[{"title":"Immunological self tolerance: Lessons from mathematical modeling","quality_controlled":0,"page":"77 - 100","publisher":"Elsevier","abstract":[{"lang":"eng","text":"One of the fundamental properties of the immune system is its capacity to avoid autoimmune diseases. The mechanism underlying this process, known as self-tolerance, is hitherto unresolved but seems to involve the control of clonal expansion of autoreactive lymphocytes. This article reviews mathematical modeling of self-tolerance, addressing two specific hypotheses. The first hypothesis posits that self-tolerance is mediated by tuning of activation thresholds, which makes autoreactive T lymphocytes reversibly &quot;anergic&quot; and unable to proliferate. The second hypothesis posits that the proliferation of autoreactive T lymphocytes is instead controlled by specific regulatory T lymphocytes. Models representing the population dynamics of autoreactive T lymphocytes according to these two hypotheses were derived. For each model we identified how cell density affects tolerance, and predicted the corresponding phase spaces and bifurcations. We show that the simple induction of proliferative anergy, as modeled here, has a density dependence that is only partially compatible with adoptive transfers of tolerance, and that the models of tolerance mediated by specific regulatory T cells are closer to the observations."}],"citation":{"mla":"Carneiro, Jorge, et al. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” <i>Journal of Computational and Applied Mathematics</i>, vol. 184, no. 1, Elsevier, 2005, pp. 77–100, doi:<a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">10.1016/j.cam.2004.10.025</a>.","apa":"Carneiro, J., Paixao, T., Milutinovic, D., Sousa, J., Leon, K., Gardner, R., &#38; Faro, J. (2005). Immunological self tolerance: Lessons from mathematical modeling. <i>Journal of Computational and Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">https://doi.org/10.1016/j.cam.2004.10.025</a>","short":"J. Carneiro, T. Paixao, D. Milutinovic, J. Sousa, K. Leon, R. Gardner, J. Faro, Journal of Computational and Applied Mathematics 184 (2005) 77–100.","ama":"Carneiro J, Paixao T, Milutinovic D, et al. Immunological self tolerance: Lessons from mathematical modeling. <i>Journal of Computational and Applied Mathematics</i>. 2005;184(1):77-100. doi:<a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">10.1016/j.cam.2004.10.025</a>","chicago":"Carneiro, Jorge, Tiago Paixao, Dejan Milutinovic, João Sousa, Kalet Leon, Rui Gardner, and Jose Faro. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” <i>Journal of Computational and Applied Mathematics</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">https://doi.org/10.1016/j.cam.2004.10.025</a>.","ista":"Carneiro J, Paixao T, Milutinovic D, Sousa J, Leon K, Gardner R, Faro J. 2005. Immunological self tolerance: Lessons from mathematical modeling. Journal of Computational and Applied Mathematics. 184(1), 77–100.","ieee":"J. Carneiro <i>et al.</i>, “Immunological self tolerance: Lessons from mathematical modeling,” <i>Journal of Computational and Applied Mathematics</i>, vol. 184, no. 1. Elsevier, pp. 77–100, 2005."},"acknowledgement":"The work was financially supported by Fundação para a Ciência e Tecnologia: grants  P/BIA/10094/1998,  POCTI/36413/99,  and  POCTI/MGI/46477/2002; and fellowships to JF (Praxis/BCC/18972/98), JS (BD/13546/97), KL (SFRH/BPD+/1157/2002), DM (SFRH/BD/2960/2000) and TP (SFRH/BD/10550/2002).","doi":"10.1016/j.cam.2004.10.025","intvolume":"       184","month":"12","date_updated":"2021-01-12T07:00:32Z","status":"public","publication":"Journal of Computational and Applied Mathematics","publist_id":"3863","date_published":"2005-12-01T00:00:00Z","_id":"2895","volume":184,"publication_status":"published","date_created":"2018-12-11T12:00:12Z","extern":1,"issue":"1","year":"2005","author":[{"full_name":"Carneiro, Jorge","last_name":"Carneiro","first_name":"Jorge"},{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Tiago Paixao"},{"last_name":"Milutinovic","first_name":"Dejan","full_name":"Milutinovic, Dejan"},{"full_name":"Sousa, João","last_name":"Sousa","first_name":"João"},{"first_name":"Kalet","last_name":"Leon","full_name":"Leon, Kalet"},{"last_name":"Gardner","first_name":"Rui","full_name":"Gardner, Rui"},{"first_name":"Jose","last_name":"Faro","full_name":"Faro, Jose"}],"day":"01","type":"journal_article"},{"quality_controlled":"1","title":"Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first?","publisher":"Springer","page":"67 - 73","doi":"10.1007/s00709-005-0104-8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In plants, cell polarity is an issue more recurring than in other systems, because plants, due to their adaptive and flexible development, often change cell polarity postembryonically according to intrinsic cues and demands of the environment. Recent findings on the directional movement of the plant signalling molecule auxin provide a unique connection between individual cell polarity and the establishment of polarity at the tissue, organ, and whole-plant levels. Decisions about the subcellular polar targeting of PIN auxin transport components determine the direction of auxin flow between cells and consequently mediate multiple developmental events. In addition, mutations or chemical interference with PIN-based auxin transport result in abnormal cell divisions. Thus, the complicated links between cell polarity establishment, auxin transport, cytoskeleton, and oriented cell divisions now begin to emerge. Here we review the available literature on the issues of cell polarity in both plants and animals to extend our understanding on the generation, maintenance, and transmission of cell polarity in plants."}],"citation":{"ista":"Dhonukshe P, Kleine Vehn J, Friml J. 2005. Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first? Protoplasma. 226(1–2), 67–73.","ieee":"P. Dhonukshe, J. Kleine Vehn, and J. Friml, “Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first?,” <i>Protoplasma</i>, vol. 226, no. 1–2. Springer, pp. 67–73, 2005.","mla":"Dhonukshe, Pankaj, et al. “Cell Polarity, Auxin Transport and Cytoskeleton Mediated Division Planes: Who Comes First?” <i>Protoplasma</i>, vol. 226, no. 1–2, Springer, 2005, pp. 67–73, doi:<a href=\"https://doi.org/10.1007/s00709-005-0104-8\">10.1007/s00709-005-0104-8</a>.","apa":"Dhonukshe, P., Kleine Vehn, J., &#38; Friml, J. (2005). Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first? <i>Protoplasma</i>. Springer. <a href=\"https://doi.org/10.1007/s00709-005-0104-8\">https://doi.org/10.1007/s00709-005-0104-8</a>","short":"P. Dhonukshe, J. Kleine Vehn, J. Friml, Protoplasma 226 (2005) 67–73.","ama":"Dhonukshe P, Kleine Vehn J, Friml J. Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first? <i>Protoplasma</i>. 2005;226(1-2):67-73. doi:<a href=\"https://doi.org/10.1007/s00709-005-0104-8\">10.1007/s00709-005-0104-8</a>","chicago":"Dhonukshe, Pankaj, Jürgen Kleine Vehn, and Jiří Friml. “Cell Polarity, Auxin Transport and Cytoskeleton Mediated Division Planes: Who Comes First?” <i>Protoplasma</i>. Springer, 2005. <a href=\"https://doi.org/10.1007/s00709-005-0104-8\">https://doi.org/10.1007/s00709-005-0104-8</a>."},"intvolume":"       226","date_updated":"2021-01-12T07:40:22Z","month":"10","status":"public","date_published":"2005-10-01T00:00:00Z","publist_id":"3701","publication":"Protoplasma","_id":"3000","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:47Z","volume":226,"oa_version":"None","extern":"1","issue":"1-2","year":"2005","type":"journal_article","day":"01","author":[{"full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe","first_name":"Pankaj"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}]},{"date_published":"2005-06-30T00:00:00Z","publication":"Nature","publist_id":"3702","_id":"3001","month":"06","date_updated":"2021-01-12T07:40:23Z","status":"public","citation":{"mla":"Paciorek, Tomasz, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” <i>Nature</i>, vol. 435, no. 7046, Nature Publishing Group, 2005, pp. 1251–56, doi:<a href=\"https://doi.org/10.1038/nature03633\">10.1038/nature03633</a>.","apa":"Paciorek, T., Zažímalová, E., Ruthardt, N., Petrášek, J., Stierhof, Y., Kleine Vehn, J., … Friml, J. (2005). Auxin inhibits endocytosis and promotes its own efflux from cells. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature03633\">https://doi.org/10.1038/nature03633</a>","short":"T. Paciorek, E. Zažímalová, N. Ruthardt, J. Petrášek, Y. Stierhof, J. Kleine Vehn, D. Morris, N. Emans, G. Jürgens, N. Geldner, J. Friml, Nature 435 (2005) 1251–1256.","ama":"Paciorek T, Zažímalová E, Ruthardt N, et al. Auxin inhibits endocytosis and promotes its own efflux from cells. <i>Nature</i>. 2005;435(7046):1251-1256. doi:<a href=\"https://doi.org/10.1038/nature03633\">10.1038/nature03633</a>","chicago":"Paciorek, Tomasz, Eva Zažímalová, Nadia Ruthardt, Jan Petrášek, York Stierhof, Jürgen Kleine Vehn, David Morris, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” <i>Nature</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nature03633\">https://doi.org/10.1038/nature03633</a>.","ista":"Paciorek T, Zažímalová E, Ruthardt N, Petrášek J, Stierhof Y, Kleine Vehn J, Morris D, Emans N, Jürgens G, Geldner N, Friml J. 2005. Auxin inhibits endocytosis and promotes its own efflux from cells. Nature. 435(7046), 1251–1256.","ieee":"T. Paciorek <i>et al.</i>, “Auxin inhibits endocytosis and promotes its own efflux from cells,” <i>Nature</i>, vol. 435, no. 7046. Nature Publishing Group, pp. 1251–1256, 2005."},"abstract":[{"text":"One of the mechanisms by which signalling molecules regulate cellular behaviour is modulating subcellular protein translocation. This mode of regulation is often based on specialized vesicle trafficking, termed constitutive cycling, which consists of repeated internalization and recycling of proteins to and from the plasma membrane. No such mechanism of hormone action has been shown in plants although several proteins, including the PIN auxin efflux facilitators, exhibit constitutive cycling. Here we show that a major regulator of plant development, auxin, inhibits endocytosis. This effect is specific to biologically active auxins and requires activity of the Calossin-like protein BIG. By inhibiting the internalization step of PIN constitutive cycling, auxin increases levels of PINs at the plasma membrane. Concomitantly, auxin promotes its own efflux from cells by a vesicle-trafficking-dependent mechanism. Furthermore, asymmetric auxin translocation during gravitropism is correlated with decreased PIN internalization. Our data imply a previously undescribed mode of plant hormone action: by modulating PIN protein trafficking, auxin regulates PIN abundance and activity at the cell surface, providing a mechanism for the feedback regulation of auxin transport.","lang":"eng"}],"doi":"10.1038/nature03633","intvolume":"       435","title":"Auxin inhibits endocytosis and promotes its own efflux from cells","quality_controlled":0,"page":"1251 - 1256","publisher":"Nature Publishing Group","issue":"7046","year":"2005","author":[{"first_name":"Tomasz","last_name":"Paciorek","full_name":"Paciorek, Tomasz"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"first_name":"Nadia","last_name":"Ruthardt","full_name":"Ruthardt, Nadia"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Stierhof, York-Dieter","last_name":"Stierhof","first_name":"York"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Morris","first_name":"David","full_name":"Morris, David A"},{"last_name":"Emans","first_name":"Neil","full_name":"Emans, Neil"},{"full_name":"Jürgens, Gerd","last_name":"Jürgens","first_name":"Gerd"},{"last_name":"Geldner","first_name":"Niko","full_name":"Geldner, Niko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"}],"type":"journal_article","day":"30","extern":1,"volume":435,"publication_status":"published","date_created":"2018-12-11T12:00:47Z"},{"quality_controlled":0,"title":"Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression","publisher":"Company of Biologists","page":"4521 - 4531","doi":"10.1242/dev.02027","abstract":[{"lang":"eng","text":"Plant development displays an exceptional plasticity and adaptability that involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar auxin flow, which requires polarly localized transport facilitators of the PIN family, largely contributes to the establishment and maintenance of the auxin gradients. Functionally overlapping action of PIN proteins mediates multiple developmental processes, including embryo formation, organ development and tropisms. Here we show that PIN proteins exhibit synergistic interactions, which involve cross-regulation of PIN gene expression in pin mutants or plants with inhibited auxin transport. Auxin itself positively feeds back on PIN gene expression in a tissue-specific manner through an AUX/IAA-dependent signalling pathway. This regulatory switch is indicative of a mechanism by which the loss of a specific PIN protein is compensated for by auxin-dependent ectopic: expression of its homologues. The compensatory properties of the PIN-dependent transport network might enable the stabilization of auxin gradients and potentially contribute to the robustness of plant adaptive development."}],"citation":{"ieee":"A. Vieten <i>et al.</i>, “Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression,” <i>Development</i>, vol. 132, no. 20. Company of Biologists, pp. 4521–4531, 2005.","ista":"Vieten A, Vanneste S, Wiśniewska J, Benková E, Benjamins R, Beeckman T, Luschnig C, Friml J. 2005. Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. Development. 132(20), 4521–4531.","short":"A. Vieten, S. Vanneste, J. Wiśniewska, E. Benková, R. Benjamins, T. Beeckman, C. Luschnig, J. Friml, Development 132 (2005) 4521–4531.","ama":"Vieten A, Vanneste S, Wiśniewska J, et al. Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. <i>Development</i>. 2005;132(20):4521-4531. doi:<a href=\"https://doi.org/10.1242/dev.02027\">10.1242/dev.02027</a>","chicago":"Vieten, Anne, Steffen Vanneste, Justyna Wiśniewska, Eva Benková, René Benjamins, Tom Beeckman, Christian Luschnig, and Jiří Friml. “Functional Redundancy of PIN Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.” <i>Development</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/dev.02027\">https://doi.org/10.1242/dev.02027</a>.","mla":"Vieten, Anne, et al. “Functional Redundancy of PIN Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.” <i>Development</i>, vol. 132, no. 20, Company of Biologists, 2005, pp. 4521–31, doi:<a href=\"https://doi.org/10.1242/dev.02027\">10.1242/dev.02027</a>.","apa":"Vieten, A., Vanneste, S., Wiśniewska, J., Benková, E., Benjamins, R., Beeckman, T., … Friml, J. (2005). Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.02027\">https://doi.org/10.1242/dev.02027</a>"},"intvolume":"       132","date_updated":"2021-01-12T07:40:23Z","month":"10","status":"public","publication":"Development","publist_id":"3700","date_published":"2005-10-01T00:00:00Z","_id":"3003","date_created":"2018-12-11T12:00:48Z","publication_status":"published","volume":132,"extern":1,"year":"2005","issue":"20","day":"01","type":"journal_article","author":[{"last_name":"Vieten","first_name":"Anne","full_name":"Vieten, Anne"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Justyna","last_name":"Wiśniewska","full_name":"Wiśniewska, Justyna"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"first_name":"René","last_name":"Benjamins","full_name":"Benjamins, René"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"}]},{"year":"2005","issue":"9","type":"journal_article","day":"01","author":[{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"first_name":"Olivier","last_name":"Meurette","full_name":"Meurette, Olivier"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Ljung, Karin","first_name":"Karin","last_name":"Ljung"},{"first_name":"Göran","last_name":"Sandberg","full_name":"Sandberg, Göran"},{"full_name":"Hooykaas, Paul","last_name":"Hooykaas","first_name":"Paul"},{"first_name":"Remko","last_name":"Offringa","full_name":"Offringa, Remko"}],"publication_status":"published","date_created":"2018-12-11T12:00:48Z","volume":17,"extern":1,"date_updated":"2021-01-12T07:40:24Z","month":"07","status":"public","publist_id":"3698","publication":"Plant Cell","date_published":"2005-07-01T00:00:00Z","_id":"3004","quality_controlled":0,"title":"Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis","publisher":"American Society of Plant Biologists","page":"2517 - 2526","doi":"10.1105/tpc.105.034637","abstract":[{"lang":"eng","text":"Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients."}],"citation":{"ista":"Weijers D, Sauer M, Meurette O, Friml J, Ljung K, Sandberg G, Hooykaas P, Offringa R. 2005. Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell. 17(9), 2517–2526.","ieee":"D. Weijers <i>et al.</i>, “Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis,” <i>Plant Cell</i>, vol. 17, no. 9. American Society of Plant Biologists, pp. 2517–2526, 2005.","apa":"Weijers, D., Sauer, M., Meurette, O., Friml, J., Ljung, K., Sandberg, G., … Offringa, R. (2005). Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.105.034637\">https://doi.org/10.1105/tpc.105.034637</a>","mla":"Weijers, Dolf, et al. “Maintenance of Embryonic Auxin Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” <i>Plant Cell</i>, vol. 17, no. 9, American Society of Plant Biologists, 2005, pp. 2517–26, doi:<a href=\"https://doi.org/10.1105/tpc.105.034637\">10.1105/tpc.105.034637</a>.","chicago":"Weijers, Dolf, Michael Sauer, Olivier Meurette, Jiří Friml, Karin Ljung, Göran Sandberg, Paul Hooykaas, and Remko Offringa. “Maintenance of Embryonic Auxin Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2005. <a href=\"https://doi.org/10.1105/tpc.105.034637\">https://doi.org/10.1105/tpc.105.034637</a>.","ama":"Weijers D, Sauer M, Meurette O, et al. Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. <i>Plant Cell</i>. 2005;17(9):2517-2526. doi:<a href=\"https://doi.org/10.1105/tpc.105.034637\">10.1105/tpc.105.034637</a>","short":"D. Weijers, M. Sauer, O. Meurette, J. Friml, K. Ljung, G. Sandberg, P. Hooykaas, R. Offringa, Plant Cell 17 (2005) 2517–2526."},"intvolume":"        17"},{"publisher":"Nature Publishing Group","page":"26 - 31","quality_controlled":0,"title":"Conformational changes in the Arp2 3 complex leading to actin nucleation","intvolume":"        12","doi":"10.1038/nsmb870","citation":{"chicago":"Rodal, Avital, Olga Sokolova, Deborah Robins, Karen Daugherty, Simon Hippenmeyer, Howard Riezman, Nikolaus Grigorieff, and Bruce Goode. “Conformational Changes in the Arp2 3 Complex Leading to Actin Nucleation.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nsmb870\">https://doi.org/10.1038/nsmb870</a>.","short":"A. Rodal, O. Sokolova, D. Robins, K. Daugherty, S. Hippenmeyer, H. Riezman, N. Grigorieff, B. Goode, Nature Structural and Molecular Biology 12 (2005) 26–31.","ama":"Rodal A, Sokolova O, Robins D, et al. Conformational changes in the Arp2 3 complex leading to actin nucleation. <i>Nature Structural and Molecular Biology</i>. 2005;12(1):26-31. doi:<a href=\"https://doi.org/10.1038/nsmb870\">10.1038/nsmb870</a>","apa":"Rodal, A., Sokolova, O., Robins, D., Daugherty, K., Hippenmeyer, S., Riezman, H., … Goode, B. (2005). Conformational changes in the Arp2 3 complex leading to actin nucleation. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb870\">https://doi.org/10.1038/nsmb870</a>","mla":"Rodal, Avital, et al. “Conformational Changes in the Arp2 3 Complex Leading to Actin Nucleation.” <i>Nature Structural and Molecular Biology</i>, vol. 12, no. 1, Nature Publishing Group, 2005, pp. 26–31, doi:<a href=\"https://doi.org/10.1038/nsmb870\">10.1038/nsmb870</a>.","ieee":"A. Rodal <i>et al.</i>, “Conformational changes in the Arp2 3 complex leading to actin nucleation,” <i>Nature Structural and Molecular Biology</i>, vol. 12, no. 1. Nature Publishing Group, pp. 26–31, 2005.","ista":"Rodal A, Sokolova O, Robins D, Daugherty K, Hippenmeyer S, Riezman H, Grigorieff N, Goode B. 2005. Conformational changes in the Arp2 3 complex leading to actin nucleation. Nature Structural and Molecular Biology. 12(1), 26–31."},"abstract":[{"text":"The two actin-related subunits of the Arp2/3 complex, Arp2 and Arp3, are proposed to form a pseudo actin dimer that nucleates actin polymerization. However, in the crystal structure of the inactive complex, they are too far apart to form such a nucleus. Here, we show using EM that yeast and bovine Arp2/3 complexes exist in a distribution among open, intermediate and closed conformations. The crystal structure docks well into the open conformation. The activator WASp binds at the cleft between Arp2 and Arp3, and all WASp-bound complexes are closed. The inhibitor coronin binds near the p35 subunit, and all coronin-bound complexes are open. Activating and loss-of-function mutations in the p35 subunit skew conformational distribution in opposite directions, closed and open, respectively. We conclude that WASp stabilizes p35-dependent closure of the complex, holding Arp2 and Arp3 closer together to nucleate an actin filament.","lang":"eng"}],"status":"public","date_updated":"2021-01-12T07:41:21Z","month":"01","_id":"3141","publication":"Nature Structural and Molecular Biology","date_published":"2005-01-01T00:00:00Z","publist_id":"3554","date_created":"2018-12-11T12:01:38Z","publication_status":"published","volume":12,"extern":1,"day":"01","type":"journal_article","author":[{"last_name":"Rodal","first_name":"Avital","full_name":"Rodal, Avital A"},{"last_name":"Sokolova","first_name":"Olga","full_name":"Sokolova, Olga"},{"full_name":"Robins, Deborah B","last_name":"Robins","first_name":"Deborah"},{"full_name":"Daugherty, Karen M","first_name":"Karen","last_name":"Daugherty"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Simon Hippenmeyer"},{"first_name":"Howard","last_name":"Riezman","full_name":"Riezman, Howard"},{"full_name":"Grigorieff, Nikolaus","first_name":"Nikolaus","last_name":"Grigorieff"},{"first_name":"Bruce","last_name":"Goode","full_name":"Goode, Bruce L"}],"issue":"1","year":"2005"},{"author":[{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Simon Hippenmeyer"},{"full_name":"Vrieseling, Eline","first_name":"Eline","last_name":"Vrieseling"},{"first_name":"Markus","last_name":"Sigrist","full_name":"Sigrist, Markus"},{"last_name":"Portmann","first_name":"Thomas","full_name":"Portmann, Thomas"},{"last_name":"Laengle","first_name":"Celia","full_name":"Laengle, Celia"},{"first_name":"David","last_name":"Ladle","full_name":"Ladle, David R"},{"full_name":"Arber, Silvia","first_name":"Silvia","last_name":"Arber"}],"day":"01","type":"journal_article","issue":"5","year":"2005","extern":1,"license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":3,"date_created":"2018-12-11T12:01:38Z","publication_status":"published","_id":"3143","date_published":"2005-05-01T00:00:00Z","publication":"PLoS Biology","publist_id":"3552","status":"public","month":"05","date_updated":"2021-01-12T07:41:21Z","intvolume":"         3","citation":{"chicago":"Hippenmeyer, Simon, Eline Vrieseling, Markus Sigrist, Thomas Portmann, Celia Laengle, David Ladle, and Silvia Arber. “A Developmental Switch in the Response of DRG Neurons to ETS Transcription Factor Signaling.” <i>PLoS Biology</i>. Public Library of Science, 2005. <a href=\"https://doi.org/10.1371/journal.pbio.0030159\">https://doi.org/10.1371/journal.pbio.0030159</a>.","short":"S. Hippenmeyer, E. Vrieseling, M. Sigrist, T. Portmann, C. Laengle, D. Ladle, S. Arber, PLoS Biology 3 (2005) 0878–0890.","ama":"Hippenmeyer S, Vrieseling E, Sigrist M, et al. A developmental switch in the response of DRG neurons to ETS transcription factor signaling. <i>PLoS Biology</i>. 2005;3(5):0878-0890. doi:<a href=\"https://doi.org/10.1371/journal.pbio.0030159\">10.1371/journal.pbio.0030159</a>","apa":"Hippenmeyer, S., Vrieseling, E., Sigrist, M., Portmann, T., Laengle, C., Ladle, D., &#38; Arber, S. (2005). A developmental switch in the response of DRG neurons to ETS transcription factor signaling. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.0030159\">https://doi.org/10.1371/journal.pbio.0030159</a>","mla":"Hippenmeyer, Simon, et al. “A Developmental Switch in the Response of DRG Neurons to ETS Transcription Factor Signaling.” <i>PLoS Biology</i>, vol. 3, no. 5, Public Library of Science, 2005, pp. 0878–90, doi:<a href=\"https://doi.org/10.1371/journal.pbio.0030159\">10.1371/journal.pbio.0030159</a>.","ieee":"S. Hippenmeyer <i>et al.</i>, “A developmental switch in the response of DRG neurons to ETS transcription factor signaling,” <i>PLoS Biology</i>, vol. 3, no. 5. Public Library of Science, pp. 0878–0890, 2005.","ista":"Hippenmeyer S, Vrieseling E, Sigrist M, Portmann T, Laengle C, Ladle D, Arber S. 2005. A developmental switch in the response of DRG neurons to ETS transcription factor signaling. PLoS Biology. 3(5), 0878–0890."},"abstract":[{"text":"Two ETS transcription factors of the Pea3 subfamily are induced in subpopulations of dorsal root ganglion (DRG) sensory and spinal motor neurons by target-derived factors. Their expression controls late aspects of neuronal differentiation such as target invasion and branching. Here, we show that the late onset of ETS gene expression is an essential requirement for normal sensory neuron differentiation. We provide genetic evidence in the mouse that precocious ETS expression in DRG sensory neurons perturbs axonal projections, the acquisition of terminal differentiation markers, and their dependence on neurotrophic support. Together, our findings indicate that DRG sensory neurons exhibit a temporal developmental switch that can be revealed by distinct responses to ETS transcription factor signaling at sequential steps of neuronal maturation.","lang":"eng"}],"doi":"10.1371/journal.pbio.0030159","page":"0878 - 0890","publisher":"Public Library of Science","title":"A developmental switch in the response of DRG neurons to ETS transcription factor signaling","quality_controlled":0},{"conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"day":"25","type":"conference","author":[{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"first_name":"Sanjiv","last_name":"Kumar","full_name":"Kumar, Sanjiv"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Vladimir Kolmogorov"},{"full_name":"Blake, Andrew","first_name":"Andrew","last_name":"Blake"}],"year":"2005","extern":1,"publication_status":"published","date_created":"2018-12-11T12:01:50Z","volume":1,"_id":"3175","publist_id":"3503","date_published":"2005-07-25T00:00:00Z","status":"public","date_updated":"2021-01-12T07:41:35Z","month":"07","intvolume":"         1","doi":"10.1109/CVPR.2005.130","citation":{"ista":"Rother C, Kumar S, Kolmogorov V, Blake A. 2005. Digital tapestry. CVPR: Computer Vision and Pattern Recognition vol. 1, 589–596.","ieee":"C. Rother, S. Kumar, V. Kolmogorov, and A. Blake, “Digital tapestry,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 1, pp. 589–596.","mla":"Rother, Carsten, et al. <i>Digital Tapestry</i>. Vol. 1, IEEE, 2005, pp. 589–96, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.130\">10.1109/CVPR.2005.130</a>.","apa":"Rother, C., Kumar, S., Kolmogorov, V., &#38; Blake, A. (2005). Digital tapestry (Vol. 1, pp. 589–596). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.130\">https://doi.org/10.1109/CVPR.2005.130</a>","short":"C. Rother, S. Kumar, V. Kolmogorov, A. Blake, in:, IEEE, 2005, pp. 589–596.","ama":"Rother C, Kumar S, Kolmogorov V, Blake A. Digital tapestry. In: Vol 1. IEEE; 2005:589-596. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.130\">10.1109/CVPR.2005.130</a>","chicago":"Rother, Carsten, Sanjiv Kumar, Vladimir Kolmogorov, and Andrew Blake. “Digital Tapestry,” 1:589–96. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.130\">https://doi.org/10.1109/CVPR.2005.130</a>."},"abstract":[{"lang":"eng","text":"This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov Random Field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with &quot;almost&quot; metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented."}],"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/rother_cvpr05.pdf"}],"publisher":"IEEE","page":"589 - 596","quality_controlled":0,"title":"Digital tapestry"},{"publication_status":"published","date_created":"2018-12-11T12:01:50Z","extern":1,"year":"2005","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"last_name":"Criminisi","first_name":"Antonio","full_name":"Criminisi, Antonio"},{"first_name":"Andrew","last_name":"Blake","full_name":"Blake, Andrew"},{"full_name":"Cross, Geoffrey","last_name":"Cross","first_name":"Geoffrey"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"day":"01","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"title":"Bi-layer segmentation of binocular stereo video","quality_controlled":0,"page":"1186 - 1186","publisher":"IEEE","citation":{"ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: IEEE; 2005:1186-1186. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.90\">10.1109/CVPR.2005.90</a>","short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 1186–1186.","chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 1186–1186. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.90\">https://doi.org/10.1109/CVPR.2005.90</a>.","mla":"Kolmogorov, Vladimir, et al. <i>Bi-Layer Segmentation of Binocular Stereo Video</i>. IEEE, 2005, pp. 1186–1186, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.90\">10.1109/CVPR.2005.90</a>.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005). Bi-layer segmentation of binocular stereo video (pp. 1186–1186). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.90\">https://doi.org/10.1109/CVPR.2005.90</a>","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, pp. 1186–1186.","ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition, 1186–1186."},"abstract":[{"text":"This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.\n","lang":"eng"}],"doi":"10.1109/CVPR.2005.90","month":"01","date_updated":"2021-01-12T07:41:35Z","status":"public","publist_id":"3504","date_published":"2005-01-01T00:00:00Z","_id":"3176"},{"abstract":[{"lang":"eng","text":"Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method."}],"citation":{"ieee":"V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 316–323.","ista":"Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323.","short":"V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323.","ama":"Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product message passing. In: AUAI Press; 2005:316-323.","chicago":"Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005.","mla":"Kolmogorov, Vladimir, and Martin Wainwright. <i>On the Optimality of Tree Reweighted Max Product Message Passing</i>. AUAI Press, 2005, pp. 316–23.","apa":"Kolmogorov, V., &#38; Wainwright, M. (2005). On the optimality of tree reweighted max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press."},"quality_controlled":0,"title":"On the optimality of tree reweighted max product message passing","main_file_link":[{"url":"http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf","open_access":"0"}],"publisher":"AUAI Press","page":"316 - 323","date_published":"2005-07-01T00:00:00Z","publist_id":"3500","_id":"3181","date_updated":"2021-01-12T07:41:38Z","month":"07","status":"public","extern":1,"date_created":"2018-12-11T12:01:51Z","publication_status":"published","year":"2005","day":"01","type":"conference","conference":{"name":"UAI: Uncertainty in Artificial Intelligence"},"author":[{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wainwright, Martin J","last_name":"Wainwright","first_name":"Martin"}]},{"extern":1,"volume":1,"publication_status":"published","date_created":"2018-12-11T12:01:52Z","year":"2005","author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuri","last_name":"Boykov","full_name":"Boykov, Yuri"}],"type":"conference","day":"05","conference":{"name":"ICCV: International Conference on Computer Vision"},"abstract":[{"text":"In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such &quot;submodular&quot; metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the &quot;shrinking&quot; problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints.","lang":"eng"}],"citation":{"ieee":"V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts or global optimization of length area and flux,” presented at the ICCV: International Conference on Computer Vision, 2005, vol. 1, pp. 564–571.","ista":"Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts or global optimization of length area and flux. ICCV: International Conference on Computer Vision vol. 1, 564–571.","chicago":"Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005. <a href=\"https://doi.org/10.1109/ICCV.2005.252\">https://doi.org/10.1109/ICCV.2005.252</a>.","ama":"Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:<a href=\"https://doi.org/10.1109/ICCV.2005.252\">10.1109/ICCV.2005.252</a>","short":"V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571.","apa":"Kolmogorov, V., &#38; Boykov, Y. (2005). What metrics can be approximated by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2005.252\">https://doi.org/10.1109/ICCV.2005.252</a>","mla":"Kolmogorov, Vladimir, and Yuri Boykov. <i>What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux</i>. Vol. 1, IEEE, 2005, pp. 564–71, doi:<a href=\"https://doi.org/10.1109/ICCV.2005.252\">10.1109/ICCV.2005.252</a>."},"doi":"10.1109/ICCV.2005.252","intvolume":"         1","title":"What metrics can be approximated by geo cuts or global optimization of length area and flux","quality_controlled":0,"page":"564 - 571","publisher":"IEEE","publist_id":"3501","date_published":"2005-12-05T00:00:00Z","_id":"3182","month":"12","date_updated":"2021-01-12T07:41:38Z","status":"public"},{"_id":"3183","publist_id":"3502","date_published":"2005-07-25T00:00:00Z","status":"public","month":"07","date_updated":"2021-01-12T07:41:38Z","intvolume":"         2","citation":{"ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol. 2, 407–414.","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 2, pp. 407–414.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005). Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.91\">https://doi.org/10.1109/CVPR.2005.91</a>","mla":"Kolmogorov, Vladimir, et al. <i>Bi-Layer Segmentation of Binocular Stereo Video</i>. Vol. 2, IEEE, 2005, pp. 407–14, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.91\">10.1109/CVPR.2005.91</a>.","chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.91\">https://doi.org/10.1109/CVPR.2005.91</a>.","ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.91\">10.1109/CVPR.2005.91</a>","short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 407–414."},"abstract":[{"lang":"eng","text":"This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar perfomance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output."}],"doi":"10.1109/CVPR.2005.91","page":"407 - 414","publisher":"IEEE","main_file_link":[{"url":"http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf","open_access":"0"}],"title":"Bi-layer segmentation of binocular stereo video","quality_controlled":0,"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"},{"last_name":"Criminisi","first_name":"Antonio","full_name":"Criminisi, Antonio"},{"full_name":"Blake, Andrew","last_name":"Blake","first_name":"Andrew"},{"first_name":"Geoffrey","last_name":"Cross","full_name":"Cross, Geoffrey"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"}],"day":"25","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"year":"2005","extern":1,"volume":2,"date_created":"2018-12-11T12:01:52Z","publication_status":"published"},{"status":"public","date_updated":"2021-01-12T07:41:50Z","month":"09","_id":"3211","date_published":"2005-09-12T00:00:00Z","publist_id":"3469","publisher":"Springer","page":"527 - 545","quality_controlled":0,"title":"Improved security analyses for CBC MACs","intvolume":"      3621","acknowledgement":"Pietrzak was supported by the Swiss National Science Foundation, project No. 200020-103847/1.","doi":"10.1007/11535218_32","abstract":[{"lang":"eng","text":"We present an improved bound on the advantage of any q-query adversary at distinguishing between the CBC MAC over a random n-bit permutation and a random function outputting n bits. The result assumes that no message queried is a prefix of any other, as is the case when all messages to be MACed have the same length. We go on to give an improved analysis of the encrypted CBC MAC, where there is no restriction on queried messages. Letting m be the block length of the longest query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate into improved guarantees on the probability of forging these MACs."}],"alternative_title":["LNCS"],"citation":{"ieee":"M. Bellare, K. Z. Pietrzak, and P. Rogaway, “Improved security analyses for CBC MACs,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 527–545.","ista":"Bellare M, Pietrzak KZ, Rogaway P. 2005. Improved security analyses for CBC MACs. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 527–545.","chicago":"Bellare, Mihir, Krzysztof Z Pietrzak, and Phillip Rogaway. “Improved Security Analyses for CBC MACs,” 3621:527–45. Springer, 2005. <a href=\"https://doi.org/10.1007/11535218_32\">https://doi.org/10.1007/11535218_32</a>.","short":"M. Bellare, K.Z. Pietrzak, P. Rogaway, in:, Springer, 2005, pp. 527–545.","ama":"Bellare M, Pietrzak KZ, Rogaway P. Improved security analyses for CBC MACs. In: Vol 3621. Springer; 2005:527-545. doi:<a href=\"https://doi.org/10.1007/11535218_32\">10.1007/11535218_32</a>","apa":"Bellare, M., Pietrzak, K. Z., &#38; Rogaway, P. (2005). Improved security analyses for CBC MACs (Vol. 3621, pp. 527–545). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/11535218_32\">https://doi.org/10.1007/11535218_32</a>","mla":"Bellare, Mihir, et al. <i>Improved Security Analyses for CBC MACs</i>. Vol. 3621, Springer, 2005, pp. 527–45, doi:<a href=\"https://doi.org/10.1007/11535218_32\">10.1007/11535218_32</a>."},"type":"conference","conference":{"name":"CRYPTO: International Cryptology Conference"},"day":"12","author":[{"full_name":"Bellare, Mihir","last_name":"Bellare","first_name":"Mihir"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak"},{"first_name":"Phillip","last_name":"Rogaway","full_name":"Rogaway, Phillip"}],"year":"2005","date_created":"2018-12-11T12:02:02Z","publication_status":"published","volume":3621,"extern":1},{"_id":"3212","date_published":"2005-09-12T00:00:00Z","publist_id":"3470","status":"public","date_updated":"2021-01-12T07:41:50Z","month":"09","intvolume":"      3621","acknowledgement":"Supported by NSF CAREER Award CCR-0133806 and TC Grant No.CCR-0311095. Supported by the Swiss National Science Foundation, project No. 200020-103847/1","doi":"10.1007/11535218_27","citation":{"ieee":"Y. Dodis, R. Oliveira, and K. Z. Pietrzak, “On the generic insecurity of the full domain hash,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 449–466.","ista":"Dodis Y, Oliveira R, Pietrzak KZ. 2005. On the generic insecurity of the full domain hash. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 449–466.","chicago":"Dodis, Yevgeniy, Roberto Oliveira, and Krzysztof Z Pietrzak. “On the Generic Insecurity of the Full Domain Hash,” 3621:449–66. Springer, 2005. <a href=\"https://doi.org/10.1007/11535218_27\">https://doi.org/10.1007/11535218_27</a>.","ama":"Dodis Y, Oliveira R, Pietrzak KZ. On the generic insecurity of the full domain hash. In: Vol 3621. Springer; 2005:449-466. doi:<a href=\"https://doi.org/10.1007/11535218_27\">10.1007/11535218_27</a>","short":"Y. Dodis, R. Oliveira, K.Z. Pietrzak, in:, Springer, 2005, pp. 449–466.","apa":"Dodis, Y., Oliveira, R., &#38; Pietrzak, K. Z. (2005). On the generic insecurity of the full domain hash (Vol. 3621, pp. 449–466). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/11535218_27\">https://doi.org/10.1007/11535218_27</a>","mla":"Dodis, Yevgeniy, et al. <i>On the Generic Insecurity of the Full Domain Hash</i>. Vol. 3621, Springer, 2005, pp. 449–66, doi:<a href=\"https://doi.org/10.1007/11535218_27\">10.1007/11535218_27</a>."},"alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use.\nIn this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model."}],"publisher":"Springer","page":"449 - 466","quality_controlled":0,"title":"On the generic insecurity of the full domain hash","type":"conference","day":"12","conference":{"name":"CRYPTO: International Cryptology Conference"},"author":[{"full_name":"Dodis, Yevgeniy","first_name":"Yevgeniy","last_name":"Dodis"},{"full_name":"Oliveira, Roberto","first_name":"Roberto","last_name":"Oliveira"},{"full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"}],"year":"2005","extern":1,"date_created":"2018-12-11T12:02:03Z","publication_status":"published","volume":3621},{"_id":"3213","publist_id":"3468","date_published":"2005-09-12T00:00:00Z","status":"public","month":"09","date_updated":"2021-01-12T07:41:50Z","intvolume":"      3621","citation":{"apa":"Pietrzak, K. Z. (2005). Composition does not imply adaptive security (Vol. 3621, pp. 55–65). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/11535218_4\">https://doi.org/10.1007/11535218_4</a>","mla":"Pietrzak, Krzysztof Z. <i>Composition Does Not Imply Adaptive Security</i>. Vol. 3621, Springer, 2005, pp. 55–65, doi:<a href=\"https://doi.org/10.1007/11535218_4\">10.1007/11535218_4</a>.","chicago":"Pietrzak, Krzysztof Z. “Composition Does Not Imply Adaptive Security,” 3621:55–65. Springer, 2005. <a href=\"https://doi.org/10.1007/11535218_4\">https://doi.org/10.1007/11535218_4</a>.","ama":"Pietrzak KZ. Composition does not imply adaptive security. In: Vol 3621. Springer; 2005:55-65. doi:<a href=\"https://doi.org/10.1007/11535218_4\">10.1007/11535218_4</a>","short":"K.Z. Pietrzak, in:, Springer, 2005, pp. 55–65.","ista":"Pietrzak KZ. 2005. Composition does not imply adaptive security. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 55–65.","ieee":"K. Z. Pietrzak, “Composition does not imply adaptive security,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 55–65."},"abstract":[{"text":"We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case.\nIn this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.","lang":"eng"}],"alternative_title":["LNCS"],"doi":"10.1007/11535218_4","acknowledgement":"Supported by the Swiss National Science Foundation, project No. 200020-103847/1.","page":"55 - 65","publisher":"Springer","title":"Composition does not imply adaptive security","quality_controlled":0,"author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak"}],"day":"12","type":"conference","conference":{"name":"CRYPTO: International Cryptology Conference"},"year":"2005","extern":1,"volume":3621,"publication_status":"published","date_created":"2018-12-11T12:02:03Z"},{"doi":"10.1146/annurev.cellbio.21.090704.151152","language":[{"iso":"eng"}],"intvolume":"        21","quality_controlled":"1","title":"Pushing the envelope: Structure, function, and dynamics of the nuclear periphery","page":"347-380","external_id":{"pmid":["16212499"]},"publication":"Annual Review of Cell and Developmental Biology","publication_identifier":{"eissn":["1530-8995"],"issn":["1081-0706"]},"status":"public","extern":"1","article_type":"original","keyword":["Cell Biology","Developmental Biology"],"volume":21,"oa_version":"None","article_processing_charge":"No","day":"10","type":"journal_article","citation":{"ieee":"M. Hetzer, T. C. Walther, and I. W. Mattaj, “Pushing the envelope: Structure, function, and dynamics of the nuclear periphery,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 21. Annual Reviews, pp. 347–380, 2005.","ista":"Hetzer M, Walther TC, Mattaj IW. 2005. Pushing the envelope: Structure, function, and dynamics of the nuclear periphery. Annual Review of Cell and Developmental Biology. 21, 347–380.","ama":"Hetzer M, Walther TC, Mattaj IW. Pushing the envelope: Structure, function, and dynamics of the nuclear periphery. <i>Annual Review of Cell and Developmental Biology</i>. 2005;21:347-380. doi:<a href=\"https://doi.org/10.1146/annurev.cellbio.21.090704.151152\">10.1146/annurev.cellbio.21.090704.151152</a>","short":"M. Hetzer, T.C. Walther, I.W. Mattaj, Annual Review of Cell and Developmental Biology 21 (2005) 347–380.","chicago":"Hetzer, Martin, Tobias C. Walther, and Iain W. Mattaj. “Pushing the Envelope: Structure, Function, and Dynamics of the Nuclear Periphery.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2005. <a href=\"https://doi.org/10.1146/annurev.cellbio.21.090704.151152\">https://doi.org/10.1146/annurev.cellbio.21.090704.151152</a>.","mla":"Hetzer, Martin, et al. “Pushing the Envelope: Structure, Function, and Dynamics of the Nuclear Periphery.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 21, Annual Reviews, 2005, pp. 347–80, doi:<a href=\"https://doi.org/10.1146/annurev.cellbio.21.090704.151152\">10.1146/annurev.cellbio.21.090704.151152</a>.","apa":"Hetzer, M., Walther, T. C., &#38; Mattaj, I. W. (2005). Pushing the envelope: Structure, function, and dynamics of the nuclear periphery. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.cellbio.21.090704.151152\">https://doi.org/10.1146/annurev.cellbio.21.090704.151152</a>"},"abstract":[{"lang":"eng","text":"The nuclear envelope (NE) is a highly specialized membrane that delineates the eukaryotic cell nucleus. It is composed of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) and, in metazoa, the lamina. The NE not only regulates the trafficking of macromolecules between nucleoplasm and cytosol but also provides anchoring sites for chromatin and the cytoskeleton. Through these interactions, the NE helps position the nucleus within the cell and chromosomes within the nucleus, thereby regulating the expression of certain genes. The NE is not static, rather it is continuously remodeled during cell division. The most dramatic example of NE reorganization occurs during mitosis in metazoa when the NE undergoes a complete cycle of disassembly and reformation. Despite the importance of the NE for eukaryotic cell life, relatively little is known about its biogenesis or many of its functions. We thus are far from understanding the molecular etiology of a diverse group of NE-associated diseases."}],"publisher":"Annual Reviews","date_published":"2005-11-10T00:00:00Z","_id":"11120","scopus_import":"1","date_updated":"2022-07-18T08:57:34Z","month":"11","publication_status":"published","date_created":"2022-04-07T07:56:52Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","year":"2005","author":[{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W"},{"full_name":"Walther, Tobias C.","last_name":"Walther","first_name":"Tobias C."},{"first_name":"Iain W.","last_name":"Mattaj","full_name":"Mattaj, Iain W."}],"pmid":1},{"month":"09","date_updated":"2023-02-09T11:54:40Z","scopus_import":"1","status":"public","publication_identifier":{"isbn":["9781595931689"]},"publication":"Proceedings of the 16th ACM conference on Hypertext and hypermedia","date_published":"2005-09-06T00:00:00Z","_id":"11698","title":"Hyperlink analysis on the world wide web","quality_controlled":"1","page":"1-3","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"abstract":[{"text":"We give a short survey of the use of hyperlink analysis in web search engine ranking and sketch other applications of hyperlink analysis in the web space.","lang":"eng"}],"citation":{"short":"M.H. Henzinger, in:, Proceedings of the 16th ACM Conference on Hypertext and Hypermedia, Association for Computing Machinery, 2005, pp. 1–3.","ama":"Henzinger MH. Hyperlink analysis on the world wide web. In: <i>Proceedings of the 16th ACM Conference on Hypertext and Hypermedia</i>. Association for Computing Machinery; 2005:1-3. doi:<a href=\"https://doi.org/10.1145/1083356.1083357\">10.1145/1083356.1083357</a>","chicago":"Henzinger, Monika H. “Hyperlink Analysis on the World Wide Web.” In <i>Proceedings of the 16th ACM Conference on Hypertext and Hypermedia</i>, 1–3. Association for Computing Machinery, 2005. <a href=\"https://doi.org/10.1145/1083356.1083357\">https://doi.org/10.1145/1083356.1083357</a>.","mla":"Henzinger, Monika H. “Hyperlink Analysis on the World Wide Web.” <i>Proceedings of the 16th ACM Conference on Hypertext and Hypermedia</i>, Association for Computing Machinery, 2005, pp. 1–3, doi:<a href=\"https://doi.org/10.1145/1083356.1083357\">10.1145/1083356.1083357</a>.","apa":"Henzinger, M. H. (2005). Hyperlink analysis on the world wide web. In <i>Proceedings of the 16th ACM conference on Hypertext and hypermedia</i> (pp. 1–3). Salzburg, Austria: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/1083356.1083357\">https://doi.org/10.1145/1083356.1083357</a>","ieee":"M. H. Henzinger, “Hyperlink analysis on the world wide web,” in <i>Proceedings of the 16th ACM conference on Hypertext and hypermedia</i>, Salzburg, Austria, 2005, pp. 1–3.","ista":"Henzinger MH. 2005. Hyperlink analysis on the world wide web. Proceedings of the 16th ACM conference on Hypertext and hypermedia. HYPERTEXT: Conference on Hypertext and Hypermedia, 1–3."},"doi":"10.1145/1083356.1083357","year":"2005","article_processing_charge":"No","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H"}],"conference":{"start_date":"2005-09-06","location":"Salzburg, Austria","name":"HYPERTEXT: Conference on Hypertext and Hypermedia","end_date":"2005-09-09"},"type":"conference","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2022-07-29T10:47:23Z","oa_version":"None","extern":"1","keyword":["Hyperlink Analysis","World Wide Web"]},{"extern":"1","article_type":"original","volume":55,"oa_version":"Published Version","related_material":{"record":[{"id":"11926","relation":"earlier_version","status":"public"}]},"article_processing_charge":"No","issue":"1","type":"journal_article","day":"01","doi":"10.1016/j.jalgor.2004.11.001","language":[{"iso":"eng"}],"intvolume":"        55","quality_controlled":"1","title":"An online throughput-competitive algorithm for multicast routing and admission control","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.jalgor.2004.11.001","open_access":"1"}],"page":"1-20","publication":"Journal of Algorithms","publication_identifier":{"issn":["0196-6774"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-08-08T12:03:00Z","publication_status":"published","year":"2005","author":[{"full_name":"Goel, Ashish","first_name":"Ashish","last_name":"Goel"},{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"first_name":"Serge","last_name":"Plotkin","full_name":"Plotkin, Serge"}],"abstract":[{"text":"We present the first polylog-competitive online algorithm for the general multicast admission control and routing problem in the throughput model. The ratio of the number of requests accepted by the optimum offline algorithm to the expected number of requests accepted by our algorithm is O((log n + log log M)(log n + log M) log n), where M is the number of multicast groups and n is the number of nodes in the graph. We show that this is close to optimum by presenting an\r\nΩ(log n log M) lower bound on this ratio for any randomized online algorithm against an oblivious adversary, when M is much larger than the link capacities. Our lower bound applies even in the restricted case where the link capacities are much larger than bandwidth requested by a single multicast. We also present a simple proof showing that it is impossible to be competitive against an adaptive online adversary.\r\nAs in the previous online routing algorithms, our algorithm uses edge-costs when deciding on which is the best path to use. In contrast to the previous competitive algorithms in the throughput model, our cost is not a direct function of the edge load. The new cost definition allows us to decouple the effects of routing and admission decisions of different multicast groups.","lang":"eng"}],"citation":{"ieee":"A. Goel, M. H. Henzinger, and S. Plotkin, “An online throughput-competitive algorithm for multicast routing and admission control,” <i>Journal of Algorithms</i>, vol. 55, no. 1. Elsevier, pp. 1–20, 2005.","ista":"Goel A, Henzinger MH, Plotkin S. 2005. An online throughput-competitive algorithm for multicast routing and admission control. Journal of Algorithms. 55(1), 1–20.","short":"A. Goel, M.H. Henzinger, S. Plotkin, Journal of Algorithms 55 (2005) 1–20.","ama":"Goel A, Henzinger MH, Plotkin S. An online throughput-competitive algorithm for multicast routing and admission control. <i>Journal of Algorithms</i>. 2005;55(1):1-20. doi:<a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">10.1016/j.jalgor.2004.11.001</a>","chicago":"Goel, Ashish, Monika H Henzinger, and Serge Plotkin. “An Online Throughput-Competitive Algorithm for Multicast Routing and Admission Control.” <i>Journal of Algorithms</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">https://doi.org/10.1016/j.jalgor.2004.11.001</a>.","mla":"Goel, Ashish, et al. “An Online Throughput-Competitive Algorithm for Multicast Routing and Admission Control.” <i>Journal of Algorithms</i>, vol. 55, no. 1, Elsevier, 2005, pp. 1–20, doi:<a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">10.1016/j.jalgor.2004.11.001</a>.","apa":"Goel, A., Henzinger, M. H., &#38; Plotkin, S. (2005). An online throughput-competitive algorithm for multicast routing and admission control. <i>Journal of Algorithms</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgor.2004.11.001\">https://doi.org/10.1016/j.jalgor.2004.11.001</a>"},"publisher":"Elsevier","date_published":"2005-04-01T00:00:00Z","_id":"11763","date_updated":"2023-02-21T16:33:22Z","scopus_import":"1","month":"04"},{"_id":"8028","date_published":"2005-11-16T00:00:00Z","date_updated":"2021-01-12T08:16:37Z","month":"11","citation":{"ama":"Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire neurons. <i>Journal of Neuroscience</i>. 2005;25(46):10786-10795. doi:<a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">10.1523/jneurosci.3508-05.2005</a>","short":"T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795.","chicago":"Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2005. <a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">https://doi.org/10.1523/jneurosci.3508-05.2005</a>.","mla":"Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>, vol. 25, no. 46, Society for Neuroscience, 2005, pp. 10786–95, doi:<a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">10.1523/jneurosci.3508-05.2005</a>.","apa":"Vogels, T. P., &#38; Abbott, L. F. (2005). Signal propagation and logic gating in networks of integrate-and-fire neurons. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">https://doi.org/10.1523/jneurosci.3508-05.2005</a>","ieee":"T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks of integrate-and-fire neurons,” <i>Journal of Neuroscience</i>, vol. 25, no. 46. Society for Neuroscience, pp. 10786–10795, 2005.","ista":"Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795."},"abstract":[{"text":"Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.","lang":"eng"}],"publisher":"Society for Neuroscience","author":[{"orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"},{"first_name":"L. F.","last_name":"Abbott","full_name":"Abbott, L. F."}],"year":"2005","pmid":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication_status":"published","date_created":"2020-06-25T13:12:33Z","publication":"Journal of Neuroscience","external_id":{"pmid":["16291952"]},"publication_identifier":{"issn":["0270-6474","1529-2401"]},"status":"public","intvolume":"        25","doi":"10.1523/jneurosci.3508-05.2005","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/"}],"oa":1,"page":"10786-10795","quality_controlled":"1","title":"Signal propagation and logic gating in networks of integrate-and-fire neurons","day":"16","type":"journal_article","issue":"46","article_processing_charge":"No","article_type":"original","extern":"1","oa_version":"Published Version","volume":25},{"article_type":"review","extern":"1","oa_version":"None","volume":28,"day":"21","type":"journal_article","issue":"1","article_processing_charge":"No","intvolume":"        28","language":[{"iso":"eng"}],"doi":"10.1146/annurev.neuro.28.061604.135637","page":"357-376","title":"Neural network dynamics","quality_controlled":"1","publication":"Annual Review of Neuroscience","external_id":{"pmid":["16022600"]},"publication_identifier":{"issn":["0147-006X","1545-4126"]},"status":"public","publication_status":"published","date_created":"2020-06-25T13:13:11Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"last_name":"Vogels","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"},{"last_name":"Rajan","first_name":"Kanaka","full_name":"Rajan, Kanaka"},{"full_name":"Abbott, L.F.","first_name":"L.F.","last_name":"Abbott"}],"year":"2005","pmid":1,"citation":{"short":"T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005) 357–376.","ama":"Vogels TP, Rajan K, Abbott LF. Neural network dynamics. <i>Annual Review of Neuroscience</i>. 2005;28(1):357-376. doi:<a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">10.1146/annurev.neuro.28.061604.135637</a>","chicago":"Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.” <i>Annual Review of Neuroscience</i>. Annual Reviews, 2005. <a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>.","mla":"Vogels, Tim P., et al. “Neural Network Dynamics.” <i>Annual Review of Neuroscience</i>, vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:<a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">10.1146/annurev.neuro.28.061604.135637</a>.","apa":"Vogels, T. P., Rajan, K., &#38; Abbott, L. F. (2005). Neural network dynamics. <i>Annual Review of Neuroscience</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>","ieee":"T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” <i>Annual Review of Neuroscience</i>, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005.","ista":"Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review of Neuroscience. 28(1), 357–376."},"abstract":[{"text":"Neural network modeling is often concerned with stimulus-driven responses, but most of the activity in the brain is internally generated. Here, we review network models of internally generated activity, focusing on three types of network dynamics: (a) sustained responses to transient stimuli, which provide a model of working memory; (b) oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits. We also review propagation of stimulus-driven activity through spontaneously active networks. Exploring these aspects of neural network dynamics is critical for understanding how neural circuits produce cognitive function.","lang":"eng"}],"publisher":"Annual Reviews","_id":"8029","date_published":"2005-07-21T00:00:00Z","month":"07","date_updated":"2021-01-12T08:16:37Z"}]