[{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/","open_access":"1"}],"status":"public","type":"journal_article","_id":"1611","date_created":"2018-12-11T11:53:01Z","author":[{"full_name":"Whitfield, Jason","first_name":"Jason","last_name":"Whitfield"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"full_name":"Clifton, Ben","last_name":"Clifton","first_name":"Ben"},{"full_name":"Radziejewski, Johanna","last_name":"Radziejewski","first_name":"Johanna"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"},{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"first_name":"Colin","last_name":"Jackson","full_name":"Jackson, Colin"}],"oa_version":"Submitted Version","project":[{"grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"}],"quality_controlled":"1","volume":24,"language":[{"iso":"eng"}],"issue":"9","month":"09","doi":"10.1002/pro.2721","page":"1412 - 1422","year":"2015","day":"01","oa":1,"publication":"Protein Science","publist_id":"5555","intvolume":"        24","scopus_import":1,"external_id":{"pmid":["26061224"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Whitfield <i>et al.</i>, “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” <i>Protein Science</i>, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015.","ama":"Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. <i>Protein Science</i>. 2015;24(9):1412-1422. doi:<a href=\"https://doi.org/10.1002/pro.2721\">10.1002/pro.2721</a>","chicago":"Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” <i>Protein Science</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/pro.2721\">https://doi.org/10.1002/pro.2721</a>.","ista":"Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.","apa":"Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. <i>Protein Science</i>. Wiley. <a href=\"https://doi.org/10.1002/pro.2721\">https://doi.org/10.1002/pro.2721</a>","mla":"Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” <i>Protein Science</i>, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:<a href=\"https://doi.org/10.1002/pro.2721\">10.1002/pro.2721</a>.","short":"J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422."},"department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T06:52:00Z","title":"Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction","pmid":1,"date_published":"2015-09-01T00:00:00Z","publisher":"Wiley","publication_status":"published","abstract":[{"lang":"eng","text":"Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding &quot;core&quot; that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue."}]},{"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","author":[{"last_name":"Strüber","first_name":"Michael","full_name":"Strüber, Michael"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bartos, Marlene","last_name":"Bartos","first_name":"Marlene"}],"has_accepted_license":"1","month":"01","file":[{"relation":"main_file","creator":"dernst","file_id":"5838","checksum":"6703309a1f58493cf5a704211fb6ebed","file_size":1280860,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:07Z","date_created":"2019-01-17T07:52:40Z","file_name":"2015_PNAS_Strueber.pdf"}],"issue":"4","language":[{"iso":"eng"}],"volume":112,"date_created":"2018-12-11T11:53:02Z","_id":"1614","type":"journal_article","status":"public","ec_funded":1,"department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:52:01Z","citation":{"ieee":"M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” <i>PNAS</i>, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.","apa":"Strüber, M., Jonas, P. M., &#38; Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1412996112\">https://doi.org/10.1073/pnas.1412996112</a>","chicago":"Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1412996112\">https://doi.org/10.1073/pnas.1412996112</a>.","ista":"Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225.","ama":"Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. <i>PNAS</i>. 2015;112(4):1220-1225. doi:<a href=\"https://doi.org/10.1073/pnas.1412996112\">10.1073/pnas.1412996112</a>","short":"M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.","mla":"Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” <i>PNAS</i>, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:<a href=\"https://doi.org/10.1073/pnas.1412996112\">10.1073/pnas.1412996112</a>."},"external_id":{"pmid":["25583495"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. "}],"ddc":["570"],"pmid":1,"file_date_updated":"2020-07-14T12:45:07Z","date_published":"2015-01-27T00:00:00Z","publisher":"National Academy of Sciences","title":"Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells","oa":1,"day":"27","page":"1220 - 1225","year":"2015","doi":"10.1073/pnas.1412996112","scopus_import":1,"publist_id":"5552","intvolume":"       112","publication":"PNAS"},{"language":[{"iso":"eng"}],"volume":51,"article_processing_charge":"No","month":"11","issue":"11","author":[{"full_name":"Lee, Ji-Woong","last_name":"Lee","first_name":"Ji-Woong"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"quality_controlled":"1","oa_version":"Published Version","publication_identifier":{"issn":["1359-7345"],"eissn":["1364-548X"]},"status":"public","main_file_link":[{"url":"https://doi.org/10.1039/C4CC08541H","open_access":"1"}],"date_created":"2023-08-01T09:44:48Z","article_type":"original","type":"journal_article","_id":"13395","pmid":1,"date_published":"2015-11-18T00:00:00Z","publisher":"Royal Society of Chemistry","title":"Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2","publication_status":"published","abstract":[{"lang":"eng","text":"Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate."}],"external_id":{"pmid":["25417754"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-08-07T13:01:53Z","citation":{"ieee":"J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2,” <i>Chemical Communications</i>, vol. 51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.","ista":"Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.","chicago":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” <i>Chemical Communications</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c4cc08541h\">https://doi.org/10.1039/c4cc08541h</a>.","ama":"Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. <i>Chemical Communications</i>. 2015;51(11):2036-2039. doi:<a href=\"https://doi.org/10.1039/c4cc08541h\">10.1039/c4cc08541h</a>","apa":"Lee, J.-W., &#38; Klajn, R. (2015). Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. <i>Chemical Communications</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c4cc08541h\">https://doi.org/10.1039/c4cc08541h</a>","mla":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” <i>Chemical Communications</i>, vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:<a href=\"https://doi.org/10.1039/c4cc08541h\">10.1039/c4cc08541h</a>.","short":"J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039."},"intvolume":"        51","publication":"Chemical Communications","keyword":["Materials Chemistry","Metals and Alloys","Surfaces","Coatings and Films","General Chemistry","Ceramics and Composites","Electronic","Optical and Magnetic Materials","Catalysis"],"scopus_import":"1","year":"2015","doi":"10.1039/c4cc08541h","day":"18","page":"2036-2039","oa":1},{"oa":1,"day":"02","page":"403-421","year":"2015","doi":"10.1039/c4fd00265b","scopus_import":"1","keyword":["Physical and Theoretical Chemistry"],"publication":"Faraday Discussions","intvolume":"       181","citation":{"mla":"Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” <i>Faraday Discussions</i>, vol. 181, Royal Society of Chemistry, 2015, pp. 403–21, doi:<a href=\"https://doi.org/10.1039/c4fd00265b\">10.1039/c4fd00265b</a>.","short":"G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin, G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421.","apa":"Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin, A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c4fd00265b\">https://doi.org/10.1039/c4fd00265b</a>","chicago":"Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c4fd00265b\">https://doi.org/10.1039/c4fd00265b</a>.","ama":"Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly of iron oxide nanocubes. <i>Faraday Discussions</i>. 2015;181:403-421. doi:<a href=\"https://doi.org/10.1039/c4fd00265b\">10.1039/c4fd00265b</a>","ista":"Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 181, 403–421.","ieee":"G. Singh <i>et al.</i>, “Magnetic field-induced self-assembly of iron oxide nanocubes,” <i>Faraday Discussions</i>, vol. 181. Royal Society of Chemistry, pp. 403–421, 2015."},"date_updated":"2023-08-07T13:06:23Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25920522"]},"abstract":[{"text":"Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light.","lang":"eng"}],"publication_status":"published","title":"Magnetic field-induced self-assembly of iron oxide nanocubes","date_published":"2015-01-02T00:00:00Z","publisher":"Royal Society of Chemistry","pmid":1,"_id":"13397","type":"journal_article","article_type":"original","date_created":"2023-08-01T09:45:17Z","status":"public","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"main_file_link":[{"url":"https://doi.org/10.1039/C4FD00265B","open_access":"1"}],"oa_version":"Published Version","quality_controlled":"1","author":[{"first_name":"Gurvinder","last_name":"Singh","full_name":"Singh, Gurvinder"},{"first_name":"Henry","last_name":"Chan","full_name":"Chan, Henry"},{"last_name":"Udayabhaskararao","first_name":"T.","full_name":"Udayabhaskararao, T."},{"full_name":"Gelman, Elijah","last_name":"Gelman","first_name":"Elijah"},{"full_name":"Peddis, Davide","first_name":"Davide","last_name":"Peddis"},{"last_name":"Baskin","first_name":"Artem","full_name":"Baskin, Artem"},{"full_name":"Leitus, Gregory","last_name":"Leitus","first_name":"Gregory"},{"last_name":"Král","first_name":"Petr","full_name":"Král, Petr"},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"month":"01","article_processing_charge":"No","volume":181,"language":[{"iso":"eng"}]},{"status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/","open_access":"1"}],"date_created":"2018-12-11T11:51:42Z","_id":"1383","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":1,"month":"07","issue":"7","article_number":"15094","author":[{"last_name":"Yu","first_name":"Luo","full_name":"Yu, Luo"},{"full_name":"Scholl, Stefan","first_name":"Stefan","last_name":"Scholl"},{"full_name":"Doering, Anett","last_name":"Doering","first_name":"Anett"},{"first_name":"Zhang","last_name":"Yi","full_name":"Yi, Zhang"},{"full_name":"Irani, Niloufer","last_name":"Irani","first_name":"Niloufer"},{"last_name":"Di Rubbo","first_name":"Simone","full_name":"Di Rubbo, Simone"},{"full_name":"Neumetzler, Lutz","last_name":"Neumetzler","first_name":"Lutz"},{"last_name":"Krishnamoorthy","first_name":"Praveen","full_name":"Krishnamoorthy, Praveen"},{"full_name":"Van Houtte, Isabelle","first_name":"Isabelle","last_name":"Van Houtte"},{"full_name":"Mylle, Evelien","last_name":"Mylle","first_name":"Evelien"},{"last_name":"Bischoff","first_name":"Volker","full_name":"Bischoff, Volker"},{"last_name":"Vernhettes","first_name":"Samantha","full_name":"Vernhettes, Samantha"},{"first_name":"Johan","last_name":"Winne","full_name":"Winne, Johan"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"York","last_name":"Stierhof","full_name":"Stierhof, York"},{"full_name":"Schumacher, Karin","first_name":"Karin","last_name":"Schumacher"},{"last_name":"Persson","first_name":"Staffan","full_name":"Persson, Staffan"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"quality_controlled":"1","oa_version":"Submitted Version","intvolume":"         1","publist_id":"5827","publication":"Nature Plants","scopus_import":1,"doi":"10.1038/nplants.2015.94","day":"06","year":"2015","oa":1,"publisher":"Nature Publishing Group","date_published":"2015-07-06T00:00:00Z","pmid":1,"title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","abstract":[{"lang":"eng","text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["27250258"]},"date_updated":"2021-01-12T06:50:18Z","department":[{"_id":"JiFr"}],"citation":{"apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. 2015;1(7). doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094.","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>.","ieee":"L. Yu <i>et al.</i>, “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” <i>Nature Plants</i>, vol. 1, no. 7. Nature Publishing Group, 2015.","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>.","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015)."}},{"oa":1,"year":"2015","day":"01","page":"144","doi":"10.15479/at:ista:1401","acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","supervisor":[{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"publist_id":"5806","citation":{"short":"V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.","mla":"Sharmanska, Viktoriia. <i>Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views</i>. Institute of Science and Technology Austria, 2015, doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>.","apa":"Sharmanska, V. (2015). <i>Learning with attributes for object recognition: Parametric and non-parametrics views</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>","chicago":"Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>.","ista":"Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria.","ama":"Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>","ieee":"V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015."},"department":[{"_id":"ChLa"},{"_id":"GradSch"}],"date_updated":"2023-09-07T11:40:11Z","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"PhD","ddc":["000"],"publication_status":"published","abstract":[{"lang":"eng","text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views."}],"title":"Learning with attributes for object recognition: Parametric and non-parametrics views","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-11-17T13:47:24Z","date_published":"2015-04-01T00:00:00Z","_id":"1401","type":"dissertation","date_created":"2018-12-11T11:51:48Z","main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","oa_version":"Published Version","author":[{"full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","first_name":"Viktoriia","last_name":"Sharmanska"}],"file":[{"content_type":"application/pdf","date_updated":"2021-02-22T11:33:17Z","date_created":"2021-02-22T11:33:17Z","file_name":"2015_Thesis_Sharmanska.pdf","relation":"main_file","success":1,"creator":"dernst","file_id":"9177","checksum":"3605b402bb6934e09ae4cf672c84baf7","file_size":7964342,"access_level":"open_access"},{"file_name":"2015_Thesis_Sharmanska_pdfa.pdf","date_created":"2021-11-16T14:40:45Z","date_updated":"2021-11-17T13:47:24Z","content_type":"application/pdf","access_level":"closed","file_size":7372241,"checksum":"e37593b3ee75bf3180629df2d6ca8f4e","file_id":"10297","creator":"cchlebak","relation":"main_file"}],"has_accepted_license":"1","month":"04","article_processing_charge":"No","language":[{"iso":"eng"}]},{"issue":"11","article_number":"112135","month":"11","article_processing_charge":"No","volume":635,"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Walt, Samuel G","last_name":"Walt","first_name":"Samuel G"},{"last_name":"Ram","first_name":"N Bhargava","full_name":"Ram, N Bhargava"},{"full_name":"von Conta, Aaron","last_name":"von Conta","first_name":"Aaron"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"last_name":"Atala","first_name":"Marcos","full_name":"Atala, Marcos"},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"}],"type":"journal_article","_id":"14014","article_type":"original","date_created":"2023-08-10T06:37:44Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1742-6596/635/11/112135"}],"status":"public","publication_identifier":{"issn":["1742-6588"],"eissn":["1742-6596"]},"abstract":[{"lang":"eng","text":"We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons."}],"publication_status":"published","title":"Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography","publisher":"IOP Publishing","date_published":"2015-11-01T00:00:00Z","citation":{"ieee":"S. G. Walt, N. B. Ram, A. von Conta, D. R. Baykusheva, M. Atala, and H. J. Wörner, “Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography,” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11. IOP Publishing, 2015.","apa":"Walt, S. G., Ram, N. B., von Conta, A., Baykusheva, D. R., Atala, M., &#38; Wörner, H. J. (2015). Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. <i>Journal of Physics: Conference Series</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">https://doi.org/10.1088/1742-6596/635/11/112135</a>","ama":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. <i>Journal of Physics: Conference Series</i>. 2015;635(11). doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">10.1088/1742-6596/635/11/112135</a>","chicago":"Walt, Samuel G, N Bhargava Ram, Aaron von Conta, Denitsa Rangelova Baykusheva, Marcos Atala, and Hans Jakob Wörner. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” <i>Journal of Physics: Conference Series</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">https://doi.org/10.1088/1742-6596/635/11/112135</a>.","ista":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. 2015. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 635(11), 112135.","short":"S.G. Walt, N.B. Ram, A. von Conta, D.R. Baykusheva, M. Atala, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).","mla":"Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">10.1088/1742-6596/635/11/112135</a>."},"date_updated":"2023-08-22T08:51:33Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Physics and Astronomy"],"scopus_import":"1","publication":"Journal of Physics: Conference Series","intvolume":"       635","oa":1,"day":"01","year":"2015","doi":"10.1088/1742-6596/635/11/112135"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T08:49:14Z","extern":"1","citation":{"ista":"Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 635(11), 112136.","ama":"Kraus PM, Mignolet B, Baykusheva DR, et al. Attosecond charge migration and its laser control. <i>Journal of Physics: Conference Series</i>. 2015;635(11). doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">10.1088/1742-6596/635/11/112136</a>","chicago":"Kraus, P M, B Mignolet, Denitsa Rangelova Baykusheva, A Rupenyan, L Horný, E F Penka, O I Tolstikhin, et al. “Attosecond Charge Migration and Its Laser Control.” <i>Journal of Physics: Conference Series</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">https://doi.org/10.1088/1742-6596/635/11/112136</a>.","apa":"Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Attosecond charge migration and its laser control. <i>Journal of Physics: Conference Series</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">https://doi.org/10.1088/1742-6596/635/11/112136</a>","ieee":"P. M. Kraus <i>et al.</i>, “Attosecond charge migration and its laser control,” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11. IOP Publishing, 2015.","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).","mla":"Kraus, P. M., et al. “Attosecond Charge Migration and Its Laser Control.” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11, 112136, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">10.1088/1742-6596/635/11/112136</a>."},"publisher":"IOP Publishing","date_published":"2015-07-01T00:00:00Z","title":"Attosecond charge migration and its laser control","abstract":[{"text":"We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes.","lang":"eng"}],"publication_status":"published","day":"01","doi":"10.1088/1742-6596/635/11/112136","year":"2015","oa":1,"intvolume":"       635","publication":"Journal of Physics: Conference Series","scopus_import":"1","keyword":["General Physics and Astronomy"],"author":[{"full_name":"Kraus, P M","first_name":"P M","last_name":"Kraus"},{"full_name":"Mignolet, B","first_name":"B","last_name":"Mignolet"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Rupenyan, A","last_name":"Rupenyan","first_name":"A"},{"full_name":"Horný, L","first_name":"L","last_name":"Horný"},{"full_name":"Penka, E F","first_name":"E F","last_name":"Penka"},{"first_name":"O I","last_name":"Tolstikhin","full_name":"Tolstikhin, O I"},{"first_name":"J","last_name":"Schneider","full_name":"Schneider, J"},{"full_name":"Jensen, F","first_name":"F","last_name":"Jensen"},{"full_name":"Madsen, L B","first_name":"L B","last_name":"Madsen"},{"first_name":"A D","last_name":"Bandrauk","full_name":"Bandrauk, A D"},{"last_name":"Remacle","first_name":"F","full_name":"Remacle, F"},{"last_name":"Wörner","first_name":"H J","full_name":"Wörner, H J"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":635,"month":"07","issue":"11","article_number":"112136","status":"public","publication_identifier":{"eissn":["1742-6596"],"issn":["1742-6588"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1742-6596/635/11/112136"}],"date_created":"2023-08-10T06:37:53Z","type":"journal_article","_id":"14015","article_type":"original"},{"article_type":"original","_id":"14016","type":"journal_article","date_created":"2023-08-10T06:38:01Z","publication_identifier":{"eissn":["2041-1723"]},"main_file_link":[{"url":"https://doi.org/10.1038/ncomms8039","open_access":"1"}],"status":"public","oa_version":"Published Version","quality_controlled":"1","author":[{"first_name":"P. M.","last_name":"Kraus","full_name":"Kraus, P. M."},{"last_name":"Tolstikhin","first_name":"O. I.","full_name":"Tolstikhin, O. I."},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Rupenyan, A.","last_name":"Rupenyan","first_name":"A."},{"full_name":"Schneider, J.","last_name":"Schneider","first_name":"J."},{"first_name":"C. Z.","last_name":"Bisgaard","full_name":"Bisgaard, C. Z."},{"first_name":"T.","last_name":"Morishita","full_name":"Morishita, T."},{"full_name":"Jensen, F.","first_name":"F.","last_name":"Jensen"},{"full_name":"Madsen, L. B.","first_name":"L. B.","last_name":"Madsen"},{"full_name":"Wörner, H. J.","last_name":"Wörner","first_name":"H. J."}],"article_number":"7039","month":"05","volume":6,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa":1,"year":"2015","doi":"10.1038/ncomms8039","day":"05","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"publication":"Nature Communications","intvolume":"         6","citation":{"mla":"Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” <i>Nature Communications</i>, vol. 6, 7039, Springer Nature, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms8039\">10.1038/ncomms8039</a>.","short":"P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015).","apa":"Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ncomms8039\">https://doi.org/10.1038/ncomms8039</a>","ista":"Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 6, 7039.","chicago":"Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” <i>Nature Communications</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/ncomms8039\">https://doi.org/10.1038/ncomms8039</a>.","ama":"Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms8039\">10.1038/ncomms8039</a>","ieee":"P. M. Kraus <i>et al.</i>, “Observation of laser-induced electronic structure in oriented polyatomic molecules,” <i>Nature Communications</i>, vol. 6. Springer Nature, 2015."},"extern":"1","date_updated":"2023-08-22T08:52:56Z","external_id":{"pmid":["25940229"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies."}],"title":"Observation of laser-induced electronic structure in oriented polyatomic molecules","pmid":1,"publisher":"Springer Nature","date_published":"2015-05-05T00:00:00Z"},{"date_published":"2015-02-19T00:00:00Z","publisher":"American Physical Society","title":"Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation","abstract":[{"lang":"eng","text":"The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1504.03933"]},"date_updated":"2023-08-22T08:56:34Z","extern":"1","citation":{"ista":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 91(2), 023421.","chicago":"Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” <i>Physical Review A</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/physreva.91.023421\">https://doi.org/10.1103/physreva.91.023421</a>.","ama":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. <i>Physical Review A</i>. 2015;91(2). doi:<a href=\"https://doi.org/10.1103/physreva.91.023421\">10.1103/physreva.91.023421</a>","apa":"Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., &#38; Rohringer, N. (2015). Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.91.023421\">https://doi.org/10.1103/physreva.91.023421</a>","ieee":"S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer, “Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation,” <i>Physical Review A</i>, vol. 91, no. 2. American Physical Society, 2015.","mla":"Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” <i>Physical Review A</i>, vol. 91, no. 2, 023421, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/physreva.91.023421\">10.1103/physreva.91.023421</a>.","short":"S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical Review A 91 (2015)."},"intvolume":"        91","arxiv":1,"publication":"Physical Review A","scopus_import":"1","keyword":["Atomic and Molecular Physics","and Optics"],"day":"19","doi":"10.1103/physreva.91.023421","year":"2015","oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":91,"month":"02","issue":"2","article_number":"023421","author":[{"last_name":"Zhang","first_name":"Song Bin","full_name":"Zhang, Song Bin"},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"last_name":"Kraus","first_name":"Peter M.","full_name":"Kraus, Peter M."},{"full_name":"Wörner, Hans Jakob","last_name":"Wörner","first_name":"Hans Jakob"},{"full_name":"Rohringer, Nina","first_name":"Nina","last_name":"Rohringer"}],"quality_controlled":"1","oa_version":"Preprint","status":"public","publication_identifier":{"issn":["1050-2947"],"eissn":["1094-1622"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.03933"}],"date_created":"2023-08-10T06:38:10Z","type":"journal_article","_id":"14017","article_type":"original"},{"publist_id":"5782","conference":{"location":"Montreal, Canada","name":"NIPS: Neural Information Processing Systems","end_date":"2015-12-12","start_date":"2015-12-07"},"intvolume":"        28","_id":"1424","type":"conference","oa":1,"date_created":"2018-12-11T11:51:56Z","status":"public","main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}],"page":"3070 - 3078","day":"01","year":"2015","acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","publication_status":"published","month":"12","abstract":[{"lang":"eng","text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data."}],"title":"Statistical topological data analysis-A kernel perspective","volume":28,"language":[{"iso":"eng"}],"publisher":"Neural Information Processing Systems","date_published":"2015-12-01T00:00:00Z","oa_version":"Submitted Version","citation":{"mla":"Kwitt, Roland, et al. <i>Statistical Topological Data Analysis-A Kernel Perspective</i>. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.","short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., &#38; Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.","chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015."},"quality_controlled":"1","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:50:38Z","alternative_title":["Advances in Neural Information Processing Systems"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kwitt","first_name":"Roland","full_name":"Kwitt, Roland"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","full_name":"Huber, Stefan","first_name":"Stefan","last_name":"Huber","orcid":"0000-0002-8871-5814"},{"full_name":"Niethammer, Marc","first_name":"Marc","last_name":"Niethammer"},{"last_name":"Lin","first_name":"Weili","full_name":"Lin, Weili"},{"orcid":"0000-0002-9683-0724","last_name":"Bauer","first_name":"Ulrich","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"}]},{"status":"public","main_file_link":[{"url":"http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks","open_access":"1"}],"date_created":"2018-12-11T11:51:57Z","_id":"1425","type":"conference","ec_funded":1,"conference":{"end_date":"2015-12-12","start_date":"2015-12-07","name":"NIPS: Neural Information Processing Systems","location":"Montreal, Canada"},"author":[{"full_name":"Pentina, Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","last_name":"Pentina"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"None","language":[{"iso":"eng"}],"volume":2015,"month":"01","day":"01","year":"2015","page":"1540 - 1548","oa":1,"intvolume":"      2015","publist_id":"5781","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","alternative_title":["Advances in Neural Information Processing Systems"],"date_updated":"2021-01-12T06:50:39Z","department":[{"_id":"ChLa"}],"citation":{"mla":"Pentina, Anastasia, and Christoph Lampert. <i>Lifelong Learning with Non-i.i.d. Tasks</i>. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.","short":"A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015, pp. 1540–1548.","ieee":"A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.","ama":"Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems; 2015:1540-1548.","ista":"Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548.","chicago":"Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.","apa":"Pentina, A., &#38; Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems."},"date_published":"2015-01-01T00:00:00Z","publisher":"Neural Information Processing Systems","title":"Lifelong learning with non-i.i.d. tasks","abstract":[{"text":"In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm.","lang":"eng"}],"publication_status":"published"},{"oa_version":"Preprint","citation":{"ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, 1455–62. ACM, 2015. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>.","ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2015:1455-1462. doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>","apa":"Paixao, T., Sudholt, D., Heredia, J., &#38; Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i> (pp. 1455–1462). Madrid, Spain: ACM. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, Madrid, Spain, 2015, pp. 1455–1462.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2015, pp. 1455–62, doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>."},"project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"quality_controlled":"1","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2021-01-12T06:50:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"last_name":"Heredia","first_name":"Jorge","full_name":"Heredia, Jorge"},{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"}],"month":"07","publication_status":"published","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"title":"First steps towards a runtime comparison of natural and artificial evolution","publisher":"ACM","language":[{"iso":"eng"}],"date_published":"2015-07-11T00:00:00Z","_id":"1430","type":"conference","date_created":"2018-12-11T11:51:58Z","oa":1,"page":"1455 - 1462","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.06260"}],"status":"public","doi":"10.1145/2739480.2754758","year":"2015","day":"11","scopus_import":1,"publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","publist_id":"5768","conference":{"location":"Madrid, Spain","name":"GECCO: Genetic and evolutionary computation conference","end_date":"2015-07-15","start_date":"2015-07-11"},"ec_funded":1},{"date_created":"2023-09-06T12:52:47Z","article_type":"letter_note","type":"journal_article","_id":"14303","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.nanolett.5b01461"}],"status":"public","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Kick, B","last_name":"Kick","first_name":"B"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","first_name":"Florian M","last_name":"Praetorius"},{"first_name":"H","last_name":"Dietz","full_name":"Dietz, H"},{"full_name":"Weuster-Botz, D","first_name":"D","last_name":"Weuster-Botz"}],"month":"06","issue":"7","language":[{"iso":"eng"}],"volume":15,"article_processing_charge":"No","oa":1,"page":"4672-4676","doi":"10.1021/acs.nanolett.5b01461","year":"2015","day":"01","intvolume":"        15","publication":"Nano Letters","extern":"1","date_updated":"2023-11-07T11:56:32Z","citation":{"short":"B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676.","mla":"Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” <i>Nano Letters</i>, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">10.1021/acs.nanolett.5b01461</a>.","ieee":"B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” <i>Nano Letters</i>, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015.","apa":"Kick, B., Praetorius, F. M., Dietz, H., &#38; Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. <i>Nano Letters</i>. ACS Publications. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">https://doi.org/10.1021/acs.nanolett.5b01461</a>","chicago":"Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” <i>Nano Letters</i>. ACS Publications, 2015. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">https://doi.org/10.1021/acs.nanolett.5b01461</a>.","ista":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676.","ama":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. <i>Nano Letters</i>. 2015;15(7):4672-4676. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">10.1021/acs.nanolett.5b01461</a>"},"external_id":{"pmid":["26028443"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale."}],"pmid":1,"publisher":"ACS Publications","date_published":"2015-06-01T00:00:00Z","title":"Efficient production of single-stranded phage DNA as scaffolds for DNA origami"},{"has_accepted_license":"1","month":"05","issue":"4","file":[{"success":1,"relation":"main_file","file_size":2416780,"access_level":"open_access","creator":"cziletti","file_id":"9058","checksum":"b97d62433581875c1b85210c5f6ae370","date_updated":"2021-02-02T13:22:19Z","date_created":"2021-02-02T13:22:19Z","content_type":"application/pdf","file_name":"2015_ScienceAdvances_Palacci.pdf"}],"article_number":"e1400214","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":1,"quality_controlled":"1","oa_version":"Published Version","author":[{"orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Sacanna, Stefano","first_name":"Stefano","last_name":"Sacanna"},{"first_name":"Anaïs","last_name":"Abramian","full_name":"Abramian, Anaïs"},{"full_name":"Barral, Jérémie","last_name":"Barral","first_name":"Jérémie"},{"full_name":"Hanson, Kasey","last_name":"Hanson","first_name":"Kasey"},{"first_name":"Alexander Y.","last_name":"Grosberg","full_name":"Grosberg, Alexander Y."},{"full_name":"Pine, David J.","first_name":"David J.","last_name":"Pine"},{"last_name":"Chaikin","first_name":"Paul M.","full_name":"Chaikin, Paul M."}],"date_created":"2021-02-02T13:15:02Z","type":"journal_article","_id":"9057","article_type":"original","publication_identifier":{"issn":["2375-2548"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","status":"public","abstract":[{"text":"Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.","lang":"eng"}],"publication_status":"published","ddc":["530"],"date_published":"2015-05-01T00:00:00Z","publisher":"American Association for the Advancement of Science ","file_date_updated":"2021-02-02T13:22:19Z","pmid":1,"title":"Artificial rheotaxis","date_updated":"2023-02-23T13:47:52Z","extern":"1","citation":{"short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” <i>Science Advances</i>, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:<a href=\"https://doi.org/10.1126/sciadv.1400214\">10.1126/sciadv.1400214</a>.","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” <i>Science Advances</i>. American Association for the Advancement of Science , 2015. <a href=\"https://doi.org/10.1126/sciadv.1400214\">https://doi.org/10.1126/sciadv.1400214</a>.","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. <i>Science Advances</i>. 2015;1(4). doi:<a href=\"https://doi.org/10.1126/sciadv.1400214\">10.1126/sciadv.1400214</a>","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. <i>Science Advances</i>. American Association for the Advancement of Science . <a href=\"https://doi.org/10.1126/sciadv.1400214\">https://doi.org/10.1126/sciadv.1400214</a>","ieee":"J. A. Palacci <i>et al.</i>, “Artificial rheotaxis,” <i>Science Advances</i>, vol. 1, no. 4. American Association for the Advancement of Science , 2015."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"external_id":{"arxiv":["1505.05111"],"pmid":["26601175"]},"scopus_import":"1","intvolume":"         1","arxiv":1,"publication":"Science Advances","oa":1,"day":"01","year":"2015","doi":"10.1126/sciadv.1400214"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Lefauve, A., Muller, C. J., &#38; Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2014jc010598\">https://doi.org/10.1002/2014jc010598</a>","ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. <i>Journal of Geophysical Research: Oceans</i>. 2015;120(7):4760-4777. doi:<a href=\"https://doi.org/10.1002/2014jc010598\">10.1002/2014jc010598</a>","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union, 2015. <a href=\"https://doi.org/10.1002/2014jc010598\">https://doi.org/10.1002/2014jc010598</a>.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” <i>Journal of Geophysical Research: Oceans</i>, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” <i>Journal of Geophysical Research: Oceans</i>, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:<a href=\"https://doi.org/10.1002/2014jc010598\">10.1002/2014jc010598</a>.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777."},"extern":"1","date_updated":"2022-01-24T13:45:41Z","title":"A three-dimensional map of tidal dissipation over abyssal hills","publisher":"American Geophysical Union","date_published":"2015-06-08T00:00:00Z","publication_status":"published","abstract":[{"text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere.","lang":"eng"}],"page":"4760-4777","doi":"10.1002/2014jc010598","year":"2015","day":"08","oa":1,"publication":"Journal of Geophysical Research: Oceans","intvolume":"       120","author":[{"last_name":"Lefauve","first_name":"Adrien","full_name":"Lefauve, Adrien"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"first_name":"Angélique","last_name":"Melet","full_name":"Melet, Angélique"}],"oa_version":"Published Version","quality_controlled":"1","volume":120,"article_processing_charge":"No","language":[{"iso":"eng"}],"issue":"7","month":"06","publication_identifier":{"issn":["2169-9275"]},"status":"public","main_file_link":[{"url":"https://doi.org/10.1002/2014JC010598","open_access":"1"}],"article_type":"original","type":"journal_article","_id":"9141","date_created":"2021-02-15T14:21:49Z"},{"oa":1,"day":"21","doi":"10.7554/eLife.09206","year":"2015","publication":"eLife","intvolume":"         4","publist_id":"6512","citation":{"mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” <i>ELife</i>, vol. 4, e09206, eLife Sciences Publications, 2015, doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” <i>ELife</i>. eLife Sciences Publications, 2015. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>.","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. <i>eLife</i>. 2015;4. doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>","ieee":"I. Sehring <i>et al.</i>, “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” <i>eLife</i>, vol. 4. eLife Sciences Publications, 2015."},"date_updated":"2021-01-12T08:21:58Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["539","570"],"abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events."}],"publication_status":"published","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","file_date_updated":"2020-07-14T12:48:15Z","date_published":"2015-10-21T00:00:00Z","publisher":"eLife Sciences Publications","type":"journal_article","_id":"928","date_created":"2018-12-11T11:49:15Z","status":"public","oa_version":"Published Version","quality_controlled":"1","author":[{"last_name":"Sehring","first_name":"Ivonne","full_name":"Sehring, Ivonne"},{"first_name":"Pierre","last_name":"Recho","full_name":"Recho, Pierre"},{"full_name":"Denker, Elsa","last_name":"Denker","first_name":"Elsa"},{"last_name":"Kourakis","first_name":"Matthew","full_name":"Kourakis, Matthew"},{"last_name":"Mathiesen","first_name":"Birthe","full_name":"Mathiesen, Birthe"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Dong, Bo","last_name":"Dong","first_name":"Bo"},{"last_name":"Jiang","first_name":"Di","full_name":"Jiang, Di"}],"file":[{"file_name":"2015_eLife_Sehring.pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-20T15:50:56Z","content_type":"application/pdf","file_size":7202224,"access_level":"open_access","creator":"dernst","file_id":"5769","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","relation":"main_file"}],"article_number":"e09206","has_accepted_license":"1","month":"10","volume":4,"language":[{"iso":"eng"}]},{"title":"Physics of active jamming during collective cellular motion in a monolayer","publisher":"National Academy of Sciences","date_published":"2015-12-15T00:00:00Z","pmid":1,"abstract":[{"text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26627719"]},"citation":{"mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319.","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. 2015;112(50):15314-15319. doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>","chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., &#38; Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” <i>PNAS</i>, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015."},"date_updated":"2021-01-12T08:22:01Z","extern":"1","publication":"PNAS","intvolume":"       112","publist_id":"6511","doi":"10.1073/pnas.1510973112","year":"2015","page":"15314 - 15319","day":"15","oa":1,"volume":112,"language":[{"iso":"eng"}],"issue":"50","month":"12","author":[{"full_name":"García, Simón","last_name":"García","first_name":"Simón"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"},{"full_name":"Silberzan, Pascal","last_name":"Silberzan","first_name":"Pascal"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"oa_version":"None","quality_controlled":"1","status":"public","main_file_link":[{"url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf","open_access":"1"}],"type":"journal_article","_id":"933","date_created":"2018-12-11T11:49:16Z"},{"scopus_import":"1","intvolume":"        29","publication":"Genes and Development","oa":1,"year":"2015","day":"15","doi":"10.1101/gad.269902.115","page":"2517–2531","abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"publication_status":"published","ddc":["570"],"file_date_updated":"2021-06-08T09:55:10Z","date_published":"2015-12-15T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press","pmid":1,"title":"Evolution and function of genomic imprinting in plants","date_updated":"2021-12-14T07:58:15Z","department":[{"_id":"DaZi"}],"extern":"1","citation":{"chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"pmid":["26680300"]},"date_created":"2021-06-08T09:56:24Z","type":"journal_article","_id":"9532","article_type":"review","status":"public","publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"month":"12","has_accepted_license":"1","issue":"24","file":[{"file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","date_updated":"2021-06-08T09:55:10Z","date_created":"2021-06-08T09:55:10Z","content_type":"application/pdf","file_size":1116846,"access_level":"open_access","creator":"asandaue","checksum":"086a88cfca4677646da26ed960cb02e9","file_id":"9533","relation":"main_file","success":1}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":29,"quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}]},{"month":"11","language":[{"iso":"eng"}],"volume":49,"article_processing_charge":"No","quality_controlled":"1","oa_version":"Preprint","author":[{"first_name":"Michael","last_name":"Krivelevich","full_name":"Krivelevich, Michael"},{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"date_created":"2021-06-21T06:40:34Z","article_type":"original","_id":"9575","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1501.04816","open_access":"1"}],"publication_identifier":{"issn":["1571-0653"]},"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight."}],"publisher":"Elsevier","date_published":"2015-11-01T00:00:00Z","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","extern":"1","date_updated":"2023-02-23T14:01:28Z","citation":{"ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49. Elsevier, pp. 181–187, 2015.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. 2015;49:181-187. doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>.","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49, Elsevier, 2015, pp. 181–87, doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>."},"external_id":{"arxiv":["1501.04816"]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","scopus_import":"1","arxiv":1,"intvolume":"        49","publication":"Electronic Notes in Discrete Mathematics","oa":1,"day":"01","doi":"10.1016/j.endm.2015.06.027","year":"2015","page":"181-187"}]