[{"extern":"1","doi":"10.1016/j.anbehav.2004.09.005","status":"public","author":[{"first_name":"Ludivine","full_name":"De Menten, Ludivine","last_name":"De Menten"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"last_name":"Aron","full_name":"Aron, Serge","first_name":"Serge"}],"publist_id":"2237","intvolume":"        69","title":"Primary sex ratio adjustment by ant queens in response to local mate competition","day":"01","publisher":"Elsevier","volume":69,"month":"05","date_published":"2005-05-01T00:00:00Z","issue":"5","oa_version":"None","citation":{"ista":"De Menten L, Cremer S, Heinze J, Aron S. 2005. Primary sex ratio adjustment by ant queens in response to local mate competition. Animal Behaviour. 69(5), 1031–1035.","ieee":"L. De Menten, S. Cremer, J. Heinze, and S. Aron, “Primary sex ratio adjustment by ant queens in response to local mate competition,” <i>Animal Behaviour</i>, vol. 69, no. 5. Elsevier, pp. 1031–1035, 2005.","mla":"De Menten, Ludivine, et al. “Primary Sex Ratio Adjustment by Ant Queens in Response to Local Mate Competition.” <i>Animal Behaviour</i>, vol. 69, no. 5, Elsevier, 2005, pp. 1031–35, doi:<a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">10.1016/j.anbehav.2004.09.005</a>.","chicago":"De Menten, Ludivine, Sylvia Cremer, Jürgen Heinze, and Serge Aron. “Primary Sex Ratio Adjustment by Ant Queens in Response to Local Mate Competition.” <i>Animal Behaviour</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">https://doi.org/10.1016/j.anbehav.2004.09.005</a>.","ama":"De Menten L, Cremer S, Heinze J, Aron S. Primary sex ratio adjustment by ant queens in response to local mate competition. <i>Animal Behaviour</i>. 2005;69(5):1031-1035. doi:<a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">10.1016/j.anbehav.2004.09.005</a>","short":"L. De Menten, S. Cremer, J. Heinze, S. Aron, Animal Behaviour 69 (2005) 1031–1035.","apa":"De Menten, L., Cremer, S., Heinze, J., &#38; Aron, S. (2005). Primary sex ratio adjustment by ant queens in response to local mate competition. <i>Animal Behaviour</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">https://doi.org/10.1016/j.anbehav.2004.09.005</a>"},"page":"1031 - 1035","abstract":[{"text":"In the ant Cardiocondyla obscurior, wingless males compete with nestmate males for access to female mating\r\npartners, leading to local mate competition (LMC). Queen number varies between colonies, resulting in\r\nvariation in the strength of LMC. Cremer &amp; Heinze (2002, Proceedings of the Royal Society of London, Series B,\r\n269, 417–422) showed that colonies responded to increasing queen number by producing a less femalebiased\r\nsex ratio, as predicted by LMC theory. However, the proximate mechanisms responsible for this\r\nvariation in the sex ratio could not be determined because the study was restricted to adult sex ratios.With\r\nLMC, the primary sex ratio (proportion of haploid eggs laid by the queen) is expected to be female biased,\r\nwhich lowers the conflict between queens and workers over sex allocation. We compared the primary sex\r\nratios laid by queens in monogynous and in polygynous experimental colonies of C. obscurior. The\r\nproportion of haploid eggs laid by queens was significantly lower in single-queen than in multiple-queen\r\ncolonies. Furthermore, queens rapidly adjusted their primary sex ratios to changes in colony queen\r\nnumber. This is the first report of an adaptive adjustment of the primary sex ratio in response to LMC by\r\nant queens.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","publication":"Animal Behaviour","date_created":"2018-12-11T12:05:52Z","date_updated":"2021-01-12T07:53:10Z","_id":"3915","year":"2005"},{"extern":"1","status":"public","doi":"10.1016/j.cub.2005.01.036","author":[{"full_name":"Schrempf, Alexandra","last_name":"Schrempf","first_name":"Alexandra"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"title":"Sexual cooperation: mating increases longevity in ant queens","publist_id":"2238","intvolume":"        15","volume":15,"day":"08","publisher":"Cell Press","month":"02","date_published":"2005-02-08T00:00:00Z","issue":"3","oa_version":"None","citation":{"ieee":"A. Schrempf, J. Heinze, and S. Cremer, “Sexual cooperation: mating increases longevity in ant queens,” <i>Current Biology</i>, vol. 15, no. 3. Cell Press, pp. 267–270, 2005.","mla":"Schrempf, Alexandra, et al. “Sexual Cooperation: Mating Increases Longevity in Ant Queens.” <i>Current Biology</i>, vol. 15, no. 3, Cell Press, 2005, pp. 267–70, doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">10.1016/j.cub.2005.01.036</a>.","ama":"Schrempf A, Heinze J, Cremer S. Sexual cooperation: mating increases longevity in ant queens. <i>Current Biology</i>. 2005;15(3):267-270. doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">10.1016/j.cub.2005.01.036</a>","chicago":"Schrempf, Alexandra, Jürgen Heinze, and Sylvia Cremer. “Sexual Cooperation: Mating Increases Longevity in Ant Queens.” <i>Current Biology</i>. Cell Press, 2005. <a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">https://doi.org/10.1016/j.cub.2005.01.036</a>.","short":"A. Schrempf, J. Heinze, S. Cremer, Current Biology 15 (2005) 267–270.","apa":"Schrempf, A., Heinze, J., &#38; Cremer, S. (2005). Sexual cooperation: mating increases longevity in ant queens. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">https://doi.org/10.1016/j.cub.2005.01.036</a>","ista":"Schrempf A, Heinze J, Cremer S. 2005. Sexual cooperation: mating increases longevity in ant queens. Current Biology. 15(3), 267–270."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Divergent reproductive interests of males and females often cause sexual conflict [1] and [2]. Males of many species manipulate females by transferring seminal fluids that boost female short-term fecundity while decreasing their life expectancy and future reproductivity [3] and [4]. The life history of ants, however, is expected to reduce sexual conflict; whereas most insect females show repeated phases of mating and reproduction, antqueens mate only during a short period early in life and undergo a lifelong commitment to their mates by storing sperm [5]. Furthermore, sexual offspring can only be reared after a sterile worker force has been built up [5]. Therefore, the males should also profit from a long female lifespan. In the antCardiocondyla obscurior, mating indeed has a positive effect on the lifetime reproductive success of queens. Queens that mated to either one fertile or one sterilized male lived considerably longer and started laying eggs earlier than virgin queens. Only queens that received viable sperm from fertile males showed increased fecundity. The lack of a trade-off between fecundity and longevity is unexpected, given evolutionary theories of aging [6]. Our data instead reveal the existence of sexual cooperation in ants."}],"page":"267 - 270","type":"journal_article","language":[{"iso":"eng"}],"publication":"Current Biology","date_created":"2018-12-11T12:05:52Z","date_updated":"2021-01-12T07:53:10Z","_id":"3916","year":"2005"},{"type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"19 - 29","abstract":[{"text":"Resident dendritic cells (DC) within the T cell area of the lymph node take up soluble antigens that enter via the afferent lymphatics before antigen carrying DC arrive from the periphery. The reticular network within the lymph node is a conduit system forming the infrastructure for the fast delivery of soluble substances from the afferent lymph to the lumen of high endothelial venules (HEVs). Using high-resolution light microscopy and 3D reconstruction, we show here that these conduits are unique basement membrane-like structures ensheathed by fibroblastic reticular cells with occasional resident DC embedded within this cell layer. Conduit-associated DC are capable of taking up and processing soluble antigens transported within the conduits, whereas immigrated mature DC occur remote from the reticular fibers. The conduit system is, therefore, not a closed compartment that shuttles substances through the lymph node but represents the morphological equivalent to the filtering function of the lymph node.","lang":"eng"}],"citation":{"ieee":"M. K. Sixt <i>et al.</i>, “The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node,” <i>Immunity</i>, vol. 22, no. 1. Cell Press, pp. 19–29, 2005.","mla":"Sixt, Michael K., et al. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” <i>Immunity</i>, vol. 22, no. 1, Cell Press, 2005, pp. 19–29, doi:<a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">10.1016/j.immuni.2004.11.013</a>.","ama":"Sixt MK, Kanazawa N, Selg M, et al. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. <i>Immunity</i>. 2005;22(1):19-29. doi:<a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">10.1016/j.immuni.2004.11.013</a>","chicago":"Sixt, Michael K, Nobuo Kanazawa, Manuel Selg, Thomas Samson, Gunnel Roos, Dieter Reinhardt, Reinhard Pabst, Manfred Lutz, and Lydia Sorokin. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” <i>Immunity</i>. Cell Press, 2005. <a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">https://doi.org/10.1016/j.immuni.2004.11.013</a>.","apa":"Sixt, M. K., Kanazawa, N., Selg, M., Samson, T., Roos, G., Reinhardt, D., … Sorokin, L. (2005). The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. <i>Immunity</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">https://doi.org/10.1016/j.immuni.2004.11.013</a>","short":"M.K. Sixt, N. Kanazawa, M. Selg, T. Samson, G. Roos, D. Reinhardt, R. Pabst, M. Lutz, L. Sorokin, Immunity 22 (2005) 19–29.","ista":"Sixt MK, Kanazawa N, Selg M, Samson T, Roos G, Reinhardt D, Pabst R, Lutz M, Sorokin L. 2005. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. 22(1), 19–29."},"issue":"1","oa_version":"None","_id":"3933","date_updated":"2021-01-12T07:53:18Z","year":"2005","date_created":"2018-12-11T12:05:58Z","publication":"Immunity","doi":"10.1016/j.immuni.2004.11.013","status":"public","extern":"1","month":"01","date_published":"2005-01-25T00:00:00Z","day":"25","publisher":"Cell Press","volume":22,"title":"The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node","intvolume":"        22","publist_id":"2195","author":[{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"},{"last_name":"Kanazawa","full_name":"Kanazawa, Nobuo","first_name":"Nobuo"},{"first_name":"Manuel","last_name":"Selg","full_name":"Selg, Manuel"},{"first_name":"Thomas","last_name":"Samson","full_name":"Samson, Thomas"},{"last_name":"Roos","full_name":"Roos, Gunnel","first_name":"Gunnel"},{"first_name":"Dieter","full_name":"Reinhardt, Dieter","last_name":"Reinhardt"},{"first_name":"Reinhard","last_name":"Pabst","full_name":"Pabst, Reinhard"},{"first_name":"Manfred","last_name":"Lutz","full_name":"Lutz, Manfred"},{"first_name":"Lydia","last_name":"Sorokin","full_name":"Sorokin, Lydia"}]},{"date_created":"2018-12-11T12:06:16Z","conference":{"name":"PSB: Pacific Symposium on Biocomputing"},"year":"2005","_id":"3982","date_updated":"2021-01-12T07:53:38Z","citation":{"mla":"Wang, Yusu, et al. <i>Coarse and Reliable Geometric Alignment for Protein Docking</i>. World Scientific Publishing, 2005, pp. 64–75, doi:<a href=\"https://doi.org/10.1142/9789812702456_0007\">10.1142/9789812702456_0007</a>.","ieee":"Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph, “Coarse and reliable geometric alignment for protein docking,” presented at the PSB: Pacific Symposium on Biocomputing, 2005, pp. 64–75.","apa":"Wang, Y., Agarwal, P., Brown, P., Edelsbrunner, H., &#38; Rudolph, J. (2005). Coarse and reliable geometric alignment for protein docking (pp. 64–75). Presented at the PSB: Pacific Symposium on Biocomputing, World Scientific Publishing. <a href=\"https://doi.org/10.1142/9789812702456_0007\">https://doi.org/10.1142/9789812702456_0007</a>","short":"Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, J. Rudolph, in:, World Scientific Publishing, 2005, pp. 64–75.","chicago":"Wang, Yusu, Pankaj Agarwal, Paul Brown, Herbert Edelsbrunner, and Johannes Rudolph. “Coarse and Reliable Geometric Alignment for Protein Docking,” 64–75. World Scientific Publishing, 2005. <a href=\"https://doi.org/10.1142/9789812702456_0007\">https://doi.org/10.1142/9789812702456_0007</a>.","ama":"Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. Coarse and reliable geometric alignment for protein docking. In: World Scientific Publishing; 2005:64-75. doi:<a href=\"https://doi.org/10.1142/9789812702456_0007\">10.1142/9789812702456_0007</a>","ista":"Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. 2005. Coarse and reliable geometric alignment for protein docking. PSB: Pacific Symposium on Biocomputing, 64–75."},"type":"conference","publication_status":"published","abstract":[{"text":"We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems.","lang":"eng"}],"page":"64 - 75","title":"Coarse and reliable geometric alignment for protein docking","publist_id":"2143","author":[{"first_name":"Yusu","last_name":"Wang","full_name":"Wang, Yusu"},{"full_name":"Agarwal, Pankaj K","last_name":"Agarwal","first_name":"Pankaj"},{"first_name":"Paul","full_name":"Brown, Paul","last_name":"Brown"},{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Rudolph","full_name":"Rudolph, Johannes","first_name":"Johannes"}],"month":"01","date_published":"2005-01-01T00:00:00Z","publisher":"World Scientific Publishing","day":"01","quality_controlled":0,"extern":1,"status":"public","doi":"10.1142/9789812702456_0007"},{"doi":"10.1021/bi0516879","status":"public","extern":1,"quality_controlled":0,"day":"24","volume":44,"publisher":"ACS","date_published":"2005-11-24T00:00:00Z","month":"11","author":[{"first_name":"Jungsan","last_name":"Sohn","full_name":"Sohn, Jungsan"},{"first_name":"Jerry","last_name":"Parks","full_name":"Parks, Jerry M"},{"first_name":"Gregory","full_name":"Buhrman, Gregory","last_name":"Buhrman"},{"first_name":"Paul","full_name":"Brown, Paul","last_name":"Brown"},{"last_name":"Kristjánsdóttir","full_name":"Kristjánsdóttir, Kolbrun","first_name":"Kolbrun"},{"first_name":"Alexias","full_name":"Safi, Alexias","last_name":"Safi"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner"},{"first_name":"Weitao","full_name":"Yang, Weitao T","last_name":"Yang"},{"last_name":"Rudolph","full_name":"Rudolph, Johannes","first_name":"Johannes"}],"publist_id":"2144","intvolume":"        44","title":"Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate","page":"16563 - 16573","abstract":[{"text":"Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling anticancer targets because their overexpression has been associated with numerous cancers. However, drug discovery targeting these phosphatases has been hampered by the lack of structural information about how Cdc25s interact with their native protein substrates, the cyclin-dependent kinases. Herein, we predict a docked orientation for Cdc25B with its Cdk2-pTpY-CycA protein substrate by a rigid-body docking method and refine the docked models with full-scale molecular dynamics simulations and minimization. We validate the stable ensemble structure experimentally by a variety of in vitro and in vivo techniques. Specifically, we compare our model with a crystal structure of the substrate-trapping mutant of Cdc25B. We identify and validate in vivo a novel hot-spot residue on Cdc25B (Arg492) that plays a central role in protein substrate recognition. We identify a hot-spot residue on the Substrate Cdk2 (Asp206) and confirm its interaction with hot-spot residues on Cdc25 using hot-spot swapping and double mutant cycles to derive interaction energies. Our experimentally validated model is consistent with previous studies of Cdk2 and its interaction partners and initiates the opportunity for drug discovery of inhibitors that target the remote binding sites of this protein-protein interaction.","lang":"eng"}],"publication_status":"published","type":"journal_article","issue":"50","citation":{"ama":"Sohn J, Parks J, Buhrman G, et al. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. <i>Biochemistry</i>. 2005;44(50):16563-16573. doi:<a href=\"https://doi.org/10.1021/bi0516879\">10.1021/bi0516879</a>","chicago":"Sohn, Jungsan, Jerry Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjánsdóttir, Alexias Safi, Herbert Edelsbrunner, Weitao Yang, and Johannes Rudolph. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” <i>Biochemistry</i>. ACS, 2005. <a href=\"https://doi.org/10.1021/bi0516879\">https://doi.org/10.1021/bi0516879</a>.","short":"J. Sohn, J. Parks, G. Buhrman, P. Brown, K. Kristjánsdóttir, A. Safi, H. Edelsbrunner, W. Yang, J. Rudolph, Biochemistry 44 (2005) 16563–16573.","apa":"Sohn, J., Parks, J., Buhrman, G., Brown, P., Kristjánsdóttir, K., Safi, A., … Rudolph, J. (2005). Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. <i>Biochemistry</i>. ACS. <a href=\"https://doi.org/10.1021/bi0516879\">https://doi.org/10.1021/bi0516879</a>","ieee":"J. Sohn <i>et al.</i>, “Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate,” <i>Biochemistry</i>, vol. 44, no. 50. ACS, pp. 16563–16573, 2005.","mla":"Sohn, Jungsan, et al. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” <i>Biochemistry</i>, vol. 44, no. 50, ACS, 2005, pp. 16563–73, doi:<a href=\"https://doi.org/10.1021/bi0516879\">10.1021/bi0516879</a>.","ista":"Sohn J, Parks J, Buhrman G, Brown P, Kristjánsdóttir K, Safi A, Edelsbrunner H, Yang W, Rudolph J. 2005. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 44(50), 16563–16573."},"_id":"3983","year":"2005","date_updated":"2021-01-12T07:53:39Z","publication":"Biochemistry","date_created":"2018-12-11T12:06:16Z"},{"title":"The limitations of adaptive dynamics as a model of evolution","intvolume":"        18","publist_id":"1982","author":[{"full_name":"Nicholas Barton","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Jitka Polechova"}],"date_published":"2005-09-01T00:00:00Z","month":"09","day":"01","publisher":"Wiley-Blackwell","volume":18,"quality_controlled":0,"extern":1,"status":"public","doi":"10.1111/j.1420-9101.2005.00943.x","date_created":"2018-12-11T12:07:10Z","publication":"Journal of Evolutionary Biology","_id":"4138","date_updated":"2021-01-12T07:54:47Z","year":"2005","citation":{"ista":"Barton NH, Polechova J. 2005. The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. 18(5), 1186–1190.","ama":"Barton NH, Polechova J. The limitations of adaptive dynamics as a model of evolution. <i>Journal of Evolutionary Biology</i>. 2005;18(5):1186-1190. doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">10.1111/j.1420-9101.2005.00943.x</a>","chicago":"Barton, Nicholas H, and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">https://doi.org/10.1111/j.1420-9101.2005.00943.x</a>.","short":"N.H. Barton, J. Polechova, Journal of Evolutionary Biology 18 (2005) 1186–1190.","apa":"Barton, N. H., &#38; Polechova, J. (2005). The limitations of adaptive dynamics as a model of evolution. <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">https://doi.org/10.1111/j.1420-9101.2005.00943.x</a>","ieee":"N. H. Barton and J. Polechova, “The limitations of adaptive dynamics as a model of evolution,” <i>Journal of Evolutionary Biology</i>, vol. 18, no. 5. Wiley-Blackwell, pp. 1186–1190, 2005.","mla":"Barton, Nicholas H., and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” <i>Journal of Evolutionary Biology</i>, vol. 18, no. 5, Wiley-Blackwell, 2005, pp. 1186–90, doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">10.1111/j.1420-9101.2005.00943.x</a>."},"issue":"5","type":"journal_article","publication_status":"published","page":"1186 - 1190","abstract":[{"lang":"eng","text":"Adaptive dynamics describes the evolution of an asexual population through the successive substitution of mutations of small effect. Waxman &amp; Gavrilets (2005) give an excellent overview of the method and its applications. In this note, we focus on the plausibility of the key assumption that mutations have small effects, and the consequences of relaxing that assumption. We argue that: (i) successful mutations often have large effects; (ii) such mutations generate a qualitatively different evolutionary pattern, which is inherently stochastic; and (iii) in models of competition for a continuous resource, selection becomes very weak once several phenotypes are established. This makes the effects of introducing new mutations unpredictable using the methods of adaptive dynamics.\n\nWe should make clear at the outset that our criticism is of methods that rely on local analysis of fitness gradients (eqn 2 of Waxman &amp; Gavrilets, 2005), and not of the broader idea that evolution can be understood by examining the invasion of successive mutations. We use the term ‘adaptive dynamics’ to refer to the former technique, and contrast it with a more general population genetic analysis of probabilities of invasion."}]},{"author":[{"first_name":"Florian","last_name":"Ulrich","full_name":"Ulrich, Florian"},{"first_name":"Michael","full_name":"Krieg, Michael","last_name":"Krieg"},{"last_name":"Schötz","full_name":"Schötz, Eva","first_name":"Eva"},{"first_name":"Vinzenz","full_name":"Link, Vinzenz","last_name":"Link"},{"first_name":"Irinka","full_name":"Castanon, Irinka","last_name":"Castanon"},{"first_name":"Viktor","full_name":"Schnabel, Viktor","last_name":"Schnabel"},{"full_name":"Taubenberger, Anna","last_name":"Taubenberger","first_name":"Anna"},{"first_name":"Daniel","last_name":"Müller","full_name":"Müller, Daniel"},{"full_name":"Puech, Pierre","last_name":"Puech","first_name":"Pierre"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","title":"Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin","publist_id":"1977","intvolume":"         9","day":"01","publisher":"Cell Press","volume":9,"month":"10","date_published":"2005-10-01T00:00:00Z","extern":"1","status":"public","doi":"10.1016/j.devcel.2005.08.011","publication":"Developmental Cell","date_created":"2018-12-11T12:07:12Z","_id":"4144","year":"2005","date_updated":"2021-01-12T07:54:50Z","issue":"4","oa_version":"None","citation":{"ista":"Ulrich F, Krieg M, Schötz E, Link V, Castanon I, Schnabel V, Taubenberger A, Müller D, Puech P, Heisenberg C-PJ. 2005. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. 9(4), 555–564.","mla":"Ulrich, Florian, et al. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” <i>Developmental Cell</i>, vol. 9, no. 4, Cell Press, 2005, pp. 555–64, doi:<a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">10.1016/j.devcel.2005.08.011</a>.","ieee":"F. Ulrich <i>et al.</i>, “Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin,” <i>Developmental Cell</i>, vol. 9, no. 4. Cell Press, pp. 555–564, 2005.","short":"F. Ulrich, M. Krieg, E. Schötz, V. Link, I. Castanon, V. Schnabel, A. Taubenberger, D. Müller, P. Puech, C.-P.J. Heisenberg, Developmental Cell 9 (2005) 555–564.","apa":"Ulrich, F., Krieg, M., Schötz, E., Link, V., Castanon, I., Schnabel, V., … Heisenberg, C.-P. J. (2005). Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">https://doi.org/10.1016/j.devcel.2005.08.011</a>","ama":"Ulrich F, Krieg M, Schötz E, et al. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. <i>Developmental Cell</i>. 2005;9(4):555-564. doi:<a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">10.1016/j.devcel.2005.08.011</a>","chicago":"Ulrich, Florian, Michael Krieg, Eva Schötz, Vinzenz Link, Irinka Castanon, Viktor Schnabel, Anna Taubenberger, Daniel Müller, Pierre Puech, and Carl-Philipp J Heisenberg. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” <i>Developmental Cell</i>. Cell Press, 2005. <a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">https://doi.org/10.1016/j.devcel.2005.08.011</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","page":"555 - 564","abstract":[{"lang":"eng","text":"Wnt11 plays a central role in tissue morphogenesis during vertebrate gastrulation, but the molecular and cellular mechanisms by which Wnt11 exerts its effects remain poorly understood. Here, we show that Wnt11 functions during zebrafish gastrulation by regulating the cohesion of mesodermal and endodermal (mesendodermal) progenitor cells. Importantly, we demonstrate that Wnt11 activity in this process is mediated by the GTPase Rab5, a key regulator of early endocytosis, as blocking Rab5c activity in wild-type embryos phenocopies slb/wnt11 mutants, and enhancing Rab5c activity in slb/wnt11 mutant embryos rescues the mutant phenotype. In addition, we find that Wnt11 and Rab5c control the endocytosis of E-cadherin and are required in mesendodermal cells for E-cadherin-mediated cell cohesion. Together, our results suggest that Wnt11 controls tissue morphogenesis by modulating E-cadherin-mediated cell cohesion through Rab5c, a novel mechanism of Wnt signaling in gastrulation."}],"type":"journal_article","language":[{"iso":"eng"}]},{"doi":"10.1242/​jcs.02547","status":"public","extern":"1","month":"01","date_published":"2005-01-01T00:00:00Z","day":"01","volume":118,"publisher":"Company of Biologists","title":"Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy","article_processing_charge":"No","publist_id":"1964","intvolume":"       118","author":[{"first_name":"Pierre","last_name":"Puech","full_name":"Puech, Pierre"},{"first_name":"Anna","last_name":"Taubenberger","full_name":"Taubenberger, Anna"},{"full_name":"Ulrich, Florian","last_name":"Ulrich","first_name":"Florian"},{"first_name":"Michael","full_name":"Krieg, Michael","last_name":"Krieg"},{"last_name":"Mueller","full_name":"Mueller, Daniel","first_name":"Daniel"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"type":"journal_article","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, progenitor cells of different germ layers acquire specific adhesive properties that contribute to germ layer formation and separation. Wnt signals have been suggested to function in this process by modulating the different levels of adhesion between the germ layers, however, direct evidence for this is still lacking. Here we show that Wnt11, a key signal regulating gastrulation movements, is needed for the adhesion of zebrafish mesendodermal progenitor cells to fibronectin, an abundant extracellular matrix component during gastrulation. To measure this effect, we developed an assay to quantify the adhesion of single zebrafish primary mesendodermal progenitors using atomic-force microscopy (AFM). We observed significant differences in detachment force and work between cultured mesendodermal progenitors from wild-type embryos and from slb/wit11 mutant embryos, which carry a loss-of-function mutation in the wnt11 gene, when tested on fibronectin-coated substrates. These differences were probably due to reduced adhesion to the fibronectin substrate as neither the overall cell morphology nor the cell elasticity grossly differed between wild-type and mutant cells. Furthermore, in the presence of inhibitors of fibronectin-integrin binding, such as RGD peptides, the adhesion force and work were strongly decreased, indicating that integrins are involved in the binding of mesendodermal progenitors in our assay. These findings demonstrate that AFM can be used to quantitatively determine the substrate-adhesion of cultured primary gastrulating cells and provide insight into the role of Wnt11 signalling in modulating cell adhesion at the single cell scale."}],"page":"4199 - 4206","citation":{"mla":"Puech, Pierre, et al. “Measuring Cell Adhesion Forces of Primary Gastrulating Cells from Zebrafish Using Atomic Force Microscopy.” <i>Journal of Cell Science</i>, vol. 118, no. 18, Company of Biologists, 2005, pp. 4199–206, doi:<a href=\"https://doi.org/10.1242/​jcs.02547\">10.1242/​jcs.02547</a>.","ieee":"P. Puech, A. Taubenberger, F. Ulrich, M. Krieg, D. Mueller, and C.-P. J. Heisenberg, “Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy,” <i>Journal of Cell Science</i>, vol. 118, no. 18. Company of Biologists, pp. 4199–4206, 2005.","short":"P. Puech, A. Taubenberger, F. Ulrich, M. Krieg, D. Mueller, C.-P.J. Heisenberg, Journal of Cell Science 118 (2005) 4199–4206.","apa":"Puech, P., Taubenberger, A., Ulrich, F., Krieg, M., Mueller, D., &#38; Heisenberg, C.-P. J. (2005). Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/​jcs.02547\">https://doi.org/10.1242/​jcs.02547</a>","ama":"Puech P, Taubenberger A, Ulrich F, Krieg M, Mueller D, Heisenberg C-PJ. Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. <i>Journal of Cell Science</i>. 2005;118(18):4199-4206. doi:<a href=\"https://doi.org/10.1242/​jcs.02547\">10.1242/​jcs.02547</a>","chicago":"Puech, Pierre, Anna Taubenberger, Florian Ulrich, Michael Krieg, Daniel Mueller, and Carl-Philipp J Heisenberg. “Measuring Cell Adhesion Forces of Primary Gastrulating Cells from Zebrafish Using Atomic Force Microscopy.” <i>Journal of Cell Science</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/​jcs.02547\">https://doi.org/10.1242/​jcs.02547</a>.","ista":"Puech P, Taubenberger A, Ulrich F, Krieg M, Mueller D, Heisenberg C-PJ. 2005. Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. Journal of Cell Science. 118(18), 4199–4206."},"oa_version":"None","issue":"18","date_updated":"2021-01-12T07:54:54Z","_id":"4155","year":"2005","date_created":"2018-12-11T12:07:16Z","publication":"Journal of Cell Science"},{"status":"public","doi":"10.1242/dev.01611","extern":"1","month":"02","date_published":"2005-02-15T00:00:00Z","publisher":"Company of Biologists","day":"15","volume":132,"intvolume":"       132","publist_id":"1952","article_processing_charge":"No","title":"Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones","author":[{"last_name":"Norton","full_name":"Norton, Will","first_name":"Will"},{"first_name":"Maryam","last_name":"Mangoli","full_name":"Mangoli, Maryam"},{"first_name":"Zsolt","last_name":"Lele","full_name":"Lele, Zsolt"},{"full_name":"Pogoda, Hans","last_name":"Pogoda","first_name":"Hans"},{"first_name":"Brianne","last_name":"Diamond","full_name":"Diamond, Brianne"},{"first_name":"Sara","full_name":"Mercurio, Sara","last_name":"Mercurio"},{"first_name":"Claire","last_name":"Russell","full_name":"Russell, Claire"},{"first_name":"Hiroki","last_name":"Teraoka","full_name":"Teraoka, Hiroki"},{"full_name":"Stickney, Heather","last_name":"Stickney","first_name":"Heather"},{"first_name":"Gerd","last_name":"Rauch","full_name":"Rauch, Gerd"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Corinne","full_name":"Houart, Corinne","last_name":"Houart"},{"first_name":"Thomas","full_name":"Schilling, Thomas","last_name":"Schilling"},{"last_name":"Frohnhoefer","full_name":"Frohnhoefer, Hans","first_name":"Hans"},{"last_name":"Rastegar","full_name":"Rastegar, Sepand","first_name":"Sepand"},{"full_name":"Neumann, Carl","last_name":"Neumann","first_name":"Carl"},{"full_name":"Gardiner, R Mark","last_name":"Gardiner","first_name":"R Mark"},{"last_name":"Strähle","full_name":"Strähle, Uwe","first_name":"Uwe"},{"full_name":"Geisler, Robert","last_name":"Geisler","first_name":"Robert"},{"last_name":"Rees","full_name":"Rees, Michelle","first_name":"Michelle"},{"first_name":"William","full_name":"Talbot, William","last_name":"Talbot"},{"first_name":"Stephen","last_name":"Wilson","full_name":"Wilson, Stephen"}],"type":"journal_article","language":[{"iso":"eng"}],"page":"645 - 658","abstract":[{"lang":"eng","text":"In this study, we elucidate the roles of the winged-helix transcription factor Foxa2 in ventral CNS development in zebrafish. Through cloning of monorail (mol), which we find encodes the transcription factor Foxa2, and phenotypic analysis of mol(-/-) embryos, we show that floorplate is induced in the absence of Foxa2 function but fails to further differentiate. In mol(-/-) mutants, expression of Foxa and Hh family genes is not maintained in floorplate cells and lateral expansion of the floorplate fails to occur. Our results suggest that this is due to defects both in the regulation of Hh activity in medial floorplate cells as well as cell-autonomous requirements for Foxa2 in the prospective laterally positioned floorplate cells themselves. Foxa2 is also required for induction and/or patterning of several distinct cell types in the ventral CNS. Serotonergic neurones of the raphe nucleus and the trochlear motor nucleus are absent in mol(-/-) embryos, and oculomotor and facial motoneurones ectopically occupy ventral CNS midline positions in the midbrain and hindbrain. There is also a severe reduction of prospective oligodendrocytes in the midbrain and hindbrain. Finally, in the absence of Foxa2, at least two likely Hh pathway target genes are ectopically expressed in more dorsal regions of the midbrain and hindbrain ventricular neuroepithelium, raising the possibility that Foxa2 activity may normally be required to limit the range of action of secreted Hh proteins."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"W. Norton <i>et al.</i>, “Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones,” <i>Development</i>, vol. 132, no. 4. Company of Biologists, pp. 645–658, 2005.","mla":"Norton, Will, et al. “Monorail/Foxa2 Regulates Floorplate Differentiation and Specification of Oligodendrocytes, Serotonergic Raphe Neurones and Cranial Motoneurones.” <i>Development</i>, vol. 132, no. 4, Company of Biologists, 2005, pp. 645–58, doi:<a href=\"https://doi.org/10.1242/dev.01611\">10.1242/dev.01611</a>.","ama":"Norton W, Mangoli M, Lele Z, et al. Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. <i>Development</i>. 2005;132(4):645-658. doi:<a href=\"https://doi.org/10.1242/dev.01611\">10.1242/dev.01611</a>","chicago":"Norton, Will, Maryam Mangoli, Zsolt Lele, Hans Pogoda, Brianne Diamond, Sara Mercurio, Claire Russell, et al. “Monorail/Foxa2 Regulates Floorplate Differentiation and Specification of Oligodendrocytes, Serotonergic Raphe Neurones and Cranial Motoneurones.” <i>Development</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/dev.01611\">https://doi.org/10.1242/dev.01611</a>.","apa":"Norton, W., Mangoli, M., Lele, Z., Pogoda, H., Diamond, B., Mercurio, S., … Wilson, S. (2005). Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.01611\">https://doi.org/10.1242/dev.01611</a>","short":"W. Norton, M. Mangoli, Z. Lele, H. Pogoda, B. Diamond, S. Mercurio, C. Russell, H. Teraoka, H. Stickney, G. Rauch, C.-P.J. Heisenberg, C. Houart, T. Schilling, H. Frohnhoefer, S. Rastegar, C. Neumann, R.M. Gardiner, U. Strähle, R. Geisler, M. Rees, W. Talbot, S. Wilson, Development 132 (2005) 645–658.","ista":"Norton W, Mangoli M, Lele Z, Pogoda H, Diamond B, Mercurio S, Russell C, Teraoka H, Stickney H, Rauch G, Heisenberg C-PJ, Houart C, Schilling T, Frohnhoefer H, Rastegar S, Neumann C, Gardiner RM, Strähle U, Geisler R, Rees M, Talbot W, Wilson S. 2005. Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. Development. 132(4), 645–658."},"issue":"4","oa_version":"None","_id":"4167","date_updated":"2021-01-12T07:55:00Z","year":"2005","date_created":"2018-12-11T12:07:21Z","publication":"Development"},{"author":[{"full_name":"Montero, Juan","last_name":"Montero","first_name":"Juan"},{"full_name":"Carvalho, Lara","last_name":"Carvalho","first_name":"Lara"},{"full_name":"Wilsch Bräuninger, Michaela","last_name":"Wilsch Bräuninger","first_name":"Michaela"},{"full_name":"Kilian, Beate","last_name":"Kilian","first_name":"Beate"},{"full_name":"Mustafa, Chigdem","last_name":"Mustafa","first_name":"Chigdem"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"publist_id":"1947","intvolume":"       132","title":"Shield formation at the onset of zebrafish gastrulation","article_processing_charge":"No","day":"15","publisher":"Company of Biologists","volume":132,"month":"03","date_published":"2005-03-15T00:00:00Z","extern":"1","doi":"10.1242/dev.01667","status":"public","publication":"Development","date_created":"2018-12-11T12:07:22Z","_id":"4171","date_updated":"2021-01-12T07:55:02Z","year":"2005","issue":"6","oa_version":"None","citation":{"ista":"Montero J, Carvalho L, Wilsch Bräuninger M, Kilian B, Mustafa C, Heisenberg C-PJ. 2005. Shield formation at the onset of zebrafish gastrulation. Development. 132(6), 1187–1198.","apa":"Montero, J., Carvalho, L., Wilsch Bräuninger, M., Kilian, B., Mustafa, C., &#38; Heisenberg, C.-P. J. (2005). Shield formation at the onset of zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.01667\">https://doi.org/10.1242/dev.01667</a>","short":"J. Montero, L. Carvalho, M. Wilsch Bräuninger, B. Kilian, C. Mustafa, C.-P.J. Heisenberg, Development 132 (2005) 1187–1198.","ama":"Montero J, Carvalho L, Wilsch Bräuninger M, Kilian B, Mustafa C, Heisenberg C-PJ. Shield formation at the onset of zebrafish gastrulation. <i>Development</i>. 2005;132(6):1187-1198. doi:<a href=\"https://doi.org/10.1242/dev.01667\">10.1242/dev.01667</a>","chicago":"Montero, Juan, Lara Carvalho, Michaela Wilsch Bräuninger, Beate Kilian, Chigdem Mustafa, and Carl-Philipp J Heisenberg. “Shield Formation at the Onset of Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/dev.01667\">https://doi.org/10.1242/dev.01667</a>.","mla":"Montero, Juan, et al. “Shield Formation at the Onset of Zebrafish Gastrulation.” <i>Development</i>, vol. 132, no. 6, Company of Biologists, 2005, pp. 1187–98, doi:<a href=\"https://doi.org/10.1242/dev.01667\">10.1242/dev.01667</a>.","ieee":"J. Montero, L. Carvalho, M. Wilsch Bräuninger, B. Kilian, C. Mustafa, and C.-P. J. Heisenberg, “Shield formation at the onset of zebrafish gastrulation,” <i>Development</i>, vol. 132, no. 6. Company of Biologists, pp. 1187–1198, 2005."},"abstract":[{"lang":"eng","text":"During vertebrate gastrulation, the three germ layers, ectoderm, mesoderm and endoderm are formed, and the resulting progenitor cells are brought into the positions from which they will later contribute more complex tissues and organs. A core element in this process is the internalization of mesodermal and endodermal progenitors at the onset of gastrulation. Although many of the molecules that induce mesendoderm have been identified, much less is known about the cellular mechanisms underlying mesendodermal cell internalization and germ layer formation. Here we show that at the onset of zebrafish gastrulation, mesendodermal progenitors in dorsal/axial regions of the germ ring internalize by single cell delamination. Once internalized, mesendodermal progenitors upregulate ECadherin (Cadherin 1) expression, become increasingly motile and eventually migrate along the overlying epiblast (ectodermal) cell layer towards the animal pole of the gastrula. When E-Cadherin function is compromised, mesendodermal progenitors still internalize, but, with gastrulation proceeding, fail to elongate and efficiently migrate along the epiblast, whereas epiblast cells themselves exhibit reduced radial cell intercalation movements. This indicates that cadherin-mediated cell-cell adhesion is needed within the forming shield for both epiblast cell intercalation, and mesendodermal progenitor cell elongation and migration during zebrafish gastrulation. Our data provide insight into the cellular mechanisms underlying mesendodermal progenitor cell internalization and subsequent migration during zebrafish gastrulation, and the role of cadherin-mediated cell-cell adhesion in these processes."}],"page":"1187 - 1198","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article"},{"type":"journal_article","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","page":"S112 - S113","abstract":[{"lang":"eng","text":"The spreading of an epithelial cell sheet over a substrate is a common process during embryogenesis. Typical examples include epiboly during zebrafish gastrulation and Drosophila dorsal closure. We provide evidence that in both cases, actin-based contraction of the leading edge of the epithelium is of critical importance."}],"citation":{"ista":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2005. Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. Mechanisms of Development. 122(Supplement 1), S112–S113.","mla":"Köppen, Mathias, et al. “Misshapen Mediates Actin-Based Cell Contraction during Zebrafish Epiboly and Drosophila Dorsal Closure.” <i>Mechanisms of Development</i>, vol. 122, no. Supplement 1, Elsevier, 2005, pp. S112–13, doi:<a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">10.1016/j.mod.2005.06.010</a>.","ieee":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure,” <i>Mechanisms of Development</i>, vol. 122, no. Supplement 1. Elsevier, pp. S112–S113, 2005.","short":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Mechanisms of Development 122 (2005) S112–S113.","apa":"Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., &#38; Heisenberg, C.-P. J. (2005). Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">https://doi.org/10.1016/j.mod.2005.06.010</a>","chicago":"Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Misshapen Mediates Actin-Based Cell Contraction during Zebrafish Epiboly and Drosophila Dorsal Closure.” <i>Mechanisms of Development</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">https://doi.org/10.1016/j.mod.2005.06.010</a>.","ama":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. <i>Mechanisms of Development</i>. 2005;122(Supplement 1):S112-S113. doi:<a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">10.1016/j.mod.2005.06.010</a>"},"oa_version":"None","issue":"Supplement 1","year":"2005","_id":"4183","date_updated":"2021-01-12T07:55:07Z","date_created":"2018-12-11T12:07:27Z","publication":"Mechanisms of Development","doi":"10.1016/j.mod.2005.06.010","status":"public","extern":"1","month":"01","date_published":"2005-01-01T00:00:00Z","publisher":"Elsevier","volume":122,"day":"01","title":"Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure","article_processing_charge":"No","intvolume":"       122","publist_id":"1936","author":[{"last_name":"Köppen","full_name":"Köppen, Mathias","first_name":"Mathias"},{"last_name":"Fernández","full_name":"Fernández, Beatriz","first_name":"Beatriz"},{"full_name":"Carvalho, Lara","last_name":"Carvalho","first_name":"Lara"},{"first_name":"António","full_name":"Jacinto, António","last_name":"Jacinto"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"acknowledgement":"Poster Abstract"},{"publication":"Evolution; International Journal of Organic Evolution","date_created":"2018-12-11T12:07:50Z","year":"2005","_id":"4249","date_updated":"2021-01-12T07:55:36Z","issue":"6","citation":{"ista":"Polechova J, Barton NH. 2005. Speciation through competition: A critical review. Evolution; International Journal of Organic Evolution. 59(6), 1194–1210.","ama":"Polechova J, Barton NH. Speciation through competition: A critical review. <i>Evolution; International Journal of Organic Evolution</i>. 2005;59(6):1194-1210. doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">10.1111/j.0014-3820.2005.tb01771.x</a>","chicago":"Polechova, Jitka, and Nicholas H Barton. “Speciation through Competition: A Critical Review.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">https://doi.org/10.1111/j.0014-3820.2005.tb01771.x</a>.","apa":"Polechova, J., &#38; Barton, N. H. (2005). Speciation through competition: A critical review. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">https://doi.org/10.1111/j.0014-3820.2005.tb01771.x</a>","short":"J. Polechova, N.H. Barton, Evolution; International Journal of Organic Evolution 59 (2005) 1194–1210.","ieee":"J. Polechova and N. H. Barton, “Speciation through competition: A critical review,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 59, no. 6. Wiley-Blackwell, pp. 1194–1210, 2005.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Speciation through Competition: A Critical Review.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 59, no. 6, Wiley-Blackwell, 2005, pp. 1194–210, doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">10.1111/j.0014-3820.2005.tb01771.x</a>."},"abstract":[{"lang":"eng","text":"We examined causes of speciation in asexual populations in both sympatry and parapatry, providing an alternative explanation for the speciation patterns reported by Dieckmann and Doebeli (1999) and Doebeli and Dieckmann (2003). Both in sympatry and parapatry, they find that speciation occurs relatively easily. We reveal that in the sympatric clonal model, the equilibrium distribution is continuous and the disruptive selection driving evolution of discrete clusters is only transient. Hence, if discrete phenotypes are to remain stable in the sympatric sexual model, there should be some source of nontransient disruptive selection that will drive evolution of assortment. We analyze sexually reproducing populations using the Bulmer’s infinitesimal model and show that cost-free assortment alone leads to speciation and disruptive selection only arises when the optimal distribution cannot be matched—in this example, because the phenotypic range is limited. In addition, Doebeli and Dieckmann’s analyses assumed a high genetic variance and a high mutation rate. Thus, these theoretical models do not support the conclusion that sympatric speciation is a likely outcome of competition for resources. In their parapatric model (Doebeli and Dieckmann 2003), clustering into distinct phenotypes is driven by edge effects, rather than by frequency-dependent competition."}],"page":"1194 - 1210","publication_status":"published","type":"journal_article","author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","full_name":"Jitka Polechova","orcid":"0000-0003-0951-3112","first_name":"Jitka"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"publist_id":"1849","intvolume":"        59","title":"Speciation through competition: A critical review","publisher":"Wiley-Blackwell","volume":59,"day":"01","month":"06","date_published":"2005-06-01T00:00:00Z","extern":1,"quality_controlled":0,"status":"public","doi":"10.1111/j.0014-3820.2005.tb01771.x"},{"title":"Evolution of recombination due to random drift","intvolume":"       169","publist_id":"1846","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Nicholas Barton","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarah","last_name":"Otto","full_name":"Otto, Sarah P"}],"month":"03","date_published":"2005-03-01T00:00:00Z","volume":169,"day":"01","publisher":"Genetics Society of America","quality_controlled":0,"extern":1,"status":"public","doi":"10.1534/genetics.104.032821","date_created":"2018-12-11T12:07:51Z","publication":"Genetics","year":"2005","_id":"4251","date_updated":"2021-01-12T07:55:37Z","citation":{"ieee":"N. H. Barton and S. Otto, “Evolution of recombination due to random drift,” <i>Genetics</i>, vol. 169, no. 4. Genetics Society of America, pp. 2353–2370, 2005.","mla":"Barton, Nicholas H., and Sarah Otto. “Evolution of Recombination Due to Random Drift.” <i>Genetics</i>, vol. 169, no. 4, Genetics Society of America, 2005, pp. 2353–70, doi:<a href=\"https://doi.org/10.1534/genetics.104.032821\">10.1534/genetics.104.032821</a>.","chicago":"Barton, Nicholas H, and Sarah Otto. “Evolution of Recombination Due to Random Drift.” <i>Genetics</i>. Genetics Society of America, 2005. <a href=\"https://doi.org/10.1534/genetics.104.032821\">https://doi.org/10.1534/genetics.104.032821</a>.","ama":"Barton NH, Otto S. Evolution of recombination due to random drift. <i>Genetics</i>. 2005;169(4):2353-2370. doi:<a href=\"https://doi.org/10.1534/genetics.104.032821\">10.1534/genetics.104.032821</a>","short":"N.H. Barton, S. Otto, Genetics 169 (2005) 2353–2370.","apa":"Barton, N. H., &#38; Otto, S. (2005). Evolution of recombination due to random drift. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.104.032821\">https://doi.org/10.1534/genetics.104.032821</a>","ista":"Barton NH, Otto S. 2005. Evolution of recombination due to random drift. Genetics. 169(4), 2353–2370."},"issue":"4","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts independently (i.e. multiplicatively) upon all loci. Negative disequilibrium reduces the variance in fitness and hence, by FISHER's Fundamental Theorem (1930), slows the rate of increase in mean fitness. Modifiers that increase recombination eliminate the negative disequilibria that impede selection and consequently increase in frequency by 'hitch-hiking'. In addition, recombinant progeny are more fit on average than non-recombinant progeny when there is negative linkage disequilibrium and loci interact multiplicatively. For both these reasons, stochastic fluctuations in linkage disequilibrium in finite populations favor the evolution of increased rates of recombination, even in the absence of epistatic interactions among loci and even when disequilibrium is initially absent. The method developed within this paper quantifies the strength of selection on a modifier allele that increases recombination due to stochastically generated linkage disequilibria. The analysis indicates that, in a population subject to multiplicative selection, genetic associations generated by drift do select for increased recombination, a result that is confirmed by Monte Carlo simulations. Selection for a modifier that increases recombination is highest when linkage among all loci is tight, when beneficial alleles rise from low to high frequency, and when the population size is small."}],"page":"2353 - 2370"},{"_id":"4252","year":"2005","date_updated":"2021-01-12T07:55:38Z","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569515/","open_access":"1"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","date_created":"2018-12-11T12:07:51Z","publication_status":"published","abstract":[{"text":"Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, ‘mutation–selection models’, that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of ‘balancing selection models’. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some","lang":"eng"}],"page":"1411 - 1425","type":"journal_article","issue":"1459","citation":{"ieee":"T. Johnson and N. H. Barton, “Theoretical models of selection and mutationon quantitative traits,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 360, no. 1459. Royal Society, The, pp. 1411–1425, 2005.","mla":"Johnson, Toby, and Nicholas H. Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 360, no. 1459, Royal Society, The, 2005, pp. 1411–25, doi:<a href=\"https://doi.org/10.1098/rstb.2005.1667\">10.1098/rstb.2005.1667</a>.","chicago":"Johnson, Toby, and Nicholas H Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2005. <a href=\"https://doi.org/10.1098/rstb.2005.1667\">https://doi.org/10.1098/rstb.2005.1667</a>.","ama":"Johnson T, Barton NH. Theoretical models of selection and mutationon quantitative traits. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2005;360(1459):1411-1425. doi:<a href=\"https://doi.org/10.1098/rstb.2005.1667\">10.1098/rstb.2005.1667</a>","apa":"Johnson, T., &#38; Barton, N. H. (2005). Theoretical models of selection and mutationon quantitative traits. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2005.1667\">https://doi.org/10.1098/rstb.2005.1667</a>","short":"T. Johnson, N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360 (2005) 1411–1425.","ista":"Johnson T, Barton NH. 2005. Theoretical models of selection and mutationon quantitative traits. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360(1459), 1411–1425."},"publisher":"Royal Society, The","day":"29","volume":360,"month":"07","date_published":"2005-07-29T00:00:00Z","author":[{"first_name":"Toby","full_name":"Johnson, Toby","last_name":"Johnson"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Nicholas Barton","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"title":"Theoretical models of selection and mutationon quantitative traits","intvolume":"       360","publist_id":"1847","doi":"10.1098/rstb.2005.1667","status":"public","extern":1,"quality_controlled":0},{"extern":1,"quality_controlled":0,"doi":"1550","status":"public","author":[{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski,Andreas"},{"first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Wies","last_name":"Wies"}],"title":"Boolean Heaps","publist_id":"1092","day":"01","publisher":"Springer","date_published":"2005-01-01T00:00:00Z","month":"01","alternative_title":["LNCS 3672"],"citation":{"ista":"Podelski A, Wies T. 2005. Boolean Heaps. SAS: Static Analysis Symposium, LNCS 3672, , 267–282.","apa":"Podelski, A., &#38; Wies, T. (2005). Boolean Heaps (pp. 267–282). Presented at the SAS: Static Analysis Symposium, Springer. <a href=\"https://doi.org/1550\">https://doi.org/1550</a>","short":"A. Podelski, T. Wies, in:, Springer, 2005, pp. 267–282.","ama":"Podelski A, Wies T. Boolean Heaps. In: Springer; 2005:267-282. doi:<a href=\"https://doi.org/1550\">1550</a>","chicago":"Podelski, Andreas, and Thomas Wies. “Boolean Heaps,” 267–82. Springer, 2005. <a href=\"https://doi.org/1550\">https://doi.org/1550</a>.","mla":"Podelski, Andreas, and Thomas Wies. <i>Boolean Heaps</i>. Springer, 2005, pp. 267–82, doi:<a href=\"https://doi.org/1550\">1550</a>.","ieee":"A. Podelski and T. Wies, “Boolean Heaps,” presented at the SAS: Static Analysis Symposium, 2005, pp. 267–282."},"publication_status":"published","page":"267 - 282","type":"conference","conference":{"name":"SAS: Static Analysis Symposium"},"date_created":"2018-12-11T12:08:29Z","_id":"4367","date_updated":"2021-01-12T07:56:27Z","year":"2005"},{"conference":{"name":"POPL: Principles of Programming Languages"},"date_created":"2018-12-11T12:08:41Z","_id":"4404","year":"2005","date_updated":"2021-01-12T07:56:44Z","citation":{"ista":"Alur R, Cerny P, Madhusudan P, Nam W. 2005. Synthesis of interface specifications for Java classes. POPL: Principles of Programming Languages, 98–109.","mla":"Alur, Rajeev, et al. <i>Synthesis of Interface Specifications for Java Classes</i>. ACM, 2005, pp. 98–109, doi:<a href=\"https://doi.org/1542\">1542</a>.","ieee":"R. Alur, P. Cerny, P. Madhusudan, and W. Nam, “Synthesis of interface specifications for Java classes,” presented at the POPL: Principles of Programming Languages, 2005, pp. 98–109.","apa":"Alur, R., Cerny, P., Madhusudan, P., &#38; Nam, W. (2005). Synthesis of interface specifications for Java classes (pp. 98–109). Presented at the POPL: Principles of Programming Languages, ACM. <a href=\"https://doi.org/1542\">https://doi.org/1542</a>","short":"R. Alur, P. Cerny, P. Madhusudan, W. Nam, in:, ACM, 2005, pp. 98–109.","chicago":"Alur, Rajeev, Pavol Cerny, P. Madhusudan, and Wonhong Nam. “Synthesis of Interface Specifications for Java Classes,” 98–109. ACM, 2005. <a href=\"https://doi.org/1542\">https://doi.org/1542</a>.","ama":"Alur R, Cerny P, Madhusudan P, Nam W. Synthesis of interface specifications for Java classes. In: ACM; 2005:98-109. doi:<a href=\"https://doi.org/1542\">1542</a>"},"publication_status":"published","page":"98 - 109","type":"conference","author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Pavol Cerny","first_name":"Pavol"},{"first_name":"P.","full_name":"Madhusudan,P.","last_name":"Madhusudan"},{"full_name":"Nam,Wonhong","last_name":"Nam","first_name":"Wonhong"}],"title":"Synthesis of interface specifications for Java classes","publist_id":"1053","day":"01","publisher":"ACM","date_published":"2005-01-01T00:00:00Z","month":"01","extern":1,"quality_controlled":0,"status":"public","doi":"1542"},{"year":"2005","_id":"4412","date_updated":"2021-01-12T07:56:47Z","date_created":"2018-12-11T12:08:43Z","conference":{"name":"RTSS: Real-Time Systems Symposium"},"type":"conference","page":"99 - 110","abstract":[{"text":"The periodic resource model for hierarchical, compositional scheduling abstracts task groups by resource requirements. We study this model in the presence of dataflow constraints between the tasks within a group (intragroup dependencies), and between tasks in different groups (inter-group dependencies). We consider two natural semantics for dataflow constraints, namely, RTW (real-time workshop) semantics and LET (logical execution time) semantics. We show that while RTW semantics offers better end-to-end latency on the task group level, LET semantics allows tighter resource bounds in the abstraction hierarchy and therefore provides better composability properties. This result holds both for intragroup and intergroup dependencies, as well as for shared and for distributed resources.","lang":"eng"}],"publication_status":"published","citation":{"ieee":"S. Matic and T. A. Henzinger, “Trading end-to-end latency for composability,” presented at the RTSS: Real-Time Systems Symposium, 2005, pp. 99–110.","mla":"Matic, Slobodan, and Thomas A. Henzinger. <i>Trading End-to-End Latency for Composability</i>. IEEE, 2005, pp. 99–110, doi:<a href=\"https://doi.org/10.1109/RTSS.2005.43\">10.1109/RTSS.2005.43</a>.","chicago":"Matic, Slobodan, and Thomas A Henzinger. “Trading End-to-End Latency for Composability,” 99–110. IEEE, 2005. <a href=\"https://doi.org/10.1109/RTSS.2005.43\">https://doi.org/10.1109/RTSS.2005.43</a>.","ama":"Matic S, Henzinger TA. Trading end-to-end latency for composability. In: IEEE; 2005:99-110. doi:<a href=\"https://doi.org/10.1109/RTSS.2005.43\">10.1109/RTSS.2005.43</a>","apa":"Matic, S., &#38; Henzinger, T. A. (2005). Trading end-to-end latency for composability (pp. 99–110). Presented at the RTSS: Real-Time Systems Symposium, IEEE. <a href=\"https://doi.org/10.1109/RTSS.2005.43\">https://doi.org/10.1109/RTSS.2005.43</a>","short":"S. Matic, T.A. Henzinger, in:, IEEE, 2005, pp. 99–110.","ista":"Matic S, Henzinger TA. 2005. Trading end-to-end latency for composability. RTSS: Real-Time Systems Symposium, 99–110."},"date_published":"2005-01-01T00:00:00Z","month":"01","day":"01","publisher":"IEEE","publist_id":"317","title":"Trading end-to-end latency for composability","author":[{"first_name":"Slobodan","full_name":"Matic, Slobodan","last_name":"Matic"},{"full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"}],"status":"public","doi":"10.1109/RTSS.2005.43","quality_controlled":0,"extern":1},{"citation":{"ieee":"C. Kirsch, M. Sanvido, and T. A. Henzinger, “A programmable microkernel for real-time systems,” presented at the VEE: Virtual Execution Environments, 2005, pp. 35–45.","mla":"Kirsch, Christoph, et al. <i>A Programmable Microkernel for Real-Time Systems</i>. ACM, 2005, pp. 35–45, doi:<a href=\"https://doi.org/10.1145/1064979.1064986\">10.1145/1064979.1064986</a>.","chicago":"Kirsch, Christoph, Marco Sanvido, and Thomas A Henzinger. “A Programmable Microkernel for Real-Time Systems,” 35–45. ACM, 2005. <a href=\"https://doi.org/10.1145/1064979.1064986\">https://doi.org/10.1145/1064979.1064986</a>.","ama":"Kirsch C, Sanvido M, Henzinger TA. A programmable microkernel for real-time systems. In: ACM; 2005:35-45. doi:<a href=\"https://doi.org/10.1145/1064979.1064986\">10.1145/1064979.1064986</a>","short":"C. Kirsch, M. Sanvido, T.A. Henzinger, in:, ACM, 2005, pp. 35–45.","apa":"Kirsch, C., Sanvido, M., &#38; Henzinger, T. A. (2005). A programmable microkernel for real-time systems (pp. 35–45). Presented at the VEE: Virtual Execution Environments, ACM. <a href=\"https://doi.org/10.1145/1064979.1064986\">https://doi.org/10.1145/1064979.1064986</a>","ista":"Kirsch C, Sanvido M, Henzinger TA. 2005. A programmable microkernel for real-time systems. VEE: Virtual Execution Environments, 35–45."},"type":"conference","abstract":[{"text":"We present a new software system architecture for the implementation of hard real-time applications. The core of the system is a microkernel whose reactivity (interrupt handling as in synchronous reactive programs) and proactivity (task scheduling as in traditional RTOSs) are fully programmable. The microkernel, which we implemented on a StrongARM processor, consists of two interacting domain-specific virtual machines, a reactive E (Embedded) machine and a proactive S (Scheduling) machine. The microkernel code (or microcode) that runs on the microkernel is partitioned into E and S code. E code manages the interaction of the system with the physical environment: the execution of E code is triggered by environment interrupts, which signal external events such as the arrival of a message or sensor value, and it releases application tasks to the S machine. S code manages the interaction of the system with the processor: the execution of S code is triggered by hardware interrupts, which signal internal events such as the completion of a task or time slice, and it dispatches application tasks to the CPU, possibly preempting a running task. This partition of the system orthogonalizes the two main concerns of real-time implementations: E code refers to environment time and thus defines the reactivity of the system in a hardware- and scheduler-independent fashion; S code refers to CPU time and defines a system scheduler. If both time lines can be reconciled, then the code is called time safe; violations of time safety are handled again in a programmable way, by run-time exceptions. The separation of E from S code permits the independent programming, verification, optimization, composition, dynamic adaptation, and reuse of both reaction and scheduling mechanisms. Our measurements show that the system overhead is very acceptable even for large sets of task, generally in the 0.2--0.3% range.","lang":"eng"}],"page":"35 - 45","publication_status":"published","date_created":"2018-12-11T12:08:45Z","conference":{"name":"VEE: Virtual Execution Environments"},"_id":"4418","year":"2005","date_updated":"2021-01-12T07:56:49Z","quality_controlled":0,"extern":1,"doi":"10.1145/1064979.1064986","status":"public","publist_id":"311","title":"A programmable microkernel for real-time systems","author":[{"last_name":"Kirsch","full_name":"Kirsch, Christoph M","first_name":"Christoph"},{"last_name":"Sanvido","full_name":"Sanvido, Marco A","first_name":"Marco"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"month":"01","date_published":"2005-01-01T00:00:00Z","day":"01","publisher":"ACM"},{"publication":"ACM Transactions on Computational Logic (TOCL)","date_created":"2018-12-11T12:08:56Z","date_updated":"2021-01-12T07:57:05Z","_id":"4454","year":"2005","issue":"1","citation":{"ista":"Henzinger TA, Majumdar R, Raskin J. 2005. A classification of symbolic transition systems. ACM Transactions on Computational Logic (TOCL). 6(1), 1–32.","apa":"Henzinger, T. A., Majumdar, R., &#38; Raskin, J. (2005). A classification of symbolic transition systems. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/1042038.1042039\">https://doi.org/10.1145/1042038.1042039</a>","short":"T.A. Henzinger, R. Majumdar, J. Raskin, ACM Transactions on Computational Logic (TOCL) 6 (2005) 1–32.","ama":"Henzinger TA, Majumdar R, Raskin J. A classification of symbolic transition systems. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2005;6(1):1-32. doi:<a href=\"https://doi.org/10.1145/1042038.1042039\">10.1145/1042038.1042039</a>","chicago":"Henzinger, Thomas A, Ritankar Majumdar, and Jean Raskin. “A Classification of Symbolic Transition Systems.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2005. <a href=\"https://doi.org/10.1145/1042038.1042039\">https://doi.org/10.1145/1042038.1042039</a>.","mla":"Henzinger, Thomas A., et al. “A Classification of Symbolic Transition Systems.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 6, no. 1, ACM, 2005, pp. 1–32, doi:<a href=\"https://doi.org/10.1145/1042038.1042039\">10.1145/1042038.1042039</a>.","ieee":"T. A. Henzinger, R. Majumdar, and J. Raskin, “A classification of symbolic transition systems,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 6, no. 1. ACM, pp. 1–32, 2005."},"publication_status":"published","abstract":[{"text":"We define five increasingly comprehensive classes of infinite-state systems, called STS1--STS5, whose state spaces have finitary structure. For four of these classes, we provide examples from hybrid systems.STS1 These are the systems with finite bisimilarity quotients. They can be analyzed symbolically by iteratively applying predecessor and Boolean operations on state sets, starting from a finite number of observable state sets. Any such iteration is guaranteed to terminate in that only a finite number of state sets can be generated. This enables model checking of the μ-calculus.STS2 These are the systems with finite similarity quotients. They can be analyzed symbolically by iterating the predecessor and positive Boolean operations. This enables model checking of the existential and universal fragments of the μ-calculus.STS3 These are the systems with finite trace-equivalence quotients. They can be analyzed symbolically by iterating the predecessor operation and a restricted form of positive Boolean operations (intersection is restricted to intersection with observables). This enables model checking of all ω-regular properties, including linear temporal logic.STS4 These are the systems with finite distance-equivalence quotients (two states are equivalent if for every distance d, the same observables can be reached in d transitions). The systems in this class can be analyzed symbolically by iterating the predecessor operation and terminating when no new state sets are generated. This enables model checking of the existential conjunction-free and universal disjunction-free fragments of the μ-calculus.STS5 These are the systems with finite bounded-reachability quotients (two states are equivalent if for every distance d, the same observables can be reached in d or fewer transitions). The systems in this class can be analyzed symbolically by iterating the predecessor operation and terminating when no new states are encountered (this is a weaker termination condition than above). This enables model checking of reachability properties.","lang":"eng"}],"page":"1 - 32","type":"journal_article","author":[{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","last_name":"Henzinger"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar S"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean"}],"title":"A classification of symbolic transition systems","publist_id":"272","intvolume":"         6","publisher":"ACM","volume":6,"day":"01","date_published":"2005-01-01T00:00:00Z","month":"01","extern":1,"quality_controlled":0,"doi":"10.1145/1042038.1042039","status":"public"},{"intvolume":"      3829","publist_id":"273","title":"Quantifying similarities between timed systems","acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF grants CCR-0208875, CCR-0225610, and CCR-0427202.","author":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar S","last_name":"Majumdar"},{"first_name":"Vinayak","full_name":"Prabhu, Vinayak S","last_name":"Prabhu"}],"date_published":"2005-12-13T00:00:00Z","month":"12","publisher":"Springer","day":"13","volume":3829,"quality_controlled":0,"extern":1,"status":"public","doi":"10.1007/11603009_18","date_created":"2018-12-11T12:08:56Z","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"_id":"4455","year":"2005","date_updated":"2021-01-12T07:57:05Z","citation":{"ista":"Henzinger TA, Majumdar R, Prabhu V. 2005. Quantifying similarities between timed systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 3829, 226–241.","chicago":"Henzinger, Thomas A, Ritankar Majumdar, and Vinayak Prabhu. “Quantifying Similarities between Timed Systems,” 3829:226–41. Springer, 2005. <a href=\"https://doi.org/10.1007/11603009_18\">https://doi.org/10.1007/11603009_18</a>.","ama":"Henzinger TA, Majumdar R, Prabhu V. Quantifying similarities between timed systems. In: Vol 3829. Springer; 2005:226-241. doi:<a href=\"https://doi.org/10.1007/11603009_18\">10.1007/11603009_18</a>","apa":"Henzinger, T. A., Majumdar, R., &#38; Prabhu, V. (2005). Quantifying similarities between timed systems (Vol. 3829, pp. 226–241). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. <a href=\"https://doi.org/10.1007/11603009_18\">https://doi.org/10.1007/11603009_18</a>","short":"T.A. Henzinger, R. Majumdar, V. Prabhu, in:, Springer, 2005, pp. 226–241.","ieee":"T. A. Henzinger, R. Majumdar, and V. Prabhu, “Quantifying similarities between timed systems,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2005, vol. 3829, pp. 226–241.","mla":"Henzinger, Thomas A., et al. <i>Quantifying Similarities between Timed Systems</i>. Vol. 3829, Springer, 2005, pp. 226–41, doi:<a href=\"https://doi.org/10.1007/11603009_18\">10.1007/11603009_18</a>."},"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We define quantitative similarity functions between timed transition systems that measure the degree of closeness of two systems as a real, in contrast to the traditional boolean yes/no approach to timed simulation and language inclusion. Two systems are close if for each timed trace of one system, there exists a corresponding timed trace in the other system with the same sequence of events and closely corresponding event timings. We show that timed CTL is robust with respect to our quantitative version of bisimilarity, in particular, if a system satisfies a formula, then every close system satisfies a close formula. We also define a discounted version of CTL over timed systems, which assigns to every CTL formula a real value that is obtained by discounting real time. We prove the robustness of discounted CTL by establishing that close states in the bisimilarity metric have close values for all discounted CTL formulas.","lang":"eng"}],"page":"226 - 241","publication_status":"published"}]