:56:32Z","oa_version":"None","date_updated":"2025-07-10T11:52:16Z","language":[{"iso":"eng"}],"page":"255 - 264","author":[{"first_name":"Sibu","full_name":"Simon, Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"full_name":"Dobrev, Petre","last_name":"Dobrev","first_name":"Petre"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","volume":1056},{"type":"journal_article","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.tcs.2013.11.032","intvolume":"       521","day":"13","department":[{"_id":"KrCh"}],"date_published":"2014-02-13T00:00:00Z","doi":"10.1016/j.tcs.2013.11.032","citation":{"mla":"Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>, vol. 521, Elsevier, 2014, pp. 73–91, doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>.","chicago":"Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>.","short":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer Science 521 (2014) 73–91.","ista":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps in Muller and parity games. Theoretical Computer Science. 521, 73–91.","ieee":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps in Muller and parity games,” <i>Theoretical Computer Science</i>, vol. 521. Elsevier, pp. 73–91, 2014.","apa":"Grinshpun, A., Phalitnonkiat, P., Rubin, S., &#38; Tarfulea, A. (2014). Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>","ama":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. 2014;521:73-91. doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>"},"publication_identifier":{"issn":["0304-3975"]},"scopus_import":"1","quality_controlled":"1","publication":"Theoretical Computer Science","publist_id":"4703","abstract":[{"text":"Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. ","lang":"eng"}],"month":"02","oa":1,"_id":"2246","main_file_link":[{"url":"http://arxiv.org/abs/1303.3777","open_access":"1"}],"language":[{"iso":"eng"}],"date_updated":"2026-04-16T10:08:15Z","page":"73 - 91","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2014","corr_author":"1","author":[{"full_name":"Grinshpun, Andrey","last_name":"Grinshpun","first_name":"Andrey"},{"last_name":"Phalitnonkiat","full_name":"Phalitnonkiat, Pakawat","first_name":"Pakawat"},{"last_name":"Rubin","full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha"},{"full_name":"Tarfulea, Andrei","last_name":"Tarfulea","first_name":"Andrei"}],"status":"public","volume":521,"isi":1,"article_processing_charge":"No","title":"Alternating traps in Muller and parity games","date_created":"2018-12-11T11:56:33Z","publisher":"Elsevier","external_id":{"arxiv":["1303.3777"],"isi":["000331433100007"]},"oa_version":"Submitted Version","arxiv":1},{"publication_identifier":{"issn":["1552-5007"]},"citation":{"mla":"Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12, doi:<a href=\"https://doi.org/10.1002/jez.b.22545\">10.1002/jez.b.22545</a>.","chicago":"Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/jez.b.22545\">https://doi.org/10.1002/jez.b.22545</a>.","short":"D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322 (2014) 1–12.","ista":"Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 322(1), 1–12.","ieee":"D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic approach to avian digit homology,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 322, no. 1. Wiley-Blackwell, pp. 1–12, 2014.","apa":"Capek, D., Metscher, B., &#38; Müller, G. (2014). Thumbs down: A molecular-morphogenetic approach to avian digit homology. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/jez.b.22545\">https://doi.org/10.1002/jez.b.22545</a>","ama":"Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach to avian digit homology. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2014;322(1):1-12. doi:<a href=\"https://doi.org/10.1002/jez.b.22545\">10.1002/jez.b.22545</a>"},"doi":"10.1002/jez.b.22545","scopus_import":"1","department":[{"_id":"CaHe"}],"date_published":"2014-01-01T00:00:00Z","type":"journal_article","fulldoi":"https://doi.org/10.1002/jez.b.22545","publication_status":"published","intvolume":"       322","day":"01","month":"01","_id":"2248","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","publist_id":"4701","abstract":[{"text":"Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.","lang":"eng"}],"quality_controlled":"1","volume":322,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","author":[{"orcid":"0000-0001-5199-9940","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","full_name":"Capek, Daniel","last_name":"Capek"},{"last_name":"Metscher","full_name":"Metscher, Brian","first_name":"Brian"},{"last_name":"Müller","full_name":"Müller, Gerd","first_name":"Gerd"}],"status":"public","page":"1 - 12","language":[{"iso":"eng"}],"date_updated":"2025-09-29T11:18:02Z","issue":"1","oa_version":"None","external_id":{"isi":["000335377400001"]},"date_created":"2018-12-11T11:56:33Z","publisher":"Wiley-Blackwell","article_processing_charge":"No","title":"Thumbs down: A molecular-morphogenetic approach to avian digit homology"},{"oa_version":"Submitted Version","issue":"1","external_id":{"isi":["000328661300008"]},"date_created":"2018-12-11T11:56:34Z","publisher":"Wiley-Blackwell","article_processing_charge":"No","title":"Inter-regulation of the unfolded protein response and auxin signaling","volume":77,"isi":1,"year":"2014","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","author":[{"first_name":"Yani","last_name":"Chen","full_name":"Chen, Yani"},{"last_name":"Aung","full_name":"Aung, Kyaw","first_name":"Kyaw"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"first_name":"Kathryn","last_name":"Walicki","full_name":"Walicki, Kathryn"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Brandizzí","full_name":"Brandizzí, Federica","first_name":"Federica"}],"page":"97 - 107","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/","open_access":"1"}],"date_updated":"2026-04-16T10:08:30Z","oa":1,"month":"01","_id":"2249","publist_id":"4699","publication":"Plant Journal","abstract":[{"lang":"eng","text":"The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes."}],"quality_controlled":"1","citation":{"ieee":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation of the unfolded protein response and auxin signaling,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.","apa":"Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., &#38; Brandizzí, F. (2014). Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>","ama":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. 2014;77(1):97-107. doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>","mla":"Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107, doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>.","chicago":"Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>.","short":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal 77 (2014) 97–107.","ista":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107."},"doi":"10.1111/tpj.12373","publication_identifier":{"issn":["0960-7412"]},"scopus_import":"1","department":[{"_id":"JiFr"}],"date_published":"2014-01-01T00:00:00Z","publication_status":"published","fulldoi":"https://doi.org/10.1111/tpj.12373","type":"journal_article","day":"01","intvolume":"        77"},{"date_updated":"2025-09-29T11:16:03Z","language":[{"iso":"eng"}],"page":"130 - 135","author":[{"first_name":"Sujal","last_name":"Phadke","full_name":"Phadke, Sujal"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pham, Tuan","last_name":"Pham","first_name":"Tuan"},{"full_name":"Pham, Stephanie","last_name":"Pham","first_name":"Stephanie"},{"full_name":"Zufall, Rebecca","last_name":"Zufall","first_name":"Rebecca"}],"corr_author":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","isi":1,"volume":105,"title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","article_processing_charge":"No","publisher":"Oxford University Press","date_created":"2018-12-11T11:56:35Z","external_id":{"isi":["000328427800013"]},"issue":"1","oa_version":"None","intvolume":"       105","day":"01","type":"journal_article","fulldoi":"https://doi.org/10.1093/jhered/est063","publication_status":"published","date_published":"2014-01-01T00:00:00Z","department":[{"_id":"NiBa"}],"scopus_import":"1","publication_identifier":{"issn":["0022-1503"]},"citation":{"ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>.","mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>.","ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. 2014;105(1):130-135. doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., &#38; Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>","ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” <i>Journal of Heredity</i>, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014."},"doi":"10.1093/jhered/est063","quality_controlled":"1","abstract":[{"lang":"eng","text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila."}],"publication":"Journal of Heredity","publist_id":"4695","_id":"2252","month":"01"},{"issue":"1","ddc":["580"],"oa_version":"Published Version","external_id":{"isi":["000328661300009"]},"publisher":"Wiley-Blackwell","date_created":"2018-12-11T11:56:35Z","title":"Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth","article_processing_charge":"No","isi":1,"volume":77,"author":[{"first_name":"Aurélien","full_name":"Bailly, Aurélien","last_name":"Bailly"},{"full_name":"Wang, Bangjun","last_name":"Wang","first_name":"Bangjun"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"first_name":"Stephan","last_name":"Pollmann","full_name":"Pollmann, Stephan"},{"first_name":"Daniel","last_name":"Schenck","full_name":"Schenck, Daniel"},{"first_name":"Hartwig","last_name":"Lüthen","full_name":"Lüthen, Hartwig"},{"last_name":"Schulz","full_name":"Schulz, Alexander","first_name":"Alexander"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","page":"108 - 118","date_updated":"2026-06-18T18:33:25Z","main_file_link":[{"url":"https://doi.org/10.1111/tpj.12369","open_access":"1"}],"language":[{"iso":"eng"}],"_id":"2253","month":"01","oa":1,"abstract":[{"text":"Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.","lang":"eng"}],"publication":"Plant Journal","publist_id":"4694","quality_controlled":"1","scopus_import":"1","publication_identifier":{"issn":["0960-7412"]},"citation":{"mla":"Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>.","chicago":"Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>.","ista":"Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 77(1), 108–118.","short":"A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz, J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.","apa":"Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., … Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>","ieee":"A. Bailly <i>et al.</i>, “Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.","ama":"Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. 2014;77(1):108-118. doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>"},"doi":"10.1111/tpj.12369","article_type":"original","date_published":"2014-01-01T00:00:00Z","department":[{"_id":"JiFr"}],"project":[{"name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur","_id":"256BDAB0-B435-11E9-9278-68D0E5697425"}],"intvolume":"        77","day":"01","type":"journal_article","publication_status":"published","fulldoi":"https://doi.org/10.1111/tpj.12369"},{"_id":"2254","oa":1,"month":"01","quality_controlled":"1","abstract":[{"lang":"eng","text":"Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus."}],"publist_id":"4692","publication":"Neuron","date_published":"2014-01-08T00:00:00Z","department":[{"_id":"PeJo"}],"file":[{"file_name":"IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf","checksum":"438547cfcd9045a22f065f2019f07849","file_id":"4773","relation":"main_file","date_updated":"2020-07-14T12:45:35Z","file_size":4373072,"content_type":"application/pdf","date_created":"2018-12-12T10:09:48Z","creator":"system","access_level":"open_access"}],"has_accepted_license":"1","scopus_import":"1","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2013.09.046","citation":{"apa":"Pernia-Andrade, A., &#38; Jonas, P. M. (2014). Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>","ieee":"A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations,” <i>Neuron</i>, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.","ama":"Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. 2014;81(1):140-152. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>.","chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>.","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152.","ista":"Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 81(1), 140–152."},"day":"08","intvolume":"        81","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.neuron.2013.09.046","type":"journal_article","project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548"},{"call_identifier":"FWF","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses"}],"external_id":{"isi":["000329559000015"]},"ec_funded":1,"file_date_updated":"2020-07-14T12:45:35Z","ddc":["570"],"oa_version":"Published Version","issue":"1","pubrep_id":"422","title":"Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations","article_processing_charge":"No","publisher":"Elsevier","date_created":"2018-12-11T11:56:35Z","status":"public","corr_author":"1","author":[{"last_name":"Pernia-Andrade","full_name":"Pernia-Andrade, Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87","first_name":"Alejandro"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"year":"2014","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"volume":81,"date_updated":"2026-04-16T10:08:53Z","language":[{"iso":"eng"}],"page":"140 - 152"},{"abstract":[{"lang":"eng","text":"Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction."}],"publist_id":"4689","publication":"PLoS Computational Biology","quality_controlled":"1","acknowledgement":"This work was funded by NSF grant IIS-0613435, NSF grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508, the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation, ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES: ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651.","_id":"2257","oa":1,"month":"01","day":"02","intvolume":"        10","fulldoi":"https://doi.org/10.1371/journal.pcbi.1003408","publication_status":"published","type":"journal_article","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_size":2194790,"relation":"main_file","date_updated":"2020-07-14T12:45:35Z","date_created":"2018-12-12T10:12:46Z","access_level":"open_access","creator":"system","checksum":"c720222c5e924a4acb17f23b9381a6ca","file_name":"IST-2016-436-v1+1_journal.pcbi.1003408.pdf","file_id":"4965"}],"scopus_import":"1","publication_identifier":{"issn":["1553-734X"]},"doi":"10.1371/journal.pcbi.1003408","citation":{"ista":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 10(1), e1003408.","short":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).","chicago":"Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” <i>PLoS Computational Biology</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">https://doi.org/10.1371/journal.pcbi.1003408</a>.","mla":"Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” <i>PLoS Computational Biology</i>, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">10.1371/journal.pcbi.1003408</a>.","ama":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. <i>PLoS Computational Biology</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">10.1371/journal.pcbi.1003408</a>","ieee":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” <i>PLoS Computational Biology</i>, vol. 10, no. 1. Public Library of Science, 2014.","apa":"Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., &#38; Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">https://doi.org/10.1371/journal.pcbi.1003408</a>"},"date_published":"2014-01-02T00:00:00Z","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","date_created":"2018-12-11T11:56:36Z","related_material":{"record":[{"id":"5562","relation":"research_data","status":"public"}]},"title":"Searching for collective behavior in a large network of sensory neurons","pubrep_id":"436","article_processing_charge":"No","file_date_updated":"2020-07-14T12:45:35Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"issue":"1","external_id":{"isi":["000337948500010"]},"article_number":"e1003408","date_updated":"2025-09-29T11:14:06Z","language":[{"iso":"eng"}],"isi":1,"volume":10,"status":"public","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Amodei","full_name":"Amodei, Dario","first_name":"Dario"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"corr_author":"1","year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"date_created":"2018-12-11T11:56:38Z","publisher":"Oxford University Press","article_processing_charge":"No","title":"DICE, an efficient system for iterative genomic editing in human pluripotent stem cells","pubrep_id":"961","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["571","610"],"oa_version":"Preprint","issue":"5","file_date_updated":"2020-07-14T12:45:35Z","external_id":{"isi":["000333093600005"]},"article_number":"e34","language":[{"iso":"eng"}],"date_updated":"2025-09-29T11:13:18Z","volume":42,"isi":1,"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","author":[{"full_name":"Zhu, Fangfang","last_name":"Zhu","first_name":"Fangfang"},{"last_name":"Gamboa","full_name":"Gamboa, Matthew","first_name":"Matthew"},{"full_name":"Farruggio, Alfonso","last_name":"Farruggio","first_name":"Alfonso"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Tasic","full_name":"Tasic, Bosiljka","first_name":"Bosiljka"},{"last_name":"Schüle","full_name":"Schüle, Birgitt","first_name":"Birgitt"},{"full_name":"Chen Tsai, Yanru","last_name":"Chen Tsai","first_name":"Yanru"},{"last_name":"Calos","full_name":"Calos, Michele","first_name":"Michele"}],"publist_id":"4684","publication":"Nucleic Acids Research","abstract":[{"text":"To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.","lang":"eng"}],"acknowledgement":"California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]. Funding for open access charge: California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]\r\nCC BY 3,0","quality_controlled":"1","oa":1,"month":"03","_id":"2261","fulldoi":"https://doi.org/10.1093/nar/gkt1290","publication_status":"published","type":"journal_article","day":"05","intvolume":"        42","citation":{"ieee":"F. Zhu <i>et al.</i>, “DICE, an efficient system for iterative genomic editing in human pluripotent stem cells,” <i>Nucleic Acids Research</i>, vol. 42, no. 5. Oxford University Press, 2014.","apa":"Zhu, F., Gamboa, M., Farruggio, A., Hippenmeyer, S., Tasic, B., Schüle, B., … Calos, M. (2014). DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkt1290\">https://doi.org/10.1093/nar/gkt1290</a>","ama":"Zhu F, Gamboa M, Farruggio A, et al. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. <i>Nucleic Acids Research</i>. 2014;42(5). doi:<a href=\"https://doi.org/10.1093/nar/gkt1290\">10.1093/nar/gkt1290</a>","mla":"Zhu, Fangfang, et al. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” <i>Nucleic Acids Research</i>, vol. 42, no. 5, e34, Oxford University Press, 2014, doi:<a href=\"https://doi.org/10.1093/nar/gkt1290\">10.1093/nar/gkt1290</a>.","chicago":"Zhu, Fangfang, Matthew Gamboa, Alfonso Farruggio, Simon Hippenmeyer, Bosiljka Tasic, Birgitt Schüle, Yanru Chen Tsai, and Michele Calos. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” <i>Nucleic Acids Research</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/nar/gkt1290\">https://doi.org/10.1093/nar/gkt1290</a>.","short":"F. Zhu, M. Gamboa, A. Farruggio, S. Hippenmeyer, B. Tasic, B. Schüle, Y. Chen Tsai, M. Calos, Nucleic Acids Research 42 (2014).","ista":"Zhu F, Gamboa M, Farruggio A, Hippenmeyer S, Tasic B, Schüle B, Chen Tsai Y, Calos M. 2014. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. 42(5), e34."},"doi":"10.1093/nar/gkt1290","has_accepted_license":"1","file":[{"date_created":"2018-12-12T10:09:15Z","access_level":"open_access","creator":"system","file_size":11044478,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:35Z","file_id":"4738","checksum":"e9268f5f96a820f04d7ebbf85927c3cb","file_name":"IST-2018-961-v1+1_2014_Hippenmeyer_DICE.pdf"}],"scopus_import":"1","department":[{"_id":"SiHi"}],"date_published":"2014-03-05T00:00:00Z"},{"day":"03","publication_status":"published","fulldoi":"https://doi.org/10.1109/ICCV.2013.365","type":"conference","date_published":"2014-03-03T00:00:00Z","department":[{"_id":"VlKo"}],"has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:45:36Z","relation":"main_file","file_size":378601,"content_type":"application/pdf","creator":"system","access_level":"open_access","date_created":"2018-12-12T10:09:30Z","file_name":"IST-2016-566-v1+1_iccv13_part_enumeration.pdf","checksum":"4a74b5c92d6dcd2348c2c10ec8dd18bf","file_id":"4754"}],"scopus_import":"1","citation":{"mla":"Olsson, Carl, et al. <i>Partial Enumeration and Curvature Regularization</i>. IEEE, 2014, pp. 2936–43, doi:<a href=\"https://doi.org/10.1109/ICCV.2013.365\">10.1109/ICCV.2013.365</a>.","chicago":"Olsson, Carl, Johannes Ulen, Yuri Boykov, and Vladimir Kolmogorov. “Partial Enumeration and Curvature Regularization,” 2936–43. IEEE, 2014. <a href=\"https://doi.org/10.1109/ICCV.2013.365\">https://doi.org/10.1109/ICCV.2013.365</a>.","short":"C. Olsson, J. Ulen, Y. Boykov, V. Kolmogorov, in:, IEEE, 2014, pp. 2936–2943.","ista":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. 2014. Partial enumeration and curvature regularization. ICCV: International Conference on Computer Vision, 2936–2943.","ieee":"C. Olsson, J. Ulen, Y. Boykov, and V. Kolmogorov, “Partial enumeration and curvature regularization,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2014, pp. 2936–2943.","apa":"Olsson, C., Ulen, J., Boykov, Y., &#38; Kolmogorov, V. (2014). Partial enumeration and curvature regularization (pp. 2936–2943). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2013.365\">https://doi.org/10.1109/ICCV.2013.365</a>","ama":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. Partial enumeration and curvature regularization. In: IEEE; 2014:2936-2943. doi:<a href=\"https://doi.org/10.1109/ICCV.2013.365\">10.1109/ICCV.2013.365</a>"},"doi":"10.1109/ICCV.2013.365","quality_controlled":"1","abstract":[{"text":"Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches. \r\nThis partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed. \r\nOur main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach.\r\n","lang":"eng"}],"publist_id":"4669","conference":{"location":"Sydney, Australia","start_date":"2013-12-01","name":"ICCV: International Conference on Computer Vision","end_date":"2013-12-08"},"_id":"2275","oa":1,"month":"03","date_updated":"2025-09-29T14:28:16Z","language":[{"iso":"eng"}],"page":"2936 - 2943","status":"public","author":[{"full_name":"Olsson, Carl","last_name":"Olsson","first_name":"Carl"},{"first_name":"Johannes","last_name":"Ulen","full_name":"Ulen, Johannes"},{"full_name":"Boykov, Yuri","last_name":"Boykov","first_name":"Yuri"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"}],"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"pubrep_id":"566","title":"Partial enumeration and curvature regularization","article_processing_charge":"No","publisher":"IEEE","date_created":"2018-12-11T11:56:42Z","external_id":{"isi":["000351830500367"]},"file_date_updated":"2020-07-14T12:45:36Z","oa_version":"Submitted Version","ddc":["000"]}]