[{"publication":"Nature","citation":{"ieee":"B. Hof, J. Westerweel, T. Schneider, and B. Eckhardt, “Finite lifetime of turbulence in shear flows,” Nature, vol. 443, no. 7107. Nature Publishing Group, pp. 59–62, 2006.","apa":"Hof, B., Westerweel, J., Schneider, T., & Eckhardt, B. (2006). Finite lifetime of turbulence in shear flows. Nature. Nature Publishing Group. https://doi.org/10.1038/nature05089","ista":"Hof B, Westerweel J, Schneider T, Eckhardt B. 2006. Finite lifetime of turbulence in shear flows. Nature. 443(7107), 59–62.","ama":"Hof B, Westerweel J, Schneider T, Eckhardt B. Finite lifetime of turbulence in shear flows. Nature. 2006;443(7107):59-62. doi:10.1038/nature05089","chicago":"Hof, Björn, Jerry Westerweel, Tobias Schneider, and Bruno Eckhardt. “Finite Lifetime of Turbulence in Shear Flows.” Nature. Nature Publishing Group, 2006. https://doi.org/10.1038/nature05089.","short":"B. Hof, J. Westerweel, T. Schneider, B. Eckhardt, Nature 443 (2006) 59–62.","mla":"Hof, Björn, et al. “Finite Lifetime of Turbulence in Shear Flows.” Nature, vol. 443, no. 7107, Nature Publishing Group, 2006, pp. 59–62, doi:10.1038/nature05089."},"quality_controlled":0,"page":"59 - 62","date_published":"2006-09-07T00:00:00Z","doi":"10.1038/nature05089","month":"09","day":"07","year":"2006","_id":"2791","publication_status":"published","title":"Finite lifetime of turbulence in shear flows","status":"public","publisher":"Nature Publishing Group","intvolume":" 443","author":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Björn Hof"},{"last_name":"Westerweel","first_name":"Jerry","full_name":"Westerweel, Jerry"},{"last_name":"Schneider","first_name":"Tobias","full_name":"Schneider, Tobias M"},{"full_name":"Eckhardt, Bruno","last_name":"Eckhardt","first_name":"Bruno"}],"date_updated":"2021-01-12T06:59:44Z","date_created":"2018-12-11T11:59:37Z","volume":443,"type":"journal_article","abstract":[{"lang":"eng","text":"Generally, the motion of fluids is smooth and laminar at low speeds but becomes highly disordered and turbulent as the velocity increases. The transition from laminar to turbulent flow can involve a sequence of instabilities in which the system realizes progressively more complicated states, or it can occur suddenly. Once the transition has taken place, it is generally assumed that, under steady conditions, the turbulent state will persist indefinitely. The flow of a fluid down a straight pipe provides a ubiquitous example of a shear flow undergoing a sudden transition from laminar to turbulent motion. Extensive calculations and experimental studies have shown that, at relatively low flow rates, turbulence in pipes is transient, and is characterized by an exponential distribution of lifetimes. They also suggest that for Reynolds numbers exceeding a critical value the lifetime diverges (that is, becomes infinitely large), marking a change from transient to persistent turbulence. Here we present experimental data and numerical calculations covering more than two decades of lifetimes, showing that the lifetime does not in fact diverge but rather increases exponentially with the Reynolds number. This implies that turbulence in pipes is only a transient event (contrary to the commonly accepted view), and that the turbulent and laminar states remain dynamically connected, suggesting avenues for turbulence control."}],"publist_id":"4098","issue":"7107","extern":1},{"abstract":[{"text":"Transition to turbulence in pipe flow has posed a riddle in fluid dynamics since the pioneering experiments of Reynolds[1]. Although the laminar flow is linearly stable for all flow rates, practical pipe flows become turbulent at large enough flow speeds. Turbulence arises suddenly and fully without distinct steps and without a clear critical point. The complexity of this problem has puzzled mathematicians, physicists and engineers for more than a century and no satisfactory explanation of this problem has been given. In a very recent theoretical approach it has been suggested that unstable solutions of the Navier Stokes equations may hold the key to understanding this problem. In numerical studies such unstable states have been identified as exact solutions for the idealized case of a pipe with periodic boundary conditions[2, 3]. These solutions have the form of waves extending through the entire pipe and travelling in the streamwise direction at a phase speed close to the bulk velocity of the fluid. With the aid of a recently developed high-speed stereoscopic Particle Image Velocimetry (PIV) system, we were able to observe transients of such unstable solutions in turbulent pipe flow[4].","lang":"eng"}],"publist_id":"4097","extern":1,"type":"journal_article","author":[{"full_name":"Björn Hof","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"van Doorne, Casimir W","first_name":"Casimir","last_name":"Van Doorne"},{"full_name":"Westerweel, Jerry","last_name":"Westerweel","first_name":"Jerry"},{"full_name":"Nieuwstadt, Frans T","first_name":"Frans","last_name":"Nieuwstadt"}],"date_updated":"2021-01-12T06:59:45Z","date_created":"2018-12-11T11:59:37Z","volume":78,"_id":"2792","year":"2006","title":"Observation of nonlinear travelling waves in turbulent pipe flow","publication_status":"published","status":"public","publisher":"Springer","intvolume":" 78","day":"18","month":"01","date_published":"2006-01-18T00:00:00Z","doi":"10.1007/1-4020-4159-4_11","publication":"Fluid Mechanics and its Applications","citation":{"ama":"Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. Observation of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and its Applications. 2006;78:109-114. doi:10.1007/1-4020-4159-4_11","ieee":"B. Hof, C. Van Doorne, J. Westerweel, and F. Nieuwstadt, “Observation of nonlinear travelling waves in turbulent pipe flow,” Fluid Mechanics and its Applications, vol. 78. Springer, pp. 109–114, 2006.","apa":"Hof, B., Van Doorne, C., Westerweel, J., & Nieuwstadt, F. (2006). Observation of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and Its Applications. Springer. https://doi.org/10.1007/1-4020-4159-4_11","ista":"Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. 2006. Observation of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and its Applications. 78, 109–114.","short":"B. Hof, C. Van Doorne, J. Westerweel, F. Nieuwstadt, Fluid Mechanics and Its Applications 78 (2006) 109–114.","mla":"Hof, Björn, et al. “Observation of Nonlinear Travelling Waves in Turbulent Pipe Flow.” Fluid Mechanics and Its Applications, vol. 78, Springer, 2006, pp. 109–14, doi:10.1007/1-4020-4159-4_11.","chicago":"Hof, Björn, Casimir Van Doorne, Jerry Westerweel, and Frans Nieuwstadt. “Observation of Nonlinear Travelling Waves in Turbulent Pipe Flow.” Fluid Mechanics and Its Applications. Springer, 2006. https://doi.org/10.1007/1-4020-4159-4_11."},"quality_controlled":0,"page":"109 - 114"},{"type":"journal_article","publist_id":"3864","issue":"8","abstract":[{"text":"IL-10 is a potent anti-inflammatory and immunomodulatory cytokine, exerting major effects in the degree and quality of the immune response. Using a newly generated IL-10 reporter mouse model, which easily allows the study of IL-10 expression from each allele in a single cell, we report here for the first time that IL-10 is predominantly monoallelic expressed in CD4+ T cells. Furthermore, we have compelling evidence that this expression pattern is not due to parental imprinting, allelic exclusion, or strong allelic bias. Instead, our results support a stochastic regulation mechanism, in which the probability to initiate allelic transcription depends on the strength of TCR signaling and subsequent capacity to overcome restrictions imposed by chromatin hypoacetylation. In vivo Ag-experienced T cells show a higher basal probability to transcribe IL-10 when compared with naive cells, yet still show mostly monoallelic IL-10 expression. Finally, statistical analysis on allelic expression data shows transcriptional independence between both alleles. We conclude that CD4+ T cells have a low probability for IL-10 allelic activation resulting in a predominantly monoallelic expression pattern, and that IL-10 expression appears to be stochastically regulated by controlling the frequency of expressing cells, rather than absolute protein levels per cell.","lang":"eng"}],"extern":1,"_id":"2894","year":"2006","intvolume":" 177","publisher":"American Association of Immunologists","title":"Stochastic Monoallelic Expression of IL 10 in T Cells","status":"public","publication_status":"published","author":[{"last_name":"Calado","first_name":"Dinis","full_name":"Calado, Dinis P"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Tiago Paixao"},{"full_name":"Holmberg, Dan","last_name":"Holmberg","first_name":"Dan"},{"full_name":"Haury, Matthias","first_name":"Matthias","last_name":"Haury"}],"volume":177,"date_created":"2018-12-11T12:00:11Z","date_updated":"2021-01-12T07:00:32Z","day":"01","month":"01","citation":{"chicago":"Calado, Dinis, Tiago Paixao, Dan Holmberg, and Matthias Haury. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology. American Association of Immunologists, 2006. https://doi.org/10.4049/jimmunol.177.8.5358 .","short":"D. Calado, T. Paixao, D. Holmberg, M. Haury, Journal of Immunology 177 (2006) 5358–5364.","mla":"Calado, Dinis, et al. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology, vol. 177, no. 8, American Association of Immunologists, 2006, pp. 5358–64, doi:10.4049/jimmunol.177.8.5358 .","apa":"Calado, D., Paixao, T., Holmberg, D., & Haury, M. (2006). Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. American Association of Immunologists. https://doi.org/10.4049/jimmunol.177.8.5358 ","ieee":"D. Calado, T. Paixao, D. Holmberg, and M. Haury, “Stochastic Monoallelic Expression of IL 10 in T Cells,” Journal of Immunology, vol. 177, no. 8. American Association of Immunologists, pp. 5358–5364, 2006.","ista":"Calado D, Paixao T, Holmberg D, Haury M. 2006. Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. 177(8), 5358–5364.","ama":"Calado D, Paixao T, Holmberg D, Haury M. Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. 2006;177(8):5358-5364. doi:10.4049/jimmunol.177.8.5358 "},"publication":"Journal of Immunology","page":"5358 - 5364","quality_controlled":0,"doi":"10.4049/jimmunol.177.8.5358 ","date_published":"2006-01-01T00:00:00Z"},{"page":"423 - 427","quality_controlled":0,"citation":{"apa":"Kolmogorov, V., & Zabih, R. (2006). Graph cut algorithms for binocular stereo with occlusions. In Handbook of Mathematical Models in Computer Vision (pp. 423–427). Springer. https://doi.org/10.1007/0-387-28831-7_26","ieee":"V. Kolmogorov and R. Zabih, “Graph cut algorithms for binocular stereo with occlusions,” in Handbook of Mathematical Models in Computer Vision, Springer, 2006, pp. 423–427.","ista":"Kolmogorov V, Zabih R. 2006.Graph cut algorithms for binocular stereo with occlusions. In: Handbook of Mathematical Models in Computer Vision. , 423–427.","ama":"Kolmogorov V, Zabih R. Graph cut algorithms for binocular stereo with occlusions. In: Handbook of Mathematical Models in Computer Vision. Springer; 2006:423-427. doi:10.1007/0-387-28831-7_26","chicago":"Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular Stereo with Occlusions.” In Handbook of Mathematical Models in Computer Vision, 423–27. Springer, 2006. https://doi.org/10.1007/0-387-28831-7_26.","short":"V. Kolmogorov, R. Zabih, in:, Handbook of Mathematical Models in Computer Vision, Springer, 2006, pp. 423–427.","mla":"Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular Stereo with Occlusions.” Handbook of Mathematical Models in Computer Vision, Springer, 2006, pp. 423–27, doi:10.1007/0-387-28831-7_26."},"publication":"Handbook of Mathematical Models in Computer Vision","date_published":"2006-01-01T00:00:00Z","doi":"10.1007/0-387-28831-7_26","month":"01","day":"01","publisher":"Springer","publication_status":"published","title":"Graph cut algorithms for binocular stereo with occlusions","status":"public","_id":"2921","year":"2006","date_created":"2018-12-11T12:00:21Z","date_updated":"2021-01-12T07:00:42Z","author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ramin","last_name":"Zabih","full_name":"Zabih, Ramin"}],"type":"book_chapter","extern":1,"publist_id":"3816","abstract":[{"text":"Most binocular stereo algorithms assume that all scene elements are visible from both cameras. Scene elements that are visible from only one camera, known as occlusions, pose an important challenge for stereo. Occlusions are important for segmentation, because they appear near discontinuities. However, stereo algorithms tend to ignore occlusions because of their difficulty. One reason is that occlusions require the input images to be treated symmetrically, which complicates the problem formulation. Worse, certain depth maps imply physically impossible scene configurations, and must be excluded from the output. In this chapter we approach the problem of binocular stereo with occlusions from an energy minimization viewpoint. We begin by reviewing traditional stereo methods that do not handle occlusions. If occlusions are ignored, it is easy to formulate the stereo problem as a pixel labeling problem, which leads to an energy function that is common in early vision. This kind of energy function can he minimized using graph cuts, which is a combinatorial optimization technique that has proven to be very effective for low-level vision problems. Motivated by this, we have designed two graph cut stereo algorithms that are designed to handle occlusions. These algorithms produce promising experimental results on real data with ground truth.","lang":"eng"}]},{"type":"book_chapter","alternative_title":["Plant Cell Monographs"],"publist_id":"3699","abstract":[{"lang":"eng","text":"Arabidopsis thaliana is currently the most important model organism for basic molecular plant research. It is also a favourable model for developmental biology, as its embryogenesis follows a nearly invariant pattern of cell divisions and cell type specifications. Study of embryogenesis can involve genetic, physiological or biochemical approaches, but is always limited by the inaccessibility of the embryos which develop deep inside maternal tissue. Thus, for developmental studies, there is an increasing demand for methods which allow embryogenesis under artificial conditions, providing better accessibility to experimental manipulation. In this chapter, we address theoretical aspects of embryo culture, give some thoughts on which embryo culture system is suited best for which application and finally discuss three current methods which have been successfully used in Arabidopsis embryo culture. © 2006 Springer-Verlag Berlin Heidelberg."}],"extern":1,"_id":"3002","year":"2006","publisher":"Springer","intvolume":" 2","editor":[{"last_name":"Mujib","first_name":"Abdul","full_name":"Mujib, Abdul"},{"full_name":"Šamaj, Jozef","first_name":"Jozef","last_name":"Šamaj"}],"title":"In vitro culture of Arabidopsis embryos","publication_status":"published","status":"public","author":[{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml"}],"volume":2,"date_updated":"2021-01-12T07:40:23Z","date_created":"2018-12-11T12:00:48Z","month":"01","day":"01","citation":{"short":"M. Sauer, J. Friml, in:, A. Mujib, J. Šamaj (Eds.), Somatic Embryogenesis, Springer, 2006, pp. 343–354.","mla":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.” Somatic Embryogenesis, edited by Abdul Mujib and Jozef Šamaj, vol. 2, Springer, 2006, pp. 343–54, doi:10.1007/7089_020.","chicago":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.” In Somatic Embryogenesis, edited by Abdul Mujib and Jozef Šamaj, 2:343–54. Springer, 2006. https://doi.org/10.1007/7089_020.","ama":"Sauer M, Friml J. In vitro culture of Arabidopsis embryos. In: Mujib A, Šamaj J, eds. Somatic Embryogenesis. Vol 2. Springer; 2006:343-354. doi:10.1007/7089_020","ieee":"M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos,” in Somatic Embryogenesis, vol. 2, A. Mujib and J. Šamaj, Eds. Springer, 2006, pp. 343–354.","apa":"Sauer, M., & Friml, J. (2006). In vitro culture of Arabidopsis embryos. In A. Mujib & J. Šamaj (Eds.), Somatic Embryogenesis (Vol. 2, pp. 343–354). Springer. https://doi.org/10.1007/7089_020","ista":"Sauer M, Friml J. 2006.In vitro culture of Arabidopsis embryos. In: Somatic Embryogenesis. Plant Cell Monographs, vol. 2, 343–354."},"publication":"Somatic Embryogenesis","page":"343 - 354","quality_controlled":0,"date_published":"2006-01-01T00:00:00Z","doi":"10.1007/7089_020"},{"extern":1,"issue":"5775","publist_id":"3690","abstract":[{"text":"Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux.","lang":"eng"}],"type":"journal_article","volume":312,"date_updated":"2021-01-12T07:40:27Z","date_created":"2018-12-11T12:00:51Z","author":[{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"full_name":"Mravec, Jozef","first_name":"Jozef","last_name":"Mravec"},{"full_name":"Bouchard, Rodolphe","last_name":"Bouchard","first_name":"Rodolphe"},{"first_name":"Joshua","last_name":"Blakeslee","full_name":"Blakeslee, Joshua"},{"full_name":"Melinda Abas","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","last_name":"Abas"},{"first_name":"Daniela","last_name":"Seifertová","full_name":"Seifertová, Daniela"},{"last_name":"Wiśniewska","first_name":"Justyna","full_name":"Wiśniewska, Justyna"},{"full_name":"Tadele, Zerihun","first_name":"Zerihun","last_name":"Tadele"},{"last_name":"Kubeš","first_name":"Martin","full_name":"Kubeš, Martin"},{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"last_name":"Dhonukshe","first_name":"Pankaj","full_name":"Dhonukshe, Pankaj"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"full_name":"Perry, Lucie","first_name":"Lucie","last_name":"Perry"},{"full_name":"Křeček, Pavel","first_name":"Pavel","last_name":"Křeček"},{"full_name":"Lee, Ok Ran","first_name":"Ok","last_name":"Lee"},{"last_name":"Fink","first_name":"Gerald","full_name":"Fink, Gerald R"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"first_name":"Angus","last_name":"Murphy","full_name":"Murphy, Angus S"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"intvolume":" 312","publisher":"American Association for the Advancement of Science","publication_status":"published","title":"PIN proteins perform a rate-limiting function in cellular auxin efflux","status":"public","year":"2006","_id":"3012","month":"05","day":"12","doi":"10.1126/science.1123542","date_published":"2006-05-12T00:00:00Z","page":"914 - 918","quality_controlled":0,"citation":{"ieee":"J. Petrášek et al., “PIN proteins perform a rate-limiting function in cellular auxin efflux,” Science, vol. 312, no. 5775. American Association for the Advancement of Science, pp. 914–918, 2006.","apa":"Petrášek, J., Mravec, J., Bouchard, R., Blakeslee, J., Abas, M. F., Seifertová, D., … Friml, J. (2006). PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1123542","ista":"Petrášek J, Mravec J, Bouchard R, Blakeslee J, Abas MF, Seifertová D, Wiśniewska J, Tadele Z, Kubeš M, Čovanová M, Dhonukshe P, Skůpa P, Benková E, Perry L, Křeček P, Lee O, Fink G, Geisler M, Murphy A, Luschnig C, Zažímalová E, Friml J. 2006. PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. 312(5775), 914–918.","ama":"Petrášek J, Mravec J, Bouchard R, et al. PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. 2006;312(5775):914-918. doi:10.1126/science.1123542","chicago":"Petrášek, Jan, Jozef Mravec, Rodolphe Bouchard, Joshua Blakeslee, Melinda F Abas, Daniela Seifertová, Justyna Wiśniewska, et al. “PIN Proteins Perform a Rate-Limiting Function in Cellular Auxin Efflux.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1123542.","short":"J. Petrášek, J. Mravec, R. Bouchard, J. Blakeslee, M.F. Abas, D. Seifertová, J. Wiśniewska, Z. Tadele, M. Kubeš, M. Čovanová, P. Dhonukshe, P. Skůpa, E. Benková, L. Perry, P. Křeček, O. Lee, G. Fink, M. Geisler, A. Murphy, C. Luschnig, E. Zažímalová, J. Friml, Science 312 (2006) 914–918.","mla":"Petrášek, Jan, et al. “PIN Proteins Perform a Rate-Limiting Function in Cellular Auxin Efflux.” Science, vol. 312, no. 5775, American Association for the Advancement of Science, 2006, pp. 914–18, doi:10.1126/science.1123542."},"publication":"Science"},{"abstract":[{"lang":"eng","text":"The formation of the leaf vascular pattern has fascinated biologists for centuries. In the early leaf primordium, complex networks of procambial cells emerge from homogeneous subepidermal tissue. The molecular nature of the underlying positional information is unknown, but various lines of evidence implicate gradually restricted transport routes of the plant hormone auxin in defining sites of procambium formation. Here we show that a crucial member of the AtPIN family of auxin-efflux-associated proteins, AtPIN1, is expressed prior to pre-procambial and procambial cell fate markers in domains that become restricted toward sites of procambium formation. Subcellular AtPIN1 polarity indicates that auxin is directed to distinct "convergence points" in the epidermis, from where it defines the positions of major veins. Integrated polarities in all emerging veins indicate auxin drainage toward pre-existing veins, but veins display divergent polarities as they become connected at both ends. Auxin application and transport inhibition reveal that convergence point positioning and AtPIN1 expression domain dynamics are self-organizing, auxin-transport-dependent processes. We derive a model for self-regulated, reiterative patterning of all vein orders and postulate at its onset a common epidermal auxin-focusing mechanism for major-vein positioning and phyllotactic patterning."}],"issue":"8","publist_id":"3692","extern":1,"type":"journal_article","author":[{"last_name":"Scarpella","first_name":"Enrico","full_name":"Scarpella, Enrico"},{"last_name":"Marcos","first_name":"Danielle","full_name":"Marcos, Danielle"},{"full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Berleth","first_name":"Thomas","full_name":"Berleth, Thomas"}],"date_updated":"2021-01-12T07:40:26Z","date_created":"2018-12-11T12:00:51Z","volume":20,"_id":"3010","year":"2006","status":"public","publication_status":"published","title":"Control of leaf vascular patterning by polar auxin transport","intvolume":" 20","publisher":"Cold Spring Harbor Laboratory Press","month":"04","day":"15","doi":"10.1101/gad.1402406","date_published":"2006-04-15T00:00:00Z","publication":"Genes and Development","citation":{"chicago":"Scarpella, Enrico, Danielle Marcos, Jiří Friml, and Thomas Berleth. “Control of Leaf Vascular Patterning by Polar Auxin Transport.” Genes and Development. Cold Spring Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.1402406.","short":"E. Scarpella, D. Marcos, J. Friml, T. Berleth, Genes and Development 20 (2006) 1015–1027.","mla":"Scarpella, Enrico, et al. “Control of Leaf Vascular Patterning by Polar Auxin Transport.” Genes and Development, vol. 20, no. 8, Cold Spring Harbor Laboratory Press, 2006, pp. 1015–27, doi:10.1101/gad.1402406.","ieee":"E. Scarpella, D. Marcos, J. Friml, and T. Berleth, “Control of leaf vascular patterning by polar auxin transport,” Genes and Development, vol. 20, no. 8. Cold Spring Harbor Laboratory Press, pp. 1015–1027, 2006.","apa":"Scarpella, E., Marcos, D., Friml, J., & Berleth, T. (2006). Control of leaf vascular patterning by polar auxin transport. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.1402406","ista":"Scarpella E, Marcos D, Friml J, Berleth T. 2006. Control of leaf vascular patterning by polar auxin transport. Genes and Development. 20(8), 1015–1027.","ama":"Scarpella E, Marcos D, Friml J, Berleth T. Control of leaf vascular patterning by polar auxin transport. Genes and Development. 2006;20(8):1015-1027. doi:10.1101/gad.1402406"},"quality_controlled":0,"page":"1015 - 1027"},{"month":"03","day":"01","page":"249 - 256","quality_controlled":0,"citation":{"chicago":"Abas, Lindy, René Benjamins, Nenad Malenica, Tomasz Paciorek, Justyna Wiśniewska, Jeanette Moulinier Anzola, Tobias Sieberer, Jiří Friml, and Christian Luschnig. “Intracellular Trafficking and Proteolysis of the Arabidopsis Auxin-Efflux Facilitator PIN2 Are Involved in Root Gravitropism.” Nature Cell Biology. Nature Publishing Group, 2006. https://doi.org/10.1038/ncb1369.","short":"L. Abas, R. Benjamins, N. Malenica, T. Paciorek, J. Wiśniewska, J. Moulinier Anzola, T. Sieberer, J. Friml, C. Luschnig, Nature Cell Biology 8 (2006) 249–256.","mla":"Abas, Lindy, et al. “Intracellular Trafficking and Proteolysis of the Arabidopsis Auxin-Efflux Facilitator PIN2 Are Involved in Root Gravitropism.” Nature Cell Biology, vol. 8, no. 3, Nature Publishing Group, 2006, pp. 249–56, doi:10.1038/ncb1369.","apa":"Abas, L., Benjamins, R., Malenica, N., Paciorek, T., Wiśniewska, J., Moulinier Anzola, J., … Luschnig, C. (2006). Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1369","ieee":"L. Abas et al., “Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism,” Nature Cell Biology, vol. 8, no. 3. Nature Publishing Group, pp. 249–256, 2006.","ista":"Abas L, Benjamins R, Malenica N, Paciorek T, Wiśniewska J, Moulinier Anzola J, Sieberer T, Friml J, Luschnig C. 2006. Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. Nature Cell Biology. 8(3), 249–256.","ama":"Abas L, Benjamins R, Malenica N, et al. Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. Nature Cell Biology. 2006;8(3):249-256. doi:10.1038/ncb1369"},"publication":"Nature Cell Biology","doi":"10.1038/ncb1369","date_published":"2006-03-01T00:00:00Z","type":"journal_article","extern":1,"issue":"3","publist_id":"3694","abstract":[{"lang":"eng","text":"Root gravitropism describes the orientation of root growth along the gravity vector and is mediated by differential cell elongation in the root meristem. This response requires the coordinated, asymmetric distribution of the phytohormone auxin within the root meristem, and depends on the concerted activities of PIN proteins and AUX1 - members of the auxin transport pathway. Here, we show that intracellular trafficking and proteasome activity combine to control PIN2 degradation during root gravitropism. Following gravi-stimulation, proteasome-dependent variations in PIN2 localization and degradation at the upper and lower sides of the root result in asymmetric distribution of PIN2. Ubiquitination of PIN2 occurs in a proteasome-dependent manner, indicating that the proteasome is involved in the control of PIN2 turnover. Stabilization of PIN2 affects its abundance and distribution, and leads to defects in auxin distribution and gravitropic responses. We describe the effects of auxin on PIN2 localization and protein levels, indicating that redistribution of auxin during the gravitropic response may be involved in the regulation of PIN2 protein."}],"intvolume":" 8","publisher":"Nature Publishing Group","publication_status":"published","status":"public","title":"Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism","_id":"3007","year":"2006","volume":8,"date_updated":"2021-01-12T07:40:25Z","date_created":"2018-12-11T12:00:50Z","author":[{"last_name":"Abas","first_name":"Lindy","full_name":"Abas, Lindy"},{"full_name":"Benjamins, René","first_name":"René","last_name":"Benjamins"},{"last_name":"Malenica","first_name":"Nenad","full_name":"Malenica, Nenad"},{"full_name":"Paciorek, Tomasz","first_name":"Tomasz","last_name":"Paciorek"},{"full_name":"Wiśniewska, Justyna","last_name":"Wiśniewska","first_name":"Justyna"},{"first_name":"Jeanette","last_name":"Moulinier Anzola","full_name":"Moulinier-Anzola, Jeanette C"},{"full_name":"Sieberer, Tobias","last_name":"Sieberer","first_name":"Tobias"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"}]},{"volume":10,"date_updated":"2021-01-12T07:40:24Z","date_created":"2018-12-11T12:00:49Z","author":[{"last_name":"Dhonukshe","first_name":"Pankaj","full_name":"Dhonukshe, Pankaj"},{"last_name":"Baluška","first_name":"František","full_name":"Baluška, František"},{"full_name":"Schlicht, Markus","first_name":"Markus","last_name":"Schlicht"},{"full_name":"Hlavacka, Andrej","last_name":"Hlavacka","first_name":"Andrej"},{"last_name":"Šamaj","first_name":"Jozef","full_name":"Šamaj, Jozef"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Gadella","first_name":"Theodorus","full_name":"Gadella, Theodorus W"}],"publisher":"Cell Press","intvolume":" 10","publication_status":"published","status":"public","title":"Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis","_id":"3006","year":"2006","extern":1,"publist_id":"3696","issue":"1","abstract":[{"text":"Dividing plant cells perform a remarkable task of building a new cell wall within the cytoplasm in a few minutes. A long-standing paradigm claims that this primordial cell wall, known as the cell plate, is generated by delivery of newly synthesized material from Golgi apparatus-originated secretory vesicles. Here, we show that, in diverse plant species, cell surface material, including plasma membrane proteins, cell wall components, and exogenously applied endocytic tracers, is rapidly delivered to the forming cell plate. Importantly, this occurs even when de novo protein synthesis is blocked. In addition, cytokinesis-specific syntaxin KNOLLE as well as plasma membrane (PM) resident proteins localize to endosomes that fuse to initiate the cell plate. The rate of endocytosis is strongly enhanced during cell plate formation, and its genetic or pharmacological inhibition leads to cytokinesis defects. Our results reveal that endocytic delivery of cell surface material significantly contributes to cell plate formation during plant cytokinesis. ","lang":"eng"}],"type":"journal_article","doi":"10.1016/j.devcel.2005.11.015","date_published":"2006-01-01T00:00:00Z","page":"137 - 150","quality_controlled":0,"citation":{"mla":"Dhonukshe, Pankaj, et al. “Endocytosis of Cell Surface Material Mediates Cell Plate Formation during Plant Cytokinesis.” Developmental Cell, vol. 10, no. 1, Cell Press, 2006, pp. 137–50, doi:10.1016/j.devcel.2005.11.015.","short":"P. Dhonukshe, F. Baluška, M. Schlicht, A. Hlavacka, J. Šamaj, J. Friml, T. Gadella, Developmental Cell 10 (2006) 137–150.","chicago":"Dhonukshe, Pankaj, František Baluška, Markus Schlicht, Andrej Hlavacka, Jozef Šamaj, Jiří Friml, and Theodorus Gadella. “Endocytosis of Cell Surface Material Mediates Cell Plate Formation during Plant Cytokinesis.” Developmental Cell. Cell Press, 2006. https://doi.org/10.1016/j.devcel.2005.11.015.","ama":"Dhonukshe P, Baluška F, Schlicht M, et al. Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Developmental Cell. 2006;10(1):137-150. doi:10.1016/j.devcel.2005.11.015","ista":"Dhonukshe P, Baluška F, Schlicht M, Hlavacka A, Šamaj J, Friml J, Gadella T. 2006. Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Developmental Cell. 10(1), 137–150.","apa":"Dhonukshe, P., Baluška, F., Schlicht, M., Hlavacka, A., Šamaj, J., Friml, J., & Gadella, T. (2006). Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2005.11.015","ieee":"P. Dhonukshe et al., “Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis,” Developmental Cell, vol. 10, no. 1. Cell Press, pp. 137–150, 2006."},"publication":"Developmental Cell","month":"01","day":"01"},{"month":"05","day":"12","date_published":"2006-05-12T00:00:00Z","doi":"10.1126/science.1121356","citation":{"ista":"Wiśniewska J, Xu J, Seifertová D, Brewer P, Růžička K, Blilou I, Rouquié D, Benková E, Scheres B, Friml J. 2006. Polar PIN localization directs auxin flow in plants. Science. 312(5775).","apa":"Wiśniewska, J., Xu, J., Seifertová, D., Brewer, P., Růžička, K., Blilou, I., … Friml, J. (2006). Polar PIN localization directs auxin flow in plants. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1121356","ieee":"J. Wiśniewska et al., “Polar PIN localization directs auxin flow in plants,” Science, vol. 312, no. 5775. American Association for the Advancement of Science, 2006.","ama":"Wiśniewska J, Xu J, Seifertová D, et al. Polar PIN localization directs auxin flow in plants. Science. 2006;312(5775). doi:10.1126/science.1121356","chicago":"Wiśniewska, Justyna, Jian Xu, Daniela Seifertová, Philip Brewer, Kamil Růžička, Ikram Blilou, David Rouquié, Eva Benková, Ben Scheres, and Jiří Friml. “Polar PIN Localization Directs Auxin Flow in Plants.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121356.","mla":"Wiśniewska, Justyna, et al. “Polar PIN Localization Directs Auxin Flow in Plants.” Science, vol. 312, no. 5775, American Association for the Advancement of Science, 2006, doi:10.1126/science.1121356.","short":"J. Wiśniewska, J. Xu, D. Seifertová, P. Brewer, K. Růžička, I. Blilou, D. Rouquié, E. Benková, B. Scheres, J. Friml, Science 312 (2006)."},"publication":"Science","quality_controlled":0,"publist_id":"3691","issue":"5775","abstract":[{"text":"Polar flow of the phytohormone auxin requires plasma membrane‐associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed the importance of PIN polar positions for directional auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity signals directly demonstrates that PIN polarity is a primary factor in determining the direction of auxin flow in meristematic tissues. This finding provides a crucial piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN polarity.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"first_name":"Justyna","last_name":"Wiśniewska","full_name":"Wiśniewska, Justyna"},{"full_name":"Xu, Jian","last_name":"Xu","first_name":"Jian"},{"full_name":"Seifertová, Daniela","first_name":"Daniela","last_name":"Seifertová"},{"full_name":"Brewer, Philip B","last_name":"Brewer","first_name":"Philip"},{"last_name":"Růžička","first_name":"Kamil","full_name":"Růžička, Kamil"},{"last_name":"Blilou","first_name":"Ikram","full_name":"Blilou, Ikram"},{"full_name":"Rouquié, David","first_name":"David","last_name":"Rouquié"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Eva Benková"},{"full_name":"Scheres, Ben","first_name":"Ben","last_name":"Scheres"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"volume":312,"date_updated":"2021-01-12T07:40:27Z","date_created":"2018-12-11T12:00:51Z","_id":"3011","year":"2006","publisher":"American Association for the Advancement of Science","intvolume":" 312","publication_status":"published","title":"Polar PIN localization directs auxin flow in plants","status":"public"},{"_id":"3005","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Apical-basal polarity: Why plant cells don't stand on their heads","intvolume":" 11","publisher":"Cell Press","author":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Benfey, Philip","first_name":"Philip","last_name":"Benfey"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"},{"full_name":"Berleth, Thomas","last_name":"Berleth","first_name":"Thomas"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"last_name":"Grebe","first_name":"Markus","full_name":"Grebe, Markus"},{"full_name":"Heisler, Marcus","first_name":"Marcus","last_name":"Heisler"},{"full_name":"Hejátko, Jan","first_name":"Jan","last_name":"Hejátko"},{"last_name":"Jürgens","first_name":"Gerd","full_name":"Jürgens, Gerd"},{"full_name":"Laux, Thomas","last_name":"Laux","first_name":"Thomas"},{"last_name":"Lindsey","first_name":"Keith","full_name":"Lindsey, Keith"},{"last_name":"Lukowitz","first_name":"Wolfgang","full_name":"Lukowitz, Wolfgang"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"last_name":"Offringa","first_name":"Remko","full_name":"Offringa, Remko"},{"first_name":"Ben","last_name":"Scheres","full_name":"Scheres, Ben"},{"full_name":"Swarup, Ranjan","last_name":"Swarup","first_name":"Ranjan"},{"full_name":"Torres Ruiz, Ramón","last_name":"Torres Ruiz","first_name":"Ramón"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"}],"date_created":"2018-12-11T12:00:49Z","date_updated":"2021-01-12T07:40:24Z","volume":11,"oa_version":"None","type":"journal_article","publist_id":"3697","issue":"1","extern":"1","publication":"Trends in Plant Science","citation":{"ista":"Friml J, Benfey P, Benková E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejátko J, Jürgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, Scheres B, Swarup R, Torres Ruiz R, Weijers D, Zažímalová E. 2006. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 11(1), 12–14.","apa":"Friml, J., Benfey, P., Benková, E., Bennett, M., Berleth, T., Geldner, N., … Zažímalová, E. (2006). Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2005.11.010","ieee":"J. Friml et al., “Apical-basal polarity: Why plant cells don’t stand on their heads,” Trends in Plant Science, vol. 11, no. 1. Cell Press, pp. 12–14, 2006.","ama":"Friml J, Benfey P, Benková E, et al. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 2006;11(1):12-14. doi:10.1016/j.tplants.2005.11.010","chicago":"Friml, Jiří, Philip Benfey, Eva Benková, Malcolm Bennett, Thomas Berleth, Niko Geldner, Markus Grebe, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science. Cell Press, 2006. https://doi.org/10.1016/j.tplants.2005.11.010.","mla":"Friml, Jiří, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science, vol. 11, no. 1, Cell Press, 2006, pp. 12–14, doi:10.1016/j.tplants.2005.11.010.","short":"J. Friml, P. Benfey, E. Benková, M. Bennett, T. Berleth, N. Geldner, M. Grebe, M. Heisler, J. Hejátko, G. Jürgens, T. Laux, K. Lindsey, W. Lukowitz, C. Luschnig, R. Offringa, B. Scheres, R. Swarup, R. Torres Ruiz, D. Weijers, E. Zažímalová, Trends in Plant Science 11 (2006) 12–14."},"page":"12 - 14","doi":"10.1016/j.tplants.2005.11.010","date_published":"2006-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"01"},{"month":"01","day":"20","doi":"10.1126/science.1121790","date_published":"2006-01-20T00:00:00Z","quality_controlled":0,"page":"385 - 388","publication":"Science","citation":{"chicago":"Xu, Jian, Hugo Hofhuis, Renze Heidstra, Michael Sauer, Jiří Friml, and Ben Scheres. “A Molecular Framework for Plant Regeneration.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121790.","short":"J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, B. Scheres, Science 311 (2006) 385–388.","mla":"Xu, Jian, et al. “A Molecular Framework for Plant Regeneration.” Science, vol. 311, no. 5759, American Association for the Advancement of Science, 2006, pp. 385–88, doi:10.1126/science.1121790.","apa":"Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J., & Scheres, B. (2006). A molecular framework for plant regeneration. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1121790","ieee":"J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, and B. Scheres, “A molecular framework for plant regeneration,” Science, vol. 311, no. 5759. American Association for the Advancement of Science, pp. 385–388, 2006.","ista":"Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. 2006. A molecular framework for plant regeneration. Science. 311(5759), 385–388.","ama":"Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. A molecular framework for plant regeneration. Science. 2006;311(5759):385-388. doi:10.1126/science.1121790"},"extern":1,"abstract":[{"text":"Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution.","lang":"eng"}],"issue":"5759","publist_id":"3695","type":"journal_article","date_created":"2018-12-11T12:00:50Z","date_updated":"2021-01-12T07:40:25Z","volume":311,"author":[{"full_name":"Xu, Jian","first_name":"Jian","last_name":"Xu"},{"first_name":"Hugo","last_name":"Hofhuis","full_name":"Hofhuis, Hugo"},{"first_name":"Renze","last_name":"Heidstra","full_name":"Heidstra, Renze"},{"full_name":"Sauer, Michael","first_name":"Michael","last_name":"Sauer"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"first_name":"Ben","last_name":"Scheres","full_name":"Scheres, Ben"}],"status":"public","publication_status":"published","title":"A molecular framework for plant regeneration","intvolume":" 311","publisher":"American Association for the Advancement of Science","year":"2006","_id":"3008"},{"month":"01","day":"01","oa":1,"external_id":{"pmid":[" 16554435"]},"citation":{"short":"T. Paciorek, J. Friml, Journal of Cell Science 119 (2006) 1199–1202.","mla":"Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science, vol. 119, no. 7, Company of Biologists, 2006, pp. 1199–202, doi:10.1242/jcs.02910.","chicago":"Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02910.","ama":"Paciorek T, Friml J. Auxin signaling. Journal of Cell Science. 2006;119(7):1199-1202. doi:10.1242/jcs.02910","apa":"Paciorek, T., & Friml, J. (2006). Auxin signaling. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02910","ieee":"T. Paciorek and J. Friml, “Auxin signaling,” Journal of Cell Science, vol. 119, no. 7. Company of Biologists, pp. 1199–1202, 2006.","ista":"Paciorek T, Friml J. 2006. Auxin signaling. Journal of Cell Science. 119(7), 1199–1202."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/16554435","open_access":"1"}],"publication":"Journal of Cell Science","page":"1199 - 1202","quality_controlled":"1","date_published":"2006-01-01T00:00:00Z","doi":"10.1242/jcs.02910","language":[{"iso":"eng"}],"type":"journal_article","issue":"7","publist_id":"3693","extern":"1","pmid":1,"_id":"3009","year":"2006","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists","intvolume":" 119","status":"public","title":"Auxin signaling","publication_status":"published","author":[{"full_name":"Paciorek, Tomasz","last_name":"Paciorek","first_name":"Tomasz"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"volume":119,"oa_version":"Published Version","date_updated":"2021-01-12T07:40:25Z","date_created":"2018-12-11T12:00:50Z"},{"month":"10","day":"15","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1101/gad.390806","date_published":"2006-10-15T00:00:00Z","page":"2902 - 2911","publication":"Genes and Development","citation":{"mla":"Sauer, Michael, et al. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development, vol. 20, no. 20, Cold Spring Harbor Laboratory Press, 2006, pp. 2902–11, doi:10.1101/gad.390806.","short":"M. Sauer, J. Balla, C. Luschnig, J. Wiśniewska, V. Reinöhl, J. Friml, E. Benková, Genes and Development 20 (2006) 2902–2911.","chicago":"Sauer, Michael, Jozef Balla, Christian Luschnig, Justyna Wiśniewska, Vilém Reinöhl, Jiří Friml, and Eva Benková. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development. Cold Spring Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.390806.","ama":"Sauer M, Balla J, Luschnig C, et al. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 2006;20(20):2902-2911. doi:10.1101/gad.390806","ista":"Sauer M, Balla J, Luschnig C, Wiśniewska J, Reinöhl V, Friml J, Benková E. 2006. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 20(20), 2902–2911.","apa":"Sauer, M., Balla, J., Luschnig, C., Wiśniewska, J., Reinöhl, V., Friml, J., & Benková, E. (2006). Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.390806","ieee":"M. Sauer et al., “Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity,” Genes and Development, vol. 20, no. 20. Cold Spring Harbor Laboratory Press, pp. 2902–2911, 2006."},"extern":"1","abstract":[{"text":"Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants.","lang":"eng"}],"publist_id":"3686","issue":"20","type":"journal_article","date_updated":"2021-11-16T07:53:09Z","date_created":"2018-12-11T12:00:53Z","volume":20,"oa_version":"None","author":[{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"full_name":"Wiśniewska, Justyna","first_name":"Justyna","last_name":"Wiśniewska"},{"first_name":"Vilém","last_name":"Reinöhl","full_name":"Reinöhl, Vilém"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"related_material":{"link":[{"relation":"erratum","url":"http://genesdev.cshlp.org/content/21/11/1431.short"}]},"status":"public","publication_status":"published","title":"Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity","publisher":"Cold Spring Harbor Laboratory Press","intvolume":" 20","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"3016","year":"2006"},{"month":"12","day":"01","quality_controlled":"1","page":"2738 - 2754","publication":"Cellular and Molecular Life Sciences","citation":{"apa":"Tanaka, H., Dhonukshe, P., Brewer, P., & Friml, J. (2006). Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. Birkhäuser. https://doi.org/10.1007/s00018-006-6116-5","ieee":"H. Tanaka, P. Dhonukshe, P. Brewer, and J. Friml, “Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development,” Cellular and Molecular Life Sciences, vol. 63, no. 23. Birkhäuser, pp. 2738–2754, 2006.","ista":"Tanaka H, Dhonukshe P, Brewer P, Friml J. 2006. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 63(23), 2738–2754.","ama":"Tanaka H, Dhonukshe P, Brewer P, Friml J. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 2006;63(23):2738-2754. doi:10.1007/s00018-006-6116-5","chicago":"Tanaka, Hirokazu, Pankaj Dhonukshe, Philip Brewer, and Jiří Friml. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences. Birkhäuser, 2006. https://doi.org/10.1007/s00018-006-6116-5.","short":"H. Tanaka, P. Dhonukshe, P. Brewer, J. Friml, Cellular and Molecular Life Sciences 63 (2006) 2738–2754.","mla":"Tanaka, Hirokazu, et al. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences, vol. 63, no. 23, Birkhäuser, 2006, pp. 2738–54, doi:10.1007/s00018-006-6116-5."},"language":[{"iso":"eng"}],"doi":"10.1007/s00018-006-6116-5","date_published":"2006-12-01T00:00:00Z","type":"journal_article","extern":"1","abstract":[{"text":"The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events.","lang":"eng"}],"issue":"23","publist_id":"3685","title":"Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development","publication_status":"published","status":"public","intvolume":" 63","publisher":"Birkhäuser","_id":"3017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2006","date_updated":"2021-01-12T07:40:29Z","date_created":"2018-12-11T12:00:53Z","oa_version":"None","volume":63,"author":[{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"last_name":"Dhonukshe","first_name":"Pankaj","full_name":"Dhonukshe, Pankaj"},{"last_name":"Brewer","first_name":"Philip","full_name":"Brewer, Philip"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}]},{"quality_controlled":0,"page":"3171 - 3181","publication":"Plant Cell","citation":{"ista":"Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. 2006. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 18(11), 3171–3181.","apa":"Kleine Vehn, J., Dhonukshe, P., Swarup, R., Bennett, M., & Friml, J. (2006). Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.106.042770","ieee":"J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, and J. Friml, “Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1,” Plant Cell, vol. 18, no. 11. American Society of Plant Biologists, pp. 3171–3181, 2006.","ama":"Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 2006;18(11):3171-3181. doi:10.1105/tpc.106.042770","chicago":"Kleine Vehn, Jürgen, Pankaj Dhonukshe, Ranjan Swarup, Malcolm Bennett, and Jiří Friml. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell. American Society of Plant Biologists, 2006. https://doi.org/10.1105/tpc.106.042770.","mla":"Kleine Vehn, Jürgen, et al. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell, vol. 18, no. 11, American Society of Plant Biologists, 2006, pp. 3171–81, doi:10.1105/tpc.106.042770.","short":"J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, J. Friml, Plant Cell 18 (2006) 3171–3181."},"date_published":"2006-11-01T00:00:00Z","doi":"10.1105/tpc.106.042770","month":"11","day":"01","publication_status":"published","title":"Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1","status":"public","publisher":"American Society of Plant Biologists","intvolume":" 18","year":"2006","_id":"3018","date_updated":"2021-01-12T07:40:29Z","date_created":"2018-12-11T12:00:53Z","volume":18,"author":[{"full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe","first_name":"Pankaj"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"first_name":"Malcolm","last_name":"Bennett","full_name":"Bennett, Malcolm"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport."}],"issue":"11","publist_id":"3684"},{"publisher":"Nature Publishing Group","intvolume":" 1","title":"In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples","publication_status":"published","status":"public","year":"2006","_id":"3020","volume":1,"date_updated":"2021-01-12T07:40:30Z","date_created":"2018-12-11T12:00:54Z","author":[{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"full_name":"Blilou, Ikram","last_name":"Blilou","first_name":"Ikram"},{"full_name":"Brewer, Philip B","last_name":"Brewer","first_name":"Philip"},{"full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheres, Ben","last_name":"Scheres","first_name":"Ben"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Eva Benková"}],"type":"journal_article","extern":1,"issue":"4","publist_id":"3683","abstract":[{"lang":"eng","text":"High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used."}],"page":"1939 - 1946","quality_controlled":0,"citation":{"chicago":"Hejátko, Jan, Ikram Blilou, Philip Brewer, Jiří Friml, Ben Scheres, and Eva Benková. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.333.","mla":"Hejátko, Jan, et al. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 1939–46, doi:10.1038/nprot.2006.333.","short":"J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, E. Benková, Nature Protocols 1 (2006) 1939–1946.","ista":"Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. 2006. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 1(4), 1939–1946.","ieee":"J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, and E. Benková, “In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 1939–1946, 2006.","apa":"Hejátko, J., Blilou, I., Brewer, P., Friml, J., Scheres, B., & Benková, E. (2006). In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.333","ama":"Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 2006;1(4):1939-1946. doi:10.1038/nprot.2006.333"},"publication":"Nature Protocols","date_published":"2006-11-01T00:00:00Z","doi":"10.1038/nprot.2006.333","day":"01","month":"11"},{"status":"public","title":"Immunocytochemical techniques for whole mount in situ protein localization in plants","publication_status":"published","publisher":"Nature Publishing Group","intvolume":" 1","_id":"3015","year":"2006","date_updated":"2021-01-12T07:40:28Z","date_created":"2018-12-11T12:00:52Z","volume":1,"author":[{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"first_name":"Tomasz","last_name":"Paciorek","full_name":"Paciorek, Tomasz"},{"full_name":"Eva Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount 'immunolocalization' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days."}],"publist_id":"3688","issue":"1","quality_controlled":0,"page":"98 - 103","publication":"Nature Protocols","citation":{"ama":"Sauer M, Paciorek T, Benková E, Friml J. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 2006;1(1):98-103. doi:10.1038/nprot.2006.15","ista":"Sauer M, Paciorek T, Benková E, Friml J. 2006. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 1(1), 98–103.","ieee":"M. Sauer, T. Paciorek, E. Benková, and J. Friml, “Immunocytochemical techniques for whole mount in situ protein localization in plants,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 98–103, 2006.","apa":"Sauer, M., Paciorek, T., Benková, E., & Friml, J. (2006). Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.15","mla":"Sauer, Michael, et al. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 98–103, doi:10.1038/nprot.2006.15.","short":"M. Sauer, T. Paciorek, E. Benková, J. Friml, Nature Protocols 1 (2006) 98–103.","chicago":"Sauer, Michael, Tomasz Paciorek, Eva Benková, and Jiří Friml. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.15."},"date_published":"2006-06-01T00:00:00Z","doi":"10.1038/nprot.2006.15","day":"01","month":"06"},{"page":"104 - 107","quality_controlled":0,"citation":{"short":"T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, J. Friml, Nature Protocols 1 (2006) 104–107.","mla":"Paciorek, Tomasz, et al. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 104–07, doi:10.1038/nprot.2006.16.","chicago":"Paciorek, Tomasz, Michael Sauer, Jozef Balla, Justyna Wiśniewska, and Jiří Friml. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.16.","ama":"Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 2006;1(1):104-107. doi:10.1038/nprot.2006.16","apa":"Paciorek, T., Sauer, M., Balla, J., Wiśniewska, J., & Friml, J. (2006). Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.16","ieee":"T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, and J. Friml, “Immunocytochemical technique for protein localization in sections of plant tissues,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 104–107, 2006.","ista":"Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. 2006. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 1(1), 104–107."},"publication":"Nature Protocols","doi":"10.1038/nprot.2006.16","date_published":"2006-06-01T00:00:00Z","month":"06","day":"01","intvolume":" 1","publisher":"Nature Publishing Group","title":"Immunocytochemical technique for protein localization in sections of plant tissues","status":"public","publication_status":"published","year":"2006","_id":"3013","volume":1,"date_created":"2018-12-11T12:00:52Z","date_updated":"2021-01-12T07:40:27Z","author":[{"full_name":"Paciorek, Tomasz","first_name":"Tomasz","last_name":"Paciorek"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"last_name":"Wiśniewska","first_name":"Justyna","full_name":"Wiśniewska, Justyna"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"}],"type":"journal_article","extern":1,"publist_id":"3689","issue":"1","abstract":[{"lang":"eng","text":"There is a growing demand for methods that allow rapid and reliable in situ localization of proteins in plant cells. The immunocytochemistry protocol presented here can be used routinely to observe protein localization patterns in tissue sections of various plant species. This protocol is especially suitable for plant species with more-complex tissue architecture (such as maize, Zea mays), which makes it difficult to use an easier whole-mount procedure for protein localization. To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding and tissue-sectioning step. The protocol consists of the following procedures: chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing, rehydration, blocking and antibody incubation. The detailed protocol, recommended controls and troubleshooting are presented here, along with examples of applications."}]},{"page":"1462 - 1467","quality_controlled":0,"citation":{"ama":"Brewer P, Heisler M, Hejátko J, Friml J, Benková E. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 2006;1(3):1462-1467. doi:10.1038/nprot.2006.226","ista":"Brewer P, Heisler M, Hejátko J, Friml J, Benková E. 2006. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 1(3), 1462–1467.","ieee":"P. Brewer, M. Heisler, J. Hejátko, J. Friml, and E. Benková, “In situ hybridization for mRNA detection in Arabidopsis tissue sections,” Nature Protocols, vol. 1, no. 3. Nature Publishing Group, pp. 1462–1467, 2006.","apa":"Brewer, P., Heisler, M., Hejátko, J., Friml, J., & Benková, E. (2006). In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.226","mla":"Brewer, Philip, et al. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols, vol. 1, no. 3, Nature Publishing Group, 2006, pp. 1462–67, doi:10.1038/nprot.2006.226.","short":"P. Brewer, M. Heisler, J. Hejátko, J. Friml, E. Benková, Nature Protocols 1 (2006) 1462–1467.","chicago":"Brewer, Philip, Marcus Heisler, Jan Hejátko, Jiří Friml, and Eva Benková. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.226."},"publication":"Nature Protocols","date_published":"2006-08-01T00:00:00Z","doi":"10.1038/nprot.2006.226","month":"08","day":"01","intvolume":" 1","publisher":"Nature Publishing Group","status":"public","publication_status":"published","title":"In situ hybridization for mRNA detection in Arabidopsis tissue sections","_id":"3014","year":"2006","volume":1,"date_created":"2018-12-11T12:00:52Z","date_updated":"2021-01-12T07:40:28Z","author":[{"full_name":"Brewer, Philip B","first_name":"Philip","last_name":"Brewer"},{"first_name":"Marcus","last_name":"Heisler","full_name":"Heisler, Marcus G"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Eva Benková"}],"type":"journal_article","extern":1,"issue":"3","publist_id":"3687","abstract":[{"text":"Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days.","lang":"eng"}]},{"publication":"Annual Review of Cell and Developmental Biology","citation":{"ama":"Kunwar P, Siekhaus DE, Lehmann R. In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. 2006;22:237-265. doi:10.1146/annurev.cellbio.22.010305.103337","apa":"Kunwar, P., Siekhaus, D. E., & Lehmann, R. (2006). In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev.cellbio.22.010305.103337","ieee":"P. Kunwar, D. E. Siekhaus, and R. Lehmann, “In vivo migration A germ cell perspective,” Annual Review of Cell and Developmental Biology, vol. 22. Annual Reviews, pp. 237–265, 2006.","ista":"Kunwar P, Siekhaus DE, Lehmann R. 2006. In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. 22, 237–265.","short":"P. Kunwar, D.E. Siekhaus, R. Lehmann, Annual Review of Cell and Developmental Biology 22 (2006) 237–265.","mla":"Kunwar, Prabhat, et al. “In Vivo Migration A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology, vol. 22, Annual Reviews, 2006, pp. 237–65, doi:10.1146/annurev.cellbio.22.010305.103337.","chicago":"Kunwar, Prabhat, Daria E Siekhaus, and Ruth Lehmann. “In Vivo Migration A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2006. https://doi.org/10.1146/annurev.cellbio.22.010305.103337."},"quality_controlled":0,"page":"237 - 265","date_published":"2006-06-14T00:00:00Z","doi":"10.1146/annurev.cellbio.22.010305.103337","month":"06","day":"14","_id":"3152","year":"2006","publication_status":"published","title":"In vivo migration A germ cell perspective","status":"public","intvolume":" 22","publisher":"Annual Reviews","author":[{"full_name":"Kunwar, Prabhat S","last_name":"Kunwar","first_name":"Prabhat"},{"full_name":"Daria Siekhaus","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"},{"full_name":"Lehmann, Ruth","last_name":"Lehmann","first_name":"Ruth"}],"date_updated":"2021-01-12T07:41:25Z","date_created":"2018-12-11T12:01:42Z","volume":22,"type":"journal_article","abstract":[{"lang":"eng","text":"The basic concepts of the molecular machinery that mediates cell migration have been gleaned from cell culture systems. However, the three-dimensional environment within an organism presents migrating cells with a much greater challenge. They must move between and among other cells while interpreting multiple attractive and repulsive cues to choose their proper path. They must coordinate their cell adhesion with their surroundings and know when to start and stop moving. New insights into the control of these remaining mysteries have emerged from genetic dissection and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos. In this review, we first describe germ cell migration in cellular and mechanistic detail in these different model systems. We then compare these systems to highlight the emerging principles. Finally, we contrast the migration of germ cells with that of immune and cancer cells to outline the conserved and different mechanisms."}],"publist_id":"3543","extern":1},{"month":"07","day":"05","main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/criminisi_cvpr06.pdf"}],"citation":{"chicago":"Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov. “Bilayer Segmentation of Live Video,” 1:53–60. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.69.","mla":"Criminisi, Antonio, et al. Bilayer Segmentation of Live Video. Vol. 1, IEEE, 2006, pp. 53–60, doi:10.1109/CVPR.2006.69.","short":"A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, IEEE, 2006, pp. 53–60.","ista":"Criminisi A, Cross G, Blake A, Kolmogorov V. 2006. Bilayer segmentation of live video. CVPR: Computer Vision and Pattern Recognition vol. 1, 53–60.","ieee":"A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer segmentation of live video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2006, vol. 1, pp. 53–60.","apa":"Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2006). Bilayer segmentation of live video (Vol. 1, pp. 53–60). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.69","ama":"Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer segmentation of live video. In: Vol 1. IEEE; 2006:53-60. doi:10.1109/CVPR.2006.69"},"page":"53 - 60","quality_controlled":0,"date_published":"2006-07-05T00:00:00Z","doi":"10.1109/CVPR.2006.69","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","publist_id":"3494","abstract":[{"text":"This paper presents an algorithm capable of real-time separation of foreground from background in monocular video sequences. Automatic segmentation of layers from colour/contrast or from motion alone is known to be error-prone. Here motion, colour and contrast cues are probabilistically fused together with spatial and temporal priors to infer layers accurately and efficiently. Central to our algorithm is the fact that pixel velocities are not needed, thus removing the need for optical flow estimation, with its tendency to error and computational expense. Instead, an efficient motion vs non-motion classifier is trained to operate directly and jointly on intensity-change and contrast. Its output is then fused with colour information. The prior on segmentation is represented by a second order, temporal, Hidden Markov Model, together with a spatial MRF favouring coherence except where contrast is high. Finally, accurate layer segmentation and explicit occlusion detection are efficiently achieved by binary graph cut. The segmentation accuracy of the proposed algorithm is quantitatively evaluated with respect to existing ground-truth data and found to be comparable to the accuracy of a state of the art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated in the application of live background substitution and shown to generate convincingly good quality composite video.","lang":"eng"}],"extern":1,"_id":"3189","year":"2006","intvolume":" 1","publisher":"IEEE","title":"Bilayer segmentation of live video","publication_status":"published","status":"public","author":[{"first_name":"Antonio","last_name":"Criminisi","full_name":"Criminisi, Antonio"},{"last_name":"Cross","first_name":"Geoffrey","full_name":"Cross, Geoffrey"},{"full_name":"Blake, Andrew","first_name":"Andrew","last_name":"Blake"},{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":1,"date_updated":"2021-01-12T07:41:40Z","date_created":"2018-12-11T12:01:54Z"},{"page":"1568 - 1583","quality_controlled":0,"citation":{"ama":"Kolmogorov V. Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(10):1568-1583. doi:10.1109/TPAMI.2006.200","ieee":"V. Kolmogorov, “Convergent tree reweighted message passing for energy minimization,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 10. IEEE, pp. 1568–1583, 2006.","apa":"Kolmogorov, V. (2006). Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.200","ista":"Kolmogorov V. 2006. Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(10), 1568–1583.","short":"V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 1568–1583.","mla":"Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 10, IEEE, 2006, pp. 1568–83, doi:10.1109/TPAMI.2006.200.","chicago":"Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.200."},"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67371/trw_maxproduct_aistats05.pdf"}],"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","date_published":"2006-08-21T00:00:00Z","doi":"10.1109/TPAMI.2006.200","month":"08","day":"21","intvolume":" 28","publisher":"IEEE","status":"public","title":"Convergent tree reweighted message passing for energy minimization","publication_status":"published","_id":"3190","year":"2006","volume":28,"date_created":"2018-12-11T12:01:55Z","date_updated":"2021-01-12T07:41:41Z","author":[{"full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"type":"journal_article","extern":1,"publist_id":"3495","issue":"10","abstract":[{"lang":"eng","text":"Algorithms for discrete energy minimization are of fundamental importance in computer vision. In this paper, we focus on the recent technique proposed by Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW). It was inspired by the problem of maximizing a lower bound on the energy. However, the algorithm is not guaranteed to increase this bound - it may actually go down. In addition, TRW does not always converge. We develop a modification of this algorithm which we call sequential tree-reweighted message passing. Its main property is that the bound is guaranteed not to decrease. We also give a weak tree agreement condition which characterizes local maxima of the bound with respect to TRW algorithms. We prove that our algorithm has a limit point that achieves weak tree agreement. Finally, we show that, our algorithm requires half as much memory as traditional message passing approaches. Experimental results demonstrate that on certain synthetic and real problems, our algorithm outperforms both the ordinary belief propagation and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition, on stereo problems with Potts interactions, we obtain a lower energy than graph cuts."}]},{"date_created":"2018-12-11T12:01:54Z","date_updated":"2021-01-12T07:41:40Z","author":[{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"last_name":"Minka","first_name":"Thomas","full_name":"Minka, Thomas P"},{"full_name":"Blake, Andrew","last_name":"Blake","first_name":"Andrew"}],"status":"public","title":"Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs","publication_status":"published","publisher":"IEEE","year":"2006","_id":"3188","extern":1,"abstract":[{"text":"We introduce the term cosegmentation which denotes the task of segmenting simultaneously the common parts of an image pair. A generative model for cosegmentation is presented. Inference in the model leads to minimizing an energy with an MRF term encoding spatial coherency and a global constraint which attempts to match the appearance histograms of the common parts. This energy has not been proposed previously and its optimization is challenging and NP-hard. For this problem a novel optimization scheme which we call trust region graph cuts is presented. We demonstrate that this framework has the potential to improve a wide range of research: Object driven image retrieval, video tracking and segmentation, and interactive image editing. The power of the framework lies in its generality, the common part can be a rigid/non-rigid object (or scene), observed from different viewpoints or even similar objects of the same class.","lang":"eng"}],"publist_id":"3493","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"date_published":"2006-07-05T00:00:00Z","doi":"10.1109/CVPR.2006.91","quality_controlled":0,"page":"993 - 1000","citation":{"chicago":"Rother, Carsten, Vladimir Kolmogorov, Thomas Minka, and Andrew Blake. “Cosegmentation of Image Pairs by Histogram Matching - Incorporating a Global Constraint into MRFs,” 993–1000. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.91.","short":"C. Rother, V. Kolmogorov, T. Minka, A. Blake, in:, IEEE, 2006, pp. 993–1000.","mla":"Rother, Carsten, et al. Cosegmentation of Image Pairs by Histogram Matching - Incorporating a Global Constraint into MRFs. IEEE, 2006, pp. 993–1000, doi:10.1109/CVPR.2006.91.","ieee":"C. Rother, V. Kolmogorov, T. Minka, and A. Blake, “Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs,” presented at the CVPR: Computer Vision and Pattern Recognition, 2006, pp. 993–1000.","apa":"Rother, C., Kolmogorov, V., Minka, T., & Blake, A. (2006). Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs (pp. 993–1000). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.91","ista":"Rother C, Kolmogorov V, Minka T, Blake A. 2006. Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs. CVPR: Computer Vision and Pattern Recognition, 993–1000.","ama":"Rother C, Kolmogorov V, Minka T, Blake A. Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs. In: IEEE; 2006:993-1000. doi:10.1109/CVPR.2006.91"},"day":"05","month":"07"},{"month":"07","day":"11","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"doi":"10.1007/11761679_24","date_published":"2006-07-11T00:00:00Z","citation":{"mla":"Maurer, Ueli, et al. Luby Rackoff Ciphers from Weak Round Functions . Vol. 4004, Springer, 2006, pp. 391–408, doi:10.1007/11761679_24.","short":"U. Maurer, Y. Oswald, K.Z. Pietrzak, J. Sjödin, in:, Springer, 2006, pp. 391–408.","chicago":"Maurer, Ueli, Yvonne Oswald, Krzysztof Z Pietrzak, and Johan Sjödin. “Luby Rackoff Ciphers from Weak Round Functions ,” 4004:391–408. Springer, 2006. https://doi.org/10.1007/11761679_24.","ama":"Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. Luby Rackoff ciphers from weak round functions . In: Vol 4004. Springer; 2006:391-408. doi:10.1007/11761679_24","ista":"Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. 2006. Luby Rackoff ciphers from weak round functions . EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 391–408.","apa":"Maurer, U., Oswald, Y., Pietrzak, K. Z., & Sjödin, J. (2006). Luby Rackoff ciphers from weak round functions (Vol. 4004, pp. 391–408). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_24","ieee":"U. Maurer, Y. Oswald, K. Z. Pietrzak, and J. Sjödin, “Luby Rackoff ciphers from weak round functions ,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol. 4004, pp. 391–408."},"quality_controlled":0,"page":"391 - 408","abstract":[{"lang":"eng","text":"The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key.\nLuby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers.\nBut the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation."}],"publist_id":"3465","extern":1,"type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Maurer, Ueli M","last_name":"Maurer","first_name":"Ueli"},{"full_name":"Oswald, Yvonne A","first_name":"Yvonne","last_name":"Oswald"},{"full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Sjödin, Johan","last_name":"Sjödin","first_name":"Johan"}],"date_updated":"2021-01-12T07:41:51Z","date_created":"2018-12-11T12:02:03Z","volume":4004,"acknowledgement":"Most of this work was done while the K. Pietrzak was a PhD student at ETH where he was supported by the Swiss National Science Foundation, project No. 200020- 103847/1. Currently he is partially supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 ECRYPT.","_id":"3214","year":"2006","publication_status":"published","title":"Luby Rackoff ciphers from weak round functions ","status":"public","intvolume":" 4004","publisher":"Springer"},{"acknowledgement":"Supported in part by NSF career award CCR-0133806 and NSF grant CCR-0311095. Supported by the Swiss National Science Foundation, project No. 200020-103847/1.","_id":"3215","year":"2006","status":"public","title":"Separating sources for encryption and secret sharing","publication_status":"published","publisher":"Springer","intvolume":" 3876","author":[{"first_name":"Yevgeniy","last_name":"Dodis","full_name":"Dodis, Yevgeniy"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak"},{"first_name":"Bartosz","last_name":"Przydatek","full_name":"Przydatek, Bartosz"}],"date_updated":"2021-01-12T07:41:51Z","date_created":"2018-12-11T12:02:04Z","volume":3876,"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Most cryptographic primitives such as encryption, authentication or secret sharing require randomness. Usually one assumes that perfect randomness is available, but those primitives might also be realized under weaker assumptions. In this work we continue the study of building secure cryptographic primitives from imperfect random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows that there exists a (high-entropy) source of randomness allowing for perfect encryption of a bit, and yet from which one cannot extract even a single weakly random bit, separating encryption from extraction. Our main result separates encryption from 2-out-2 secret sharing (both in the information-theoretic and in the computational settings): any source which can be used to achieve one-bit encryption also can be used for 2-out-2 secret sharing of one bit, but the converse is false, even for high-entropy sources. Therefore, possibility of extraction strictly implies encryption, which in turn strictly implies 2-out-2 secret sharing.","lang":"eng"}],"publist_id":"3466","extern":1,"citation":{"chicago":"Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Bartosz Przydatek. “Separating Sources for Encryption and Secret Sharing,” 3876:601–16. Springer, 2006. https://doi.org/10.1007/11681878_31.","mla":"Dodis, Yevgeniy, et al. Separating Sources for Encryption and Secret Sharing. Vol. 3876, Springer, 2006, pp. 601–16, doi:10.1007/11681878_31.","short":"Y. Dodis, K.Z. Pietrzak, B. Przydatek, in:, Springer, 2006, pp. 601–616.","ista":"Dodis Y, Pietrzak KZ, Przydatek B. 2006. Separating sources for encryption and secret sharing. TCC: Theory of Cryptography Conference, LNCS, vol. 3876, 601–616.","apa":"Dodis, Y., Pietrzak, K. Z., & Przydatek, B. (2006). Separating sources for encryption and secret sharing (Vol. 3876, pp. 601–616). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/11681878_31","ieee":"Y. Dodis, K. Z. Pietrzak, and B. Przydatek, “Separating sources for encryption and secret sharing,” presented at the TCC: Theory of Cryptography Conference, 2006, vol. 3876, pp. 601–616.","ama":"Dodis Y, Pietrzak KZ, Przydatek B. Separating sources for encryption and secret sharing. In: Vol 3876. Springer; 2006:601-616. doi:10.1007/11681878_31"},"quality_controlled":0,"page":"601 - 616","conference":{"name":"TCC: Theory of Cryptography Conference"},"doi":"10.1007/11681878_31","date_published":"2006-04-11T00:00:00Z","month":"04","day":"11"},{"day":"11","month":"07","quality_controlled":0,"page":"328 - 338","citation":{"chicago":"Pietrzak, Krzysztof Z. “Composition Implies Adaptive Security in Minicrypt,” 4004:328–38. Springer, 2006. https://doi.org/10.1007/11761679_20.","short":"K.Z. Pietrzak, in:, Springer, 2006, pp. 328–338.","mla":"Pietrzak, Krzysztof Z. Composition Implies Adaptive Security in Minicrypt. Vol. 4004, Springer, 2006, pp. 328–38, doi:10.1007/11761679_20.","apa":"Pietrzak, K. Z. (2006). Composition implies adaptive security in minicrypt (Vol. 4004, pp. 328–338). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_20","ieee":"K. Z. Pietrzak, “Composition implies adaptive security in minicrypt,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol. 4004, pp. 328–338.","ista":"Pietrzak KZ. 2006. Composition implies adaptive security in minicrypt. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 328–338.","ama":"Pietrzak KZ. Composition implies adaptive security in minicrypt. In: Vol 4004. Springer; 2006:328-338. doi:10.1007/11761679_20"},"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"doi":"10.1007/11761679_20","date_published":"2006-07-11T00:00:00Z","alternative_title":["LNCS"],"type":"conference","extern":1,"abstract":[{"text":"To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true.\nTo our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not.","lang":"eng"}],"publist_id":"3464","title":"Composition implies adaptive security in minicrypt","status":"public","publication_status":"published","publisher":"Springer","intvolume":" 4004","acknowledgement":"Author was supported during the writing of this work by the Swiss National Science Foundation, project No. 200020-103847/1. Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932","_id":"3217","year":"2006","date_updated":"2021-01-12T07:41:52Z","date_created":"2018-12-11T12:02:04Z","volume":4004,"author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak"}]},{"conference":{"name":"ICALP: Automata, Languages and Programming"},"date_published":"2006-07-28T00:00:00Z","doi":"10.1007/11787006_15","citation":{"mla":"Pietrzak, Krzysztof Z. A Tight Bound for EMAC. Vol. 4052, Springer, 2006, pp. 168–79, doi:10.1007/11787006_15.","short":"K.Z. Pietrzak, in:, Springer, 2006, pp. 168–179.","chicago":"Pietrzak, Krzysztof Z. “A Tight Bound for EMAC,” 4052:168–79. Springer, 2006. https://doi.org/10.1007/11787006_15.","ama":"Pietrzak KZ. A tight bound for EMAC. In: Vol 4052. Springer; 2006:168-179. doi:10.1007/11787006_15","ista":"Pietrzak KZ. 2006. A tight bound for EMAC. ICALP: Automata, Languages and Programming, LNCS, vol. 4052, 168–179.","apa":"Pietrzak, K. Z. (2006). A tight bound for EMAC (Vol. 4052, pp. 168–179). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11787006_15","ieee":"K. Z. Pietrzak, “A tight bound for EMAC,” presented at the ICALP: Automata, Languages and Programming, 2006, vol. 4052, pp. 168–179."},"quality_controlled":0,"page":"168 - 179","month":"07","day":"28","author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Krzysztof Pietrzak"}],"date_updated":"2021-01-12T07:41:52Z","date_created":"2018-12-11T12:02:04Z","volume":4052,"_id":"3216","year":"2006","acknowledgement":"Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 ECRYPT.","status":"public","publication_status":"published","title":"A tight bound for EMAC","publisher":"Springer","intvolume":" 4052","abstract":[{"lang":"eng","text":"We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04].\nThe bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found."}],"publist_id":"3463","extern":1,"type":"conference","alternative_title":["LNCS"]},{"quality_controlled":0,"page":"143 - 155","publication":"Neuron","citation":{"mla":"O’Neill, Joseph, et al. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron, vol. 49, no. 1, Elsevier, 2006, pp. 143–55, doi:10.1016/j.neuron.2005.10.037.","short":"J. O’Neill, T. Senior, J.L. Csicsvari, Neuron 49 (2006) 143–155.","chicago":"O’Neill, Joseph, Timothy Senior, and Jozsef L Csicsvari. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.10.037.","ama":"O’Neill J, Senior T, Csicsvari JL. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 2006;49(1):143-155. doi:10.1016/j.neuron.2005.10.037","ista":"O’Neill J, Senior T, Csicsvari JL. 2006. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 49(1), 143–155.","ieee":"J. O’Neill, T. Senior, and J. L. Csicsvari, “Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior,” Neuron, vol. 49, no. 1. Elsevier, pp. 143–155, 2006.","apa":"O’Neill, J., Senior, T., & Csicsvari, J. L. (2006). Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.10.037"},"date_published":"2006-01-05T00:00:00Z","doi":"10.1016/j.neuron.2005.10.037","day":"05","month":"01","title":"Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior","status":"public","publication_status":"published","publisher":"Elsevier","intvolume":" 49","_id":"3522","year":"2006","date_created":"2018-12-11T12:03:46Z","date_updated":"2021-01-12T07:44:03Z","volume":49,"author":[{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","first_name":"Joseph","full_name":"Joseph O'Neill"},{"full_name":"Senior,Timothy","first_name":"Timothy","last_name":"Senior"},{"last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Jozsef Csicsvari"}],"type":"journal_article","extern":1,"abstract":[{"text":"We observed sharp wave/ripples (SWR) during exploration within brief (< 2.4 s) interruptions of or during theta oscillations. CA1 network responses of SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility or sleep were similar. However, neuronal activity during eSWR was location dependent, and eSWR-related firing was stronger inside the place field than outside. The eSPW-related firing increase was stronger than the baseline increase inside compared to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs. Pairs of cells with similar place fields and/or correlated firing during exploration showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential activation of place cells was not required for the reactivation of waking co-firing patterns; cell pairs with symmetrical cross-correlations still showed reactivated waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing during eSWRs facilitates initial associations between cells with similar place fields that enable place-related ensemble patterns to recur during subsequent sleep-SWRs.","lang":"eng"}],"publist_id":"2863","issue":"1"},{"date_published":"2006-09-01T00:00:00Z","doi":"10.1111/j.0014-3820.2006.tb00521.x","quality_controlled":0,"page":"1763 - 1776","publication":"Evolution; International Journal of Organic Evolution","citation":{"chicago":"Turelli, Michael, and Nicholas H Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x.","short":"M. Turelli, N.H. Barton, Evolution; International Journal of Organic Evolution 60 (2006) 1763–1776.","mla":"Turelli, Michael, and Nicholas H. Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution, vol. 60, no. 9, Wiley-Blackwell, 2006, pp. 1763–76, doi:10.1111/j.0014-3820.2006.tb00521.x.","ieee":"M. Turelli and N. H. Barton, “Will population bottlenecks and multilocus epistasis increase additive genetic variance?,” Evolution; International Journal of Organic Evolution, vol. 60, no. 9. Wiley-Blackwell, pp. 1763–1776, 2006.","apa":"Turelli, M., & Barton, N. H. (2006). Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x","ista":"Turelli M, Barton NH. 2006. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 60(9), 1763–1776.","ama":"Turelli M, Barton NH. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 2006;60(9):1763-1776. doi:10.1111/j.0014-3820.2006.tb00521.x"},"day":"01","month":"09","date_updated":"2021-01-12T07:44:37Z","date_created":"2018-12-11T12:04:13Z","volume":60,"author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"publication_status":"published","title":"Will population bottlenecks and multilocus epistasis increase additive genetic variance?","status":"public","intvolume":" 60","publisher":"Wiley-Blackwell","year":"2006","_id":"3607","extern":1,"abstract":[{"lang":"eng","text":"We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance–attributable to epistasis rather than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences."}],"issue":"9","publist_id":"2776","type":"journal_article"},{"publication_status":"published","title":"Objective quality measurement for geometric document image restoration","status":"public","publisher":"Springer","year":"2006","_id":"3683","date_updated":"2021-01-12T07:45:07Z","date_created":"2018-12-11T12:04:36Z","author":[{"full_name":"Christoph Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"last_name":"Breuel","first_name":"Thomas","full_name":"Breuel,Thomas M"}],"type":"conference","extern":1,"abstract":[{"lang":"eng","text":"Many algorithms to remove distortion from document images have be proposed in recent years, but so far there is no reliable method for comparing their performance. In this paper we propose a collection of methods to measure the quality of such restoration algorithms for document image which show a non-linear distortion due to perspective or page curl. For the result from these measurement to be meaningful, a common data set of ground truth is required. We therefore started with the buildup of a document image database that is meant to serve as a common data basis for all kinds of restoration from images of 3D-shaped document. The long term goal would be to establish this database and following extensions in the area of document image dewarping as an as fruitful and indispensable tool as e.g. the NIST database is for OCR, or the Caltech database is for object and face recognition."}],"publist_id":"2692","quality_controlled":0,"citation":{"chicago":"Lampert, Christoph, and Thomas Breuel. “Objective Quality Measurement for Geometric Document Image Restoration.” Springer, 2006.","short":"C. Lampert, T. Breuel, in:, Springer, 2006.","mla":"Lampert, Christoph, and Thomas Breuel. Objective Quality Measurement for Geometric Document Image Restoration. Springer, 2006.","apa":"Lampert, C., & Breuel, T. (2006). Objective quality measurement for geometric document image restoration. Presented at the DAS: Document Analysis Systems, Springer.","ieee":"C. Lampert and T. Breuel, “Objective quality measurement for geometric document image restoration,” presented at the DAS: Document Analysis Systems, 2006.","ista":"Lampert C, Breuel T. 2006. Objective quality measurement for geometric document image restoration. DAS: Document Analysis Systems.","ama":"Lampert C, Breuel T. Objective quality measurement for geometric document image restoration. In: Springer; 2006."},"main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/~chl/papers/lampert-das2006.pdf"}],"conference":{"name":"DAS: Document Analysis Systems"},"date_published":"2006-03-16T00:00:00Z","month":"03","day":"16"},{"day":"18","month":"09","citation":{"chicago":"Lampert, Christoph. “Machine Learning for Video Compression: Macroblock Mode Decision,” 936–40. IEEE, 2006. https://doi.org/10.1109/ICPR.2006.778.","short":"C. Lampert, in:, IEEE, 2006, pp. 936–940.","mla":"Lampert, Christoph. Machine Learning for Video Compression: Macroblock Mode Decision. IEEE, 2006, pp. 936–40, doi:10.1109/ICPR.2006.778.","apa":"Lampert, C. (2006). Machine learning for video compression: Macroblock mode decision (pp. 936–940). Presented at the ICPR: International Conference on Pattern Recognition, IEEE. https://doi.org/10.1109/ICPR.2006.778","ieee":"C. Lampert, “Machine learning for video compression: Macroblock mode decision,” presented at the ICPR: International Conference on Pattern Recognition, 2006, pp. 936–940.","ista":"Lampert C. 2006. Machine learning for video compression: Macroblock mode decision. ICPR: International Conference on Pattern Recognition, 936–940.","ama":"Lampert C. Machine learning for video compression: Macroblock mode decision. In: IEEE; 2006:936-940. doi:10.1109/ICPR.2006.778"},"page":"936 - 940","quality_controlled":0,"doi":"10.1109/ICPR.2006.778","date_published":"2006-09-18T00:00:00Z","conference":{"name":"ICPR: International Conference on Pattern Recognition"},"type":"conference","publist_id":"2689","abstract":[{"text":"Video compression currently is dominated by engineering and fine-tuned heuristic methods. In this paper, we propose to instead apply the well-developed machinery of machine learning in order to support the optimization of existing video encoders and the creation of new ones. Exemplarily, we show how by machine learning we can improve one encoding step that is crucial for the performance of all current video standards: macroblock mode decision. By formulating the problem in a Bayesian setup, we show that macroblock mode decision can be reduced to a classification problem with a cost function for misclassification that is sample dependent. We demonstrate how to apply different machine learning techniques to obtain suitable classifiers and we show in detailed experiments that all of these perform better than the state-of-the-art heuristic method","lang":"eng"}],"extern":1,"year":"2006","_id":"3685","publisher":"IEEE","status":"public","title":"Machine learning for video compression: Macroblock mode decision","publication_status":"published","author":[{"full_name":"Christoph Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"date_updated":"2021-01-12T07:45:08Z","date_created":"2018-12-11T12:04:37Z"},{"month":"07","day":"01","publication":"Protein Expression and Purification","citation":{"mla":"Le, Thuc, et al. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification, vol. 48, no. 1, Elsevier, 2006, pp. 28–31.","short":"T. Le, C.C. Guet, P. Cluzel, Protein Expression and Purification 48 (2006) 28–31.","chicago":"Le, Thuc, Calin C Guet, and Philippe Cluzel. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification. Elsevier, 2006.","ama":"Le T, Guet CC, Cluzel P. Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. 2006;48(1):28-31.","ista":"Le T, Guet CC, Cluzel P. 2006. Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. 48(1), 28–31.","ieee":"T. Le, C. C. Guet, and P. Cluzel, “Protein expression enhancement in efflux-deleted mutant bacteria,” Protein Expression and Purification, vol. 48, no. 1. Elsevier, pp. 28–31, 2006.","apa":"Le, T., Guet, C. C., & Cluzel, P. (2006). Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. Elsevier."},"quality_controlled":0,"page":"28 - 31","date_published":"2006-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We applied a single-cell assay to characterize how transcription dynamics affects protein expression levels of a tetracycline-inducible gene expression system. Transcriptional activity of the tetracycline promoter in response to a steady level of inducer is steady in ΔacrAB efflux mutant but pulsating in wildtype Escherichia coli cells. We found that the expression level of the green fluorescent protein is several folds higher in ΔacrAB efflux mutant than in wildtype cells."}],"publist_id":"2478","issue":"1","extern":1,"year":"2006","_id":"3750","status":"public","publication_status":"published","title":"Protein expression enhancement in efflux-deleted mutant bacteria","publisher":"Elsevier","intvolume":" 48","author":[{"first_name":"Thuc","last_name":"Le","full_name":"Le,Thuc T."},{"full_name":"Calin Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"full_name":"Cluzel,Philippe","first_name":"Philippe","last_name":"Cluzel"}],"date_updated":"2021-01-12T07:51:56Z","date_created":"2018-12-11T12:04:58Z","volume":48},{"publication":"Journal of Theoretical Biology","citation":{"short":"A. Kupczok, P. Dittrich, Journal of Theoretical Biology 238 (2006) 726–35.","mla":"Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.” Journal of Theoretical Biology, vol. 238, no. 3, Elsevier, 2006, pp. 726–35, doi:10.1016/j.jtbi.2005.06.019.","chicago":"Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.06.019.","ama":"Kupczok A, Dittrich P. Determinants of simulated RNA evolution. Journal of Theoretical Biology. 2006;238(3):726-735. doi:10.1016/j.jtbi.2005.06.019","ieee":"A. Kupczok and P. Dittrich, “Determinants of simulated RNA evolution.,” Journal of Theoretical Biology, vol. 238, no. 3. Elsevier, pp. 726–35, 2006.","apa":"Kupczok, A., & Dittrich, P. (2006). Determinants of simulated RNA evolution. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.06.019","ista":"Kupczok A, Dittrich P. 2006. Determinants of simulated RNA evolution. Journal of Theoretical Biology. 238(3), 726–35."},"quality_controlled":0,"page":"726 - 35","doi":"10.1016/j.jtbi.2005.06.019","date_published":"2006-01-01T00:00:00Z","day":"01","month":"01","_id":"3767","year":"2006","status":"public","publication_status":"published","title":"Determinants of simulated RNA evolution.","publisher":"Elsevier","intvolume":" 238","author":[{"full_name":"Anne Kupczok","first_name":"Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Dittrich","full_name":"Dittrich,Peter"}],"date_created":"2018-12-11T12:05:03Z","date_updated":"2021-01-12T07:52:03Z","volume":238,"type":"journal_article","abstract":[{"text":"Models of RNA secondary structure folding are widely used to study evolution in theory and simulation. However, systematic studies of the parameters involved are rare. In this paper, we study by simulation how RNA evolution is influenced by three different factors, namely the mutation rate, scaling of the fitness function, and distance measure. We found that for low mutation rates the qualitative evolutionary behavior is robust with respect to the scaling of the fitness function. For efficient mutation rates, which are close to the error threshold, scaling and distance measure have a strong influence on the evolutionary behavior. A global distance measure that takes sequence information additively into account lowers the error threshold. When using a local sequence-structure alignment for the distance, we observed a smoother evolution of the fitness over time. Finally, in addition to the well known error threshold, we identify another threshold of the mutation rate, called divergence threshold, where the qualitative transient behavior changes from a localized to an exploratory search.","lang":"eng"}],"issue":"3","publist_id":"2461","extern":1},{"quality_controlled":0,"page":"229 - 43","publication":"Journal of Physiology","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817792/"}],"citation":{"ama":"Aponte Y, Lien C, Reisinger E, Jonas PM. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 2006;574(Pt 1):229-243. doi:10.1113/jphysiol.2005.104042","ista":"Aponte Y, Lien C, Reisinger E, Jonas PM. 2006. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 574(Pt 1), 229–43.","apa":"Aponte, Y., Lien, C., Reisinger, E., & Jonas, P. M. (2006). Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2005.104042","ieee":"Y. Aponte, C. Lien, E. Reisinger, and P. M. Jonas, “Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus,” Journal of Physiology, vol. 574, no. Pt 1. Wiley-Blackwell, pp. 229–43, 2006.","mla":"Aponte, Yexica, et al. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology, vol. 574, no. Pt 1, Wiley-Blackwell, 2006, pp. 229–43, doi:10.1113/jphysiol.2005.104042.","short":"Y. Aponte, C. Lien, E. Reisinger, P.M. Jonas, Journal of Physiology 574 (2006) 229–43.","chicago":"Aponte, Yexica, Cheng Lien, Ellen Reisinger, and Peter M Jonas. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology. Wiley-Blackwell, 2006. https://doi.org/10.1113/jphysiol.2005.104042."},"oa":1,"doi":"10.1113/jphysiol.2005.104042","date_published":"2006-01-01T00:00:00Z","day":"01","month":"01","status":"public","title":"Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus","publication_status":"published","publisher":"Wiley-Blackwell","intvolume":" 574","year":"2006","_id":"3813","date_created":"2018-12-11T12:05:19Z","date_updated":"2021-01-12T07:52:23Z","volume":574,"author":[{"first_name":"Yexica","last_name":"Aponte","full_name":"Aponte, Yexica"},{"last_name":"Lien","first_name":"Cheng","full_name":"Lien, Cheng-Chang"},{"last_name":"Reisinger","first_name":"Ellen","full_name":"Reisinger, Ellen"},{"full_name":"Peter Jonas","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"type":"journal_article","extern":1,"abstract":[{"text":"Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed in principal neurons in the central nervous system. However, Ih in inhibitory GABAergic interneurons is less well characterized. We examined the functional properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of 5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent membrane time constant. ZD 7288 blocked a hyperpolarization-activated current in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288 were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of the activation curve of Ih was -83.9 mV, and the activation time constant at -120 mV was 190 ms. Single-cell expression analysis using reverse transcription followed by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD 7288 increased the current threshold for evoking antidromic action potentials by extracellular stimulation, consistent with the expression of Ih in BC axons. Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs, to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged, consistent with the presence of Ih in inhibitory terminals. In conclusion, our results suggest that Ih channels are expressed in the somatodendritic region, axon and presynaptic elements of fast-spiking BCs in the hippocampus.","lang":"eng"}],"issue":"Pt 1","publist_id":"2397"},{"author":[{"first_name":"Michael","last_name":"Frotscher","full_name":"Frotscher, Michael"},{"full_name":"Peter Jonas","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sloviter, Robert S","last_name":"Sloviter","first_name":"Robert"}],"date_updated":"2019-04-26T07:22:35Z","date_created":"2018-12-11T12:05:19Z","volume":326,"year":"2006","_id":"3814","status":"public","publication_status":"published","title":"Synapses formed by normal and abnormal hippocampal mossy fibers (Review)","intvolume":" 326","publisher":"Springer","abstract":[{"text":"The axon terminals (mossy fibers) of hippocampal dentate granule cells form characteristic synaptic connections with large spines or excrescences of both hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled mossy fibers and immunolabeling of target cells with interneuron markers has revealed that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic inhibitory interneurons rather than to excitatory principal cells, although the functional implications of these quantitative differences are unclear. Following a brief description of the "classical" mossy fiber synapse on excrescences of CA3 pyramidal cells, the present review focuses on the contacts formed between granule cells and GABAergic interneurons, both normally and after synaptic reorganization. In response to deafferentation of mossy cell target cells, which include both granule cells and interneurons, mossy fibers "sprout" new axon collaterals that form a band of supragranular mossy fibers in the inner molecular layer of the dentate gyrus. Although most newly formed recurrent mossy fibers establish synapses with granule cells, there is an apparently convergent input of new mossy fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are observed in chronically epileptic rats and may be the structural correlate of the granule cell hyperinhibition observed in these animals in vivo. Together, the findings reviewed here establish mossy fiber synapses as an important component of inhibitory circuits in the hippocampus.","lang":"eng"}],"publist_id":"2395","issue":"2","extern":1,"type":"review","doi":"10.1007/s00441-006-0269-2","date_published":"2006-01-01T00:00:00Z","publication":"Cell and Tissue Research","citation":{"ama":"Frotscher M, Jonas PM, Sloviter R. Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. 2006;326(2):361-367. doi:10.1007/s00441-006-0269-2","ista":"Frotscher M, Jonas PM, Sloviter R. 2006. Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. 326(2), 361–7.","ieee":"M. Frotscher, P. M. Jonas, and R. Sloviter, “Synapses formed by normal and abnormal hippocampal mossy fibers (Review),” Cell and Tissue Research, vol. 326, no. 2. Springer, pp. 361–7, 2006.","apa":"Frotscher, M., Jonas, P. M., & Sloviter, R. (2006). Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0269-2","mla":"Frotscher, Michael, et al. “Synapses Formed by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue Research, vol. 326, no. 2, Springer, 2006, pp. 361–67, doi:10.1007/s00441-006-0269-2.","short":"M. Frotscher, P.M. Jonas, R. Sloviter, Cell and Tissue Research 326 (2006) 361–7.","chicago":"Frotscher, Michael, Peter M Jonas, and Robert Sloviter. “Synapses Formed by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0269-2."},"quality_controlled":0,"page":"361 - 7","day":"01","month":"01"},{"doi":"10.1007/s00424-006-0093-2","date_published":"2006-01-01T00:00:00Z","citation":{"short":"J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 361–72.","mla":"Bischofberger, Josef, et al. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.","chicago":"Bischofberger, Josef, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology. Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.","ama":"Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2","apa":"Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2","ieee":"J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network,” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–72, 2006.","ista":"Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. 453(3), 361–72."},"publication":"Pflugers Archiv : European Journal of Physiology","page":"361 - 72","quality_controlled":0,"month":"01","day":"01","author":[{"full_name":"Bischofberger, Josef","first_name":"Josef","last_name":"Bischofberger"},{"full_name":"Engel, Dominique","first_name":"Dominique","last_name":"Engel"},{"last_name":"Frotscher","first_name":"Michael","full_name":"Frotscher, Michael"},{"full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"volume":453,"date_updated":"2021-01-12T07:52:24Z","date_created":"2018-12-11T12:05:19Z","year":"2006","_id":"3815","publisher":"Springer","intvolume":" 453","status":"public","publication_status":"published","title":"Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network","issue":"3","publist_id":"2396","abstract":[{"lang":"eng","text":"It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network."}],"extern":1,"type":"journal_article"},{"_id":"3811","year":"2006","publisher":"Elsevier","intvolume":" 49","status":"public","publication_status":"published","title":"Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates","author":[{"full_name":"Vida, Imre","last_name":"Vida","first_name":"Imre"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"},{"full_name":"Peter Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"volume":49,"date_created":"2018-12-11T12:05:18Z","date_updated":"2021-01-12T07:52:22Z","type":"journal_article","publist_id":"2398","issue":"1","abstract":[{"text":"Networks of GABAergic neurons are key elements in the generation of gamma oscillations in the brain. Computational studies suggested that the emergence of coherent oscillations requires hyperpolarizing inhibition. Here, we show that GABA(A) receptor-mediated inhibition in mature interneurons of the hippocampal dentate gyrus is shunting rather than hyperpolarizing. Unexpectedly, when shunting inhibition is incorporated into a structured interneuron network model with fast and strong synapses, coherent oscillations emerge. In comparison to hyperpolarizing inhibition, networks with shunting inhibition show several advantages. First, oscillations are generated with smaller tonic excitatory drive. Second, network frequencies are tuned to the gamma band. Finally, robustness against heterogeneity in the excitatory drive is markedly improved. In single interneurons, shunting inhibition shortens the interspike interval for low levels of drive but prolongs it for high levels, leading to homogenization of neuronal firing rates. Thus, shunting inhibition may confer increased robustness to gamma oscillations in the brain.","lang":"eng"}],"extern":1,"citation":{"chicago":"Vida, Imre, Marlene Bartos, and Peter M Jonas. “Shunting Inhibition Improves Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.11.036.","mla":"Vida, Imre, et al. “Shunting Inhibition Improves Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron, vol. 49, no. 1, Elsevier, 2006, pp. 107–17, doi:10.1016/j.neuron.2005.11.036.","short":"I. Vida, M. Bartos, P.M. Jonas, Neuron 49 (2006) 107–17.","ista":"Vida I, Bartos M, Jonas PM. 2006. Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. 49(1), 107–17.","ieee":"I. Vida, M. Bartos, and P. M. Jonas, “Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates,” Neuron, vol. 49, no. 1. Elsevier, pp. 107–17, 2006.","apa":"Vida, I., Bartos, M., & Jonas, P. M. (2006). Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.11.036","ama":"Vida I, Bartos M, Jonas PM. Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. 2006;49(1):107-117. doi:10.1016/j.neuron.2005.11.036"},"publication":"Neuron","page":"107 - 17","quality_controlled":0,"date_published":"2006-01-01T00:00:00Z","doi":"10.1016/j.neuron.2005.11.036","month":"01","day":"01"},{"date_created":"2018-12-11T12:05:20Z","date_updated":"2021-01-12T07:52:24Z","volume":326,"author":[{"full_name":"Frotscher, Michael","first_name":"Michael","last_name":"Frotscher"},{"first_name":"Eckart","last_name":"Gundelfinger","full_name":"Gundelfinger, Eckart"},{"full_name":"Peter Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"},{"first_name":"Erwin","last_name":"Neher","full_name":"Neher, Erwin"},{"full_name":"Seeburg, Peter","last_name":"Seeburg","first_name":"Peter"}],"title":"The most important recent advances in synapse research from my point of view--and what remains to be done","publication_status":"published","status":"public","publisher":"Springer","intvolume":" 326","_id":"3817","year":"2006","extern":1,"publist_id":"2394","issue":"2","type":"journal_article","date_published":"2006-01-01T00:00:00Z","doi":"10.1007/s00441-006-0325-y","quality_controlled":0,"page":"203 - 4","publication":"Cell and Tissue Research","citation":{"ista":"Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. 2006. The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. 326(2), 203–4.","ieee":"M. Frotscher, E. Gundelfinger, P. M. Jonas, E. Neher, and P. Seeburg, “The most important recent advances in synapse research from my point of view--and what remains to be done,” Cell and Tissue Research, vol. 326, no. 2. Springer, pp. 203–4, 2006.","apa":"Frotscher, M., Gundelfinger, E., Jonas, P. M., Neher, E., & Seeburg, P. (2006). The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0325-y","ama":"Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. 2006;326(2):203-204. doi:10.1007/s00441-006-0325-y","chicago":"Frotscher, Michael, Eckart Gundelfinger, Peter M Jonas, Erwin Neher, and Peter Seeburg. “The Most Important Recent Advances in Synapse Research from My Point of View--and What Remains to Be Done.” Cell and Tissue Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0325-y.","mla":"Frotscher, Michael, et al. “The Most Important Recent Advances in Synapse Research from My Point of View--and What Remains to Be Done.” Cell and Tissue Research, vol. 326, no. 2, Springer, 2006, pp. 203–04, doi:10.1007/s00441-006-0325-y.","short":"M. Frotscher, E. Gundelfinger, P.M. Jonas, E. Neher, P. Seeburg, Cell and Tissue Research 326 (2006) 203–4."},"day":"01","month":"01"},{"type":"journal_article","abstract":[{"text":"Invasive species often dramatically change native species communities by directly and indirectly out-competing native species. We studied the direct interference abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA & ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers towards three native Lasius ant species that occur at the edge of a L. neglectus supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus (OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack rate of L. neglectus and behavioural dominance throughout the aggressive encounters. Attacks of L. neglectus were performed fastest and most frequent against L. grandis, and also the highest antennation frequencies were observed in encounters between these two species. This could be due to the largest difference in body size, or due to a greater overlap in ecological niche between L. neglectus and L. grandis compared to the other two native species. There was only weak support for L. neglectus workers from the periphery of the supercolony to be more aggressive relative to workers from the centre, even though the former encounter native ant species on a daily basis at the edge of the supercolony.","lang":"eng"}],"publist_id":"2239","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3912","year":"2006","title":"Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain","publication_status":"published","status":"public","publisher":"Österreichische Gesellschaft für Entomofaunistik","intvolume":" 9","author":[{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"},{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V"},{"full_name":"Lommen, Suzanne","last_name":"Lommen","first_name":"Suzanne"},{"last_name":"Petersen","first_name":"Klaus","full_name":"Petersen, Klaus"},{"last_name":"Pedersen","first_name":"Jes","full_name":"Pedersen, Jes"}],"date_created":"2018-12-11T12:05:51Z","date_updated":"2021-01-12T07:53:09Z","volume":9,"oa_version":"None","month":"12","day":"01","publication":"Myrmecological News","citation":{"apa":"Cremer, S., Ugelvig, L. V., Lommen, S., Petersen, K., & Pedersen, J. (2006). Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. Österreichische Gesellschaft für Entomofaunistik.","ieee":"S. Cremer, L. V. Ugelvig, S. Lommen, K. Petersen, and J. Pedersen, “Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain,” Myrmecological News, vol. 9. Österreichische Gesellschaft für Entomofaunistik, pp. 13–19, 2006.","ista":"Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. 2006. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 9, 13–19.","ama":"Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 2006;9:13-19.","chicago":"Cremer, Sylvia, Line V Ugelvig, Suzanne Lommen, Klaus Petersen, and Jes Pedersen. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News. Österreichische Gesellschaft für Entomofaunistik, 2006.","short":"S. Cremer, L.V. Ugelvig, S. Lommen, K. Petersen, J. Pedersen, Myrmecological News 9 (2006) 13–19.","mla":"Cremer, Sylvia, et al. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News, vol. 9, Österreichische Gesellschaft für Entomofaunistik, 2006, pp. 13–19."},"page":"13 - 19","date_published":"2006-12-01T00:00:00Z","language":[{"iso":"eng"}]},{"date_published":"2006-08-29T00:00:00Z","doi":"10.1111/j.1439-0469.2006.00372.x","language":[{"iso":"eng"}],"publication":"Journal of Zoological Systematics and Evolutionary Research","citation":{"ieee":"K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B. Seifert, “Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study,” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.","apa":"Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., & Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x","ista":"Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. 2006. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 45(1), 82–87.","ama":"Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x","chicago":"Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.","short":"K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert, Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87.","mla":"Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87, doi:10.1111/j.1439-0469.2006.00372.x."},"page":"82 - 87","day":"29","month":"08","author":[{"full_name":"Moder, Karl","first_name":"Karl","last_name":"Moder"},{"full_name":"Schlick Steiner, Birgit","last_name":"Schlick Steiner","first_name":"Birgit"},{"last_name":"Steiner","first_name":"Florian","full_name":"Steiner, Florian"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"last_name":"Christian","first_name":"Erhard","full_name":"Christian, Erhard"},{"first_name":"Bernhard","last_name":"Seifert","full_name":"Seifert, Bernhard"}],"date_updated":"2021-01-12T07:53:10Z","date_created":"2018-12-11T12:05:52Z","volume":45,"oa_version":"None","year":"2006","_id":"3914","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study","publisher":"Wiley-Blackwell","intvolume":" 45","abstract":[{"text":"We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable.","lang":"eng"}],"issue":"1","publist_id":"2241","extern":"1","type":"journal_article"},{"extern":"1","abstract":[{"lang":"eng","text":"Many invasive ant species, such as the Argentine ant or the red imported fire ant, have huge colonies with thousands of mass-foraging workers, which quickly monopolise resources and therefore represent a considerable threat to the native ant fauna. Cardiocondyla obscurior and several other species of this myrmicine genus have similarly been transferred throughout the tropics by human activities. However, because their colonies are tiny and workers forage solitarily, Cardiocondyla are often not recognized as successful invaders. Here, we document that the life history of Cardiocondyla closely resembles that of the more conspicuous tramp species, with polygyny, intranidal mating, budding, worker sterility, low genetic variability, and possibly also unicoloniality. Given that introduced Cardiocondyla may locally reach a very high population density, the effects of these stealthy invaders on the native arthropod fauna should receive more attention."}],"publist_id":"2240","issue":"1","type":"journal_article","date_updated":"2021-01-12T07:53:09Z","date_created":"2018-12-11T12:05:51Z","volume":53,"oa_version":"None","author":[{"last_name":"Heinze","first_name":"Jürgen","full_name":"Heinze, Jürgen"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"},{"last_name":"Eckl","first_name":"Norbert","full_name":"Eckl, Norbert"},{"last_name":"Schrempf","first_name":"Alexandra","full_name":"Schrempf, Alexandra"}],"publication_status":"published","status":"public","title":"Stealthy invaders: the biology of Cardiocondyla tramp ants","intvolume":" 53","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3913","year":"2006","month":"02","day":"01","language":[{"iso":"eng"}],"doi":"10.1007/s00040-005-0847-4","date_published":"2006-02-01T00:00:00Z","page":"1 - 7","publication":"Insectes Sociaux","citation":{"ama":"Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4","apa":"Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4","ieee":"J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer, pp. 1–7, 2006.","ista":"Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.","short":"J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7.","mla":"Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.","chicago":"Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer, 2006. https://doi.org/10.1007/s00040-005-0847-4."}},{"date_published":"2006-04-01T00:00:00Z","doi":"10.1016/j.ygyno.2005.09.038","page":"28 - 39","quality_controlled":0,"citation":{"chicago":"Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology. Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038.","short":"E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic Oncology 101 (2006) 28–39.","mla":"Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology, vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038.","apa":"Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006). EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038","ieee":"E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp. 28–39, 2006.","ista":"Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 101(1), 28–39.","ama":"Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038"},"publication":"Gynecologic Oncology","day":"01","month":"04","volume":101,"date_updated":"2021-01-12T07:53:17Z","date_created":"2018-12-11T12:05:57Z","author":[{"first_name":"Emir","last_name":"Henic","full_name":"Henic, Emir"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Michael Sixt"},{"last_name":"Hansson","first_name":"Stefan","full_name":"Hansson, Stefan"},{"full_name":"Høyer-Hansen, Gunilla","last_name":"Høyer Hansen","first_name":"Gunilla"},{"last_name":"Casslén","first_name":"Bertil","full_name":"Casslén, Bertil"}],"publisher":"Elsevier","intvolume":" 101","publication_status":"published","status":"public","title":"EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor","year":"2006","_id":"3932","extern":1,"issue":"1","publist_id":"2194","abstract":[{"lang":"eng","text":"OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and tissue content of EGFR has been directly associated with poor prognosis in patients with ovarian cancer. The uPA system plays a role in pericellular proteolysis, cell migration, invasion, and is over-expressed in ovarian cancer. This study explored the effects of EGF on uPAR expression in the ovarian cancer cell line OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration assay, time-lapse video microscopy, real-time PCR, assays for cellular binding of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well as EGF-stimulated cells, is present only in the intact, not the cleaved, form. Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas non-occupied receptor sites were not increased. In addition, EGF treatment resulted in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased internalization of uPAR, since the complex is internalized together with uPAR. Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression of uPAR. In addition, we found an immediate increase of uPAR after exposing the cells to EGF and this was accompanied by a transient increase of cell migration. The increase of cell surface uPAR in response to EGF is accompanied by increased release of the soluble form of uPAR (suPAR) to the medium as well as by increased cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis inhibitor colchicine even though cell migration was inhibited, suggesting that the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased cell surface uPAR in response to EGF stimulation results from mobilization of uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and decreased internalization and degradation of uPAR. Both the anti-uPAR antibody R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa inhibited cell migration in response to uPA as well as to EGF, suggesting that EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface."}],"type":"journal_article"},{"intvolume":" 62","publisher":"Wiley-Blackwell","title":"Evaluating the quality of NMR structures by local density of protons","publication_status":"published","status":"public","year":"2006","_id":"3978","volume":62,"date_created":"2018-12-11T12:06:14Z","date_updated":"2021-01-12T07:53:36Z","author":[{"first_name":"Yih","last_name":"Ban","full_name":"Ban, Yih-En Andrew"},{"last_name":"Rudolph","first_name":"Johannes","full_name":"Rudolph, Johannes"},{"full_name":"Zhou, Pei","first_name":"Pei","last_name":"Zhou"},{"full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"type":"journal_article","extern":1,"issue":"4","publist_id":"2146","abstract":[{"lang":"eng","text":"Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures."}],"page":"852 - 864","quality_controlled":0,"citation":{"chicago":"Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.","short":"Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function and Bioinformatics 62 (2006) 852–864.","mla":"Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.","ieee":"Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality of NMR structures by local density of protons,” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.","apa":"Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811","ista":"Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 62(4), 852–864.","ama":"Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 2006;62(4):852-864. doi:10.1002/prot.20811"},"publication":"Proteins: Structure, Function and Bioinformatics","date_published":"2006-03-01T00:00:00Z","doi":"10.1002/prot.20811","day":"01","month":"03"},{"intvolume":" 53","publisher":"ACM","title":"Interface surfaces for protein-protein complexes","status":"public","publication_status":"published","year":"2006","_id":"3979","volume":53,"date_updated":"2021-01-12T07:53:37Z","date_created":"2018-12-11T12:06:14Z","author":[{"full_name":"Ban, Yih-En Andrew","first_name":"Yih","last_name":"Ban"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner"},{"first_name":"Johannes","last_name":"Rudolph","full_name":"Rudolph, Johannes"}],"type":"journal_article","extern":1,"issue":"3","publist_id":"2147","abstract":[{"text":"Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion.","lang":"eng"}],"page":"361 - 378","quality_controlled":0,"citation":{"mla":"Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957.","short":"Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378.","chicago":"Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957.","ama":"Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes. Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957","ista":"Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein complexes. Journal of the ACM. 53(3), 361–378.","apa":"Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957","ieee":"Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006."},"publication":"Journal of the ACM","doi":"10.1145/1147954.1147957","date_published":"2006-05-01T00:00:00Z","day":"01","month":"05"},{"month":"12","day":"01","doi":"10.1007/s00454-006-1265-8","date_published":"2006-12-01T00:00:00Z","page":"553 - 572","quality_controlled":0,"citation":{"ista":"Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 36(4), 553–572.","apa":"Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8","ieee":"P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer, pp. 553–572, 2006.","ama":"Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8","chicago":"Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer, 2006. https://doi.org/10.1007/s00454-006-1265-8.","mla":"Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8.","short":"P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational Geometry 36 (2006) 553–572."},"publication":"Discrete & Computational Geometry","extern":1,"publist_id":"2148","issue":"4","abstract":[{"lang":"eng","text":"Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking."}],"type":"journal_article","volume":36,"date_updated":"2021-01-12T07:53:38Z","date_created":"2018-12-11T12:06:15Z","author":[{"full_name":"Agarwal, Pankaj K","first_name":"Pankaj","last_name":"Agarwal"},{"full_name":"Herbert Edelsbrunner","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"last_name":"Harer","first_name":"John","full_name":"Harer, John"},{"full_name":"Wang, Yusu","first_name":"Yusu","last_name":"Wang"}],"intvolume":" 36","publisher":"Springer","title":"Extreme elevation on a 2-manifold","publication_status":"published","status":"public","year":"2006","_id":"3980"},{"month":"01","day":"01","page":"1250 - 1271","quality_controlled":0,"main_file_link":[{"url":"http://www.zlb.de/aktivitaeten/bd_neu/heftinhalte2006/DigitaleBib011106.pdf","open_access":"0"}],"citation":{"ieee":"P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,” Bibliotheksdienst, vol. 40, no. 11. Zentral- und Landesbibliothek Berlin, pp. 1250–1271, 2006.","apa":"Danowski, P., & Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. Zentral- und Landesbibliothek Berlin. https://doi.org/424","ista":"Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 40(11), 1250–1271.","ama":"Danowski P, Heller L. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 2006;40(11):1250-1271. doi:424","chicago":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst. Zentral- und Landesbibliothek Berlin, 2006. https://doi.org/424.","short":"P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271.","mla":"Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst, vol. 40, no. 11, Zentral- und Landesbibliothek Berlin, 2006, pp. 1250–71, doi:424."},"publication":"Bibliotheksdienst","date_published":"2006-01-01T00:00:00Z","doi":"424","type":"journal_article","extern":1,"publist_id":"1229","issue":"11","abstract":[{"text":"Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert.","lang":"eng"}],"publisher":"Zentral- und Landesbibliothek Berlin","intvolume":" 40","title":"Bibliothek 2.0 - Die Bibliothek der Zukunft?","publication_status":"published","status":"public","_id":"4345","year":"2006","volume":40,"date_updated":"2021-01-12T07:56:17Z","date_created":"2018-12-11T12:08:23Z","author":[{"last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Patrick Danowski"},{"last_name":"Heller","first_name":"Lambert","full_name":"Heller,Lambert"}]},{"_id":"4352","year":"2006","intvolume":" 74","publisher":"American Society of Tropical Medicine and Hygiene","publication_status":"published","status":"public","title":"Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil","author":[{"first_name":"Jan","last_name":"Conn","full_name":"Conn, Jan E"},{"first_name":"Joseph","last_name":"Vineis","full_name":"Vineis, Joseph H"},{"full_name":"Jonathan Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback"},{"full_name":"Onyabe, David Y","first_name":"David","last_name":"Onyabe"},{"full_name":"Wilkerson, Richard C","first_name":"Richard","last_name":"Wilkerson"},{"last_name":"Povoa","first_name":"Marinete","full_name":"Povoa, Marinete M"}],"volume":74,"date_updated":"2021-01-12T07:56:20Z","date_created":"2018-12-11T12:08:25Z","type":"journal_article","publist_id":"1108","issue":"5","abstract":[{"lang":"eng","text":"Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance."}],"extern":1,"main_file_link":[{"url":"http://www.ajtmh.org/content/74/5/798.full","open_access":"0"}],"citation":{"ama":"Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 2006;74(5):798-806.","ista":"Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 2006. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 74(5), 798–806.","ieee":"J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa, “Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil,” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene, pp. 798–806, 2006.","apa":"Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa, M. (2006). Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene.","mla":"Conn, Jan, et al. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5, American Society of Tropical Medicine and Hygiene, 2006, pp. 798–806.","short":"J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806.","chicago":"Conn, Jan, Joseph Vineis, Jonathan P Bollback, David Onyabe, Richard Wilkerson, and Marinete Povoa. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene, 2006."},"publication":"The American Journal of Tropical Medicine and Hygiene","page":"798 - 806","quality_controlled":0,"date_published":"2006-05-01T00:00:00Z","day":"01","month":"05"},{"day":"01","month":"01","doi":"10.1186/1471-2105-7-88","date_published":"2006-01-01T00:00:00Z","citation":{"chicago":"Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics. BioMed Central, 2006. https://doi.org/10.1186/1471-2105-7-88.","short":"J.P. Bollback, BMC Bioinformatics 7 (2006).","mla":"Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.","apa":"Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88","ieee":"J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.","ista":"Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 7.","ama":"Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"BMC Bioinformatics","quality_controlled":0,"publist_id":"1109","abstract":[{"text":"BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"full_name":"Jonathan Bollback","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"volume":7,"date_created":"2018-12-11T12:08:25Z","date_updated":"2021-01-12T07:56:20Z","_id":"4351","year":"2006","intvolume":" 7","publisher":"BioMed Central","status":"public","title":"SIMMAP: stochastic character mapping of discrete traits on phylogenies","publication_status":"published"},{"publist_id":"3499","abstract":[{"text":"One of the most exciting advances in early vision has been the development of efficient energy minimization algorithms. Many early vision tasks require labeling each pixel with some quantity such as depth or texture. While many such problems can be elegantly expressed in the language of Markov Random Fields (MRF's), the resulting energy minimization problems were widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. Unfortunately, most papers define their own energy function, which is minimized with a specific algorithm of their choice. As a result, the tradeoffs among different energy minimization algorithms are not well understood. In this paper we describe a set of energy minimization benchmarks, which we use to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods - graph cuts, LBP, and tree-reweighted message passing - as well as the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching and interactive segmentation. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods with minimal overhead. We expect that the availability of our benchmarks and interface will make it significantly easier for vision researchers to adopt the best method for their specific problems. Benchmarks, code, results and images are available at http://vision.middlebury.edu/MRF.","lang":"eng"}],"extern":1,"type":"conference","author":[{"full_name":"Szeliski, Richard S","last_name":"Szeliski","first_name":"Richard"},{"first_name":"Ramin","last_name":"Zabih","full_name":"Zabih, Ramin"},{"full_name":"Scharstein, Daniel","last_name":"Scharstein","first_name":"Daniel"},{"first_name":"Olga","last_name":"Veksler","full_name":"Veksler, Olga"},{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aseem","last_name":"Agarwala","full_name":"Agarwala, Aseem"},{"full_name":"Tappen, Marshall F","first_name":"Marshall","last_name":"Tappen"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"volume":3952,"date_created":"2018-12-11T12:01:51Z","date_updated":"2021-01-12T07:41:37Z","year":"2006","_id":"3180","publisher":"Springer","intvolume":" 3952","status":"public","title":"A comparative study of energy minimization methods for Markov random fields","publication_status":"published","day":"03","month":"05","date_published":"2006-05-03T00:00:00Z","doi":"10.1007/11744047_2","conference":{"name":"ECCV: European Conference on Computer Vision"},"citation":{"ama":"Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization methods for Markov random fields. In: Vol 3952. Springer; 2006:16-29. doi:10.1007/11744047_2","ieee":"R. Szeliski et al., “A comparative study of energy minimization methods for Markov random fields,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952, pp. 16–29.","apa":"Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala, A., … Rother, C. (2006). A comparative study of energy minimization methods for Markov random fields (Vol. 3952, pp. 16–29). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_2","ista":"Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C. 2006. A comparative study of energy minimization methods for Markov random fields. ECCV: European Conference on Computer Vision vol. 3952, 16–29.","short":"R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala, M. Tappen, C. Rother, in:, Springer, 2006, pp. 16–29.","mla":"Szeliski, Richard, et al. A Comparative Study of Energy Minimization Methods for Markov Random Fields. Vol. 3952, Springer, 2006, pp. 16–29, doi:10.1007/11744047_2.","chicago":"Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative Study of Energy Minimization Methods for Markov Random Fields,” 3952:16–29. Springer, 2006. https://doi.org/10.1007/11744047_2."},"main_file_link":[{"url":"http://research-srv.microsoft.com/pubs/67896/szsvkatr-eccv06.pdf","open_access":"0"}],"page":"16 - 29","quality_controlled":0}]