[{"author":[{"last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Duclercq, Jérôme","last_name":"Duclercq","first_name":"Jérôme"},{"last_name":"Weller","full_name":"Weller, Benjamin","first_name":"Benjamin"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"first_name":"Remko","last_name":"Offringa","full_name":"Offringa, Remko"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"first_name":"Angus","full_name":"Murphy, Angus","last_name":"Murphy"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"publist_id":"5160","title":"Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_updated":"2021-01-12T06:54:10Z","citation":{"ieee":"P. Marhavý et al., “Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis,” Current Biology, vol. 24, no. 9. Cell Press, pp. 1031–1037, 2014.","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.","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. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.04.002","ama":"Marhavý P, Duclercq J, Weller B, et al. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 2014;24(9):1031-1037. doi:10.1016/j.cub.2014.04.002","mla":"Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology, vol. 24, no. 9, Cell Press, 2014, pp. 1031–37, doi:10.1016/j.cub.2014.04.002.","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.","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.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.04.002."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"1934","page":"1031 - 1037","issue":"9","volume":24,"doi":"10.1016/j.cub.2014.04.002","date_published":"2014-05-05T00:00:00Z","date_created":"2018-12-11T11:54:48Z","ec_funded":1,"publication_status":"published","year":"2014","day":"05","publication":"Current Biology","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Cell Press","quality_controlled":"1","month":"05","intvolume":" 24","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."}],"oa_version":"None"},{"_id":"1932","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:10Z","department":[{"_id":"NiBa"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The existence of complex (multiple-step) genetic adaptations that are "irreducible" (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 "irreducibly complex" 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."}],"intvolume":" 68","month":"12","main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":68,"issue":"12","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014.","short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367.","ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517","apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014). Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.12517","mla":"Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.","ista":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367.","chicago":"Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1111/evo.12517."},"title":"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations","publist_id":"5162","author":[{"first_name":"Meredith","last_name":"Trotter","full_name":"Trotter, Meredith"},{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel"},{"last_name":"Peterson","full_name":"Peterson, Grant","first_name":"Grant"},{"last_name":"Peck","full_name":"Peck, Kayla","first_name":"Kayla"},{"last_name":"Masel","full_name":"Masel, Joanna","first_name":"Joanna"}],"acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","publication":"Evolution","day":"01","year":"2014","date_created":"2018-12-11T11:54:47Z","date_published":"2014-12-01T00:00:00Z","doi":"10.1111/evo.12517","page":"3357 - 3367"},{"page":"2585 - 2594","date_created":"2018-12-11T11:54:46Z","doi":"10.1109/TVCG.2014.2346432","volume":20,"issue":"12","date_published":"2014-12-31T00:00:00Z","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Visualization and Computer Graphics","day":"31","scopus_import":1,"quality_controlled":"1","publisher":"IEEE","intvolume":" 20","month":"12","abstract":[{"lang":"eng","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."}],"acknowledgement":"RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC","oa_version":"None","author":[{"full_name":"Günther, David","last_name":"Günther","first_name":"David"},{"last_name":"Jacobson","full_name":"Jacobson, Alec","first_name":"Alec"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seidel, Hans","last_name":"Seidel","first_name":"Hans"},{"first_name":"Olga","last_name":"Sorkine Hornung","full_name":"Sorkine Hornung, Olga"},{"full_name":"Weinkauf, Tino","last_name":"Weinkauf","first_name":"Tino"}],"publist_id":"5164","title":"Fast and memory-efficient topological denoising of 2D and 3D scalar fields","department":[{"_id":"HeEd"}],"citation":{"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.","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.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2346432.","apa":"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. IEEE. https://doi.org/10.1109/TVCG.2014.2346432","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. IEEE Transactions on Visualization and Computer Graphics. 2014;20(12):2585-2594. doi:10.1109/TVCG.2014.2346432","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,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12. IEEE, pp. 2585–2594, 2014.","mla":"Günther, David, et al. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12, IEEE, 2014, pp. 2585–94, doi:10.1109/TVCG.2014.2346432."},"date_updated":"2021-01-12T06:54:09Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1930"},{"date_published":"2014-04-01T00:00:00Z","volume":141,"issue":"8","doi":"10.1242/dev.102988","date_created":"2018-12-11T11:54:47Z","page":"1671 - 1682","day":"01","publication":"Development","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","month":"04","intvolume":" 141","publisher":"Company of Biologists","scopus_import":1,"quality_controlled":"1","oa_version":"None","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."}],"title":"Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates","department":[{"_id":"RySh"}],"author":[{"last_name":"Hatakeyama","full_name":"Hatakeyama, Jun","first_name":"Jun"},{"last_name":"Wakamatsu","full_name":"Wakamatsu, Yoshio","first_name":"Yoshio"},{"first_name":"Akira","last_name":"Nagafuchi","full_name":"Nagafuchi, Akira"},{"first_name":"Ryoichiro","last_name":"Kageyama","full_name":"Kageyama, Ryoichiro"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Kenji","last_name":"Shimamura","full_name":"Shimamura, Kenji"}],"publist_id":"5161","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:10Z","citation":{"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.” Development. Company of Biologists, 2014. https://doi.org/10.1242/dev.102988.","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.” Development, vol. 141, no. 8, Company of Biologists, 2014, pp. 1671–82, doi:10.1242/dev.102988.","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,” Development, vol. 141, no. 8. Company of Biologists, pp. 1671–1682, 2014.","short":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682.","apa":"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. Company of Biologists. https://doi.org/10.1242/dev.102988","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. Development. 2014;141(8):1671-1682. doi:10.1242/dev.102988"},"status":"public","type":"journal_article","_id":"1933"},{"date_updated":"2021-01-12T06:54:09Z","department":[{"_id":"GaTk"}],"_id":"1931","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":8,"issue":"MAY","oa_version":"Submitted Version","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"}],"month":"05","intvolume":" 8","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057","apa":"Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057","ieee":"C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014.","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).","mla":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.","ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.","chicago":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057."},"title":"Emergence of task-dependent representations in working memory circuits","author":[{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina"},{"full_name":"Triesch, Jochen","last_name":"Triesch","first_name":"Jochen"}],"publist_id":"5163","article_number":"57","day":"28","publication":"Frontiers in Computational Neuroscience","year":"2014","doi":"10.3389/fncom.2014.00057","date_published":"2014-05-28T00:00:00Z","date_created":"2018-12-11T11:54:46Z","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.","quality_controlled":"1","publisher":"Frontiers Research Foundation","oa":1}]