[{"publication_status":"published","date_published":"2014-11-07T00:00:00Z","doi":"10.1016/j.jtbi.2014.06.039","status":"public","language":[{"iso":"eng"}],"citation":{"short":"J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.","ieee":"J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” <i>Journal of Theoretical Biology</i>, vol. 360. Elsevier, pp. 149–162, 2014.","chicago":"Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” <i>Journal of Theoretical Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jtbi.2014.06.039\">https://doi.org/10.1016/j.jtbi.2014.06.039</a>.","ista":"Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162.","mla":"Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” <i>Journal of Theoretical Biology</i>, vol. 360, Elsevier, 2014, pp. 149–62, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.06.039\">10.1016/j.jtbi.2014.06.039</a>.","apa":"Humplik, J., Hill, A., &#38; Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2014.06.039\">https://doi.org/10.1016/j.jtbi.2014.06.039</a>","ama":"Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. <i>Journal of Theoretical Biology</i>. 2014;360:149-162. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.06.039\">10.1016/j.jtbi.2014.06.039</a>"},"intvolume":"       360","abstract":[{"text":"In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen.","lang":"eng"}],"date_updated":"2021-01-12T06:54:08Z","day":"07","month":"11","oa_version":"None","type":"journal_article","page":"149 - 162","author":[{"full_name":"Humplik, Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik"},{"full_name":"Hill, Alison","first_name":"Alison","last_name":"Hill"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"date_created":"2018-12-11T11:54:46Z","publist_id":"5166","volume":360,"title":"Evolutionary dynamics of infectious diseases in finite populations","department":[{"_id":"GaTk"}],"year":"2014","publisher":"Elsevier","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague.","scopus_import":1,"publication":"Journal of Theoretical Biology","_id":"1928"},{"quality_controlled":"1","doi":"10.1007/s10958-014-2165-8","publication_identifier":{"issn":["1072-3374"],"eissn":["1573-8795"]},"issue":"6","language":[{"iso":"eng"}],"publist_id":"5165","title":"An algorithm for cartographic generalization that preserves global topology","day":"16","author":[{"full_name":"Alexeev, V V","first_name":"V V","last_name":"Alexeev"},{"first_name":"V G","last_name":"Bogaevskaya","full_name":"Bogaevskaya, V G"},{"last_name":"Preobrazhenskaya","first_name":"M M","full_name":"Preobrazhenskaya, M M"},{"first_name":"A Y","last_name":"Ukhalov","full_name":"Ukhalov, A Y"},{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Yakimova, Olga","last_name":"Yakimova","first_name":"Olga"}],"article_type":"original","article_processing_charge":"No","scopus_import":"1","publication":"Journal of Mathematical Sciences","department":[{"_id":"HeEd"}],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-11-16T00:00:00Z","publication_status":"published","citation":{"apa":"Alexeev, V. V., Bogaevskaya, V. G., Preobrazhenskaya, M. M., Ukhalov, A. Y., Edelsbrunner, H., &#38; Yakimova, O. (2014). An algorithm for cartographic generalization that preserves global topology. <i>Journal of Mathematical Sciences</i>. Springer. <a href=\"https://doi.org/10.1007/s10958-014-2165-8\">https://doi.org/10.1007/s10958-014-2165-8</a>","mla":"Alexeev, V. V., et al. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” <i>Journal of Mathematical Sciences</i>, vol. 203, no. 6, Springer, 2014, pp. 754–60, doi:<a href=\"https://doi.org/10.1007/s10958-014-2165-8\">10.1007/s10958-014-2165-8</a>.","ista":"Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. 2014. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 203(6), 754–760.","ama":"Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. An algorithm for cartographic generalization that preserves global topology. <i>Journal of Mathematical Sciences</i>. 2014;203(6):754-760. doi:<a href=\"https://doi.org/10.1007/s10958-014-2165-8\">10.1007/s10958-014-2165-8</a>","short":"V.V. Alexeev, V.G. Bogaevskaya, M.M. Preobrazhenskaya, A.Y. Ukhalov, H. Edelsbrunner, O. Yakimova, Journal of Mathematical Sciences 203 (2014) 754–760.","chicago":"Alexeev, V V, V G Bogaevskaya, M M Preobrazhenskaya, A Y Ukhalov, Herbert Edelsbrunner, and Olga Yakimova. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” <i>Journal of Mathematical Sciences</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s10958-014-2165-8\">https://doi.org/10.1007/s10958-014-2165-8</a>.","ieee":"V. V. Alexeev, V. G. Bogaevskaya, M. M. Preobrazhenskaya, A. Y. Ukhalov, H. Edelsbrunner, and O. Yakimova, “An algorithm for cartographic generalization that preserves global topology,” <i>Journal of Mathematical Sciences</i>, vol. 203, no. 6. Springer, pp. 754–760, 2014."},"intvolume":"       203","status":"public","date_created":"2018-12-11T11:54:46Z","volume":203,"type":"journal_article","oa_version":"None","month":"11","date_updated":"2022-05-24T10:39:06Z","abstract":[{"text":"We propose an algorithm for the generalization of cartographic objects that can be used to represent maps on different scales.","lang":"eng"}],"page":"754 - 760","_id":"1929","year":"2014","acknowledgement":"We would like to offer our special thanks to students of the Department of Mathematics of Demidov Yaroslavl State University A. A. Gorokhov and V. N. Knyazev for participation in developing the program and assistance in preparation of test data. This work was supported by grant 11.G34.31.0053 from the government of the Russian Federation."},{"publisher":"IEEE","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC","department":[{"_id":"HeEd"}],"year":"2014","publication":"IEEE Transactions on Visualization and Computer Graphics","_id":"1930","scopus_import":1,"page":"2585 - 2594","author":[{"first_name":"David","last_name":"Günther","full_name":"Günther, David"},{"full_name":"Jacobson, Alec","first_name":"Alec","last_name":"Jacobson"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan","first_name":"Jan","last_name":"Reininghaus"},{"full_name":"Seidel, Hans","first_name":"Hans","last_name":"Seidel"},{"full_name":"Sorkine Hornung, Olga","first_name":"Olga","last_name":"Sorkine Hornung"},{"full_name":"Weinkauf, Tino","first_name":"Tino","last_name":"Weinkauf"}],"day":"31","abstract":[{"text":"(Figure Presented) Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications.","lang":"eng"}],"date_updated":"2021-01-12T06:54:09Z","oa_version":"None","type":"journal_article","month":"12","title":"Fast and memory-efficient topological denoising of 2D and 3D scalar fields","volume":20,"date_created":"2018-12-11T11:54:46Z","publist_id":"5164","status":"public","intvolume":"        20","language":[{"iso":"eng"}],"citation":{"short":"D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, T. Weinkauf, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 2585–2594.","ieee":"D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, and T. Weinkauf, “Fast and memory-efficient topological denoising of 2D and 3D scalar fields,” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 20, no. 12. IEEE, pp. 2585–2594, 2014.","chicago":"Günther, David, Alec Jacobson, Jan Reininghaus, Hans Seidel, Olga Sorkine Hornung, and Tino Weinkauf. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/TVCG.2014.2346432\">https://doi.org/10.1109/TVCG.2014.2346432</a>.","ista":"Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. 2014. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 20(12), 2585–2594.","mla":"Günther, David, et al. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 20, no. 12, IEEE, 2014, pp. 2585–94, doi:<a href=\"https://doi.org/10.1109/TVCG.2014.2346432\">10.1109/TVCG.2014.2346432</a>.","apa":"Günther, D., Jacobson, A., Reininghaus, J., Seidel, H., Sorkine Hornung, O., &#38; Weinkauf, T. (2014). Fast and memory-efficient topological denoising of 2D and 3D scalar fields. <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE. <a href=\"https://doi.org/10.1109/TVCG.2014.2346432\">https://doi.org/10.1109/TVCG.2014.2346432</a>","ama":"Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. <i>IEEE Transactions on Visualization and Computer Graphics</i>. 2014;20(12):2585-2594. doi:<a href=\"https://doi.org/10.1109/TVCG.2014.2346432\">10.1109/TVCG.2014.2346432</a>"},"issue":"12","publication_status":"published","date_published":"2014-12-31T00:00:00Z","doi":"10.1109/TVCG.2014.2346432","quality_controlled":"1"},{"language":[{"iso":"eng"}],"issue":"MAY","doi":"10.3389/fncom.2014.00057","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Research Foundation","department":[{"_id":"GaTk"}],"publication":"Frontiers in Computational Neuroscience","scopus_import":1,"author":[{"last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Triesch, Jochen","first_name":"Jochen","last_name":"Triesch"}],"day":"28","title":"Emergence of task-dependent representations in working memory circuits","article_number":"57","publist_id":"5163","status":"public","intvolume":"         8","citation":{"ieee":"C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” <i>Frontiers in Computational Neuroscience</i>, vol. 8, no. MAY. Frontiers Research Foundation, 2014.","chicago":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” <i>Frontiers in Computational Neuroscience</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fncom.2014.00057\">https://doi.org/10.3389/fncom.2014.00057</a>.","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).","ama":"Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. <i>Frontiers in Computational Neuroscience</i>. 2014;8(MAY). doi:<a href=\"https://doi.org/10.3389/fncom.2014.00057\">10.3389/fncom.2014.00057</a>","ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.","mla":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” <i>Frontiers in Computational Neuroscience</i>, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fncom.2014.00057\">10.3389/fncom.2014.00057</a>.","apa":"Savin, C., &#38; Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. <i>Frontiers in Computational Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncom.2014.00057\">https://doi.org/10.3389/fncom.2014.00057</a>"},"oa":1,"publication_status":"published","date_published":"2014-05-28T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/"}],"acknowledgement":"Supported in part by EC MEXT project PLICON and the LOEWE-Program “Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported by the Quandt foundation.","year":"2014","_id":"1931","abstract":[{"text":"A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity.","lang":"eng"}],"date_updated":"2021-01-12T06:54:09Z","type":"journal_article","month":"05","oa_version":"Submitted Version","volume":8,"date_created":"2018-12-11T11:54:46Z"},{"publist_id":"5162","title":"Cryptic genetic variation can make &quot;irreducible complexity&quot; a common mode of adaptation in sexual populations","day":"01","author":[{"last_name":"Trotter","first_name":"Meredith","full_name":"Trotter, Meredith"},{"first_name":"Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel"},{"first_name":"Grant","last_name":"Peterson","full_name":"Peterson, Grant"},{"last_name":"Peck","first_name":"Kayla","full_name":"Peck, Kayla"},{"last_name":"Masel","first_name":"Joanna","full_name":"Masel, Joanna"}],"ec_funded":1,"scopus_import":1,"publication":"Evolution","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1111/evo.12517","language":[{"iso":"eng"}],"issue":"12","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"date_created":"2018-12-11T11:54:47Z","volume":68,"date_updated":"2021-01-12T06:54:10Z","abstract":[{"text":"The existence of complex (multiple-step) genetic adaptations that are &quot;irreducible&quot; (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce &quot;irreducibly complex&quot; adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.","lang":"eng"}],"month":"12","type":"journal_article","oa_version":"Submitted Version","page":"3357 - 3367","_id":"1932","year":"2014","acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040         \r\n\r\nSimons Foundation\r\n\r\n","main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"date_published":"2014-12-01T00:00:00Z","publication_status":"published","oa":1,"citation":{"short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367.","ieee":"M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations,” <i>Evolution</i>, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014.","chicago":"Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make &#38;quot;Irreducible Complexity&#38;quot; a Common Mode of Adaptation in Sexual Populations.” <i>Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/evo.12517\">https://doi.org/10.1111/evo.12517</a>.","ista":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367.","mla":"Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make &#38;quot;Irreducible Complexity&#38;quot; a Common Mode of Adaptation in Sexual Populations.” <i>Evolution</i>, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:<a href=\"https://doi.org/10.1111/evo.12517\">10.1111/evo.12517</a>.","apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., &#38; Masel, J. (2014). Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/evo.12517\">https://doi.org/10.1111/evo.12517</a>","ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make &#38;quot;irreducible complexity&#38;quot; a common mode of adaptation in sexual populations. <i>Evolution</i>. 2014;68(12):3357-3367. doi:<a href=\"https://doi.org/10.1111/evo.12517\">10.1111/evo.12517</a>"},"intvolume":"        68","status":"public"},{"scopus_import":1,"_id":"1933","publication":"Development","department":[{"_id":"RySh"}],"year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists","date_created":"2018-12-11T11:54:47Z","publist_id":"5161","volume":141,"title":"Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates","oa_version":"None","month":"04","type":"journal_article","day":"01","abstract":[{"lang":"eng","text":"The development of the vertebrate brain requires an exquisite balance between proliferation and differentiation of neural progenitors. Notch signaling plays a pivotal role in regulating this balance, yet the interaction between signaling and receiving cells remains poorly understood. We have found that numerous nascent neurons and/or intermediate neurogenic progenitors expressing the ligand of Notch retain apical endfeet transiently at the ventricular lumen that form adherens junctions (AJs) with the endfeet of progenitors. Forced detachment of the apical endfeet of those differentiating cells by disrupting AJs resulted in precocious neurogenesis that was preceded by the downregulation of Notch signaling. Both Notch1 and its ligand Dll1 are distributed around AJs in the apical endfeet, and these proteins physically interact with ZO-1, a constituent of the AJ. Furthermore, live imaging of a fluorescently tagged Notch1 demonstrated its trafficking from the apical endfoot to the nucleus upon cleavage. Our results identified the apical endfoot as the central site of active Notch signaling to securely prohibit inappropriate differentiation of neural progenitors."}],"date_updated":"2021-01-12T06:54:10Z","author":[{"last_name":"Hatakeyama","first_name":"Jun","full_name":"Hatakeyama, Jun"},{"last_name":"Wakamatsu","first_name":"Yoshio","full_name":"Wakamatsu, Yoshio"},{"full_name":"Nagafuchi, Akira","last_name":"Nagafuchi","first_name":"Akira"},{"last_name":"Kageyama","first_name":"Ryoichiro","full_name":"Kageyama, Ryoichiro"},{"first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"last_name":"Shimamura","first_name":"Kenji","full_name":"Shimamura, Kenji"}],"page":"1671 - 1682","issue":"8","citation":{"ama":"Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. <i>Development</i>. 2014;141(8):1671-1682. doi:<a href=\"https://doi.org/10.1242/dev.102988\">10.1242/dev.102988</a>","ista":"Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. 2014. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 141(8), 1671–1682.","mla":"Hatakeyama, Jun, et al. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” <i>Development</i>, vol. 141, no. 8, Company of Biologists, 2014, pp. 1671–82, doi:<a href=\"https://doi.org/10.1242/dev.102988\">10.1242/dev.102988</a>.","apa":"Hatakeyama, J., Wakamatsu, Y., Nagafuchi, A., Kageyama, R., Shigemoto, R., &#38; Shimamura, K. (2014). Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.102988\">https://doi.org/10.1242/dev.102988</a>","ieee":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, and K. Shimamura, “Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates,” <i>Development</i>, vol. 141, no. 8. Company of Biologists, pp. 1671–1682, 2014.","chicago":"Hatakeyama, Jun, Yoshio Wakamatsu, Akira Nagafuchi, Ryoichiro Kageyama, Ryuichi Shigemoto, and Kenji Shimamura. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” <i>Development</i>. Company of Biologists, 2014. <a href=\"https://doi.org/10.1242/dev.102988\">https://doi.org/10.1242/dev.102988</a>.","short":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682."},"language":[{"iso":"eng"}],"intvolume":"       141","status":"public","quality_controlled":"1","date_published":"2014-04-01T00:00:00Z","doi":"10.1242/dev.102988","publication_status":"published"},{"status":"public","project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"citation":{"ista":"Marhavý P, Duclercq J, Weller B, Feraru E, Bielach A, Offringa R, Friml J, Schwechheimer C, Murphy A, Benková E. 2014. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 24(9), 1031–1037.","mla":"Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” <i>Current Biology</i>, vol. 24, no. 9, Cell Press, 2014, pp. 1031–37, doi:<a href=\"https://doi.org/10.1016/j.cub.2014.04.002\">10.1016/j.cub.2014.04.002</a>.","apa":"Marhavý, P., Duclercq, J., Weller, B., Feraru, E., Bielach, A., Offringa, R., … Benková, E. (2014). Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2014.04.002\">https://doi.org/10.1016/j.cub.2014.04.002</a>","ama":"Marhavý P, Duclercq J, Weller B, et al. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. <i>Current Biology</i>. 2014;24(9):1031-1037. doi:<a href=\"https://doi.org/10.1016/j.cub.2014.04.002\">10.1016/j.cub.2014.04.002</a>","short":"P. Marhavý, J. Duclercq, B. Weller, E. Feraru, A. Bielach, R. Offringa, J. Friml, C. Schwechheimer, A. Murphy, E. Benková, Current Biology 24 (2014) 1031–1037.","ieee":"P. Marhavý <i>et al.</i>, “Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis,” <i>Current Biology</i>, vol. 24, no. 9. Cell Press, pp. 1031–1037, 2014.","chicago":"Marhavý, Peter, Jérôme Duclercq, Benjamin Weller, Elena Feraru, Agnieszka Bielach, Remko Offringa, Jiří Friml, Claus Schwechheimer, Angus Murphy, and Eva Benková. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” <i>Current Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cub.2014.04.002\">https://doi.org/10.1016/j.cub.2014.04.002</a>."},"language":[{"iso":"eng"}],"issue":"9","intvolume":"        24","publication_status":"published","quality_controlled":"1","doi":"10.1016/j.cub.2014.04.002","date_published":"2014-05-05T00:00:00Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"year":"2014","publisher":"Cell Press","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"scopus_import":1,"publication":"Current Biology","_id":"1934","date_updated":"2021-01-12T06:54:10Z","abstract":[{"lang":"eng","text":"The plant hormones auxin and cytokinin mutually coordinate their activities to control various aspects of development [1-9], and their crosstalk occurs at multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate that cytokinin does not merely control the overall auxin flow capacity, but might also act as a polarizing cue and control the auxin stream directionality during plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter depletion at specific polar domains, thus rearranging the cellular PIN polarities and directly regulating the auxin flow direction. This selective cytokinin sensitivity correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking mutations, as well as enhanced phosphorylation in plants with modulated activities of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results reveal conceptually novel, cytokinin-driven polarization mechanism that operates in developmental processes involving rapid auxin stream redirection, such as lateral root organogenesis, in which a gradual PIN polarity switch defines the growth axis of the newly formed organ."}],"day":"05","type":"journal_article","oa_version":"None","month":"05","page":"1031 - 1037","author":[{"first_name":"Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter"},{"full_name":"Duclercq, Jérôme","first_name":"Jérôme","last_name":"Duclercq"},{"last_name":"Weller","first_name":"Benjamin","full_name":"Weller, Benjamin"},{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"full_name":"Bielach, Agnieszka","first_name":"Agnieszka","last_name":"Bielach"},{"full_name":"Offringa, Remko","last_name":"Offringa","first_name":"Remko"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"first_name":"Angus","last_name":"Murphy","full_name":"Murphy, Angus"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"}],"date_created":"2018-12-11T11:54:48Z","publist_id":"5160","volume":24,"title":"Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis"},{"language":[{"iso":"eng"}],"doi":"10.1007/s00220-014-1923-2","quality_controlled":"1","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"publication":"Communications in Mathematical Physics","scopus_import":"1","article_processing_charge":"No","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","department":[{"_id":"RoSe"}],"title":"Formation of stripes and slabs near the ferromagnetic transition","arxiv":1,"publist_id":"5159","author":[{"first_name":"Alessandro","last_name":"Giuliani","full_name":"Giuliani, Alessandro"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"day":"01","file":[{"content_type":"application/pdf","relation":"main_file","file_size":334064,"creator":"dernst","success":1,"file_name":"2014_CommMathPhysics_Giuliani.pdf","date_created":"2022-05-24T08:30:40Z","access_level":"open_access","date_updated":"2022-05-24T08:30:40Z","file_id":"11409","checksum":"c8423271cd1e1ba9e44c47af75efe7b6"}],"intvolume":"       331","citation":{"short":"A. Giuliani, É. Lieb, R. Seiringer, Communications in Mathematical Physics 331 (2014) 333–350.","chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” <i>Communications in Mathematical Physics</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00220-014-1923-2\">https://doi.org/10.1007/s00220-014-1923-2</a>.","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Formation of stripes and slabs near the ferromagnetic transition,” <i>Communications in Mathematical Physics</i>, vol. 331. Springer, pp. 333–350, 2014.","apa":"Giuliani, A., Lieb, É., &#38; Seiringer, R. (2014). Formation of stripes and slabs near the ferromagnetic transition. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-014-1923-2\">https://doi.org/10.1007/s00220-014-1923-2</a>","mla":"Giuliani, Alessandro, et al. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” <i>Communications in Mathematical Physics</i>, vol. 331, Springer, 2014, pp. 333–50, doi:<a href=\"https://doi.org/10.1007/s00220-014-1923-2\">10.1007/s00220-014-1923-2</a>.","ista":"Giuliani A, Lieb É, Seiringer R. 2014. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 331, 333–350.","ama":"Giuliani A, Lieb É, Seiringer R. Formation of stripes and slabs near the ferromagnetic transition. <i>Communications in Mathematical Physics</i>. 2014;331:333-350. doi:<a href=\"https://doi.org/10.1007/s00220-014-1923-2\">10.1007/s00220-014-1923-2</a>"},"status":"public","external_id":{"arxiv":["1304.6344"]},"ddc":["510"],"date_published":"2014-10-01T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","_id":"1935","acknowledgement":"2014 by the authors. This paper may be reproduced, in its entirety, for non-commercial purposes.\r\n\r\nThe research leading to these results has received funding from the European Research\r\nCouncil under the European Union’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694; A.G. and R.S.), the U.S. National Science Foundation (Grant PHY 0965859; E.H.L.), the Simons Foundation (Grant # 230207; E.H.L) and the NSERC (R.S.). The work is part of a project started in collaboration with Joel Lebowitz, whom we thank for many useful discussions and for his constant encouragement.","year":"2014","volume":331,"file_date_updated":"2022-05-24T08:30:40Z","date_created":"2018-12-11T11:54:48Z","page":"333 - 350","date_updated":"2022-05-24T08:32:50Z","abstract":[{"text":"We consider Ising models in d = 2 and d = 3 dimensions with nearest neighbor ferromagnetic and long-range antiferromagnetic interactions, the latter decaying as (distance)-p, p &gt; 2d, at large distances. If the strength J of the ferromagnetic interaction is larger than a critical value J c, then the ground state is homogeneous. It has been conjectured that when J is smaller than but close to J c, the ground state is periodic and striped, with stripes of constant width h = h(J), and h → ∞ as J → Jc -. (In d = 3 stripes mean slabs, not columns.) Here we rigorously prove that, if we normalize the energy in such a way that the energy of the homogeneous state is zero, then the ratio e 0(J)/e S(J) tends to 1 as J → Jc -, with e S(J) being the energy per site of the optimal periodic striped/slabbed state and e 0(J) the actual ground state energy per site of the system. Our proof comes with explicit bounds on the difference e 0(J)-e S(J) at small but positive J c-J, and also shows that in this parameter range the ground state is striped/slabbed in a certain sense: namely, if one looks at a randomly chosen window, of suitable size ℓ (very large compared to the optimal stripe size h(J)), one finds a striped/slabbed state with high probability.","lang":"eng"}],"type":"journal_article","month":"10","oa_version":"Published Version"},{"author":[{"last_name":"Arbilly","first_name":"Michal","full_name":"Arbilly, Michal"},{"full_name":"Weissman, Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman"},{"full_name":"Feldman, Marcus","first_name":"Marcus","last_name":"Feldman"},{"first_name":"Uri","last_name":"Grodzinski","full_name":"Grodzinski, Uri"}],"day":"13","title":"An arms race between producers and scroungers can drive the evolution of social cognition","publist_id":"5157","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"publication":"Behavioral Ecology","ec_funded":1,"scopus_import":1,"doi":"10.1093/beheco/aru002","quality_controlled":"1","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"issue":"3","language":[{"iso":"eng"}],"page":"487 - 495","month":"02","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures."}],"date_updated":"2021-01-12T06:54:11Z","volume":25,"date_created":"2018-12-11T11:54:48Z","year":"2014","_id":"1936","oa":1,"publication_status":"published","date_published":"2014-02-13T00:00:00Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/","open_access":"1"}],"status":"public","intvolume":"        25","citation":{"short":"M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495.","chicago":"Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” <i>Behavioral Ecology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/beheco/aru002\">https://doi.org/10.1093/beheco/aru002</a>.","ieee":"M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” <i>Behavioral Ecology</i>, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014.","apa":"Arbilly, M., Weissman, D., Feldman, M., &#38; Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. <i>Behavioral Ecology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/beheco/aru002\">https://doi.org/10.1093/beheco/aru002</a>","ista":"Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495.","mla":"Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” <i>Behavioral Ecology</i>, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:<a href=\"https://doi.org/10.1093/beheco/aru002\">10.1093/beheco/aru002</a>.","ama":"Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. <i>Behavioral Ecology</i>. 2014;25(3):487-495. doi:<a href=\"https://doi.org/10.1093/beheco/aru002\">10.1093/beheco/aru002</a>"}},{"doi":"10.1007/s00220-014-2120-z","quality_controlled":"1","project":[{"_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B"}],"issue":"1","language":[{"iso":"eng"}],"author":[{"last_name":"Bourgade","first_name":"Paul","full_name":"Bourgade, Paul"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"first_name":"Horngtzer","last_name":"Yau","full_name":"Yau, Horngtzer"}],"day":"01","title":"Edge universality of beta ensembles","publist_id":"5158","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","department":[{"_id":"LaEr"}],"publication":"Communications in Mathematical Physics","scopus_import":1,"oa":1,"publication_status":"published","date_published":"2014-11-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.5728"}],"status":"public","intvolume":"       332","citation":{"ama":"Bourgade P, Erdös L, Yau H. Edge universality of beta ensembles. <i>Communications in Mathematical Physics</i>. 2014;332(1):261-353. doi:<a href=\"https://doi.org/10.1007/s00220-014-2120-z\">10.1007/s00220-014-2120-z</a>","apa":"Bourgade, P., Erdös, L., &#38; Yau, H. (2014). Edge universality of beta ensembles. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-014-2120-z\">https://doi.org/10.1007/s00220-014-2120-z</a>","ista":"Bourgade P, Erdös L, Yau H. 2014. Edge universality of beta ensembles. Communications in Mathematical Physics. 332(1), 261–353.","mla":"Bourgade, Paul, et al. “Edge Universality of Beta Ensembles.” <i>Communications in Mathematical Physics</i>, vol. 332, no. 1, Springer, 2014, pp. 261–353, doi:<a href=\"https://doi.org/10.1007/s00220-014-2120-z\">10.1007/s00220-014-2120-z</a>.","chicago":"Bourgade, Paul, László Erdös, and Horngtzer Yau. “Edge Universality of Beta Ensembles.” <i>Communications in Mathematical Physics</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00220-014-2120-z\">https://doi.org/10.1007/s00220-014-2120-z</a>.","ieee":"P. Bourgade, L. Erdös, and H. Yau, “Edge universality of beta ensembles,” <i>Communications in Mathematical Physics</i>, vol. 332, no. 1. Springer, pp. 261–353, 2014.","short":"P. Bourgade, L. Erdös, H. Yau, Communications in Mathematical Physics 332 (2014) 261–353."},"page":"261 - 353","oa_version":"Submitted Version","type":"journal_article","month":"11","abstract":[{"text":"We prove the edge universality of the beta ensembles for any β ≥ 1, provided that the limiting spectrum is supported on a single interval, and the external potential is C4 and regular. We also prove that the edge universality holds for generalized Wigner matrices for all symmetry classes. Moreover, our results allow us to extend bulk universality for beta ensembles from analytic potentials to potentials in class C4.","lang":"eng"}],"date_updated":"2021-01-12T06:54:12Z","volume":332,"date_created":"2018-12-11T11:54:48Z","year":"2014","_id":"1937"},{"status":"public","citation":{"mla":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” <i>Journal of Bioenergetics and Biomembranes</i>, vol. 46, no. 4, Springer, 2014, pp. 247–53, doi:<a href=\"https://doi.org/10.1007/s10863-014-9554-z\">10.1007/s10863-014-9554-z</a>.","ista":"Sazanov LA. 2014. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 46(4), 247–253.","apa":"Sazanov, L. A. (2014). The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. <i>Journal of Bioenergetics and Biomembranes</i>. Springer. <a href=\"https://doi.org/10.1007/s10863-014-9554-z\">https://doi.org/10.1007/s10863-014-9554-z</a>","ama":"Sazanov LA. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. <i>Journal of Bioenergetics and Biomembranes</i>. 2014;46(4):247-253. doi:<a href=\"https://doi.org/10.1007/s10863-014-9554-z\">10.1007/s10863-014-9554-z</a>","short":"L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.","ieee":"L. A. Sazanov, “The mechanism of coupling between electron transfer and proton translocation in respiratory complex I,” <i>Journal of Bioenergetics and Biomembranes</i>, vol. 46, no. 4. Springer, pp. 247–253, 2014.","chicago":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” <i>Journal of Bioenergetics and Biomembranes</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s10863-014-9554-z\">https://doi.org/10.1007/s10863-014-9554-z</a>."},"issue":"4","extern":1,"intvolume":"        46","publication_status":"published","quality_controlled":0,"date_published":"2014-08-01T00:00:00Z","doi":"10.1007/s10863-014-9554-z","year":"2014","publisher":"Springer","publication":"Journal of Bioenergetics and Biomembranes","_id":"1979","date_updated":"2021-01-12T06:54:28Z","abstract":[{"lang":"eng","text":"NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine."}],"day":"01","type":"journal_article","month":"08","page":"247 - 253","author":[{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov","first_name":"Leonid A","last_name":"Sazanov"}],"date_created":"2018-12-11T11:55:01Z","publist_id":"5104","volume":46,"title":"The mechanism of coupling between electron transfer and proton translocation in respiratory complex I"},{"month":"03","type":"journal_article","day":"01","abstract":[{"lang":"eng","text":"Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors."}],"date_updated":"2021-01-12T06:54:29Z","page":"950 - 964","author":[{"first_name":"Adam","last_name":"Heikal","full_name":"Heikal, Adam "},{"last_name":"Nakatani","first_name":"Yoshio","full_name":"Nakatani, Yoshio"},{"full_name":"Dunn, Elyse A","last_name":"Dunn","first_name":"Elyse"},{"full_name":"Weimar, Marion R","last_name":"Weimar","first_name":"Marion"},{"last_name":"Day","first_name":"Catherine","full_name":"Day, Catherine"},{"first_name":"Edward","last_name":"Baker","full_name":"Baker, Edward N"},{"last_name":"Lott","first_name":"Shaun","full_name":"Lott, Shaun J"},{"last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov"},{"first_name":"Gregory","last_name":"Cook","full_name":"Cook, Gregory"}],"publist_id":"5103","date_created":"2018-12-11T11:55:01Z","volume":91,"title":"Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation","year":"2014","acknowledgement":"Funded by      Health Research Council of New Zealand     Royal Society of New Zealand     University of Otago     New Zealand Synchrotron Group","publisher":"Wiley-Blackwell","_id":"1980","publication":"Molecular Microbiology","publication_status":"published","quality_controlled":0,"doi":"10.1111/mmi.12507","date_published":"2014-03-01T00:00:00Z","status":"public","issue":"5","citation":{"mla":"Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” <i>Molecular Microbiology</i>, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:<a href=\"https://doi.org/10.1111/mmi.12507\">10.1111/mmi.12507</a>.","ista":"Heikal A, Nakatani Y, Dunn E, Weimar M, Day C, Baker E, Lott S, Sazanov LA, Cook G. 2014. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. 91(5), 950–964.","apa":"Heikal, A., Nakatani, Y., Dunn, E., Weimar, M., Day, C., Baker, E., … Cook, G. (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. <i>Molecular Microbiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mmi.12507\">https://doi.org/10.1111/mmi.12507</a>","ama":"Heikal A, Nakatani Y, Dunn E, et al. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. <i>Molecular Microbiology</i>. 2014;91(5):950-964. doi:<a href=\"https://doi.org/10.1111/mmi.12507\">10.1111/mmi.12507</a>","short":"A. Heikal, Y. Nakatani, E. Dunn, M. Weimar, C. Day, E. Baker, S. Lott, L.A. Sazanov, G. Cook, Molecular Microbiology 91 (2014) 950–964.","ieee":"A. Heikal <i>et al.</i>, “Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation,” <i>Molecular Microbiology</i>, vol. 91, no. 5. Wiley-Blackwell, pp. 950–964, 2014.","chicago":"Heikal, Adam, Yoshio Nakatani, Elyse Dunn, Marion Weimar, Catherine Day, Edward Baker, Shaun Lott, Leonid A Sazanov, and Gregory Cook. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” <i>Molecular Microbiology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/mmi.12507\">https://doi.org/10.1111/mmi.12507</a>."},"extern":1,"intvolume":"        91"},{"status":"public","extern":1,"intvolume":"        53","issue":"1","citation":{"apa":"Garvin, M., Bielawski, J., Sazanov, L. A., &#38; Gharrett, A. (2014). Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>","mla":"Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1, Wiley-Blackwell, 2014, pp. 1–17, doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>.","ista":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. 2014. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 53(1), 1–17.","ama":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. 2014;53(1):1-17. doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2014) 1–17.","chicago":"Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>.","ieee":"M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis of natural selection in mitochondrial complex I in metazoans,” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1. Wiley-Blackwell, pp. 1–17, 2014."},"publication_status":"published","doi":"10.1111/jzs.12079","date_published":"2014-02-01T00:00:00Z","quality_controlled":0,"acknowledgement":"Funded by      University of Alaska Center for Global Change Student Research     Cooperative Institute for Alaska Research and the Rasmuson Foundation","publisher":"Wiley-Blackwell","year":"2014","_id":"1981","publication":"Journal of Zoological Systematics and Evolutionary Research","author":[{"full_name":"Garvin, Michael R","first_name":"Michael","last_name":"Garvin"},{"last_name":"Bielawski","first_name":"Joseph","full_name":"Bielawski, Joseph P"},{"last_name":"Sazanov","first_name":"Leonid A","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gharrett","first_name":"Anthony","full_name":"Gharrett, Anthony J"}],"page":"1 - 17","type":"review","month":"02","day":"01","date_updated":"2019-04-26T07:22:06Z","abstract":[{"text":"Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may provide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.","lang":"eng"}],"volume":53,"title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","publist_id":"5102","date_created":"2018-12-11T11:55:02Z"},{"publication_status":"published","quality_controlled":0,"doi":"10.1126/science.1256773","date_published":"2014-10-10T00:00:00Z","status":"public","citation":{"ieee":"P. Nguyen <i>et al.</i>, “Spatial organization of cytokinesis signaling reconstituted in a cell-free system,” <i>Science</i>, vol. 346, no. 6206. American Association for the Advancement of Science, pp. 244–247, 2014.","chicago":"Nguyen, Phuong, Aaron Groen, Martin Loose, Keisuke Ishihara, Martin Wühr, Christine Field, and Timothy Mitchison. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1256773\">https://doi.org/10.1126/science.1256773</a>.","short":"P. Nguyen, A. Groen, M. Loose, K. Ishihara, M. Wühr, C. Field, T. Mitchison, Science 346 (2014) 244–247.","ama":"Nguyen P, Groen A, Loose M, et al. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. <i>Science</i>. 2014;346(6206):244-247. doi:<a href=\"https://doi.org/10.1126/science.1256773\">10.1126/science.1256773</a>","ista":"Nguyen P, Groen A, Loose M, Ishihara K, Wühr M, Field C, Mitchison T. 2014. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 346(6206), 244–247.","mla":"Nguyen, Phuong, et al. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” <i>Science</i>, vol. 346, no. 6206, American Association for the Advancement of Science, 2014, pp. 244–47, doi:<a href=\"https://doi.org/10.1126/science.1256773\">10.1126/science.1256773</a>.","apa":"Nguyen, P., Groen, A., Loose, M., Ishihara, K., Wühr, M., Field, C., &#38; Mitchison, T. (2014). Spatial organization of cytokinesis signaling reconstituted in a cell-free system. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1256773\">https://doi.org/10.1126/science.1256773</a>"},"issue":"6206","extern":1,"intvolume":"       346","day":"10","date_updated":"2021-01-12T06:54:32Z","abstract":[{"lang":"eng","text":"During animal cell division, the cleavage furrow is positioned by microtubules that signal to the actin cortex at the cell midplane. We developed a cell-free system to recapitulate cytokinesis signaling using cytoplasmic extract from Xenopus eggs. Microtubules grew out as asters from artificial centrosomes and met to organize antiparallel overlap zones. These zones blocked the interpenetration of neighboring asters and recruited cytokinesis midzone proteins, including the chromosomal passenger complex (CPC) and centralspindlin. The CPC was transported to overlap zones, which required two motor proteins, Kif4A and a Kif20A paralog. Using supported lipid bilayers to mimic the plasma membrane, we observed the recruitment of cleavage furrow markers, including an active RhoA reporter, at microtubule overlaps. This system opens further approaches to understanding the biophysics of cytokinesis signaling."}],"month":"10","type":"journal_article","author":[{"first_name":"Phuong","last_name":"Nguyen","full_name":"Nguyen, Phuong A"},{"first_name":"Aaron","last_name":"Groen","full_name":"Groen, Aaron C"},{"first_name":"Martin","last_name":"Loose","full_name":"Martin Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keisuke","last_name":"Ishihara","full_name":"Ishihara, Keisuke "},{"full_name":"Wühr, Martin ","last_name":"Wühr","first_name":"Martin"},{"first_name":"Christine","last_name":"Field","full_name":"Field, Christine M"},{"first_name":"Timothy","last_name":"Mitchison","full_name":"Mitchison, Timothy J"}],"page":"244 - 247","date_created":"2018-12-11T11:55:04Z","publist_id":"5093","volume":346,"title":"Spatial organization of cytokinesis signaling reconstituted in a cell-free system","year":"2014","publisher":"American Association for the Advancement of Science","acknowledgement":"This work was supported by NIH grant GM39565 (T.J.M.); MBL fellowships from the Evans Foundation, MBL Associates, and the Colwin Fund (T.J.M. and C.M.F.); HFSP fellowship LT000466/2012-L (M.L.); and NIH grant GM103785 (M.W.). ","publication":"Science","_id":"1989"},{"_id":"1990","publication":"Nature Cell Biology","year":"2014","acknowledgement":"M.L. is supported by fellowships from EMBO (ALTF 394-2011) and HFSP (LT000466/2012). Cytoskeleton dynamics research in the T.J.M. group is supported by NIH-GM39565.","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:55:05Z","publist_id":"5094","volume":16,"title":"The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns","month":"01","type":"journal_article","abstract":[{"lang":"eng","text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin superfamily GTPase, which is recruited to the membrane by the actin-related protein FtsA. Both proteins are required for the formation of the Z-ring, but if and how they influence each other's assembly dynamics is not known. Here, we reconstituted FtsA-dependent recruitment of FtsZ polymers to supported membranes, where both proteins self-organize into complex patterns, such as fast-moving filament bundles and chirally rotating rings. Using fluorescence microscopy and biochemical perturbations, we found that these large-scale rearrangements of FtsZ emerge from its polymerization dynamics and a dual, antagonistic role of FtsA: recruitment of FtsZ filaments to the membrane and negative regulation of FtsZ organization. Our findings provide a model for the initial steps of bacterial cell division and illustrate how dynamic polymers can self-organize into large-scale structures."}],"date_updated":"2021-01-12T06:54:33Z","day":"01","page":"38 - 46","author":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Martin Loose","first_name":"Martin","last_name":"Loose"},{"last_name":"Mitchison","first_name":"Timothy","full_name":"Mitchison, Timothy J"}],"issue":"1","citation":{"ieee":"M. Loose and T. Mitchison, “The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns,” <i>Nature Cell Biology</i>, vol. 16, no. 1. Nature Publishing Group, pp. 38–46, 2014.","chicago":"Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncb2885\">https://doi.org/10.1038/ncb2885</a>.","short":"M. Loose, T. Mitchison, Nature Cell Biology 16 (2014) 38–46.","ama":"Loose M, Mitchison T. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. <i>Nature Cell Biology</i>. 2014;16(1):38-46. doi:<a href=\"https://doi.org/10.1038/ncb2885\">10.1038/ncb2885</a>","ista":"Loose M, Mitchison T. 2014. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 16(1), 38–46.","mla":"Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” <i>Nature Cell Biology</i>, vol. 16, no. 1, Nature Publishing Group, 2014, pp. 38–46, doi:<a href=\"https://doi.org/10.1038/ncb2885\">10.1038/ncb2885</a>.","apa":"Loose, M., &#38; Mitchison, T. (2014). The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2885\">https://doi.org/10.1038/ncb2885</a>"},"intvolume":"        16","extern":1,"status":"public","quality_controlled":0,"doi":"10.1038/ncb2885","date_published":"2014-01-01T00:00:00Z","publication_status":"published"},{"publisher":"Cell Press","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"year":"2014","_id":"1994","publication":"Current Biology","scopus_import":1,"ec_funded":1,"page":"2786 - 2791","author":[{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"full_name":"Landberg, Katarina","first_name":"Katarina","last_name":"Landberg"},{"full_name":"Thelander, Mattias","last_name":"Thelander","first_name":"Mattias"},{"first_name":"Eva","last_name":"Medvecka","full_name":"Medvecka, Eva"},{"full_name":"Pederson, Eric","first_name":"Eric","last_name":"Pederson"},{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"last_name":"Cooper","first_name":"Endymion","full_name":"Cooper, Endymion"},{"first_name":"Mansour","last_name":"Karimi","full_name":"Karimi, Mansour"},{"full_name":"Delwiche, Charles","last_name":"Delwiche","first_name":"Charles"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"last_name":"Sundberg","first_name":"Eva","full_name":"Sundberg, Eva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí"}],"month":"12","oa_version":"None","type":"journal_article","abstract":[{"text":"The emergence and radiation of multicellular land plants was driven by crucial innovations to their body plans [1]. The directional transport of the phytohormone auxin represents a key, plant-specific mechanism for polarization and patterning in complex seed plants [2-5]. Here, we show that already in the early diverging land plant lineage, as exemplified by the moss Physcomitrella patens, auxin transport by PIN transporters is operational and diversified into ER-localized and plasma membrane-localized PIN proteins. Gain-of-function and loss-of-function analyses revealed that PIN-dependent intercellular auxin transport in Physcomitrella mediates crucial developmental transitions in tip-growing filaments and waves of polarization and differentiation in leaf-like structures. Plasma membrane PIN proteins localize in a polar manner to the tips of moss filaments, revealing an unexpected relation between polarization mechanisms in moss tip-growing cells and multicellular tissues of seed plants. Our results trace the origins of polarization and auxin-mediated patterning mechanisms and highlight the crucial role of polarized auxin transport during the evolution of multicellular land plants.","lang":"eng"}],"date_updated":"2021-01-12T06:54:34Z","day":"01","volume":24,"title":"Directional auxin transport mechanisms in early diverging land plants","date_created":"2018-12-11T11:55:06Z","publist_id":"5088","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"status":"public","intvolume":"        24","issue":"23","language":[{"iso":"eng"}],"citation":{"short":"T. Viaene, K. Landberg, M. Thelander, E. Medvecka, E. Pederson, E. Feraru, E. Cooper, M. Karimi, C. Delwiche, K. Ljung, M. Geisler, E. Sundberg, J. Friml, Current Biology 24 (2014) 2786–2791.","chicago":"Viaene, Tom, Katarina Landberg, Mattias Thelander, Eva Medvecka, Eric Pederson, Elena Feraru, Endymion Cooper, et al. “Directional Auxin Transport Mechanisms in Early Diverging Land Plants.” <i>Current Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">https://doi.org/10.1016/j.cub.2014.09.056</a>.","ieee":"T. Viaene <i>et al.</i>, “Directional auxin transport mechanisms in early diverging land plants,” <i>Current Biology</i>, vol. 24, no. 23. Cell Press, pp. 2786–2791, 2014.","apa":"Viaene, T., Landberg, K., Thelander, M., Medvecka, E., Pederson, E., Feraru, E., … Friml, J. (2014). Directional auxin transport mechanisms in early diverging land plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">https://doi.org/10.1016/j.cub.2014.09.056</a>","ista":"Viaene T, Landberg K, Thelander M, Medvecka E, Pederson E, Feraru E, Cooper E, Karimi M, Delwiche C, Ljung K, Geisler M, Sundberg E, Friml J. 2014. Directional auxin transport mechanisms in early diverging land plants. Current Biology. 24(23), 2786–2791.","mla":"Viaene, Tom, et al. “Directional Auxin Transport Mechanisms in Early Diverging Land Plants.” <i>Current Biology</i>, vol. 24, no. 23, Cell Press, 2014, pp. 2786–91, doi:<a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">10.1016/j.cub.2014.09.056</a>.","ama":"Viaene T, Landberg K, Thelander M, et al. Directional auxin transport mechanisms in early diverging land plants. <i>Current Biology</i>. 2014;24(23):2786-2791. doi:<a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">10.1016/j.cub.2014.09.056</a>"},"publication_status":"published","doi":"10.1016/j.cub.2014.09.056","date_published":"2014-12-01T00:00:00Z","quality_controlled":"1"},{"intvolume":"       113","citation":{"short":"F. Fratini, E. Mascarenhas, L. Safari, J. Poizat, D. Valente, A. Auffèves, D. Gerace, M. Santos, Physical Review Letters 113 (2014).","chicago":"Fratini, Filippo, Eduardo Mascarenhas, Laleh Safari, Jean Poizat, Daniel Valente, Alexia Auffèves, Dario Gerace, and Marcelo Santos. “Fabry-Perot Interferometer with Quantum Mirrors: Nonlinear Light Transport and Rectification.” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">https://doi.org/10.1103/PhysRevLett.113.243601</a>.","ieee":"F. Fratini <i>et al.</i>, “Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification,” <i>Physical Review Letters</i>, vol. 113, no. 24. American Physical Society, 2014.","apa":"Fratini, F., Mascarenhas, E., Safari, L., Poizat, J., Valente, D., Auffèves, A., … Santos, M. (2014). Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">https://doi.org/10.1103/PhysRevLett.113.243601</a>","mla":"Fratini, Filippo, et al. “Fabry-Perot Interferometer with Quantum Mirrors: Nonlinear Light Transport and Rectification.” <i>Physical Review Letters</i>, vol. 113, no. 24, 243601, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">10.1103/PhysRevLett.113.243601</a>.","ista":"Fratini F, Mascarenhas E, Safari L, Poizat J, Valente D, Auffèves A, Gerace D, Santos M. 2014. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. Physical Review Letters. 113(24), 243601.","ama":"Fratini F, Mascarenhas E, Safari L, et al. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. <i>Physical Review Letters</i>. 2014;113(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">10.1103/PhysRevLett.113.243601</a>"},"status":"public","date_published":"2014-12-08T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1410.5972","open_access":"1"}],"publication_status":"published","oa":1,"_id":"1995","year":"2014","volume":113,"date_created":"2018-12-11T11:55:06Z","date_updated":"2021-01-12T06:54:34Z","abstract":[{"lang":"eng","text":"Optical transport represents a natural route towards fast communications, and it is currently used in large scale data transfer. The progressive miniaturization of devices for information processing calls for the microscopic tailoring of light transport and confinement at length scales appropriate for upcoming technologies. With this goal in mind, we present a theoretical analysis of a one-dimensional Fabry-Perot interferometer built with two highly saturable nonlinear mirrors: a pair of two-level systems. Our approach captures nonlinear and nonreciprocal effects of light transport that were not reported previously. Remarkably, we show that such an elementary device can operate as a microscopic integrated optical rectifier."}],"month":"12","oa_version":"Submitted Version","type":"journal_article","language":[{"iso":"eng"}],"issue":"24","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.1103/PhysRevLett.113.243601","quality_controlled":"1","publication":"Physical Review Letters","scopus_import":1,"ec_funded":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"title":"Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification","article_number":"243601","publist_id":"5085","author":[{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"},{"first_name":"Eduardo","last_name":"Mascarenhas","full_name":"Mascarenhas, Eduardo"},{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","last_name":"Safari"},{"first_name":"Jean","last_name":"Poizat","full_name":"Poizat, Jean"},{"last_name":"Valente","first_name":"Daniel","full_name":"Valente, Daniel"},{"full_name":"Auffèves, Alexia","last_name":"Auffèves","first_name":"Alexia"},{"first_name":"Dario","last_name":"Gerace","full_name":"Gerace, Dario"},{"last_name":"Santos","first_name":"Marcelo","full_name":"Santos, Marcelo"}],"day":"08"},{"status":"public","intvolume":"       111","citation":{"apa":"Hazak, O., Obolski, U., Prat, T., Friml, J., Hadany, L., &#38; Yalovsky, S. (2014). Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1413918111\">https://doi.org/10.1073/pnas.1413918111</a>","mla":"Hazak, Ora, et al. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” <i>PNAS</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. E5471–79, doi:<a href=\"https://doi.org/10.1073/pnas.1413918111\">10.1073/pnas.1413918111</a>.","ista":"Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. 2014. Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. PNAS. 111(50), E5471–E5479.","ama":"Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. <i>PNAS</i>. 2014;111(50):E5471-E5479. doi:<a href=\"https://doi.org/10.1073/pnas.1413918111\">10.1073/pnas.1413918111</a>","short":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, S. Yalovsky, PNAS 111 (2014) E5471–E5479.","chicago":"Hazak, Ora, Uri Obolski, Tomas Prat, Jiří Friml, Lilach Hadany, and Shaul Yalovsky. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1413918111\">https://doi.org/10.1073/pnas.1413918111</a>.","ieee":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, and S. Yalovsky, “Bimodal regulation of ICR1 levels generates self-organizing auxin distribution,” <i>PNAS</i>, vol. 111, no. 50. National Academy of Sciences, pp. E5471–E5479, 2014."},"language":[{"iso":"eng"}],"issue":"50","oa":1,"publication_status":"published","date_published":"2014-12-16T00:00:00Z","doi":"10.1073/pnas.1413918111","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/","open_access":"1"}],"quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"year":"2014","publication":"PNAS","_id":"1996","scopus_import":1,"page":"E5471 - E5479","author":[{"first_name":"Ora","last_name":"Hazak","full_name":"Hazak, Ora"},{"first_name":"Uri","last_name":"Obolski","full_name":"Obolski, Uri"},{"last_name":"Prat","first_name":"Tomas","full_name":"Prat, Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"last_name":"Hadany","first_name":"Lilach","full_name":"Hadany, Lilach"},{"first_name":"Shaul","last_name":"Yalovsky","full_name":"Yalovsky, Shaul"}],"date_updated":"2021-01-12T06:54:35Z","day":"16","abstract":[{"text":"Auxin polar transport, local maxima, and gradients have become an importantmodel system for studying self-organization. Auxin distribution is regulated by auxin-dependent positive feedback loops that are not well-understood at the molecular level. Previously, we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are posttranscriptionally repressed at the site of maximum auxin accumulation at the root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential for regulating formation of auxin local maxima and gradients. ICR1 levels increase concomitant with increase in auxin response in lateral root primordia, cotyledon tips, and provascular tissues. However, in the embryo hypophysis and root meristem, when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB) [SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo hypophysis resulted in reduction of auxin accumulation and concomitant root growth arrest. ICR1 disappeared during root regeneration and lateral root initiation concomitantly with the formation of a local auxin maximum in response to external auxin treatments and transiently after gravitropic stimulation. Destabilization of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome function, and protein synthesis. A mathematical model based on these findings shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward reflux can be simulated without assuming preexisting tissue polarity. Our experimental results and mathematical modeling indicate that regulation of auxin distribution is tightly associated with auxin-dependent ICR1 levels.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","month":"12","title":"Bimodal regulation of ICR1 levels generates self-organizing auxin distribution","volume":111,"publist_id":"5083","date_created":"2018-12-11T11:55:07Z"},{"scopus_import":1,"publication":"Trends in Immunology","_id":"1998","year":"2014","department":[{"_id":"SyCr"}],"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was funded by an ERC Starting Grant by the European Research Council (to S.C.) and the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission; to L.M.).\r\nWe thank Christopher D. Pull, Sophie A.O. Armitage, Hinrich Schulenburg, Line V. Ugelvig, Matthias Konrad, Matthias Fürst, Miriam Stock, Barbara Casillas-Perez and three anonymous referees for comments on the manuscript. ","publist_id":"5081","date_created":"2018-12-11T11:55:07Z","volume":35,"title":"Individual and social immunisation in insects","abstract":[{"text":"Immune systems are able to protect the body against secondary infection with the same parasite. In insect colonies, this protection is not restricted to the level of the individual organism, but also occurs at the societal level. Here, we review recent evidence for and insights into the mechanisms underlying individual and social immunisation in insects. We disentangle general immune-protective effects from specific immune memory (priming), and examine immunisation in the context of the lifetime of an individual and that of a colony, and of transgenerational immunisation that benefits offspring. When appropriate, we discuss parallels with disease defence strategies in human societies. We propose that recurrent parasitic threats have shaped the evolution of both the individual immune systems and colony-level social immunity in insects.","lang":"eng"}],"date_updated":"2021-01-12T06:54:35Z","day":"01","type":"journal_article","oa_version":"None","month":"10","page":"471 - 482","author":[{"first_name":"Leila","last_name":"El Masri","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","full_name":"El Masri, Leila"},{"last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"citation":{"chicago":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” <i>Trends in Immunology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.it.2014.08.005\">https://doi.org/10.1016/j.it.2014.08.005</a>.","ieee":"L. El Masri and S. Cremer, “Individual and social immunisation in insects,” <i>Trends in Immunology</i>, vol. 35, no. 10. Elsevier, pp. 471–482, 2014.","short":"L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482.","ama":"El Masri L, Cremer S. Individual and social immunisation in insects. <i>Trends in Immunology</i>. 2014;35(10):471-482. doi:<a href=\"https://doi.org/10.1016/j.it.2014.08.005\">10.1016/j.it.2014.08.005</a>","apa":"El Masri, L., &#38; Cremer, S. (2014). Individual and social immunisation in insects. <i>Trends in Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.it.2014.08.005\">https://doi.org/10.1016/j.it.2014.08.005</a>","ista":"El Masri L, Cremer S. 2014. Individual and social immunisation in insects. Trends in Immunology. 35(10), 471–482.","mla":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” <i>Trends in Immunology</i>, vol. 35, no. 10, Elsevier, 2014, pp. 471–82, doi:<a href=\"https://doi.org/10.1016/j.it.2014.08.005\">10.1016/j.it.2014.08.005</a>."},"language":[{"iso":"eng"}],"issue":"10","intvolume":"        35","status":"public","quality_controlled":"1","date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.it.2014.08.005","publication_status":"published"},{"day":"01","author":[{"first_name":"Nathalie","last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie"},{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E"},{"first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5080","title":"Organisational immunity in social insects","department":[{"_id":"SyCr"}],"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"ec_funded":1,"publication":"Current Opinion in Insect Science","quality_controlled":"1","doi":"10.1016/j.cois.2014.09.001","project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"243071"}],"issue":"1","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","month":"11","abstract":[{"text":"Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses.","lang":"eng"}],"date_updated":"2024-03-25T23:30:04Z","page":"1 - 15","date_created":"2018-12-11T11:55:08Z","volume":5,"year":"2014","_id":"1999","publication_status":"published","date_published":"2014-11-01T00:00:00Z","status":"public","citation":{"apa":"Stroeymeyt, N., Casillas Perez, B. E., &#38; Cremer, S. (2014). Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>","mla":"Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>.","ista":"Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15.","ama":"Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. 2014;5(1):1-15. doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>","short":"N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15.","chicago":"Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>.","ieee":"N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1. Elsevier, pp. 1–15, 2014."},"related_material":{"record":[{"relation":"dissertation_contains","id":"6383"},{"status":"public","id":"6435","relation":"dissertation_contains"}]},"intvolume":"         5"}]