[{"year":"2014","_id":"1934","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis","status":"public","publication_status":"published","intvolume":" 24","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Cell Press","author":[{"full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","first_name":"Peter"},{"last_name":"Duclercq","first_name":"Jérôme","full_name":"Duclercq, Jérôme"},{"first_name":"Benjamin","last_name":"Weller","full_name":"Weller, Benjamin"},{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"first_name":"Agnieszka","last_name":"Bielach","full_name":"Bielach, Agnieszka"},{"full_name":"Offringa, Remko","last_name":"Offringa","first_name":"Remko"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"Schwechheimer","first_name":"Claus","full_name":"Schwechheimer, Claus"},{"full_name":"Murphy, Angus","last_name":"Murphy","first_name":"Angus"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_created":"2018-12-11T11:54:48Z","date_updated":"2021-01-12T06:54:10Z","oa_version":"None","volume":24,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"publist_id":"5160","ec_funded":1,"issue":"9","publication":"Current Biology","citation":{"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.","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.","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.","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.","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","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.","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"},"quality_controlled":"1","page":"1031 - 1037","project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7"}],"date_published":"2014-05-05T00:00:00Z","doi":"10.1016/j.cub.2014.04.002","language":[{"iso":"eng"}],"scopus_import":1,"day":"05","month":"05"},{"language":[{"iso":"eng"}],"doi":"10.1111/evo.12517","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"month":"12","volume":68,"date_updated":"2021-01-12T06:54:10Z","date_created":"2018-12-11T11:54:47Z","author":[{"last_name":"Trotter","first_name":"Meredith","full_name":"Trotter, Meredith"},{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel"},{"last_name":"Peterson","first_name":"Grant","full_name":"Peterson, Grant"},{"full_name":"Peck, Kayla","last_name":"Peck","first_name":"Kayla"},{"first_name":"Joanna","last_name":"Masel","full_name":"Masel, Joanna"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n","year":"2014","ec_funded":1,"publist_id":"5162","date_published":"2014-12-01T00:00:00Z","page":"3357 - 3367","citation":{"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.","short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 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.","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","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.","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","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."},"publication":"Evolution","day":"01","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 68","title":"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations","status":"public","_id":"1932","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"12","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"day":"31","month":"12","scopus_import":1,"doi":"10.1109/TVCG.2014.2346432","date_published":"2014-12-31T00:00:00Z","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.","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.","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.","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","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.","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","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."},"publication":"IEEE Transactions on Visualization and Computer Graphics","page":"2585 - 2594","quality_controlled":"1","issue":"12","publist_id":"5164","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"}],"type":"journal_article","author":[{"full_name":"Günther, David","last_name":"Günther","first_name":"David"},{"first_name":"Alec","last_name":"Jacobson","full_name":"Jacobson, Alec"},{"full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","first_name":"Jan"},{"first_name":"Hans","last_name":"Seidel","full_name":"Seidel, Hans"},{"last_name":"Sorkine Hornung","first_name":"Olga","full_name":"Sorkine Hornung, Olga"},{"last_name":"Weinkauf","first_name":"Tino","full_name":"Weinkauf, Tino"}],"oa_version":"None","volume":20,"date_updated":"2021-01-12T06:54:09Z","date_created":"2018-12-11T11:54:46Z","_id":"1930","acknowledgement":"RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"intvolume":" 20","publisher":"IEEE","publication_status":"published","title":"Fast and memory-efficient topological denoising of 2D and 3D scalar fields","status":"public"},{"department":[{"_id":"RySh"}],"publisher":"Company of Biologists","intvolume":" 141","title":"Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates","status":"public","publication_status":"published","year":"2014","_id":"1933","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":141,"oa_version":"None","date_updated":"2021-01-12T06:54:10Z","date_created":"2018-12-11T11:54:47Z","author":[{"full_name":"Hatakeyama, Jun","first_name":"Jun","last_name":"Hatakeyama"},{"full_name":"Wakamatsu, Yoshio","last_name":"Wakamatsu","first_name":"Yoshio"},{"full_name":"Nagafuchi, Akira","first_name":"Akira","last_name":"Nagafuchi"},{"full_name":"Kageyama, Ryoichiro","last_name":"Kageyama","first_name":"Ryoichiro"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Shimamura, Kenji","first_name":"Kenji","last_name":"Shimamura"}],"type":"journal_article","issue":"8","publist_id":"5161","abstract":[{"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.","lang":"eng"}],"page":"1671 - 1682","quality_controlled":"1","citation":{"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.","short":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682.","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.","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","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.","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.","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"},"publication":"Development","language":[{"iso":"eng"}],"date_published":"2014-04-01T00:00:00Z","doi":"10.1242/dev.102988","scopus_import":1,"month":"04","day":"01"},{"month":"05","doi":"10.3389/fncom.2014.00057","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/","open_access":"1"}],"oa":1,"quality_controlled":"1","publist_id":"5163","article_number":"57","author":[{"first_name":"Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina"},{"full_name":"Triesch, Jochen","first_name":"Jochen","last_name":"Triesch"}],"volume":8,"date_updated":"2021-01-12T06:54:09Z","date_created":"2018-12-11T11:54:46Z","year":"2014","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.","department":[{"_id":"GaTk"}],"publisher":"Frontiers Research Foundation","publication_status":"published","day":"28","scopus_import":1,"date_published":"2014-05-28T00:00:00Z","citation":{"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.","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).","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.","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","ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.","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.","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"},"publication":"Frontiers in Computational Neuroscience","issue":"MAY","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1931","intvolume":" 8","title":"Emergence of task-dependent representations in working memory circuits","status":"public"},{"date_published":"2014-11-01T00:00:00Z","page":"261 - 353","citation":{"chicago":"Bourgade, Paul, László Erdös, and Horngtzer Yau. “Edge Universality of Beta Ensembles.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2120-z.","short":"P. Bourgade, L. Erdös, H. Yau, Communications in Mathematical Physics 332 (2014) 261–353.","mla":"Bourgade, Paul, et al. “Edge Universality of Beta Ensembles.” Communications in Mathematical Physics, vol. 332, no. 1, Springer, 2014, pp. 261–353, doi:10.1007/s00220-014-2120-z.","ieee":"P. Bourgade, L. Erdös, and H. Yau, “Edge universality of beta ensembles,” Communications in Mathematical Physics, vol. 332, no. 1. Springer, pp. 261–353, 2014.","apa":"Bourgade, P., Erdös, L., & Yau, H. (2014). Edge universality of beta ensembles. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2120-z","ista":"Bourgade P, Erdös L, Yau H. 2014. Edge universality of beta ensembles. Communications in Mathematical Physics. 332(1), 261–353.","ama":"Bourgade P, Erdös L, Yau H. Edge universality of beta ensembles. Communications in Mathematical Physics. 2014;332(1):261-353. doi:10.1007/s00220-014-2120-z"},"publication":"Communications in Mathematical Physics","day":"01","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 332","title":"Edge universality of beta ensembles","status":"public","_id":"1937","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"1","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"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00220-014-2120-z","project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","grant_number":"SFB-TR3-TP10B"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1306.5728","open_access":"1"}],"month":"11","volume":332,"date_updated":"2021-01-12T06:54:12Z","date_created":"2018-12-11T11:54:48Z","author":[{"full_name":"Bourgade, Paul","last_name":"Bourgade","first_name":"Paul"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yau, Horngtzer","last_name":"Yau","first_name":"Horngtzer"}],"department":[{"_id":"LaEr"}],"publisher":"Springer","publication_status":"published","year":"2014","publist_id":"5158"},{"month":"02","day":"01","date_published":"2014-02-01T00:00:00Z","doi":"10.1111/jzs.12079","publication":"Journal of Zoological Systematics and Evolutionary Research","citation":{"chicago":"Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2014. https://doi.org/10.1111/jzs.12079.","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2014) 1–17.","mla":"Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” Journal of Zoological Systematics and Evolutionary Research, vol. 53, no. 1, Wiley-Blackwell, 2014, pp. 1–17, doi:10.1111/jzs.12079.","ieee":"M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis of natural selection in mitochondrial complex I in metazoans,” Journal of Zoological Systematics and Evolutionary Research, vol. 53, no. 1. Wiley-Blackwell, pp. 1–17, 2014.","apa":"Garvin, M., Bielawski, J., Sazanov, L. A., & Gharrett, A. (2014). Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/jzs.12079","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. Journal of Zoological Systematics and Evolutionary Research. 2014;53(1):1-17. doi:10.1111/jzs.12079"},"quality_controlled":0,"page":"1 - 17","abstract":[{"lang":"eng","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."}],"publist_id":"5102","issue":"1","extern":1,"type":"review","author":[{"first_name":"Michael","last_name":"Garvin","full_name":"Garvin, Michael R"},{"first_name":"Joseph","last_name":"Bielawski","full_name":"Bielawski, Joseph P"},{"full_name":"Leonid Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"},{"last_name":"Gharrett","first_name":"Anthony","full_name":"Gharrett, Anthony J"}],"date_updated":"2019-04-26T07:22:06Z","date_created":"2018-12-11T11:55:02Z","volume":53,"year":"2014","_id":"1981","acknowledgement":"Funded by University of Alaska Center for Global Change Student Research Cooperative Institute for Alaska Research and the Rasmuson Foundation","publication_status":"published","title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","status":"public","intvolume":" 53","publisher":"Wiley-Blackwell"},{"date_published":"2014-03-01T00:00:00Z","doi":"10.1111/mmi.12507","publication":"Molecular Microbiology","citation":{"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.” Molecular Microbiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mmi.12507.","mla":"Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507.","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.","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. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12507","ieee":"A. Heikal et al., “Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation,” Molecular Microbiology, vol. 91, no. 5. Wiley-Blackwell, pp. 950–964, 2014.","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. Molecular Microbiology. 2014;91(5):950-964. doi:10.1111/mmi.12507"},"quality_controlled":0,"page":"950 - 964","day":"01","month":"03","author":[{"full_name":"Heikal, Adam ","first_name":"Adam","last_name":"Heikal"},{"full_name":"Nakatani, Yoshio","last_name":"Nakatani","first_name":"Yoshio"},{"full_name":"Dunn, Elyse A","last_name":"Dunn","first_name":"Elyse"},{"full_name":"Weimar, Marion R","last_name":"Weimar","first_name":"Marion"},{"full_name":"Day, Catherine","last_name":"Day","first_name":"Catherine"},{"last_name":"Baker","first_name":"Edward","full_name":"Baker, Edward N"},{"full_name":"Lott, Shaun J","last_name":"Lott","first_name":"Shaun"},{"full_name":"Leonid Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"},{"full_name":"Cook, Gregory","first_name":"Gregory","last_name":"Cook"}],"date_created":"2018-12-11T11:55:01Z","date_updated":"2021-01-12T06:54:29Z","volume":91,"_id":"1980","year":"2014","acknowledgement":"Funded by Health Research Council of New Zealand Royal Society of New Zealand University of Otago New Zealand Synchrotron Group","status":"public","publication_status":"published","title":"Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation","publisher":"Wiley-Blackwell","intvolume":" 91","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."}],"publist_id":"5103","issue":"5","extern":1,"type":"journal_article"},{"page":"247 - 253","quality_controlled":0,"citation":{"ieee":"L. A. Sazanov, “The mechanism of coupling between electron transfer and proton translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4. Springer, pp. 247–253, 2014.","apa":"Sazanov, L. A. (2014). The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. Springer. https://doi.org/10.1007/s10863-014-9554-z","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.","ama":"Sazanov LA. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 2014;46(4):247-253. doi:10.1007/s10863-014-9554-z","chicago":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes. Springer, 2014. https://doi.org/10.1007/s10863-014-9554-z.","short":"L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.","mla":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4, Springer, 2014, pp. 247–53, doi:10.1007/s10863-014-9554-z."},"publication":"Journal of Bioenergetics and Biomembranes","date_published":"2014-08-01T00:00:00Z","doi":"10.1007/s10863-014-9554-z","day":"01","month":"08","intvolume":" 46","publisher":"Springer","publication_status":"published","title":"The mechanism of coupling between electron transfer and proton translocation in respiratory complex I","status":"public","year":"2014","_id":"1979","volume":46,"date_updated":"2021-01-12T06:54:28Z","date_created":"2018-12-11T11:55:01Z","author":[{"first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov"}],"type":"journal_article","extern":1,"issue":"4","publist_id":"5104","abstract":[{"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.","lang":"eng"}]},{"month":"10","day":"10","page":"244 - 247","quality_controlled":0,"citation":{"short":"P. Nguyen, A. Groen, M. Loose, K. Ishihara, M. Wühr, C. Field, T. Mitchison, Science 346 (2014) 244–247.","mla":"Nguyen, Phuong, et al. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” Science, vol. 346, no. 6206, American Association for the Advancement of Science, 2014, pp. 244–47, doi:10.1126/science.1256773.","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.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1256773.","ama":"Nguyen P, Groen A, Loose M, et al. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 2014;346(6206):244-247. doi:10.1126/science.1256773","ieee":"P. Nguyen et al., “Spatial organization of cytokinesis signaling reconstituted in a cell-free system,” Science, vol. 346, no. 6206. American Association for the Advancement of Science, pp. 244–247, 2014.","apa":"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. American Association for the Advancement of Science. https://doi.org/10.1126/science.1256773","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."},"publication":"Science","date_published":"2014-10-10T00:00:00Z","doi":"10.1126/science.1256773","type":"journal_article","extern":1,"publist_id":"5093","issue":"6206","abstract":[{"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.","lang":"eng"}],"publisher":"American Association for the Advancement of Science","intvolume":" 346","title":"Spatial organization of cytokinesis signaling reconstituted in a cell-free system","publication_status":"published","status":"public","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.). ","_id":"1989","year":"2014","volume":346,"date_created":"2018-12-11T11:55:04Z","date_updated":"2021-01-12T06:54:32Z","author":[{"first_name":"Phuong","last_name":"Nguyen","full_name":"Nguyen, Phuong A"},{"full_name":"Groen, Aaron C","first_name":"Aaron","last_name":"Groen"},{"full_name":"Martin Loose","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ishihara, Keisuke ","last_name":"Ishihara","first_name":"Keisuke"},{"full_name":"Wühr, Martin ","last_name":"Wühr","first_name":"Martin"},{"full_name":"Field, Christine M","first_name":"Christine","last_name":"Field"},{"full_name":"Mitchison, Timothy J","last_name":"Mitchison","first_name":"Timothy"}]},{"month":"01","day":"01","publication":"Nature Cell Biology","citation":{"ama":"Loose M, Mitchison T. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 2014;16(1):38-46. doi:10.1038/ncb2885","apa":"Loose, M., & Mitchison, T. (2014). The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2885","ieee":"M. Loose and T. Mitchison, “The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns,” Nature Cell Biology, vol. 16, no. 1. Nature Publishing Group, pp. 38–46, 2014.","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.","short":"M. Loose, T. Mitchison, Nature Cell Biology 16 (2014) 38–46.","mla":"Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” Nature Cell Biology, vol. 16, no. 1, Nature Publishing Group, 2014, pp. 38–46, doi:10.1038/ncb2885.","chicago":"Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2885."},"quality_controlled":0,"page":"38 - 46","date_published":"2014-01-01T00:00:00Z","doi":"10.1038/ncb2885","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."}],"issue":"1","publist_id":"5094","extern":1,"_id":"1990","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.","year":"2014","publication_status":"published","status":"public","title":"The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns","intvolume":" 16","publisher":"Nature Publishing Group","author":[{"full_name":"Martin Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"full_name":"Mitchison, Timothy J","first_name":"Timothy","last_name":"Mitchison"}],"date_updated":"2021-01-12T06:54:33Z","date_created":"2018-12-11T11:55:05Z","volume":16},{"day":"16","month":"12","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1413918111","date_published":"2014-12-16T00:00:00Z","page":"E5471 - E5479","quality_controlled":"1","citation":{"ieee":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, and S. Yalovsky, “Bimodal regulation of ICR1 levels generates self-organizing auxin distribution,” PNAS, vol. 111, no. 50. National Academy of Sciences, pp. E5471–E5479, 2014.","apa":"Hazak, O., Obolski, U., Prat, T., Friml, J., Hadany, L., & Yalovsky, S. (2014). Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1413918111","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. PNAS. 2014;111(50):E5471-E5479. doi:10.1073/pnas.1413918111","chicago":"Hazak, Ora, Uri Obolski, Tomas Prat, Jiří Friml, Lilach Hadany, and Shaul Yalovsky. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1413918111.","short":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, S. Yalovsky, PNAS 111 (2014) E5471–E5479.","mla":"Hazak, Ora, et al. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” PNAS, vol. 111, no. 50, National Academy of Sciences, 2014, pp. E5471–79, doi:10.1073/pnas.1413918111."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/"}],"publication":"PNAS","publist_id":"5083","issue":"50","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","volume":111,"date_created":"2018-12-11T11:55:07Z","date_updated":"2021-01-12T06:54:35Z","author":[{"full_name":"Hazak, Ora","last_name":"Hazak","first_name":"Ora"},{"last_name":"Obolski","first_name":"Uri","full_name":"Obolski, Uri"},{"first_name":"Tomas","last_name":"Prat","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","full_name":"Prat, Tomas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Lilach","last_name":"Hadany","full_name":"Hadany, Lilach"},{"full_name":"Yalovsky, Shaul","first_name":"Shaul","last_name":"Yalovsky"}],"publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"intvolume":" 111","status":"public","title":"Bimodal regulation of ICR1 levels generates self-organizing auxin distribution","publication_status":"published","year":"2014","_id":"1996","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"publication":"Current Biology","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.","mla":"Viaene, Tom, et al. “Directional Auxin Transport Mechanisms in Early Diverging Land Plants.” Current Biology, vol. 24, no. 23, Cell Press, 2014, pp. 2786–91, doi:10.1016/j.cub.2014.09.056.","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.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.09.056.","ama":"Viaene T, Landberg K, Thelander M, et al. Directional auxin transport mechanisms in early diverging land plants. Current Biology. 2014;24(23):2786-2791. doi:10.1016/j.cub.2014.09.056","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. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.09.056","ieee":"T. Viaene et al., “Directional auxin transport mechanisms in early diverging land plants,” Current Biology, vol. 24, no. 23. Cell Press, pp. 2786–2791, 2014.","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."},"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"page":"2786 - 2791","date_published":"2014-12-01T00:00:00Z","doi":"10.1016/j.cub.2014.09.056","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"12","year":"2014","_id":"1994","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Directional auxin transport mechanisms in early diverging land plants","intvolume":" 24","publisher":"Cell Press","department":[{"_id":"JiFr"}],"author":[{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"last_name":"Landberg","first_name":"Katarina","full_name":"Landberg, Katarina"},{"full_name":"Thelander, Mattias","last_name":"Thelander","first_name":"Mattias"},{"full_name":"Medvecka, Eva","last_name":"Medvecka","first_name":"Eva"},{"full_name":"Pederson, Eric","last_name":"Pederson","first_name":"Eric"},{"last_name":"Feraru","first_name":"Elena","full_name":"Feraru, Elena"},{"full_name":"Cooper, Endymion","last_name":"Cooper","first_name":"Endymion"},{"last_name":"Karimi","first_name":"Mansour","full_name":"Karimi, Mansour"},{"full_name":"Delwiche, Charles","last_name":"Delwiche","first_name":"Charles"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"full_name":"Sundberg, Eva","first_name":"Eva","last_name":"Sundberg"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"date_updated":"2021-01-12T06:54:34Z","date_created":"2018-12-11T11:55:06Z","oa_version":"None","volume":24,"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"}],"ec_funded":1,"publist_id":"5088","issue":"23"},{"month":"12","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.113.243601","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.5972","open_access":"1"}],"publist_id":"5085","ec_funded":1,"article_number":"243601","date_updated":"2021-01-12T06:54:34Z","date_created":"2018-12-11T11:55:06Z","volume":113,"author":[{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"full_name":"Mascarenhas, Eduardo","last_name":"Mascarenhas","first_name":"Eduardo"},{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","first_name":"Laleh"},{"full_name":"Poizat, Jean","last_name":"Poizat","first_name":"Jean"},{"last_name":"Valente","first_name":"Daniel","full_name":"Valente, Daniel"},{"first_name":"Alexia","last_name":"Auffèves","full_name":"Auffèves, Alexia"},{"full_name":"Gerace, Dario","first_name":"Dario","last_name":"Gerace"},{"last_name":"Santos","first_name":"Marcelo","full_name":"Santos, Marcelo"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2014","day":"08","scopus_import":1,"date_published":"2014-12-08T00:00:00Z","publication":"Physical Review Letters","citation":{"ama":"Fratini F, Mascarenhas E, Safari L, et al. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. Physical Review Letters. 2014;113(24). doi:10.1103/PhysRevLett.113.243601","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.","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. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.243601","ieee":"F. Fratini et al., “Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification,” Physical Review Letters, vol. 113, no. 24. American Physical Society, 2014.","mla":"Fratini, Filippo, et al. “Fabry-Perot Interferometer with Quantum Mirrors: Nonlinear Light Transport and Rectification.” Physical Review Letters, vol. 113, no. 24, 243601, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.243601.","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.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.243601."},"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."}],"issue":"24","type":"journal_article","oa_version":"Submitted Version","title":"Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification","status":"public","intvolume":" 113","_id":"1995","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"_id":"1998","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. ","year":"2014","publication_status":"published","status":"public","title":"Individual and social immunisation in insects","department":[{"_id":"SyCr"}],"publisher":"Elsevier","intvolume":" 35","author":[{"id":"349A6E66-F248-11E8-B48F-1D18A9856A87","first_name":"Leila","last_name":"El Masri","full_name":"El Masri, Leila"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"date_updated":"2021-01-12T06:54:35Z","date_created":"2018-12-11T11:55:07Z","oa_version":"None","volume":35,"type":"journal_article","abstract":[{"lang":"eng","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."}],"publist_id":"5081","issue":"10","publication":"Trends in Immunology","citation":{"chicago":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” Trends in Immunology. Elsevier, 2014. https://doi.org/10.1016/j.it.2014.08.005.","short":"L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482.","mla":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” Trends in Immunology, vol. 35, no. 10, Elsevier, 2014, pp. 471–82, doi:10.1016/j.it.2014.08.005.","apa":"El Masri, L., & Cremer, S. (2014). Individual and social immunisation in insects. Trends in Immunology. Elsevier. https://doi.org/10.1016/j.it.2014.08.005","ieee":"L. El Masri and S. Cremer, “Individual and social immunisation in insects,” Trends in Immunology, vol. 35, no. 10. Elsevier, pp. 471–482, 2014.","ista":"El Masri L, Cremer S. 2014. Individual and social immunisation in insects. Trends in Immunology. 35(10), 471–482.","ama":"El Masri L, Cremer S. Individual and social immunisation in insects. Trends in Immunology. 2014;35(10):471-482. doi:10.1016/j.it.2014.08.005"},"quality_controlled":"1","page":"471 - 482","doi":"10.1016/j.it.2014.08.005","date_published":"2014-10-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"10"},{"article_number":"0113124","license":"https://creativecommons.org/licenses/by-sa/4.0/","file_date_updated":"2020-07-14T12:45:24Z","ec_funded":1,"publist_id":"5074","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Public Library of Science","year":"2014","date_created":"2018-12-11T11:55:09Z","date_updated":"2021-01-12T06:54:39Z","volume":9,"author":[{"id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","first_name":"Sooyun","full_name":"Kim, Sooyun"}],"month":"11","quality_controlled":"1","project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0113124","type":"journal_article","abstract":[{"text":"Oriens-lacunosum moleculare (O-LM) interneurons in the CA1 region of the hippocampus play a key role in feedback inhibition and in the control of network activity. However, how these cells are efficiently activated in the network remains unclear. To address this question, I performed recordings from CA1 pyramidal neuron axons, the presynaptic fibers that provide feedback innervation of these interneurons. Two forms of axonal action potential (AP) modulation were identified. First, repetitive stimulation resulted in activity-dependent AP broadening. Broadening showed fast onset, with marked changes in AP shape following a single AP. Second, tonic depolarization in CA1 pyramidal neuron somata induced AP broadening in the axon, and depolarization-induced broadening summated with activity-dependent broadening. Outsideout patch recordings from CA1 pyramidal neuron axons revealed a high density of a-dendrotoxin (α-DTX)-sensitive, inactivating K+ channels, suggesting that K+ channel inactivation mechanistically contributes to AP broadening. To examine the functional consequences of axonal AP modulation for synaptic transmission, I performed paired recordings between synaptically connected CA1 pyramidal neurons and O-LM interneurons. CA1 pyramidal neuron-O-LM interneuron excitatory postsynaptic currents (EPSCs) showed facilitation during both repetitive stimulation and tonic depolarization of the presynaptic neuron. Both effects were mimicked and occluded by α-DTX, suggesting that they were mediated by K+ channel inactivation. Therefore, axonal AP modulation can greatly facilitate the activation of O-LM interneurons. In conclusion, modulation of AP shape in CA1 pyramidal neuron axons substantially enhances the efficacy of principal neuron-interneuron synapses, promoting the activation of O-LM interneurons in recurrent inhibitory microcircuits.","lang":"eng"}],"issue":"11","title":"Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus","ddc":["570"],"status":"public","intvolume":" 9","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2002","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":5179993,"file_name":"IST-2016-434-v1+1_journal.pone.0113124.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:52Z","date_updated":"2020-07-14T12:45:24Z","checksum":"85e4f4ea144f827272aaf376b2830564","file_id":"5107","relation":"main_file"}],"pubrep_id":"434","scopus_import":1,"day":"19","has_accepted_license":"1","publication":"PLoS One","citation":{"mla":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” PLoS One, vol. 9, no. 11, 0113124, Public Library of Science, 2014, doi:10.1371/journal.pone.0113124.","short":"S. Kim, PLoS One 9 (2014).","chicago":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0113124.","ama":"Kim S. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0113124","ista":"Kim S. 2014. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. 9(11), 0113124.","ieee":"S. Kim, “Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.","apa":"Kim, S. (2014). Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0113124"},"date_published":"2014-11-19T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2014.06.013","date_published":"2014-07-02T00:00:00Z","quality_controlled":"1","page":"8 - 10","publication":"Neuron","citation":{"ama":"O’Neill J, Csicsvari JL. Learning by example in the hippocampus. Neuron. 2014;83(1):8-10. doi:10.1016/j.neuron.2014.06.013","ista":"O’Neill J, Csicsvari JL. 2014. Learning by example in the hippocampus. Neuron. 83(1), 8–10.","ieee":"J. O’Neill and J. L. Csicsvari, “Learning by example in the hippocampus,” Neuron, vol. 83, no. 1. Elsevier, pp. 8–10, 2014.","apa":"O’Neill, J., & Csicsvari, J. L. (2014). Learning by example in the hippocampus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.06.013","mla":"O’Neill, Joseph, and Jozsef L. Csicsvari. “Learning by Example in the Hippocampus.” Neuron, vol. 83, no. 1, Elsevier, 2014, pp. 8–10, doi:10.1016/j.neuron.2014.06.013.","short":"J. O’Neill, J.L. Csicsvari, Neuron 83 (2014) 8–10.","chicago":"O’Neill, Joseph, and Jozsef L Csicsvari. “Learning by Example in the Hippocampus.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.06.013."},"month":"07","day":"02","scopus_import":1,"date_created":"2018-12-11T11:55:09Z","date_updated":"2021-01-12T06:54:39Z","volume":83,"oa_version":"None","author":[{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"}],"publication_status":"published","title":"Learning by example in the hippocampus","status":"public","department":[{"_id":"JoCs"}],"intvolume":" 83","publisher":"Elsevier","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2003","year":"2014","abstract":[{"lang":"eng","text":"Learning can be facilitated by previous knowledge when it is organized into relational representations forming schemas. In this issue of Neuron, McKenzie et al. (2014) demonstrate that the hippocampus rapidly forms interrelated, hierarchical memory representations to support schema-based learning."}],"issue":"1","publist_id":"5073","type":"journal_article"},{"scopus_import":1,"day":"01","month":"08","citation":{"ama":"Yu F, Fienberg S, Slaković A, Uhler C. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. 2014;50:133-141. doi:10.1016/j.jbi.2014.01.008","apa":"Yu, F., Fienberg, S., Slaković, A., & Uhler, C. (2014). Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. Elsevier. https://doi.org/10.1016/j.jbi.2014.01.008","ieee":"F. Yu, S. Fienberg, A. Slaković, and C. Uhler, “Scalable privacy-preserving data sharing methodology for genome-wide association studies,” Journal of Biomedical Informatics, vol. 50. Elsevier, pp. 133–141, 2014.","ista":"Yu F, Fienberg S, Slaković A, Uhler C. 2014. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. 50, 133–141.","short":"F. Yu, S. Fienberg, A. Slaković, C. Uhler, Journal of Biomedical Informatics 50 (2014) 133–141.","mla":"Yu, Fei, et al. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” Journal of Biomedical Informatics, vol. 50, Elsevier, 2014, pp. 133–41, doi:10.1016/j.jbi.2014.01.008.","chicago":"Yu, Fei, Stephen Fienberg, Alexandra Slaković, and Caroline Uhler. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” Journal of Biomedical Informatics. Elsevier, 2014. https://doi.org/10.1016/j.jbi.2014.01.008."},"main_file_link":[{"url":"http://arxiv.org/abs/1401.5193","open_access":"1"}],"oa":1,"publication":"Journal of Biomedical Informatics","page":"133 - 141","quality_controlled":"1","doi":"10.1016/j.jbi.2014.01.008","date_published":"2014-08-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"5065","abstract":[{"text":"The protection of privacy of individual-level information in genome-wide association study (GWAS) databases has been a major concern of researchers following the publication of “an attack” on GWAS data by Homer et al. (2008). Traditional statistical methods for confidentiality and privacy protection of statistical databases do not scale well to deal with GWAS data, especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach that provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, Uhler et al. (2013) proposed new methods to release aggregate GWAS data without compromising an individual’s privacy. We extend the methods developed in Uhler et al. (2013) for releasing differentially-private χ2χ2-statistics by allowing for arbitrary number of cases and controls, and for releasing differentially-private allelic test statistics. We also provide a new interpretation by assuming the controls’ data are known, which is a realistic assumption because some GWAS use publicly available data as controls. We assess the performance of the proposed methods through a risk-utility analysis on a real data set consisting of DNA samples collected by the Wellcome Trust Case Control Consortium and compare the methods with the differentially-private release mechanism proposed by Johnson and Shmatikov (2013).","lang":"eng"}],"_id":"2011","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research was partially supported by NSF Awards EMSW21-RTG and BCS-0941518 to the Department of Statistics at Carnegie Mellon University, and by NSF Grant BCS-0941553 to the Department of Statistics at Pennsylvania State University. This work was also supported in part by the National Center for Research Resources, Grant UL1 RR033184, and is now at the National Center for Advancing Translational Sciences, Grant UL1 TR000127 to Pennsylvania State University. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NSF and NIH.","publisher":"Elsevier","department":[{"_id":"CaUh"}],"intvolume":" 50","title":"Scalable privacy-preserving data sharing methodology for genome-wide association studies","status":"public","publication_status":"published","author":[{"full_name":"Yu, Fei","last_name":"Yu","first_name":"Fei"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"},{"full_name":"Slaković, Alexandra","last_name":"Slaković","first_name":"Alexandra"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline"}],"volume":50,"oa_version":"Submitted Version","date_created":"2018-12-11T11:55:12Z","date_updated":"2021-01-12T06:54:42Z"},{"language":[{"iso":"eng"}],"doi":"10.1038/nn.3700","date_published":"2014-04-25T00:00:00Z","page":"643 - 644","quality_controlled":"1","citation":{"ieee":"D. Dupret and J. L. Csicsvari, “Turning heads to remember places,” Nature Neuroscience, vol. 17, no. 5. Nature Publishing Group, pp. 643–644, 2014.","apa":"Dupret, D., & Csicsvari, J. L. (2014). Turning heads to remember places. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3700","ista":"Dupret D, Csicsvari JL. 2014. Turning heads to remember places. Nature Neuroscience. 17(5), 643–644.","ama":"Dupret D, Csicsvari JL. Turning heads to remember places. Nature Neuroscience. 2014;17(5):643-644. doi:10.1038/nn.3700","chicago":"Dupret, David, and Jozsef L Csicsvari. “Turning Heads to Remember Places.” Nature Neuroscience. Nature Publishing Group, 2014. https://doi.org/10.1038/nn.3700.","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 17 (2014) 643–644.","mla":"Dupret, David, and Jozsef L. Csicsvari. “Turning Heads to Remember Places.” Nature Neuroscience, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 643–44, doi:10.1038/nn.3700."},"publication":"Nature Neuroscience","day":"25","month":"04","scopus_import":1,"oa_version":"None","volume":17,"date_created":"2018-12-11T11:55:09Z","date_updated":"2021-01-12T06:54:40Z","author":[{"last_name":"Dupret","first_name":"David","full_name":"Dupret, David"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"intvolume":" 17","department":[{"_id":"JoCs"}],"publisher":"Nature Publishing Group","publication_status":"published","title":"Turning heads to remember places","status":"public","_id":"2005","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","issue":"5","publist_id":"5071","abstract":[{"text":"By eliciting a natural exploratory behavior in rats, head scanning, a study reveals that hippocampal place cells form new, stable firing fields in those locations where the behavior has just occurred.","lang":"eng"}],"type":"journal_article"},{"author":[{"full_name":"Klimova, Anna","first_name":"Anna","last_name":"Klimova","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rudas","first_name":"Tamás","full_name":"Rudas, Tamás"}],"date_updated":"2022-08-26T08:12:12Z","date_created":"2018-12-11T11:55:10Z","oa_version":"Published Version","year":"2014","_id":"2007","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"gIPFrm: Generalized iterative proportional fitting for relational models","department":[{"_id":"CaUh"}],"publisher":"The Comprehensive R Archive Network","abstract":[{"text":"Maximum likelihood estimation under relational models, with or without the overall effect. For more information see the reference manual","lang":"eng"}],"publist_id":"5069","type":"research_data_reference","date_published":"2014-03-20T00:00:00Z","main_file_link":[{"url":"https://CRAN.R-project.org/package=gIPFrm ","open_access":"1"}],"citation":{"chicago":"Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional Fitting for Relational Models.” The Comprehensive R Archive Network, 2014.","short":"A. Klimova, T. Rudas, (2014).","mla":"Klimova, Anna, and Tamás Rudas. GIPFrm: Generalized Iterative Proportional Fitting for Relational Models. The Comprehensive R Archive Network, 2014.","ieee":"A. Klimova and T. Rudas, “gIPFrm: Generalized iterative proportional fitting for relational models.” The Comprehensive R Archive Network, 2014.","apa":"Klimova, A., & Rudas, T. (2014). gIPFrm: Generalized iterative proportional fitting for relational models. The Comprehensive R Archive Network.","ista":"Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting for relational models, The Comprehensive R Archive Network.","ama":"Klimova A, Rudas T. gIPFrm: Generalized iterative proportional fitting for relational models. 2014."},"oa":1,"month":"03","day":"20","article_processing_charge":"No"},{"oa_version":"Published Version","file":[{"file_id":"11410","relation":"main_file","date_updated":"2022-05-24T08:41:41Z","date_created":"2022-05-24T08:41:41Z","success":1,"checksum":"6913e9bc26e9fc1c0441a739a4199229","file_name":"2014_JournNeuroscience_Matsukawa.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3963728}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2018","ddc":["570"],"title":"Netrin-G/NGL complexes encode functional synaptic diversification","status":"public","intvolume":" 34","abstract":[{"text":"Synaptic cell adhesion molecules are increasingly gaining attention for conferring specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic adhesion molecules that distribute on distinct axons, and their presence restricts the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific subdendritic segments of target neurons. However, the neural circuits and functional roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify excitatory synapses in independent hippocampal pathways. In the hippocampal CA1 area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G mutant synapses displayed opposing phenotypes in long-term and short-term plasticity through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic membranes. Our findings show that netrin-G/NGL interactions differentially control synaptic plasticity in distinct circuits via retrograde signaling mechanisms and explain how synaptic inputs are diversified to control neuronal activity.","lang":"eng"}],"issue":"47","type":"journal_article","date_published":"2014-11-19T00:00:00Z","publication":"Journal of Neuroscience","citation":{"ista":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H, Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 34(47), 15779–15792.","apa":"Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K., Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1141-14.2014","ieee":"H. Matsukawa et al., “Netrin-G/NGL complexes encode functional synaptic diversification,” Journal of Neuroscience, vol. 34, no. 47. Society for Neuroscience, pp. 15779–15792, 2014.","ama":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 2014;34(47):15779-15792. doi:10.1523/JNEUROSCI.1141-14.2014","chicago":"Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján, Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience. Society for Neuroscience, 2014. https://doi.org/10.1523/JNEUROSCI.1141-14.2014.","mla":"Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:10.1523/JNEUROSCI.1141-14.2014.","short":"H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792."},"article_type":"original","page":"15779 - 15792","day":"19","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Matsukawa, Hiroshi","last_name":"Matsukawa","first_name":"Hiroshi"},{"full_name":"Akiyoshi Nishimura, Sachiko","first_name":"Sachiko","last_name":"Akiyoshi Nishimura"},{"full_name":"Zhang, Qi","first_name":"Qi","last_name":"Zhang"},{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"},{"last_name":"Yamaguchi","first_name":"Kazuhiko","full_name":"Yamaguchi, Kazuhiko"},{"full_name":"Goto, Hiromichi","last_name":"Goto","first_name":"Hiromichi"},{"full_name":"Yaguchi, Kunio","first_name":"Kunio","last_name":"Yaguchi"},{"last_name":"Hashikawa","first_name":"Tsutomu","full_name":"Hashikawa, Tsutomu"},{"first_name":"Chie","last_name":"Sano","full_name":"Sano, Chie"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Nakashiba, Toshiaki","last_name":"Nakashiba","first_name":"Toshiaki"},{"last_name":"Itohara","first_name":"Shigeyoshi","full_name":"Itohara, Shigeyoshi"}],"date_created":"2018-12-11T11:55:14Z","date_updated":"2022-05-24T08:54:54Z","volume":34,"acknowledgement":"This work was supported by “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)” initiated by the Council for Science and Technology Policy.","year":"2014","pmid":1,"publication_status":"published","publisher":"Society for Neuroscience","department":[{"_id":"RySh"}],"file_date_updated":"2022-05-24T08:41:41Z","publist_id":"5054","doi":"10.1523/JNEUROSCI.1141-14.2014","language":[{"iso":"eng"}],"external_id":{"pmid":["25411505"]},"oa":1,"quality_controlled":"1","month":"11","publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]}},{"issue":"3-4","abstract":[{"lang":"eng","text":"We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory."}],"type":"journal_article","oa_version":"Submitted Version","_id":"2019","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 17","status":"public","title":"Phase transition in the density of states of quantum spin glasses","day":"17","scopus_import":1,"date_published":"2014-12-17T00:00:00Z","citation":{"ista":"Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464.","apa":"Erdös, L., & Schröder, D. J. (2014). Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9164-3","ieee":"L. Erdös and D. J. Schröder, “Phase transition in the density of states of quantum spin glasses,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 441–464, 2014.","ama":"Erdös L, Schröder DJ. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):441-464. doi:10.1007/s11040-014-9164-3","chicago":"Erdös, László, and Dominik J Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9164-3.","mla":"Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:10.1007/s11040-014-9164-3.","short":"L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464."},"publication":"Mathematical Physics, Analysis and Geometry","page":"441 - 464","publist_id":"5053","ec_funded":1,"author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder"}],"volume":17,"date_updated":"2021-01-12T06:54:45Z","date_created":"2018-12-11T11:55:15Z","year":"2014","publisher":"Springer","department":[{"_id":"LaEr"}],"publication_status":"published","month":"12","doi":"10.1007/s11040-014-9164-3","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.1552"}],"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"quality_controlled":"1"},{"doi":"10.1007/s10208-014-9205-0","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1209.0285","open_access":"1"}],"quality_controlled":"1","month":"10","author":[{"full_name":"Lin, Shaowei","first_name":"Shaowei","last_name":"Lin"},{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"full_name":"Sturmfels, Bernd","last_name":"Sturmfels","first_name":"Bernd"},{"full_name":"Bühlmann, Peter","first_name":"Peter","last_name":"Bühlmann"}],"volume":14,"date_created":"2018-12-11T11:55:12Z","date_updated":"2021-01-12T06:54:43Z","acknowledgement":"This work was supported in part by the US National Science Foundation (DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning program (FA8650-10-C-7020).","year":"2014","publisher":"Springer","department":[{"_id":"CaUh"}],"publication_status":"published","publist_id":"5063","date_published":"2014-10-10T00:00:00Z","citation":{"ama":"Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 2014;14(5):1079-1116. doi:10.1007/s10208-014-9205-0","ista":"Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 14(5), 1079–1116.","ieee":"S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their singularities in partial correlation testing,” Foundations of Computational Mathematics, vol. 14, no. 5. Springer, pp. 1079–1116, 2014.","apa":"Lin, S., Uhler, C., Sturmfels, B., & Bühlmann, P. (2014). Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9205-0","mla":"Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:10.1007/s10208-014-9205-0.","short":"S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116.","chicago":"Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics. Springer, 2014. https://doi.org/10.1007/s10208-014-9205-0."},"publication":"Foundations of Computational Mathematics","page":"1079 - 1116","day":"10","scopus_import":1,"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2013","intvolume":" 14","status":"public","title":"Hypersurfaces and their singularities in partial correlation testing","issue":"5","abstract":[{"lang":"eng","text":"An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n"}],"type":"journal_article"},{"type":"preprint","abstract":[{"text":" Gaussian graphical models have received considerable attention during the past four decades from the statistical and machine learning communities. In Bayesian treatments of this model, the G-Wishart distribution serves as the conjugate prior for inverse covariance matrices satisfying graphical constraints. While it is straightforward to posit the unnormalized densities, the normalizing constants of these distributions have been known only for graphs that are chordal, or decomposable. Up until now, it was unknown whether the normalizing constant for a general graph could be represented explicitly, and a considerable body of computational literature emerged that attempted to avoid this apparent intractability. We close this question by providing an explicit representation of the G-Wishart normalizing constant for general graphs.","lang":"eng"}],"publist_id":"5058","extern":1,"_id":"2017","acknowledgement":"A.L.'s research was supported by Statistics for Innovation sfi2 in Oslo.\nD.R.'s research was partially supported by the U.S. National Science Foun-dation grant DMS-1309808; and by a Romberg Guest Professorship at the Heidelberg University Graduate School for Mathematical and Computational Methods in the Sciences, funded by German Universities Excellence Initiative grant GSC 220/2.","year":"2014","title":" Exact formulas for the normalizing constants of Wishart distributions for graphical models","status":"public","publication_status":"published","publisher":"ArXiv","author":[{"full_name":"Caroline Uhler","first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216"},{"last_name":"Lenkoski","first_name":"Alex","full_name":"Lenkoski, Alex"},{"first_name":"Donald","last_name":"Richards","full_name":"Richards, Donald"}],"date_created":"2018-12-11T11:55:14Z","date_updated":"2021-01-12T06:54:44Z","month":"06","day":"18","publication":"ArXiv","citation":{"chicago":"Uhler, Caroline, Alex Lenkoski, and Donald Richards. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv. ArXiv, 2014.","mla":"Uhler, Caroline, et al. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv, ArXiv, 2014.","short":"C. Uhler, A. Lenkoski, D. Richards, ArXiv (2014).","ista":"Uhler C, Lenkoski A, Richards D. 2014. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv, .","ieee":"C. Uhler, A. Lenkoski, and D. Richards, “ Exact formulas for the normalizing constants of Wishart distributions for graphical models,” ArXiv. ArXiv, 2014.","apa":"Uhler, C., Lenkoski, A., & Richards, D. (2014). Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. ArXiv.","ama":"Uhler C, Lenkoski A, Richards D. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. 2014."},"main_file_link":[{"url":"http://arxiv.org/abs/1406.4901","open_access":"1"}],"oa":1,"quality_controlled":0,"date_published":"2014-06-18T00:00:00Z"},{"year":"2014","publication_status":"published","department":[{"_id":"SiHi"},{"_id":"Bio"}],"publisher":"Cell Press","author":[{"full_name":"Gao, Peng","first_name":"Peng","last_name":"Gao"},{"last_name":"Postiglione","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","full_name":"Postiglione, Maria P"},{"full_name":"Krieger, Teresa","last_name":"Krieger","first_name":"Teresa"},{"first_name":"Luisirene","last_name":"Hernandez","full_name":"Hernandez, Luisirene"},{"full_name":"Wang, Chao","first_name":"Chao","last_name":"Wang"},{"full_name":"Han, Zhi","first_name":"Zhi","last_name":"Han"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Papusheva, Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Papusheva"},{"full_name":"Insolera, Ryan","first_name":"Ryan","last_name":"Insolera"},{"full_name":"Chugh, Kritika","first_name":"Kritika","last_name":"Chugh"},{"first_name":"Oren","last_name":"Kodish","full_name":"Kodish, Oren"},{"full_name":"Huang, Kun","first_name":"Kun","last_name":"Huang"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"last_name":"Shi","first_name":"Song","full_name":"Shi, Song"}],"date_updated":"2021-01-12T06:54:47Z","date_created":"2018-12-11T11:55:16Z","volume":159,"file_date_updated":"2020-07-14T12:45:25Z","publist_id":"5050","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"}],"doi":"10.1016/j.cell.2014.10.027","language":[{"iso":"eng"}],"month":"11","_id":"2022","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Deterministic progenitor behavior and unitary production of neurons in the neocortex","intvolume":" 159","pubrep_id":"423","file":[{"creator":"system","file_size":4435787,"content_type":"application/pdf","file_name":"IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-12T10:08:47Z","checksum":"6c5de8329bb2ffa71cba9fda750f14ce","file_id":"4709","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program.","lang":"eng"}],"issue":"4","publication":"Cell","citation":{"short":"P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher, E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S. Hippenmeyer, S. Shi, Cell 159 (2014) 775–788.","mla":"Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell, vol. 159, no. 4, Cell Press, 2014, pp. 775–88, doi:10.1016/j.cell.2014.10.027.","chicago":"Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell. Cell Press, 2014. https://doi.org/10.1016/j.cell.2014.10.027.","ama":"Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 2014;159(4):775-788. doi:10.1016/j.cell.2014.10.027","apa":"Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.10.027","ieee":"P. Gao et al., “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” Cell, vol. 159, no. 4. Cell Press, pp. 775–788, 2014.","ista":"Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788."},"page":"775 - 788","date_published":"2014-11-06T00:00:00Z","scopus_import":1,"day":"06","has_accepted_license":"1"},{"page":"8850 - 8855","quality_controlled":"1","citation":{"ama":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 2014;111(24):8850-8855. doi:10.1073/pnas.1408233111","ista":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 111(24), 8850–8855.","ieee":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” PNAS, vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014.","apa":"Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., & Ardehali, R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1408233111","mla":"Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:10.1073/pnas.1408233111.","short":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855.","chicago":"Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman, and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1408233111."},"publication":"PNAS","language":[{"iso":"eng"}],"date_published":"2014-06-17T00:00:00Z","doi":"10.1073/pnas.1408233111","scopus_import":1,"day":"17","month":"06","department":[{"_id":"SiHi"}],"intvolume":" 111","publisher":"National Academy of Sciences","title":"Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice","status":"public","publication_status":"published","year":"2014","_id":"2020","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":111,"date_created":"2018-12-11T11:55:15Z","date_updated":"2021-01-12T06:54:46Z","author":[{"first_name":"Shah","last_name":"Ali","full_name":"Ali, Shah"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"last_name":"Saadat","first_name":"Lily","full_name":"Saadat, Lily"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"last_name":"Weissman","first_name":"Irving","full_name":"Weissman, Irving"},{"last_name":"Ardehali","first_name":"Reza","full_name":"Ardehali, Reza"}],"type":"journal_article","publist_id":"5052","issue":"24","abstract":[{"lang":"eng","text":"The mammalian heart has long been considered a postmitotic organ, implying that the total number of cardiomyocytes is set at birth. Analysis of cell division in the mammalian heart is complicated by cardiomyocyte binucleation shortly after birth, which makes it challenging to interpret traditional assays of cell turnover [Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009) Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry technique recently calculated the low, discrete rate of cardiomyocyte generation in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level understanding of postnatal cardiomyogenesis remains limited. Herein, we provide a new line of evidence for the differentiated α-myosin heavy chain-expressing cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic analysis with double markers” mouse model. We show limited, life-long, symmetric division of cardiomyocytes as a rare event that is evident in utero but significantly diminishes after the first month of life in mice; daughter cardiomyocytes divide very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore, ligation of the left anterior descending coronary artery, which causes a myocardial infarction in the mosaic analysis with double-marker mice, did not increase the rate of cardiomyocyte division above the basal level for up to 4 wk after the injury. The clonal analysis described here provides direct evidence of postnatal mammalian cardiomyogenesis."}]},{"scopus_import":1,"day":"31","month":"10","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/","open_access":"1"}],"citation":{"chicago":"William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1258996.","mla":"William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science, vol. 346, no. 6209, American Association for the Advancement of Science, 2014, pp. 626–29, doi:10.1126/science.1258996.","short":"J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629.","ista":"William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629.","ieee":"J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling,” Science, vol. 346, no. 6209. American Association for the Advancement of Science, pp. 626–629, 2014.","apa":"William, J., Hippenmeyer, S., & Luo, L. (2014). Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1258996","ama":"William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 2014;346(6209):626-629. doi:10.1126/science.1258996"},"oa":1,"publication":"Science","page":"626 - 629","quality_controlled":"1","doi":"10.1126/science.1258996","date_published":"2014-10-31T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"5051","issue":"6209","abstract":[{"lang":"eng","text":"Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development."}],"_id":"2021","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","intvolume":" 346","publisher":"American Association for the Advancement of Science","department":[{"_id":"SiHi"}],"title":"Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling","publication_status":"published","status":"public","author":[{"full_name":"William, Joo","last_name":"William","first_name":"Joo"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"}],"oa_version":"Submitted Version","volume":346,"date_updated":"2021-01-12T06:54:47Z","date_created":"2018-12-11T11:55:15Z"},{"publisher":"Society of Industrial and Applied Mathematics","editor":[{"full_name":"Cassez, Franck","first_name":"Franck","last_name":"Cassez"},{"last_name":"Raskin","first_name":"Jean-François","full_name":"Raskin, Jean-François"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2014","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1.","volume":8837,"date_created":"2018-12-11T11:55:17Z","date_updated":"2021-01-12T06:54:49Z","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"last_name":"Kwiatkowska","first_name":"Marta","full_name":"Kwiatkowska, Marta"},{"full_name":"Parker, David","first_name":"David","last_name":"Parker"},{"full_name":"Ujma, Mateusz","last_name":"Ujma","first_name":"Mateusz"}],"ec_funded":1,"publist_id":"5046","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING","grant_number":"24696","_id":"26241A12-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.2967"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-11936-6_8","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","end_date":"2014-11-07","location":"Sydney, Australia","start_date":"2014-11-03"},"month":"11","intvolume":" 8837","status":"public","title":"Verification of markov decision processes using learning algorithms","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2027","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples.","lang":"eng"}],"page":"98 - 114","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt, Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification of Markov Decision Processes Using Learning Algorithms.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1007/978-3-319-11936-6_8.","mla":"Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:10.1007/978-3-319-11936-6_8.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114.","ista":"Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M, Parker D, Ujma M. 2014. Verification of markov decision processes using learning algorithms. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm Engineering and Experiments, LNCS, vol. 8837, 98–114.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska, M., … Ujma, M. (2014). Verification of markov decision processes using learning algorithms. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 98–114). Sydney, Australia: Society of Industrial and Applied Mathematics. https://doi.org/10.1007/978-3-319-11936-6_8","ieee":"T. Brázdil et al., “Verification of markov decision processes using learning algorithms,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 98–114.","ama":"Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision processes using learning algorithms. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Society of Industrial and Applied Mathematics; 2014:98-114. doi:10.1007/978-3-319-11936-6_8"},"publication":" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","date_published":"2014-11-01T00:00:00Z","day":"01"},{"language":[{"iso":"eng"}],"doi":"10.7554/eLife.04057","project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"},{"call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"month":"12","volume":3,"date_created":"2018-12-11T11:55:19Z","date_updated":"2021-01-12T06:54:51Z","author":[{"full_name":"Arai, Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru","last_name":"Arai"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"department":[{"_id":"PeJo"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2014","publist_id":"5041","ec_funded":1,"file_date_updated":"2020-07-14T12:45:26Z","date_published":"2014-12-09T00:00:00Z","citation":{"ama":"Arai itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 2014;3. doi:10.7554/eLife.04057","ista":"Arai itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3.","ieee":"itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse,” eLife, vol. 3. eLife Sciences Publications, 2014.","apa":"Arai, itaru, & Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.04057","mla":"Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife, vol. 3, eLife Sciences Publications, 2014, doi:10.7554/eLife.04057.","short":"itaru Arai, P.M. Jonas, ELife 3 (2014).","chicago":"Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.04057."},"publication":"eLife","has_accepted_license":"1","day":"09","scopus_import":1,"file":[{"checksum":"c240f915450d4ebe8f95043a2a8c7b1a","date_created":"2018-12-12T10:14:41Z","date_updated":"2020-07-14T12:45:26Z","relation":"main_file","file_id":"5094","content_type":"application/pdf","file_size":2239563,"creator":"system","access_level":"open_access","file_name":"IST-2016-421-v1+1_e04057.full.pdf"}],"oa_version":"Submitted Version","pubrep_id":"421","intvolume":" 3","ddc":["570"],"status":"public","title":"Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2031","abstract":[{"lang":"eng","text":"A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release."}],"type":"journal_article"},{"citation":{"short":"J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014).","mla":"Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications, vol. 5, 3498, Nature Publishing Group, 2014, doi:10.1038/ncomms4498.","chicago":"Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4498.","ama":"Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 2014;5. doi:10.1038/ncomms4498","apa":"Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4498","ieee":"J. Toshima et al., “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” Nature Communications, vol. 5. Nature Publishing Group, 2014.","ista":"Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498."},"publication":"Nature Communications","date_published":"2014-03-25T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"25","intvolume":" 5","title":"Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole","ddc":["570"],"status":"public","_id":"2024","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":4803515,"creator":"system","file_name":"IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-12T10:11:11Z","checksum":"614fb6579c86d1f95bdd95eeb9ab01b0","relation":"main_file","file_id":"4864"}],"oa_version":"Submitted Version","pubrep_id":"616","type":"journal_article","abstract":[{"text":"The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and in the endocytic pathway from the plasma membrane to the vacuole. However, the intracellular location at which these two pathways converge remains unclear. In addition, the endocytic pathway is not completely blocked in yeast cells lacking all Rab5 genes, suggesting the existence of an unidentified route that bypasses the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic and VPS pathways occurs upstream of the requirement for Vps21p in these pathways. We also identify a previously unidentified endocytic pathway mediated by the AP-3 complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted cells, and thus works as an alternative route to the vacuole/lysosome. We propose that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent VPS pathway and a Rab5-independent AP-3-mediated pathway.","lang":"eng"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/ncomms4498","month":"03","publisher":"Nature Publishing Group","department":[{"_id":"DaSi"}],"publication_status":"published","year":"2014","volume":5,"date_created":"2018-12-11T11:55:16Z","date_updated":"2021-01-12T06:54:48Z","author":[{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"full_name":"Nishinoaki, Show","last_name":"Nishinoaki","first_name":"Show"},{"last_name":"Sato","first_name":"Yoshifumi","full_name":"Sato, Yoshifumi"},{"last_name":"Yamamoto","first_name":"Wataru","full_name":"Yamamoto, Wataru"},{"full_name":"Furukawa, Daiki","last_name":"Furukawa","first_name":"Daiki"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sawaguchi","first_name":"Akira","full_name":"Sawaguchi, Akira"},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"article_number":"3498","publist_id":"5048","file_date_updated":"2020-07-14T12:45:25Z"},{"month":"10","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2014.09.041","file_date_updated":"2020-07-14T12:45:25Z","publist_id":"5043","publication_status":"published","publisher":"Academic Press","department":[{"_id":"GaTk"}],"year":"2014","acknowledgement":"This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ","date_updated":"2022-08-25T14:00:47Z","date_created":"2018-12-11T11:55:18Z","volume":365,"author":[{"last_name":"Bodova","first_name":"Katarina","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bodova, Katarina"},{"last_name":"Paydarfar","first_name":"David","full_name":"Paydarfar, David"},{"full_name":"Forger, Daniel","first_name":"Daniel","last_name":"Forger"}],"related_material":{"link":[{"url":"https://doi.org/10.1016/j.jtbi.2015.03.013","relation":"erratum"}]},"scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1","page":"40 - 54","publication":" Journal of Theoretical Biology","citation":{"ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041","ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press, pp. 40–54, 2014.","apa":"Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. Academic Press. https://doi.org/10.1016/j.jtbi.2014.09.041","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 365, 40–54.","short":"K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.","mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54, doi:10.1016/j.jtbi.2014.09.041.","chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press, 2014. https://doi.org/10.1016/j.jtbi.2014.09.041."},"date_published":"2014-10-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model."}],"title":"Characterizing spiking in noisy type II neurons","status":"public","ddc":["570"],"intvolume":" 365","_id":"2028","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-12T10:17:58Z","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","file_id":"5316","relation":"main_file","creator":"system","file_size":2679222,"content_type":"application/pdf","file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf","access_level":"open_access"}],"pubrep_id":"444"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-11936-6_17","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2014-11-03","location":"Sydney, Australia","end_date":"2014-11-07"},"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"}],"quality_controlled":"1","month":"01","volume":8837,"date_created":"2018-12-11T11:55:17Z","date_updated":"2021-01-12T06:54:49Z","author":[{"last_name":"Komárková","first_name":"Zuzana","full_name":"Komárková, Zuzana"},{"full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"editor":[{"last_name":"Cassez","first_name":"Franck","full_name":"Cassez, Franck"},{"full_name":"Raskin, Jean-François","first_name":"Jean-François","last_name":"Raskin"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2014","acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","publist_id":"5045","ec_funded":1,"date_published":"2014-01-01T00:00:00Z","page":"235 - 241","citation":{"short":"Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.","mla":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:10.1007/978-3-319-11936-6_17.","chicago":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_17.","ama":"Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Springer; 2014:235-241. doi:10.1007/978-3-319-11936-6_17","apa":"Komárková, Z., & Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_17","ieee":"Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 235–241.","ista":"Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241."},"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","oa_version":"None","intvolume":" 8837","status":"public","title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","_id":"2026","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"},{"scopus_import":1,"day":"13","publication":"EPL","citation":{"ama":"Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 2014;108(2). doi:10.1209/0295-5075/108/20003","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory for the quantum Heisenberg model,” EPL, vol. 108, no. 2. IOP Publishing Ltd., 2014.","apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2014). Validity of spin-wave theory for the quantum Heisenberg model. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/108/20003","ista":"Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003.","short":"M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014).","mla":"Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL, vol. 108, no. 2, 20003, IOP Publishing Ltd., 2014, doi:10.1209/0295-5075/108/20003.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL. IOP Publishing Ltd., 2014. https://doi.org/10.1209/0295-5075/108/20003."},"date_published":"2014-10-13T00:00:00Z","type":"journal_article","abstract":[{"text":"Spin-wave theory is a key ingredient in our comprehension of quantum spin systems, and is used successfully for understanding a wide range of magnetic phenomena, including magnon condensation and stability of patterns in dipolar systems. Nevertheless, several decades of research failed to establish the validity of spin-wave theory rigorously, even for the simplest models of quantum spins. A rigorous justification of the method for the three-dimensional quantum Heisenberg ferromagnet at low temperatures is presented here. We derive sharp bounds on its free energy by combining a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic estimates and operator inequalities.","lang":"eng"}],"issue":"2","_id":"2029","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Validity of spin-wave theory for the quantum Heisenberg model","intvolume":" 108","oa_version":"Submitted Version","month":"10","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.4717"}],"oa":1,"quality_controlled":"1","doi":"10.1209/0295-5075/108/20003","language":[{"iso":"eng"}],"article_number":"20003","publist_id":"5044","year":"2014","acknowledgement":"239694; ERC; European Research Council","publication_status":"published","publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"author":[{"full_name":"Correggi, Michele","last_name":"Correggi","first_name":"Michele"},{"full_name":"Giuliani, Alessandro","first_name":"Alessandro","last_name":"Giuliani"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"date_created":"2018-12-11T11:55:18Z","date_updated":"2021-01-12T06:54:50Z","volume":108},{"month":"12","day":"08","scopus_import":1,"date_published":"2014-12-08T00:00:00Z","conference":{"end_date":"2014-12-13","location":"Montreal, Canada","start_date":"2014-12-08","name":"NIPS: Neural Information Processing Systems"},"language":[{"iso":"eng"}],"citation":{"chicago":"Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” In Advances in Neural Information Processing Systems, 1:837–45. Neural Information Processing Systems, 2014.","mla":"Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” Advances in Neural Information Processing Systems, vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45.","short":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems, 2014, pp. 837–845.","ista":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014. Mind the nuisance: Gaussian process classification using privileged noise. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 1, 837–845.","ieee":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto, “Mind the nuisance: Gaussian process classification using privileged noise,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2014, vol. 1, no. January, pp. 837–845.","apa":"Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., & Quadrianto, N. (2014). Mind the nuisance: Gaussian process classification using privileged noise. In Advances in Neural Information Processing Systems (Vol. 1, pp. 837–845). Montreal, Canada: Neural Information Processing Systems.","ama":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind the nuisance: Gaussian process classification using privileged noise. In: Advances in Neural Information Processing Systems. Vol 1. Neural Information Processing Systems; 2014:837-845."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise"}],"publication":"Advances in Neural Information Processing Systems","page":"837-845","quality_controlled":"1","issue":"January","publist_id":"5038","abstract":[{"lang":"eng","text":"The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information."}],"type":"conference","author":[{"first_name":"Daniel","last_name":"Hernandez Lobato","full_name":"Hernandez Lobato, Daniel"},{"full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","first_name":"Viktoriia","last_name":"Sharmanska"},{"last_name":"Kersting","first_name":"Kristian","full_name":"Kersting, Kristian"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"},{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"}],"volume":1,"oa_version":"Submitted Version","date_created":"2018-12-11T11:55:20Z","date_updated":"2023-02-23T10:25:24Z","year":"2014","_id":"2033","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"intvolume":" 1","publisher":"Neural Information Processing Systems","title":"Mind the nuisance: Gaussian process classification using privileged noise","publication_status":"published","status":"public"},{"publist_id":"5040","file_date_updated":"2020-07-14T12:45:26Z","article_number":"e964045","volume":1,"date_updated":"2021-01-12T06:54:51Z","date_created":"2018-12-11T11:55:19Z","author":[{"full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","first_name":"Álvaro"},{"last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva"},{"last_name":"Schelch","first_name":"Karin","full_name":"Schelch, Karin"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"full_name":"Grusch, Michael","last_name":"Grusch","first_name":"Michael"}],"department":[{"_id":"HaJa"}],"publisher":"Taylor & Francis","publication_status":"published","year":"2014","month":"12","language":[{"iso":"eng"}],"doi":"10.4161/23723548.2014.964045","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"issue":"4","abstract":[{"lang":"eng","text":"As light-based control of fundamental signaling pathways is becoming a reality, the field of optogenetics is rapidly moving beyond neuroscience. We have recently developed receptor tyrosine kinases that are activated by light and control cell proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell behaviors central to cancer progression."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"6464","checksum":"44e17ad40577ab46eb602e88a8b0b8fd","date_updated":"2020-07-14T12:45:26Z","date_created":"2019-05-16T13:39:11Z","access_level":"open_access","file_name":"2014_Taylor_Alvaro.pdf","content_type":"application/pdf","file_size":1765933,"creator":"kschuh"}],"oa_version":"Published Version","intvolume":" 1","status":"public","ddc":["570"],"title":"The optogenetic promise for oncology: Episode I","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2032","has_accepted_license":"1","day":"31","scopus_import":1,"date_published":"2014-12-31T00:00:00Z","citation":{"ista":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. 2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 1(4), e964045.","ieee":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and M. Grusch, “The optogenetic promise for oncology: Episode I,” Molecular and Cellular Oncology, vol. 1, no. 4. Taylor & Francis, 2014.","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L., & Grusch, M. (2014). The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. Taylor & Francis. https://doi.org/10.4161/23723548.2014.964045","ama":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 2014;1(4). doi:10.4161/23723548.2014.964045","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology. Taylor & Francis, 2014. https://doi.org/10.4161/23723548.2014.964045.","mla":"Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology, vol. 1, no. 4, e964045, Taylor & Francis, 2014, doi:10.4161/23723548.2014.964045.","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014)."},"publication":"Molecular and Cellular Oncology"},{"oa_version":"Submitted Version","intvolume":" 8383","title":"Enhanced chosen-ciphertext security and applications","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2045","abstract":[{"lang":"eng","text":"We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest."}],"alternative_title":["LNCS"],"type":"conference","date_published":"2014-01-01T00:00:00Z","page":"329 - 344","citation":{"chicago":"Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_19.","mla":"Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:10.1007/978-3-642-54631-0_19.","short":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344.","ista":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344.","apa":"Dachman Soled, D., Fuchsbauer, G., Mohassel, P., & O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_19","ieee":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344.","ama":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:329-344. doi:10.1007/978-3-642-54631-0_19"},"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","scopus_import":1,"volume":8383,"date_updated":"2021-01-12T06:54:57Z","date_created":"2018-12-11T11:55:24Z","author":[{"last_name":"Dachman Soled","first_name":"Dana","full_name":"Dachman Soled, Dana"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"first_name":"Payman","last_name":"Mohassel","full_name":"Mohassel, Payman"},{"last_name":"O’Neill","first_name":"Adam","full_name":"O’Neill, Adam"}],"publisher":"Springer","editor":[{"last_name":"Krawczyk","first_name":"Hugo","full_name":"Krawczyk, Hugo"}],"department":[{"_id":"KrPi"}],"publication_status":"published","acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","year":"2014","publist_id":"5006","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-54631-0_19","conference":{"location":"Buenos Aires, Argentina","start_date":"2014-03-26","end_date":"2014-03-28","name":"PKC: Public Key Crypography"},"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2012/543"}],"oa":1,"month":"01"},{"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"quality_controlled":"1","doi":"10.1186/1471-2164-15-663","language":[{"iso":"eng"}],"month":"08","year":"2014","publisher":"BioMed Central","department":[{"_id":"JoBo"}],"publication_status":"published","author":[{"full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"volume":15,"date_created":"2018-12-11T11:55:23Z","date_updated":"2021-01-12T06:54:56Z","article_number":"663","publist_id":"5009","file_date_updated":"2020-07-14T12:45:26Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","citation":{"ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663.","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014.","apa":"Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663.","short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014. https://doi.org/10.1186/1471-2164-15-663."},"publication":"BMC Genomics","date_published":"2014-08-08T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"08","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2042","intvolume":" 15","status":"public","title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","ddc":["570"],"pubrep_id":"396","file":[{"checksum":"3f6d2776b90a842a28359cc957d3d04b","date_updated":"2020-07-14T12:45:26Z","date_created":"2018-12-12T10:11:24Z","file_id":"4878","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1489769,"access_level":"open_access","file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.","lang":"eng"}]},{"day":"01","scopus_import":1,"date_published":"2014-01-01T00:00:00Z","publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments","citation":{"mla":"Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, Society of Industrial and Applied Mathematics, 2014, pp. 31–38, doi:10.1137/1.9781611973198.4.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, C. McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2014, pp. 31–38.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, 31–38. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973198.4.","ama":"Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In: McGeoch C, Meyer U, eds. Proceedings of the Workshop on Algorithm Engineering and Experiments. Society of Industrial and Applied Mathematics; 2014:31-38. doi:10.1137/1.9781611973198.4","ista":"Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in Proceedings of the Workshop on Algorithm Engineering and Experiments, Portland, USA, 2014, pp. 31–38.","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Distributed computation of persistent homology. In C. McGeoch & U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments (pp. 31–38). Portland, USA: Society of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973198.4"},"page":"31 - 38","abstract":[{"lang":"eng","text":"Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node."}],"type":"conference","oa_version":"Submitted Version","_id":"2043","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Distributed computation of persistent homology","month":"01","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","start_date":"2014-01-05","location":"Portland, USA","end_date":"2014-01-05"},"doi":"10.1137/1.9781611973198.4","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.0710"}],"quality_controlled":"1","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems"}],"ec_funded":1,"publist_id":"5008","author":[{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich"},{"last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"},{"full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus"}],"date_updated":"2021-01-12T06:54:56Z","date_created":"2018-12-11T11:55:23Z","year":"2014","publication_status":"published","editor":[{"last_name":" McGeoch","first_name":"Catherine","full_name":" McGeoch, Catherine"},{"last_name":"Meyer","first_name":"Ulrich","full_name":"Meyer, Ulrich"}],"department":[{"_id":"HeEd"}],"publisher":"Society of Industrial and Applied Mathematics"},{"publication":"Frontiers in Neural Circuits","citation":{"short":"P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014).","mla":"Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:10.3389/fncir.2014.00107.","chicago":"Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncir.2014.00107.","ama":"Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 2014;8. doi:10.3389/fncir.2014.00107","apa":"Jonas, P. M., & Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. Frontiers Research Foundation. https://doi.org/10.3389/fncir.2014.00107","ieee":"P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” Frontiers in Neural Circuits, vol. 8. Frontiers Research Foundation, 2014.","ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p."},"date_published":"2014-09-10T00:00:00Z","scopus_import":1,"day":"10","has_accepted_license":"1","_id":"2041","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits","ddc":["570"],"status":"public","intvolume":" 8","pubrep_id":"424","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5294","checksum":"3ca57b164045523f876407e9f13a9fb8","date_created":"2018-12-12T10:17:38Z","date_updated":"2020-07-14T12:45:26Z","access_level":"open_access","file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf","file_size":201110,"content_type":"application/pdf","creator":"system"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time."}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.3389/fncir.2014.00107","language":[{"iso":"eng"}],"month":"09","year":"2014","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Frontiers Research Foundation","author":[{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"},{"first_name":"John","last_name":"Lisman","full_name":"Lisman, John"}],"date_created":"2018-12-11T11:55:22Z","date_updated":"2021-01-12T06:54:55Z","volume":8,"article_number":"2p","file_date_updated":"2020-07-14T12:45:26Z","publist_id":"5010"},{"author":[{"full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","first_name":"Ulrich"},{"full_name":"Kerber, Michael","first_name":"Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299"},{"full_name":"Reininghaus, Jan","first_name":"Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:54:56Z","date_created":"2018-12-11T11:55:23Z","year":"2014","editor":[{"last_name":"Bremer","first_name":"Peer-Timo","full_name":"Bremer, Peer-Timo"},{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"},{"full_name":"Pascucci, Valerio","first_name":"Valerio","last_name":"Pascucci"},{"full_name":"Peikert, Ronald","first_name":"Ronald","last_name":"Peikert"}],"department":[{"_id":"HeEd"}],"publisher":"Springer","publication_status":"published","publist_id":"5007","ec_funded":1,"doi":"10.1007/978-3-319-04099-8_7","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.0477"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"quality_controlled":"1","month":"03","oa_version":"Submitted Version","_id":"2044","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Clear and Compress: Computing Persistent Homology in Chunks","abstract":[{"lang":"eng","text":"We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation."}],"type":"book_chapter","date_published":"2014-03-19T00:00:00Z","citation":{"short":"U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117.","mla":"Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:10.1007/978-3-319-04099-8_7.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_7.","ama":"Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Springer; 2014:103-117. doi:10.1007/978-3-319-04099-8_7","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (pp. 103–117). Springer. https://doi.org/10.1007/978-3-319-04099-8_7","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in Topological Methods in Data Analysis and Visualization III, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.","ista":"Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117."},"publication":"Topological Methods in Data Analysis and Visualization III","page":"103 - 117","day":"19","scopus_import":1,"series_title":"Mathematics and Visualization"},{"type":"journal_article","article_number":"1254927","publist_id":"5011","issue":"6204","abstract":[{"text":"Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. ","lang":"eng"}],"_id":"2040","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToBo"}],"intvolume":" 345","publisher":"American Association for the Advancement of Science","status":"public","title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","publication_status":"published","author":[{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"},{"full_name":"Ribeiro, Ana","last_name":"Ribeiro","first_name":"Ana"},{"last_name":"Pérez Valle","first_name":"Helena","full_name":"Pérez Valle, Helena"},{"first_name":"Robin","last_name":"Lovell Badge","full_name":"Lovell Badge, Robin"},{"first_name":"Vasso","last_name":"Episkopou","full_name":"Episkopou, Vasso"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"}],"volume":345,"oa_version":"Submitted Version","date_updated":"2021-01-12T06:54:55Z","date_created":"2018-12-11T11:55:22Z","scopus_import":1,"day":"26","month":"09","citation":{"mla":"Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:10.1126/science.1254927.","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1254927.","ama":"Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 2014;345(6204). doi:10.1126/science.1254927","ista":"Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927.","ieee":"A. Kicheva et al., “Coordination of progenitor specification and growth in mouse and chick spinal cord,” Science, vol. 345, no. 6204. American Association for the Advancement of Science, 2014.","apa":"Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., & Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254927"},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/","open_access":"1"}],"oa":1,"publication":"Science","quality_controlled":"1","doi":"10.1126/science.1254927","date_published":"2014-09-26T00:00:00Z","language":[{"iso":"eng"}]},{"month":"01","project":[{"name":"ROOTS Genome-wide Analysis of Root Traits","_id":"25636330-B435-11E9-9278-68D0E5697425","grant_number":"11-NSF-1070"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8067"}],"external_id":{"arxiv":["1407.8067"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-11257-2_14","conference":{"location":"Ibiza, Spain","start_date":"2014-09-17","end_date":"2014-09-19","name":"PSD: Privacy in Statistical Databases"},"publist_id":"5004","department":[{"_id":"KrPi"},{"_id":"CaUh"}],"publisher":"Springer","editor":[{"full_name":"Domingo Ferrer, Josep","first_name":"Josep","last_name":"Domingo Ferrer"}],"publication_status":"published","year":"2014","acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","volume":8744,"date_created":"2018-12-11T11:55:24Z","date_updated":"2021-01-12T06:54:57Z","author":[{"first_name":"Fei","last_name":"Yu","full_name":"Yu, Fei"},{"full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar"},{"full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fienberg","first_name":"Stephen","full_name":"Fienberg, Stephen"}],"scopus_import":1,"day":"01","page":"170 - 184","citation":{"mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:10.1007/978-3-319-11257-2_14.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. https://doi.org/10.1007/978-3-319-11257-2_14.","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8744. Springer; 2014:170-184. doi:10.1007/978-3-319-11257-2_14","ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","apa":"Yu, F., Rybar, M., Uhler, C., & Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. https://doi.org/10.1007/978-3-319-11257-2_14","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Ibiza, Spain, 2014, vol. 8744, pp. 170–184."},"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","date_published":"2014-01-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance."}],"intvolume":" 8744","status":"public","title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2047","oa_version":"Submitted Version"},{"month":"09","conference":{"location":"Rome, Italy","start_date":"2014-09-02","end_date":"2014-09-05","name":"CONCUR: Concurrency Theory"},"doi":"10.1007/978-3-662-44584-6_18","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1404.5084","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publist_id":"4993","author":[{"first_name":"Holger","last_name":"Hermanns","full_name":"Hermanns, Holger"},{"first_name":"Jan","last_name":"Krčál","full_name":"Krčál, Jan"},{"last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"}],"date_updated":"2021-01-12T06:55:00Z","date_created":"2018-12-11T11:55:27Z","volume":8704,"acknowledgement":"This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","year":"2014","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"full_name":"Gorla, Daniele","last_name":"Gorla","first_name":"Daniele"}],"day":"01","date_published":"2014-09-01T00:00:00Z","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","citation":{"ieee":"H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 249–265.","apa":"Hermanns, H., Krčál, J., & Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_18","ista":"Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265.","ama":"Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:10.1007/978-3-662-44584-6_18","chicago":"Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_18.","short":"H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265.","mla":"Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:10.1007/978-3-662-44584-6_18."},"page":"249 - 265","abstract":[{"lang":"eng","text":"In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2053","status":"public","title":"Probabilistic bisimulation: Naturally on distributions","intvolume":" 8704"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"A standard technique for solving the parameterized model checking problem is to reduce it to the classic model checking problem of finitely many finite-state systems. This work considers some of the theoretical power and limitations of this technique. We focus on concurrent systems in which processes communicate via pairwise rendezvous, as well as the special cases of disjunctive guards and token passing; specifications are expressed in indexed temporal logic without the next operator; and the underlying network topologies are generated by suitable Monadic Second Order Logic formulas and graph operations. First, we settle the exact computational complexity of the parameterized model checking problem for some of our concurrent systems, and establish new decidability results for others. Second, we consider the cases that model checking the parameterized system can be reduced to model checking some fixed number of processes, the number is known as a cutoff. We provide many cases for when such cutoffs can be computed, establish lower bounds on the size of such cutoffs, and identify cases where no cutoff exists. Third, we consider cases for which the parameterized system is equivalent to a single finite-state system (more precisely a Büchi word automaton), and establish tight bounds on the sizes of such automata.","lang":"eng"}],"publist_id":"4994","_id":"2052","acknowledgement":"The second, third, fourth and fifth authors were supported by the Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund (FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED, ICT12-059, and VRG11-005.","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","publication_status":"published","status":"public","title":"Parameterized model checking of rendezvous systems","editor":[{"last_name":"Baldan","first_name":"Paolo","full_name":"Baldan, Paolo"},{"last_name":"Gorla","first_name":"Daniele","full_name":"Gorla, Daniele"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":" 8704","department":[{"_id":"KrCh"}],"author":[{"full_name":"Aminof, Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","last_name":"Aminof","first_name":"Benjamin"},{"full_name":"Kotek, Tomer","first_name":"Tomer","last_name":"Kotek"},{"full_name":"Rubin, Sacha","last_name":"Rubin","first_name":"Sacha"},{"full_name":"Spegni, Francesco","first_name":"Francesco","last_name":"Spegni"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"date_created":"2018-12-11T11:55:26Z","date_updated":"2021-01-12T06:54:59Z","volume":8704,"oa_version":"None","month":"09","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","citation":{"short":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–124.","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–24, doi:10.1007/978-3-662-44584-6_9.","chicago":"Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut Veith. “Parameterized Model Checking of Rendezvous Systems.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_9.","ama":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking of rendezvous systems. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:109-124. doi:10.1007/978-3-662-44584-6_9","apa":"Aminof, B., Kotek, T., Rubin, S., Spegni, F., & Veith, H. (2014). Parameterized model checking of rendezvous systems. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 109–124). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_9","ieee":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 109–124.","ista":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124."},"quality_controlled":"1","page":"109 - 124","conference":{"name":"CONCUR: Concurrency Theory","end_date":"2014-09-05","start_date":"2014-09-02","location":"Rome, Italy"},"doi":"10.1007/978-3-662-44584-6_9","date_published":"2014-09-01T00:00:00Z","language":[{"iso":"eng"}]},{"ec_funded":1,"publist_id":"5005","volume":8383,"date_created":"2018-12-11T11:55:24Z","date_updated":"2021-01-12T06:54:57Z","author":[{"last_name":"Bellare","first_name":"Mihir","full_name":"Bellare, Mihir"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"}],"editor":[{"first_name":"Hugo","last_name":"Krawczyk","full_name":"Krawczyk, Hugo"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2014","acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","month":"01","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-54631-0_30","conference":{"name":"PKC: Public Key Crypography","end_date":"2014-05-28","start_date":"2014-05-26","location":"Buenos Aires, Argentina"},"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2013/413","open_access":"1"}],"oa":1,"abstract":[{"text":"We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","intvolume":" 8383","status":"public","title":"Policy-based signatures","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2046","day":"01","scopus_import":1,"date_published":"2014-01-01T00:00:00Z","page":"520 - 537","citation":{"short":"M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537.","mla":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:10.1007/978-3-642-54631-0_30.","chicago":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_30.","ama":"Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:520-537. doi:10.1007/978-3-642-54631-0_30","apa":"Bellare, M., & Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_30","ieee":"M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537.","ista":"Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537."},"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)"},{"month":"01","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1508.06546","open_access":"1"}],"external_id":{"arxiv":["1508.06546"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2013.603","publist_id":"5001","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Cambridge University Press","year":"2014","date_created":"2018-12-11T11:55:25Z","date_updated":"2021-01-12T06:54:59Z","volume":738,"author":[{"first_name":"Jakob","last_name":"Kühnen","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob"},{"full_name":"Holzner, Markus","first_name":"Markus","last_name":"Holzner"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"full_name":"Kuhlmann, Hendrik","first_name":"Hendrik","last_name":"Kuhlmann"}],"scopus_import":1,"day":"10","article_processing_charge":"No","page":"463 - 491","publication":"Journal of Fluid Mechanics","citation":{"ista":"Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491.","apa":"Kühnen, J., Holzner, M., Hof, B., & Kuhlmann, H. (2014). Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.603","ieee":"J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation of transitional flow in a toroidal pipe,” Journal of Fluid Mechanics, vol. 738. Cambridge University Press, pp. 463–491, 2014.","ama":"Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 2014;738:463-491. doi:10.1017/jfm.2013.603","chicago":"Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2014. https://doi.org/10.1017/jfm.2013.603.","mla":"Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:10.1017/jfm.2013.603.","short":"J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491."},"date_published":"2014-01-10T00:00:00Z","type":"journal_article","abstract":[{"text":"The flow instability and further transition to turbulence in a toroidal pipe (torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated experimentally. The flow inside the toroidal pipe is driven by a steel sphere fitted to the inner pipe diameter. The sphere is moved with constant azimuthal velocity from outside the torus by a moving magnet. The experiment is designed to investigate curved pipe flow by optical measurement techniques. Using stereoscopic particle image velocimetry, laser Doppler velocimetry and pressure drop measurements, the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and space-resolved velocity fields are obtained and analysed. The steady axisymmetric basic flow is strongly influenced by centrifugal effects. On an increase of the Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical bifurcation to an oscillatory flow is found in which waves travel in the streamwise direction with a phase velocity slightly faster than the mean flow. The oscillatory flow is superseded by a presumably quasi-periodic flow at a further increase of the Reynolds number before turbulence sets in. The results are found to be compatible, in general, with earlier experimental and numerical investigations on transition to turbulence in helical and curved pipes. However, important aspects of the bifurcation scenario differ considerably.","lang":"eng"}],"status":"public","title":"Experimental investigation of transitional flow in a toroidal pipe","intvolume":" 738","_id":"2050","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"conference":{"name":"NIPS: Neural Information Processing Systems"},"date_published":"2014-01-01T00:00:00Z","quality_controlled":0,"oa":1,"citation":{"short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Neural Information Processing Systems, 2014.","mla":"Marchand, Mario, et al. Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. Neural Information Processing Systems, 2014.","chicago":"Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” Neural Information Processing Systems, 2014.","ama":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: Neural Information Processing Systems; 2014.","apa":"Marchand, M., Hongyu, S., Morvant, E., Rousu, J., & Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.","ieee":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” presented at the NIPS: Neural Information Processing Systems, 2014.","ista":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. NIPS: Neural Information Processing Systems."},"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01065586"}],"month":"01","day":"01","date_created":"2018-12-11T11:55:26Z","date_updated":"2021-01-12T06:54:59Z","author":[{"full_name":"Marchand, Mario","first_name":"Mario","last_name":"Marchand"},{"full_name":"Hongyu, Su","last_name":"Hongyu","first_name":"Su"},{"full_name":"Emilie Morvant","orcid":"0000-0002-8301-7240","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","last_name":"Morvant","first_name":"Emilie"},{"full_name":"Rousu, Juho","last_name":"Rousu","first_name":"Juho"},{"last_name":"Shawe Taylor","first_name":"John","full_name":"Shawe-Taylor, John"}],"publication_status":"published","title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks","status":"public","publisher":"Neural Information Processing Systems","_id":"2051","year":"2014","extern":1,"abstract":[{"lang":"eng","text":"We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach."}],"publist_id":"4996","type":"conference"},{"publist_id":"4987","file_date_updated":"2020-07-14T12:45:27Z","department":[{"_id":"EvBe"}],"publisher":"Springer","publication_status":"published","acknowledgement":"The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14.","year":"2014","volume":251,"date_created":"2018-12-11T11:55:29Z","date_updated":"2021-01-12T06:55:02Z","author":[{"full_name":"Dubas, Ewa","first_name":"Ewa","last_name":"Dubas"},{"full_name":"Moravčíková, Jana","first_name":"Jana","last_name":"Moravčíková"},{"first_name":"Jana","last_name":"Libantová","full_name":"Libantová, Jana"},{"full_name":"Matušíková, Ildikó","last_name":"Matušíková","first_name":"Ildikó"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Zur, Iwona","first_name":"Iwona","last_name":"Zur"},{"full_name":"Krzewska, Monika","last_name":"Krzewska","first_name":"Monika"}],"month":"02","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1007/s00709-014-0616-1","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant."}],"intvolume":" 251","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","ddc":["580"],"status":"public","_id":"2059","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"5353","checksum":"d570a6073765118fc0bb83c31d96fa53","date_created":"2018-12-12T10:18:31Z","date_updated":"2020-07-14T12:45:27Z","access_level":"open_access","file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","file_size":6377990,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","pubrep_id":"394","scopus_import":1,"has_accepted_license":"1","day":"20","page":"1077 - 1087","citation":{"ista":"Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087.","ieee":"E. Dubas et al., “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” Protoplasma, vol. 251, no. 5. Springer, pp. 1077–1087, 2014.","apa":"Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., & Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0616-1","ama":"Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 2014;251(5):1077-1087. doi:10.1007/s00709-014-0616-1","chicago":"Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0616-1.","mla":"Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087."},"publication":"Protoplasma","date_published":"2014-02-20T00:00:00Z"},{"publication":"Science","citation":{"mla":"Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science, vol. 345, no. 6196, 1255263, American Association for the Advancement of Science, 2014, doi:10.1126/science.1255263.","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).","chicago":"Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1255263.","ama":"Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 2014;345(6196). doi:10.1126/science.1255263","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.","apa":"Hu, H., Gan, J., & Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1255263","ieee":"H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function,” Science, vol. 345, no. 6196. American Association for the Advancement of Science, 2014."},"date_published":"2014-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2062","status":"public","title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","ddc":["570"],"intvolume":" 345","pubrep_id":"821","oa_version":"Submitted Version","file":[{"file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf","access_level":"open_access","creator":"system","file_size":215514,"content_type":"application/pdf","file_id":"5185","relation":"main_file","date_created":"2018-12-12T10:16:00Z","date_updated":"2020-07-14T12:45:27Z","checksum":"a0036a589037d37e86364fa25cc0a82f"},{"access_level":"open_access","file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","creator":"system","content_type":"application/pdf","file_size":1732723,"file_id":"5186","relation":"main_file","checksum":"e1f57d2713725449cb898fdcb8ef47b8","date_created":"2018-12-12T10:16:01Z","date_updated":"2020-07-14T12:45:27Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes."}],"issue":"6196","oa":1,"quality_controlled":"1","project":[{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548"}],"doi":"10.1126/science.1255263","language":[{"iso":"eng"}],"month":"08","year":"2014","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"American Association for the Advancement of Science","author":[{"first_name":"Hua","last_name":"Hu","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","full_name":"Hu, Hua"},{"id":"3614E438-F248-11E8-B48F-1D18A9856A87","last_name":"Gan","first_name":"Jian","full_name":"Gan, Jian"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"date_updated":"2021-01-12T06:55:03Z","date_created":"2018-12-11T11:55:29Z","volume":345,"article_number":"1255263","file_date_updated":"2020-07-14T12:45:27Z","publist_id":"4984","ec_funded":1},{"year":"2014","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","author":[{"first_name":"Karthik","last_name":"Raveendran","full_name":"Raveendran, Karthik"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"last_name":"Türk","first_name":"Greg","full_name":"Türk, Greg"}],"volume":33,"date_created":"2018-12-11T11:55:28Z","date_updated":"2022-08-25T14:02:46Z","article_number":"137","publist_id":"4988","file_date_updated":"2020-07-14T12:45:27Z","oa":1,"project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","grant_number":"11-NSF-1070","name":"ROOTS Genome-wide Analysis of Root Traits"}],"quality_controlled":"1","doi":"10.1145/2601097.2601126","conference":{"name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","end_date":"2014-08-14","start_date":"2014-08-10","location":"Vancouver, Canada"},"language":[{"iso":"eng"}],"month":"07","_id":"2058","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 33","title":"Blending liquids","status":"public","ddc":["000"],"pubrep_id":"606","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","creator":"system","content_type":"application/pdf","file_size":8387384,"file_id":"4688","relation":"main_file","checksum":"1752760a2e71e254537f31c0d10d9c6c","date_created":"2018-12-12T10:08:27Z","date_updated":"2020-07-14T12:45:27Z"}],"type":"conference","issue":"4","abstract":[{"lang":"eng","text":"We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations."}],"citation":{"ama":"Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126","ista":"Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137.","apa":"Raveendran, K., Wojtan, C., Thuerey, N., & Türk, G. (2014). Blending liquids. In ACM Transactions on Graphics (Vol. 33). Vancouver, Canada: ACM. https://doi.org/10.1145/2601097.2601126","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4.","mla":"Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics, vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126.","short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014.","chicago":"Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In ACM Transactions on Graphics, Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601126."},"publication":"ACM Transactions on Graphics","date_published":"2014-07-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"}]