[{"type":"journal_article","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"}],"status":"public","_id":"1934","publist_id":"5160","author":[{"full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavy","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jérôme","full_name":"Duclercq, Jérôme","last_name":"Duclercq"},{"first_name":"Benjamin","last_name":"Weller","full_name":"Weller, Benjamin"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"first_name":"Remko","last_name":"Offringa","full_name":"Offringa, Remko"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"last_name":"Murphy","full_name":"Murphy, Angus","first_name":"Angus"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"title":"Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis","date_updated":"2021-01-12T06:54:10Z","citation":{"ista":"Marhavý P, Duclercq J, Weller B, Feraru E, Bielach A, Offringa R, Friml J, Schwechheimer C, Murphy A, Benková E. 2014. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 24(9), 1031–1037.","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.","short":"P. Marhavý, J. Duclercq, B. Weller, E. Feraru, A. Bielach, R. Offringa, J. Friml, C. Schwechheimer, A. Murphy, E. Benková, Current Biology 24 (2014) 1031–1037.","ieee":"P. Marhavý 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.","apa":"Marhavý, P., Duclercq, J., Weller, B., Feraru, E., Bielach, A., Offringa, R., … Benková, E. (2014). Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.04.002","ama":"Marhavý P, Duclercq J, Weller B, et al. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 2014;24(9):1031-1037. doi:10.1016/j.cub.2014.04.002","mla":"Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology, vol. 24, no. 9, Cell Press, 2014, pp. 1031–37, doi:10.1016/j.cub.2014.04.002."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"quality_controlled":"1","publisher":"Cell Press","intvolume":" 24","month":"05","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"}],"oa_version":"None","page":"1031 - 1037","ec_funded":1,"date_created":"2018-12-11T11:54:48Z","volume":24,"issue":"9","doi":"10.1016/j.cub.2014.04.002","date_published":"2014-05-05T00:00:00Z","year":"2014","publication_status":"published","language":[{"iso":"eng"}],"publication":"Current Biology","day":"05"},{"oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n","date_created":"2018-12-11T11:54:47Z","date_published":"2014-12-01T00:00:00Z","doi":"10.1111/evo.12517","page":"3357 - 3367","publication":"Evolution","day":"01","year":"2014","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"title":"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations","publist_id":"5162","author":[{"first_name":"Meredith","last_name":"Trotter","full_name":"Trotter, Meredith"},{"first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel","last_name":"Weissman"},{"first_name":"Grant","last_name":"Peterson","full_name":"Peterson, Grant"},{"last_name":"Peck","full_name":"Peck, Kayla","first_name":"Kayla"},{"first_name":"Joanna","full_name":"Masel, Joanna","last_name":"Masel"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517","apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014). Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.12517"},"intvolume":" 68","month":"12","main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","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"}],"ec_funded":1,"issue":"12","volume":68,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1932","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:54:10Z"},{"oa_version":"None","acknowledgement":"RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC","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"}],"month":"12","intvolume":" 20","quality_controlled":"1","scopus_import":1,"publisher":"IEEE","day":"31","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Visualization and Computer Graphics","year":"2014","publication_status":"published","doi":"10.1109/TVCG.2014.2346432","issue":"12","volume":20,"date_published":"2014-12-31T00:00:00Z","date_created":"2018-12-11T11:54:46Z","page":"2585 - 2594","_id":"1930","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:09Z","citation":{"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.","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.","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","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","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.","ista":"Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. 2014. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 20(12), 2585–2594.","chicago":"Günther, David, Alec Jacobson, Jan Reininghaus, Hans Seidel, Olga Sorkine Hornung, and Tino Weinkauf. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2346432."},"title":"Fast and memory-efficient topological denoising of 2D and 3D scalar fields","department":[{"_id":"HeEd"}],"publist_id":"5164","author":[{"last_name":"Günther","full_name":"Günther, David","first_name":"David"},{"first_name":"Alec","full_name":"Jacobson, Alec","last_name":"Jacobson"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"first_name":"Hans","last_name":"Seidel","full_name":"Seidel, Hans"},{"first_name":"Olga","full_name":"Sorkine Hornung, Olga","last_name":"Sorkine Hornung"},{"first_name":"Tino","full_name":"Weinkauf, Tino","last_name":"Weinkauf"}]},{"oa_version":"None","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"}],"intvolume":" 141","month":"04","scopus_import":1,"publisher":"Company of Biologists","quality_controlled":"1","publication":"Development","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:54:47Z","date_published":"2014-04-01T00:00:00Z","doi":"10.1242/dev.102988","volume":141,"issue":"8","page":"1671 - 1682","_id":"1933","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","ieee":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, and K. Shimamura, “Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates,” Development, vol. 141, no. 8. Company of Biologists, pp. 1671–1682, 2014.","short":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682.","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","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","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."},"date_updated":"2021-01-12T06:54:10Z","title":"Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates","department":[{"_id":"RySh"}],"publist_id":"5161","author":[{"last_name":"Hatakeyama","full_name":"Hatakeyama, Jun","first_name":"Jun"},{"first_name":"Yoshio","full_name":"Wakamatsu, Yoshio","last_name":"Wakamatsu"},{"first_name":"Akira","full_name":"Nagafuchi, Akira","last_name":"Nagafuchi"},{"last_name":"Kageyama","full_name":"Kageyama, Ryoichiro","first_name":"Ryoichiro"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Kenji","full_name":"Shimamura, Kenji","last_name":"Shimamura"}]},{"article_number":"57","publist_id":"5163","author":[{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina","last_name":"Savin"},{"full_name":"Triesch, Jochen","last_name":"Triesch","first_name":"Jochen"}],"title":"Emergence of task-dependent representations in working memory circuits","citation":{"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.","ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.","mla":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.","ieee":"C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014.","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).","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","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"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Frontiers Research Foundation","oa":1,"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.","date_published":"2014-05-28T00:00:00Z","doi":"10.3389/fncom.2014.00057","date_created":"2018-12-11T11:54:46Z","year":"2014","day":"28","publication":"Frontiers in Computational Neuroscience","type":"journal_article","status":"public","_id":"1931","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:54:09Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/"}],"month":"05","intvolume":" 8","abstract":[{"text":"A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity.","lang":"eng"}],"oa_version":"Submitted Version","issue":"MAY","volume":8,"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","grant_number":"SFB-TR3-TP10B","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"publist_id":"5158","author":[{"last_name":"Bourgade","full_name":"Bourgade, Paul","first_name":"Paul"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yau, Horngtzer","last_name":"Yau","first_name":"Horngtzer"}],"title":"Edge universality of beta ensembles","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.","ista":"Bourgade P, Erdös L, Yau H. 2014. Edge universality of beta ensembles. Communications in Mathematical Physics. 332(1), 261–353.","mla":"Bourgade, Paul, et al. “Edge Universality of Beta Ensembles.” Communications in Mathematical Physics, vol. 332, no. 1, Springer, 2014, pp. 261–353, doi:10.1007/s00220-014-2120-z.","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","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","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.","short":"P. Bourgade, L. Erdös, H. Yau, Communications in Mathematical Physics 332 (2014) 261–353."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer","quality_controlled":"1","page":"261 - 353","date_created":"2018-12-11T11:54:48Z","date_published":"2014-11-01T00:00:00Z","doi":"10.1007/s00220-014-2120-z","year":"2014","publication":"Communications in Mathematical Physics","day":"01","type":"journal_article","status":"public","_id":"1937","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:54:12Z","main_file_link":[{"url":"http://arxiv.org/abs/1306.5728","open_access":"1"}],"scopus_import":1,"intvolume":" 332","month":"11","abstract":[{"text":"We prove the edge universality of the beta ensembles for any β ≥ 1, provided that the limiting spectrum is supported on a single interval, and the external potential is C4 and regular. We also prove that the edge universality holds for generalized Wigner matrices for all symmetry classes. Moreover, our results allow us to extend bulk universality for beta ensembles from analytic potentials to potentials in class C4.","lang":"eng"}],"oa_version":"Submitted Version","volume":332,"issue":"1","publication_status":"published","language":[{"iso":"eng"}]},{"title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","author":[{"last_name":"Garvin","full_name":"Garvin, Michael R","first_name":"Michael"},{"first_name":"Joseph","last_name":"Bielawski","full_name":"Bielawski, Joseph P"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","last_name":"Sazanov"},{"full_name":"Gharrett, Anthony J","last_name":"Gharrett","first_name":"Anthony"}],"publist_id":"5102","extern":1,"citation":{"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.","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.","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.","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2014) 1–17.","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","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","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."},"date_updated":"2019-04-26T07:22:06Z","status":"public","type":"review","_id":"1981","date_created":"2018-12-11T11:55:02Z","date_published":"2014-02-01T00:00:00Z","issue":"1","volume":53,"doi":"10.1111/jzs.12079","page":"1 - 17","publication":"Journal of Zoological Systematics and Evolutionary Research","day":"01","publication_status":"published","year":"2014","intvolume":" 53","month":"02","publisher":"Wiley-Blackwell","quality_controlled":0,"acknowledgement":"Funded by University of Alaska Center for Global Change Student Research Cooperative Institute for Alaska Research and the Rasmuson Foundation","abstract":[{"text":"Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may provide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.","lang":"eng"}]},{"acknowledgement":"Funded by Health Research Council of New Zealand Royal Society of New Zealand University of Otago New Zealand Synchrotron Group","abstract":[{"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.","lang":"eng"}],"intvolume":" 91","month":"03","publisher":"Wiley-Blackwell","quality_controlled":0,"publication":"Molecular Microbiology","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:01Z","date_published":"2014-03-01T00:00:00Z","doi":"10.1111/mmi.12507","issue":"5","volume":91,"page":"950 - 964","_id":"1980","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T06:54:29Z","citation":{"mla":"Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507.","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","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","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.","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.","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.","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."},"title":"Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation","author":[{"last_name":"Heikal","full_name":"Heikal, Adam ","first_name":"Adam"},{"first_name":"Yoshio","last_name":"Nakatani","full_name":"Nakatani, Yoshio"},{"first_name":"Elyse","full_name":"Dunn, Elyse A","last_name":"Dunn"},{"last_name":"Weimar","full_name":"Weimar, Marion R","first_name":"Marion"},{"last_name":"Day","full_name":"Day, Catherine","first_name":"Catherine"},{"first_name":"Edward","full_name":"Baker, Edward N","last_name":"Baker"},{"first_name":"Shaun","full_name":"Lott, Shaun J","last_name":"Lott"},{"full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"first_name":"Gregory","last_name":"Cook","full_name":"Cook, Gregory"}],"publist_id":"5103"},{"publisher":"Springer","quality_controlled":0,"intvolume":" 46","month":"08","abstract":[{"lang":"eng","text":"NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine."}],"page":"247 - 253","date_created":"2018-12-11T11:55:01Z","doi":"10.1007/s10863-014-9554-z","issue":"4","volume":46,"date_published":"2014-08-01T00:00:00Z","publication_status":"published","year":"2014","publication":"Journal of Bioenergetics and Biomembranes","day":"01","type":"journal_article","status":"public","_id":"1979","author":[{"full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"publist_id":"5104","title":"The mechanism of coupling between electron transfer and proton translocation in respiratory complex I","date_updated":"2021-01-12T06:54:28Z","citation":{"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.","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.","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","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","short":"L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.","ieee":"L. A. Sazanov, “The mechanism of coupling between electron transfer and proton translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4. Springer, pp. 247–253, 2014.","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."},"extern":1},{"abstract":[{"lang":"eng","text":"During animal cell division, the cleavage furrow is positioned by microtubules that signal to the actin cortex at the cell midplane. We developed a cell-free system to recapitulate cytokinesis signaling using cytoplasmic extract from Xenopus eggs. Microtubules grew out as asters from artificial centrosomes and met to organize antiparallel overlap zones. These zones blocked the interpenetration of neighboring asters and recruited cytokinesis midzone proteins, including the chromosomal passenger complex (CPC) and centralspindlin. The CPC was transported to overlap zones, which required two motor proteins, Kif4A and a Kif20A paralog. Using supported lipid bilayers to mimic the plasma membrane, we observed the recruitment of cleavage furrow markers, including an active RhoA reporter, at microtubule overlaps. This system opens further approaches to understanding the biophysics of cytokinesis signaling."}],"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.). ","publisher":"American Association for the Advancement of Science","quality_controlled":0,"month":"10","intvolume":" 346","year":"2014","publication_status":"published","day":"10","publication":"Science","page":"244 - 247","doi":"10.1126/science.1256773","date_published":"2014-10-10T00:00:00Z","volume":346,"issue":"6206","date_created":"2018-12-11T11:55:04Z","_id":"1989","type":"journal_article","status":"public","date_updated":"2021-01-12T06:54:32Z","citation":{"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.","ista":"Nguyen P, Groen A, Loose M, Ishihara K, Wühr M, Field C, Mitchison T. 2014. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 346(6206), 244–247.","mla":"Nguyen, Phuong, et al. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” Science, vol. 346, no. 6206, American Association for the Advancement of Science, 2014, pp. 244–47, doi:10.1126/science.1256773.","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","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.","short":"P. Nguyen, A. Groen, M. Loose, K. Ishihara, M. Wühr, C. Field, T. Mitchison, Science 346 (2014) 244–247."},"extern":1,"author":[{"first_name":"Phuong","full_name":"Nguyen, Phuong A","last_name":"Nguyen"},{"first_name":"Aaron","full_name":"Groen, Aaron C","last_name":"Groen"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Loose","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"first_name":"Keisuke","last_name":"Ishihara","full_name":"Ishihara, Keisuke "},{"last_name":"Wühr","full_name":"Wühr, Martin ","first_name":"Martin"},{"first_name":"Christine","last_name":"Field","full_name":"Field, Christine M"},{"first_name":"Timothy","last_name":"Mitchison","full_name":"Mitchison, Timothy J"}],"publist_id":"5093","title":"Spatial organization of cytokinesis signaling reconstituted in a cell-free system"},{"_id":"1990","type":"journal_article","status":"public","date_updated":"2021-01-12T06:54:33Z","citation":{"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.","ista":"Loose M, Mitchison T. 2014. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 16(1), 38–46.","mla":"Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” Nature Cell Biology, vol. 16, no. 1, Nature Publishing Group, 2014, pp. 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","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","short":"M. Loose, T. Mitchison, Nature Cell Biology 16 (2014) 38–46.","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."},"extern":1,"publist_id":"5094","author":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Martin Loose"},{"first_name":"Timothy","last_name":"Mitchison","full_name":"Mitchison, Timothy J"}],"title":"The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns","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."}],"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.","quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 16","month":"01","year":"2014","publication_status":"published","publication":"Nature Cell Biology","day":"01","page":"38 - 46","date_created":"2018-12-11T11:55:05Z","issue":"1","doi":"10.1038/ncb2885","volume":16,"date_published":"2014-01-01T00:00:00Z"},{"type":"journal_article","status":"public","_id":"1996","author":[{"first_name":"Ora","full_name":"Hazak, Ora","last_name":"Hazak"},{"first_name":"Uri","last_name":"Obolski","full_name":"Obolski, Uri"},{"last_name":"Prat","full_name":"Prat, Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Hadany, Lilach","last_name":"Hadany","first_name":"Lilach"},{"first_name":"Shaul","last_name":"Yalovsky","full_name":"Yalovsky, Shaul"}],"publist_id":"5083","department":[{"_id":"JiFr"}],"title":"Bimodal regulation of ICR1 levels generates self-organizing auxin distribution","citation":{"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.","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.","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.","short":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, S. Yalovsky, PNAS 111 (2014) E5471–E5479.","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.","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","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"},"date_updated":"2021-01-12T06:54:35Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/","open_access":"1"}],"oa":1,"publisher":"National Academy of Sciences","scopus_import":1,"quality_controlled":"1","intvolume":" 111","month":"12","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"}],"oa_version":"Submitted Version","page":"E5471 - E5479","date_created":"2018-12-11T11:55:07Z","volume":111,"issue":"50","doi":"10.1073/pnas.1413918111","date_published":"2014-12-16T00:00:00Z","year":"2014","publication_status":"published","publication":"PNAS","language":[{"iso":"eng"}],"day":"16"},{"type":"journal_article","status":"public","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"_id":"1994","author":[{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"full_name":"Landberg, Katarina","last_name":"Landberg","first_name":"Katarina"},{"first_name":"Mattias","full_name":"Thelander, Mattias","last_name":"Thelander"},{"full_name":"Medvecka, Eva","last_name":"Medvecka","first_name":"Eva"},{"last_name":"Pederson","full_name":"Pederson, Eric","first_name":"Eric"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"first_name":"Endymion","last_name":"Cooper","full_name":"Cooper, Endymion"},{"first_name":"Mansour","last_name":"Karimi","full_name":"Karimi, Mansour"},{"first_name":"Charles","full_name":"Delwiche, Charles","last_name":"Delwiche"},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"},{"full_name":"Sundberg, Eva","last_name":"Sundberg","first_name":"Eva"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"5088","department":[{"_id":"JiFr"}],"title":"Directional auxin transport mechanisms in early diverging land plants","date_updated":"2021-01-12T06:54:34Z","citation":{"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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Cell Press","scopus_import":1,"month":"12","intvolume":" 24","abstract":[{"lang":"eng","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."}],"oa_version":"None","page":"2786 - 2791","volume":24,"doi":"10.1016/j.cub.2014.09.056","issue":"23","date_published":"2014-12-01T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:55:06Z","publication_status":"published","year":"2014","day":"01","language":[{"iso":"eng"}],"publication":"Current Biology"},{"date_created":"2018-12-11T11:55:06Z","date_published":"2014-12-08T00:00:00Z","doi":"10.1103/PhysRevLett.113.243601","year":"2014","publication":"Physical Review Letters","day":"08","oa":1,"quality_controlled":"1","publisher":"American Physical Society","author":[{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"},{"first_name":"Eduardo","last_name":"Mascarenhas","full_name":"Mascarenhas, Eduardo"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh","last_name":"Safari"},{"last_name":"Poizat","full_name":"Poizat, Jean","first_name":"Jean"},{"last_name":"Valente","full_name":"Valente, Daniel","first_name":"Daniel"},{"full_name":"Auffèves, Alexia","last_name":"Auffèves","first_name":"Alexia"},{"full_name":"Gerace, Dario","last_name":"Gerace","first_name":"Dario"},{"first_name":"Marcelo","last_name":"Santos","full_name":"Santos, Marcelo"}],"publist_id":"5085","title":"Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification","citation":{"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.","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.","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.","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.","short":"F. Fratini, E. Mascarenhas, L. Safari, J. Poizat, D. Valente, A. Auffèves, D. Gerace, M. Santos, Physical Review Letters 113 (2014).","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","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"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"243601","ec_funded":1,"volume":113,"issue":"24","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.5972"}],"scopus_import":1,"intvolume":" 113","month":"12","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:54:34Z","type":"journal_article","status":"public","_id":"1995"},{"language":[{"iso":"eng"}],"publication":"Trends in Immunology","day":"01","year":"2014","publication_status":"published","date_created":"2018-12-11T11:55:07Z","issue":"10","date_published":"2014-10-01T00:00:00Z","volume":35,"doi":"10.1016/j.it.2014.08.005","page":"471 - 482","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. ","oa_version":"None","abstract":[{"text":"Immune systems are able to protect the body against secondary infection with the same parasite. In insect colonies, this protection is not restricted to the level of the individual organism, but also occurs at the societal level. Here, we review recent evidence for and insights into the mechanisms underlying individual and social immunisation in insects. We disentangle general immune-protective effects from specific immune memory (priming), and examine immunisation in the context of the lifetime of an individual and that of a colony, and of transgenerational immunisation that benefits offspring. When appropriate, we discuss parallels with disease defence strategies in human societies. We propose that recurrent parasitic threats have shaped the evolution of both the individual immune systems and colony-level social immunity in insects.","lang":"eng"}],"intvolume":" 35","month":"10","quality_controlled":"1","scopus_import":1,"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:35Z","citation":{"ista":"El Masri L, Cremer S. 2014. Individual and social immunisation in insects. Trends in Immunology. 35(10), 471–482.","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.","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","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","short":"L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482.","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.","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."},"title":"Individual and social immunisation in insects","department":[{"_id":"SyCr"}],"author":[{"first_name":"Leila","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","full_name":"El Masri, Leila","last_name":"El Masri"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publist_id":"5081","_id":"1998","status":"public","type":"journal_article"},{"intvolume":" 9","month":"11","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by-sa/4.0/","issue":"11","volume":9,"language":[{"iso":"eng"}],"file":[{"file_id":"5107","checksum":"85e4f4ea144f827272aaf376b2830564","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:52Z","file_name":"IST-2016-434-v1+1_journal.pone.0113124.pdf","date_updated":"2020-07-14T12:45:24Z","file_size":5179993,"creator":"system"}],"publication_status":"published","pubrep_id":"434","status":"public","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"journal_article","_id":"2002","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:24Z","ddc":["570"],"date_updated":"2021-01-12T06:54:39Z","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","date_created":"2018-12-11T11:55:09Z","date_published":"2014-11-19T00:00:00Z","doi":"10.1371/journal.pone.0113124","publication":"PLoS One","day":"19","year":"2014","has_accepted_license":"1","project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"}],"article_number":"0113124","title":"Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus","author":[{"first_name":"Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","last_name":"Kim"}],"publist_id":"5074","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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).","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","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","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.","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."}},{"date_updated":"2021-01-12T06:54:39Z","citation":{"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.","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","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","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.","ista":"O’Neill J, Csicsvari JL. 2014. Learning by example in the hippocampus. Neuron. 83(1), 8–10."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5073","author":[{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"title":"Learning by example in the hippocampus","department":[{"_id":"JoCs"}],"_id":"2003","type":"journal_article","status":"public","publication_status":"published","year":"2014","day":"02","language":[{"iso":"eng"}],"publication":"Neuron","page":"8 - 10","date_published":"2014-07-02T00:00:00Z","doi":"10.1016/j.neuron.2014.06.013","issue":"1","volume":83,"date_created":"2018-12-11T11:55:09Z","abstract":[{"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.","lang":"eng"}],"oa_version":"None","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","month":"07","intvolume":" 83"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:42Z","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.","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.","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.","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."},"title":"Scalable privacy-preserving data sharing methodology for genome-wide association studies","department":[{"_id":"CaUh"}],"author":[{"last_name":"Yu","full_name":"Yu, Fei","first_name":"Fei"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"},{"first_name":"Alexandra","last_name":"Slaković","full_name":"Slaković, Alexandra"},{"orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"}],"publist_id":"5065","_id":"2011","status":"public","type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Biomedical Informatics","year":"2014","publication_status":"published","doi":"10.1016/j.jbi.2014.01.008","volume":50,"date_published":"2014-08-01T00:00:00Z","date_created":"2018-12-11T11:55:12Z","page":"133 - 141","oa_version":"Submitted Version","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.","abstract":[{"lang":"eng","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)."}],"month":"08","intvolume":" 50","scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.5193"}]},{"_id":"2005","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:40Z","citation":{"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.","ista":"Dupret D, Csicsvari JL. 2014. Turning heads to remember places. Nature Neuroscience. 17(5), 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.","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 17 (2014) 643–644.","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.","ama":"Dupret D, Csicsvari JL. Turning heads to remember places. Nature Neuroscience. 2014;17(5):643-644. doi:10.1038/nn.3700","apa":"Dupret, D., & Csicsvari, J. L. (2014). Turning heads to remember places. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3700"},"title":"Turning heads to remember places","department":[{"_id":"JoCs"}],"publist_id":"5071","author":[{"first_name":"David","full_name":"Dupret, David","last_name":"Dupret"},{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","abstract":[{"lang":"eng","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."}],"intvolume":" 17","month":"04","quality_controlled":"1","scopus_import":1,"publisher":"Nature Publishing Group","publication":"Nature Neuroscience","language":[{"iso":"eng"}],"day":"25","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:09Z","issue":"5","volume":17,"date_published":"2014-04-25T00:00:00Z","doi":"10.1038/nn.3700","page":"643 - 644"},{"article_processing_charge":"No","publist_id":"5069","author":[{"first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","full_name":"Klimova, Anna","last_name":"Klimova"},{"last_name":"Rudas","full_name":"Rudas, Tamás","first_name":"Tamás"}],"title":"gIPFrm: Generalized iterative proportional fitting for relational models","department":[{"_id":"CaUh"}],"citation":{"ama":"Klimova A, Rudas T. gIPFrm: Generalized iterative proportional fitting for relational models. 2014.","apa":"Klimova, A., & Rudas, T. (2014). gIPFrm: Generalized iterative proportional fitting for relational models. The Comprehensive R Archive Network.","ieee":"A. Klimova and T. 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.","ista":"Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting for relational models, The Comprehensive R Archive Network.","chicago":"Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional Fitting for Relational Models.” The Comprehensive R Archive Network, 2014."},"date_updated":"2022-08-26T08:12:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","status":"public","_id":"2007","date_created":"2018-12-11T11:55:10Z","date_published":"2014-03-20T00:00:00Z","year":"2014","day":"20","main_file_link":[{"url":"https://CRAN.R-project.org/package=gIPFrm ","open_access":"1"}],"oa":1,"publisher":"The Comprehensive R Archive Network","month":"03","abstract":[{"text":"Maximum likelihood estimation under relational models, with or without the overall effect. For more information see the reference manual","lang":"eng"}],"oa_version":"Published Version"},{"scopus_import":"1","intvolume":" 34","month":"11","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"}],"oa_version":"Published Version","pmid":1,"volume":34,"issue":"47","publication_status":"published","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2022-05-24T08:41:41Z","file_name":"2014_JournNeuroscience_Matsukawa.pdf","date_updated":"2022-05-24T08:41:41Z","file_size":3963728,"creator":"dernst","checksum":"6913e9bc26e9fc1c0441a739a4199229","file_id":"11410","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"article_type":"original","type":"journal_article","status":"public","_id":"2018","department":[{"_id":"RySh"}],"file_date_updated":"2022-05-24T08:41:41Z","date_updated":"2022-05-24T08:54:54Z","ddc":["570"],"oa":1,"publisher":"Society for Neuroscience","quality_controlled":"1","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.","page":"15779 - 15792","date_created":"2018-12-11T11:55:14Z","doi":"10.1523/JNEUROSCI.1141-14.2014","date_published":"2014-11-19T00:00:00Z","year":"2014","has_accepted_license":"1","publication":"Journal of Neuroscience","day":"19","external_id":{"pmid":["25411505"]},"article_processing_charge":"No","author":[{"first_name":"Hiroshi","last_name":"Matsukawa","full_name":"Matsukawa, Hiroshi"},{"full_name":"Akiyoshi Nishimura, Sachiko","last_name":"Akiyoshi Nishimura","first_name":"Sachiko"},{"first_name":"Qi","full_name":"Zhang, Qi","last_name":"Zhang"},{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"},{"last_name":"Yamaguchi","full_name":"Yamaguchi, Kazuhiko","first_name":"Kazuhiko"},{"last_name":"Goto","full_name":"Goto, Hiromichi","first_name":"Hiromichi"},{"first_name":"Kunio","full_name":"Yaguchi, Kunio","last_name":"Yaguchi"},{"full_name":"Hashikawa, Tsutomu","last_name":"Hashikawa","first_name":"Tsutomu"},{"first_name":"Chie","last_name":"Sano","full_name":"Sano, Chie"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Toshiaki","full_name":"Nakashiba, Toshiaki","last_name":"Nakashiba"},{"first_name":"Shigeyoshi","last_name":"Itohara","full_name":"Itohara, Shigeyoshi"}],"publist_id":"5054","title":"Netrin-G/NGL complexes encode functional synaptic diversification","citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"2019","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:45Z","department":[{"_id":"LaEr"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"12","intvolume":" 17","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1407.1552","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3-4","volume":17,"ec_funded":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464.","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","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","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.","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.","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."},"title":"Phase transition in the density of states of quantum spin glasses","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik J","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"publist_id":"5053","publisher":"Springer","quality_controlled":"1","oa":1,"day":"17","publication":"Mathematical Physics, Analysis and Geometry","year":"2014","doi":"10.1007/s11040-014-9164-3","date_published":"2014-12-17T00:00:00Z","date_created":"2018-12-11T11:55:15Z","page":"441 - 464"},{"date_updated":"2021-01-12T06:54:43Z","department":[{"_id":"CaUh"}],"_id":"2013","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"5","volume":14,"oa_version":"Submitted Version","abstract":[{"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","lang":"eng"}],"intvolume":" 14","month":"10","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0285"}],"scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116.","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","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.","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.","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."},"title":"Hypersurfaces and their singularities in partial correlation testing","author":[{"last_name":"Lin","full_name":"Lin, Shaowei","first_name":"Shaowei"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sturmfels","full_name":"Sturmfels, Bernd","first_name":"Bernd"},{"first_name":"Peter","last_name":"Bühlmann","full_name":"Bühlmann, Peter"}],"publist_id":"5063","publication":"Foundations of Computational Mathematics","day":"10","year":"2014","date_created":"2018-12-11T11:55:12Z","doi":"10.1007/s10208-014-9205-0","date_published":"2014-10-10T00:00:00Z","page":"1079 - 1116","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).","oa":1,"quality_controlled":"1","publisher":"Springer"},{"publist_id":"5058","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216","full_name":"Caroline Uhler"},{"first_name":"Alex","full_name":"Lenkoski, Alex","last_name":"Lenkoski"},{"full_name":"Richards, Donald","last_name":"Richards","first_name":"Donald"}],"title":" Exact formulas for the normalizing constants of Wishart distributions for graphical models","citation":{"short":"C. Uhler, A. Lenkoski, D. Richards, ArXiv (2014).","ieee":"C. Uhler, A. Lenkoski, and D. Richards, “ Exact formulas for the normalizing constants of Wishart distributions for graphical models,” ArXiv. ArXiv, 2014.","ama":"Uhler C, Lenkoski A, Richards D. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. 2014.","apa":"Uhler, C., Lenkoski, A., & Richards, D. (2014). Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. ArXiv.","mla":"Uhler, Caroline, et al. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv, ArXiv, 2014.","ista":"Uhler C, Lenkoski A, Richards D. 2014. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv, .","chicago":"Uhler, Caroline, Alex Lenkoski, and Donald Richards. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv. ArXiv, 2014."},"date_updated":"2021-01-12T06:54:44Z","extern":1,"type":"preprint","status":"public","_id":"2017","date_published":"2014-06-18T00:00:00Z","date_created":"2018-12-11T11:55:14Z","publication_status":"published","year":"2014","day":"18","publication":"ArXiv","publisher":"ArXiv","quality_controlled":0,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1406.4901","open_access":"1"}],"month":"06","abstract":[{"lang":"eng","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."}],"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."},{"_id":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"423","status":"public","date_updated":"2021-01-12T06:54:47Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"SiHi"},{"_id":"Bio"}],"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"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 159","month":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf","date_created":"2018-12-12T10:08:47Z","creator":"system","file_size":4435787,"date_updated":"2020-07-14T12:45:25Z","file_id":"4709","checksum":"6c5de8329bb2ffa71cba9fda750f14ce","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"issue":"4","volume":159,"project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"}],"citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5050","author":[{"full_name":"Gao, Peng","last_name":"Gao","first_name":"Peng"},{"first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","full_name":"Postiglione, Maria P","last_name":"Postiglione"},{"full_name":"Krieger, Teresa","last_name":"Krieger","first_name":"Teresa"},{"last_name":"Hernandez","full_name":"Hernandez, Luisirene","first_name":"Luisirene"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"full_name":"Han, Zhi","last_name":"Han","first_name":"Zhi"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen"},{"first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","last_name":"Papusheva","full_name":"Papusheva, Ekaterina"},{"full_name":"Insolera, Ryan","last_name":"Insolera","first_name":"Ryan"},{"last_name":"Chugh","full_name":"Chugh, Kritika","first_name":"Kritika"},{"first_name":"Oren","full_name":"Kodish, Oren","last_name":"Kodish"},{"first_name":"Kun","last_name":"Huang","full_name":"Huang, Kun"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Song","last_name":"Shi","full_name":"Shi, Song"}],"title":"Deterministic progenitor behavior and unitary production of neurons in the neocortex","oa":1,"quality_controlled":"1","publisher":"Cell Press","year":"2014","has_accepted_license":"1","publication":"Cell","day":"06","page":"775 - 788","date_created":"2018-12-11T11:55:16Z","date_published":"2014-11-06T00:00:00Z","doi":"10.1016/j.cell.2014.10.027"},{"author":[{"last_name":"Ali","full_name":"Ali, Shah","first_name":"Shah"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lily","last_name":"Saadat","full_name":"Saadat, Lily"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"last_name":"Weissman","full_name":"Weissman, Irving","first_name":"Irving"},{"full_name":"Ardehali, Reza","last_name":"Ardehali","first_name":"Reza"}],"publist_id":"5052","department":[{"_id":"SiHi"}],"title":"Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice","date_updated":"2021-01-12T06:54:46Z","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","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","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.","short":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855.","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2020","page":"8850 - 8855","issue":"24","date_published":"2014-06-17T00:00:00Z","volume":111,"doi":"10.1073/pnas.1408233111","date_created":"2018-12-11T11:55:15Z","publication_status":"published","year":"2014","day":"17","language":[{"iso":"eng"}],"publication":"PNAS","scopus_import":1,"publisher":"National Academy of Sciences","quality_controlled":"1","month":"06","intvolume":" 111","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."}],"oa_version":"None"},{"status":"public","type":"journal_article","_id":"2021","title":"Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling","department":[{"_id":"SiHi"}],"author":[{"last_name":"William","full_name":"William, Joo","first_name":"Joo"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"publist_id":"5051","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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.","ista":"William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629.","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.","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","short":"J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 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."},"date_updated":"2021-01-12T06:54:47Z","month":"10","intvolume":" 346","publisher":"American Association for the Advancement of Science","quality_controlled":"1","scopus_import":1,"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/","open_access":"1"}],"oa_version":"Submitted Version","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."}],"volume":346,"doi":"10.1126/science.1258996","date_published":"2014-10-31T00:00:00Z","issue":"6209","date_created":"2018-12-11T11:55:15Z","page":"626 - 629","day":"31","language":[{"iso":"eng"}],"publication":"Science","publication_status":"published","year":"2014"},{"intvolume":" 8837","month":"11","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.2967"}],"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"ec_funded":1,"volume":8837,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","end_date":"2014-11-07","location":"Sydney, Australia","start_date":"2014-11-03"},"type":"conference","_id":"2027","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:54:49Z","oa":1,"publisher":"Society of Industrial and Applied Mathematics","quality_controlled":"1","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.","date_created":"2018-12-11T11:55:17Z","date_published":"2014-11-01T00:00:00Z","doi":"10.1007/978-3-319-11936-6_8","page":"98 - 114","publication":" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","year":"2014","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"24696","name":"LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING","_id":"26241A12-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"editor":[{"first_name":"Franck","full_name":"Cassez, Franck","last_name":"Cassez"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"title":"Verification of markov decision processes using learning algorithms","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"first_name":"Vojtěch","full_name":"Forejt, Vojtěch","last_name":"Forejt"},{"last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Marta","last_name":"Kwiatkowska","full_name":"Kwiatkowska, Marta"},{"first_name":"David","last_name":"Parker","full_name":"Parker, David"},{"last_name":"Ujma","full_name":"Ujma, Mateusz","first_name":"Mateusz"}],"publist_id":"5046","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","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.","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.","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."}},{"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"doi":"10.7554/eLife.04057","date_published":"2014-12-09T00:00:00Z","date_created":"2018-12-11T11:55:19Z","has_accepted_license":"1","year":"2014","day":"09","publication":"eLife","project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"publist_id":"5041","author":[{"full_name":"Arai, Itaru","last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"title":"Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse","citation":{"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.","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.","short":"itaru Arai, P.M. Jonas, ELife 3 (2014).","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","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","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.","ista":"Arai itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"12","intvolume":" 3","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."}],"oa_version":"Submitted Version","volume":3,"ec_funded":1,"publication_status":"published","file":[{"file_name":"IST-2016-421-v1+1_e04057.full.pdf","date_created":"2018-12-12T10:14:41Z","file_size":2239563,"date_updated":"2020-07-14T12:45:26Z","creator":"system","file_id":"5094","checksum":"c240f915450d4ebe8f95043a2a8c7b1a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","pubrep_id":"421","_id":"2031","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:26Z","date_updated":"2021-01-12T06:54:51Z","ddc":["570"]},{"abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","scopus_import":1,"month":"03","intvolume":" 5","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4864","checksum":"614fb6579c86d1f95bdd95eeb9ab01b0","creator":"system","file_size":4803515,"date_updated":"2020-07-14T12:45:25Z","file_name":"IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf","date_created":"2018-12-12T10:11:11Z"}],"language":[{"iso":"eng"}],"volume":5,"_id":"2024","type":"journal_article","status":"public","pubrep_id":"616","date_updated":"2021-01-12T06:54:48Z","ddc":["570"],"department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:45:25Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2014","day":"25","publication":"Nature Communications","doi":"10.1038/ncomms4498","date_published":"2014-03-25T00:00:00Z","date_created":"2018-12-11T11:55:16Z","article_number":"3498","citation":{"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.","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.","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","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","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"first_name":"Show","last_name":"Nishinoaki","full_name":"Nishinoaki, Show"},{"last_name":"Sato","full_name":"Sato, Yoshifumi","first_name":"Yoshifumi"},{"first_name":"Wataru","last_name":"Yamamoto","full_name":"Yamamoto, Wataru"},{"last_name":"Furukawa","full_name":"Furukawa, Daiki","first_name":"Daiki"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Akira","full_name":"Sawaguchi, Akira","last_name":"Sawaguchi"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"publist_id":"5048","title":"Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole"},{"date_created":"2018-12-11T11:55:18Z","date_published":"2014-10-12T00:00:00Z","doi":"10.1016/j.jtbi.2014.09.041","page":"40 - 54","publication":" Journal of Theoretical Biology","day":"12","year":"2014","has_accepted_license":"1","oa":1,"publisher":"Academic Press","quality_controlled":"1","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. ","title":"Characterizing spiking in noisy type II neurons","article_processing_charge":"No","publist_id":"5043","author":[{"first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bodova","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina"},{"full_name":"Paydarfar, David","last_name":"Paydarfar","first_name":"David"},{"first_name":"Daniel","last_name":"Forger","full_name":"Forger, Daniel"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 365, 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.","short":"K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.","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.","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","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"},"related_material":{"link":[{"url":"https://doi.org/10.1016/j.jtbi.2015.03.013","relation":"erratum"}]},"volume":365,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf","date_created":"2018-12-12T10:17:58Z","creator":"system","file_size":2679222,"date_updated":"2020-07-14T12:45:25Z","file_id":"5316","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 365","month":"10","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2022-08-25T14:00:47Z","pubrep_id":"444","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","_id":"2028"},{"volume":8837,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 8837","alternative_title":["LNCS"],"oa_version":"None","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"}],"department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:54:49Z","status":"public","type":"conference","conference":{"start_date":"2014-11-03","end_date":"2014-11-07","location":"Sydney, Australia","name":"ATVA: Automated Technology for Verification and Analysis"},"_id":"2026","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-11936-6_17","date_created":"2018-12-11T11:55:17Z","page":"235 - 241","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","publisher":"Springer","quality_controlled":"1","acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","editor":[{"full_name":"Cassez, Franck","last_name":"Cassez","first_name":"Franck"},{"first_name":"Jean-François","full_name":"Raskin, Jean-François","last_name":"Raskin"}],"title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","author":[{"first_name":"Zuzana","last_name":"Komárková","full_name":"Komárková, Zuzana"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"}],"publist_id":"5045","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","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."},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"}]},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"intvolume":" 108","month":"10","main_file_link":[{"url":"http://arxiv.org/abs/1404.4717","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","volume":108,"issue":"2","_id":"2029","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:50Z","department":[{"_id":"RoSe"}],"acknowledgement":"239694; ERC; European Research Council","oa":1,"quality_controlled":"1","publisher":"IOP Publishing Ltd.","publication":"EPL","day":"13","year":"2014","date_created":"2018-12-11T11:55:18Z","date_published":"2014-10-13T00:00:00Z","doi":"10.1209/0295-5075/108/20003","article_number":"20003","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (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","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","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.","ista":"Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003."},"title":"Validity of spin-wave theory for the quantum Heisenberg model","author":[{"first_name":"Michele","full_name":"Correggi, Michele","last_name":"Correggi"},{"last_name":"Giuliani","full_name":"Giuliani, Alessandro","first_name":"Alessandro"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"5044"},{"_id":"2033","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2014-12-08","location":"Montreal, Canada","end_date":"2014-12-13"},"type":"conference","status":"public","date_updated":"2023-02-23T10:25:24Z","citation":{"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.","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.","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.","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.","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hernandez Lobato","full_name":"Hernandez Lobato, Daniel","first_name":"Daniel"},{"first_name":"Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska"},{"last_name":"Kersting","full_name":"Kersting, Kristian","first_name":"Kristian"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Novi","full_name":"Quadrianto, Novi","last_name":"Quadrianto"}],"publist_id":"5038","title":"Mind the nuisance: Gaussian process classification using privileged noise","department":[{"_id":"ChLa"}],"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."}],"oa_version":"Submitted Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise"}],"scopus_import":1,"publisher":"Neural Information Processing Systems","quality_controlled":"1","intvolume":" 1","month":"12","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems","day":"08","page":"837-845","date_created":"2018-12-11T11:55:20Z","volume":1,"issue":"January","date_published":"2014-12-08T00:00:00Z"},{"publication_status":"published","file":[{"date_created":"2019-05-16T13:39:11Z","file_name":"2014_Taylor_Alvaro.pdf","date_updated":"2020-07-14T12:45:26Z","file_size":1765933,"creator":"kschuh","file_id":"6464","checksum":"44e17ad40577ab46eb602e88a8b0b8fd","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"4","volume":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","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."}],"oa_version":"Published Version","scopus_import":1,"month":"12","intvolume":" 1","date_updated":"2021-01-12T06:54:51Z","ddc":["570"],"department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:45:26Z","_id":"2032","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","has_accepted_license":"1","year":"2014","day":"31","publication":"Molecular and Cellular Oncology","date_published":"2014-12-31T00:00:00Z","doi":"10.4161/23723548.2014.964045","date_created":"2018-12-11T11:55:19Z","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"citation":{"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.","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.","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.","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","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014).","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto"},{"orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karin","last_name":"Schelch","full_name":"Schelch, Karin"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"first_name":"Michael","full_name":"Grusch, Michael","last_name":"Grusch"}],"publist_id":"5040","title":"The optogenetic promise for oncology: Episode I","article_number":"e964045"},{"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","year":"2014","date_created":"2018-12-11T11:55:24Z","doi":"10.1007/978-3-642-54631-0_19","date_published":"2014-01-01T00:00:00Z","page":"329 - 344","acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","oa":1,"publisher":"Springer","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","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.","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.","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."},"title":"Enhanced chosen-ciphertext security and applications","editor":[{"full_name":"Krawczyk, Hugo","last_name":"Krawczyk","first_name":"Hugo"}],"author":[{"full_name":"Dachman Soled, Dana","last_name":"Dachman Soled","first_name":"Dana"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer"},{"full_name":"Mohassel, Payman","last_name":"Mohassel","first_name":"Payman"},{"last_name":"O’Neill","full_name":"O’Neill, Adam","first_name":"Adam"}],"publist_id":"5006","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":8383,"oa_version":"Submitted Version","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."}],"intvolume":" 8383","month":"01","main_file_link":[{"url":"https://eprint.iacr.org/2012/543","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"date_updated":"2021-01-12T06:54:57Z","department":[{"_id":"KrPi"}],"_id":"2045","status":"public","conference":{"name":"PKC: Public Key Crypography","start_date":"2014-03-26","end_date":"2014-03-28","location":"Buenos Aires, Argentina"},"type":"conference"},{"citation":{"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).","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.","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","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","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.","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5009","title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","article_number":"663","has_accepted_license":"1","year":"2014","day":"08","publication":"BMC Genomics","date_published":"2014-08-08T00:00:00Z","doi":"10.1186/1471-2164-15-663","date_created":"2018-12-11T11:55:23Z","quality_controlled":"1","publisher":"BioMed Central","oa":1,"date_updated":"2021-01-12T06:54:56Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"JoBo"}],"_id":"2042","type":"journal_article","tmp":{"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)","short":"CC0 (1.0)"},"status":"public","pubrep_id":"396","publication_status":"published","file":[{"file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf","date_created":"2018-12-12T10:11:24Z","file_size":1489769,"date_updated":"2020-07-14T12:45:26Z","creator":"system","file_id":"4878","checksum":"3f6d2776b90a842a28359cc957d3d04b","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"1","volume":15,"license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":1,"month":"08","intvolume":" 15"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","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.","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.","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."},"editor":[{"last_name":" McGeoch","full_name":" McGeoch, Catherine","first_name":"Catherine"},{"last_name":"Meyer","full_name":"Meyer, Ulrich","first_name":"Ulrich"}],"title":"Distributed computation of persistent homology","author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer"},{"first_name":"Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"},{"last_name":"Reininghaus","full_name":"Reininghaus, Jan","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5008","project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments","day":"01","year":"2014","date_created":"2018-12-11T11:55:23Z","doi":"10.1137/1.9781611973198.4","date_published":"2014-01-01T00:00:00Z","page":"31 - 38","oa":1,"publisher":"Society of Industrial and Applied Mathematics","quality_controlled":"1","date_updated":"2021-01-12T06:54:56Z","department":[{"_id":"HeEd"}],"_id":"2043","status":"public","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","start_date":"2014-01-05","end_date":"2014-01-05","location":"Portland, USA"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.0710"}],"scopus_import":1},{"quality_controlled":"1","publisher":"Frontiers Research Foundation","oa":1,"has_accepted_license":"1","year":"2014","day":"10","publication":"Frontiers in Neural Circuits","date_published":"2014-09-10T00:00:00Z","doi":"10.3389/fncir.2014.00107","date_created":"2018-12-11T11:55:22Z","article_number":"2p","citation":{"ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p.","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.","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","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","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"last_name":"Lisman","full_name":"Lisman, John","first_name":"John"}],"publist_id":"5010","title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"09","intvolume":" 8","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5294","checksum":"3ca57b164045523f876407e9f13a9fb8","file_size":201110,"date_updated":"2020-07-14T12:45:26Z","creator":"system","file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf","date_created":"2018-12-12T10:17:38Z"}],"language":[{"iso":"eng"}],"volume":8,"_id":"2041","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"424","date_updated":"2021-01-12T06:54:55Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"PeJo"}]},{"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"03","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.0477"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"_id":"2044","series_title":"Mathematics and Visualization","status":"public","type":"book_chapter","date_updated":"2021-01-12T06:54:56Z","department":[{"_id":"HeEd"}],"publisher":"Springer","quality_controlled":"1","oa":1,"day":"19","publication":"Topological Methods in Data Analysis and Visualization III","year":"2014","doi":"10.1007/978-3-319-04099-8_7","date_published":"2014-03-19T00:00:00Z","date_created":"2018-12-11T11:55:23Z","page":"103 - 117","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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.","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.","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."},"title":"Clear and Compress: Computing Persistent Homology in Chunks","editor":[{"full_name":"Bremer, Peer-Timo","last_name":"Bremer","first_name":"Peer-Timo"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"},{"full_name":"Peikert, Ronald","last_name":"Peikert","first_name":"Ronald"}],"publist_id":"5007","author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich"},{"first_name":"Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"}]},{"month":"09","intvolume":" 345","quality_controlled":"1","scopus_import":1,"publisher":"American Association for the Advancement of Science","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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. "}],"doi":"10.1126/science.1254927","issue":"6204","date_published":"2014-09-26T00:00:00Z","volume":345,"date_created":"2018-12-11T11:55:22Z","day":"26","language":[{"iso":"eng"}],"publication":"Science","year":"2014","publication_status":"published","status":"public","type":"journal_article","article_number":"1254927","_id":"2040","department":[{"_id":"ToBo"}],"title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","author":[{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ribeiro","full_name":"Ribeiro, Ana","first_name":"Ana"},{"full_name":"Pérez Valle, Helena","last_name":"Pérez Valle","first_name":"Helena"},{"full_name":"Lovell Badge, Robin","last_name":"Lovell Badge","first_name":"Robin"},{"first_name":"Vasso","last_name":"Episkopou","full_name":"Episkopou, Vasso"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"}],"publist_id":"5011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:55Z","citation":{"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","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","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","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.","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.","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.","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."}},{"project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070"}],"publist_id":"5004","author":[{"full_name":"Yu, Fei","last_name":"Yu","first_name":"Fei"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rybar, Michal","last_name":"Rybar"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler"},{"last_name":"Fienberg","full_name":"Fienberg, Stephen","first_name":"Stephen"}],"external_id":{"arxiv":["1407.8067"]},"title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","editor":[{"last_name":"Domingo Ferrer","full_name":"Domingo Ferrer, Josep","first_name":"Josep"}],"citation":{"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.","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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","page":"170 - 184","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-11257-2_14","date_created":"2018-12-11T11:55:24Z","year":"2014","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","type":"conference","conference":{"name":"PSD: Privacy in Statistical Databases","end_date":"2014-09-19","location":"Ibiza, Spain","start_date":"2014-09-17"},"status":"public","_id":"2047","department":[{"_id":"KrPi"},{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:57Z","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8067"}],"month":"01","intvolume":" 8744","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."}],"oa_version":"Submitted Version","volume":8744,"publication_status":"published","language":[{"iso":"eng"}]},{"title":"Probabilistic bisimulation: Naturally on distributions","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"last_name":"Gorla","full_name":"Gorla, Daniele","first_name":"Daniele"}],"author":[{"first_name":"Holger","full_name":"Hermanns, Holger","last_name":"Hermanns"},{"first_name":"Jan","last_name":"Krčál","full_name":"Krčál, Jan"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4993","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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.","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.","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","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","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.","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.","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."},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"doi":"10.1007/978-3-662-44584-6_18","date_published":"2014-09-01T00:00:00Z","date_created":"2018-12-11T11:55:27Z","page":"249 - 265","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"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.","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2021-01-12T06:55:00Z","status":"public","type":"conference","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2014-09-02","location":"Rome, Italy","end_date":"2014-09-05"},"_id":"2053","volume":8704,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 8704","alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1404.5084","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}]},{"date_updated":"2021-01-12T06:54:59Z","citation":{"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.","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4994","author":[{"id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","last_name":"Aminof","full_name":"Aminof, Benjamin"},{"first_name":"Tomer","full_name":"Kotek, Tomer","last_name":"Kotek"},{"last_name":"Rubin","full_name":"Rubin, Sacha","first_name":"Sacha"},{"first_name":"Francesco","last_name":"Spegni","full_name":"Spegni, Francesco"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"}],"department":[{"_id":"KrCh"}],"title":"Parameterized model checking of rendezvous systems","editor":[{"full_name":"Baldan, Paolo","last_name":"Baldan","first_name":"Paolo"},{"first_name":"Daniele","last_name":"Gorla","full_name":"Gorla, Daniele"}],"_id":"2052","type":"conference","conference":{"start_date":"2014-09-02","location":"Rome, Italy","end_date":"2014-09-05","name":"CONCUR: Concurrency Theory"},"status":"public","year":"2014","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","page":"109 - 124","date_published":"2014-09-01T00:00:00Z","volume":8704,"doi":"10.1007/978-3-662-44584-6_9","date_created":"2018-12-11T11:55:26Z","abstract":[{"lang":"eng","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."}],"oa_version":"None","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.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LNCS"],"quality_controlled":"1","month":"09","intvolume":" 8704"},{"citation":{"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.","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.","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.","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.","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.","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","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"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5005","author":[{"first_name":"Mihir","last_name":"Bellare","full_name":"Bellare, Mihir"},{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"}],"title":"Policy-based signatures","editor":[{"full_name":"Krawczyk, Hugo","last_name":"Krawczyk","first_name":"Hugo"}],"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"year":"2014","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","page":"520 - 537","doi":"10.1007/978-3-642-54631-0_30","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:55:24Z","acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2021-01-12T06:54:57Z","department":[{"_id":"KrPi"}],"_id":"2046","type":"conference","conference":{"name":"PKC: Public Key Crypography","start_date":"2014-05-26","end_date":"2014-05-28","location":"Buenos Aires, Argentina"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":8383,"ec_funded":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"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"https://eprint.iacr.org/2013/413","open_access":"1"}],"month":"01","intvolume":" 8383"},{"volume":738,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1508.06546","open_access":"1"}],"month":"01","intvolume":" 738","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"}],"oa_version":"Submitted Version","department":[{"_id":"BjHo"}],"date_updated":"2021-01-12T06:54:59Z","type":"journal_article","status":"public","_id":"2050","page":"463 - 491","doi":"10.1017/jfm.2013.603","date_published":"2014-01-10T00:00:00Z","date_created":"2018-12-11T11:55:25Z","year":"2014","day":"10","publication":"Journal of Fluid Mechanics","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"publist_id":"5001","author":[{"full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","last_name":"Kühnen","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"},{"last_name":"Holzner","full_name":"Holzner, Markus","first_name":"Markus"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuhlmann, Hendrik","last_name":"Kuhlmann","first_name":"Hendrik"}],"external_id":{"arxiv":["1508.06546"]},"article_processing_charge":"No","title":"Experimental investigation of transitional flow in a toroidal pipe","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.","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.","short":"J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491.","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.","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","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","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"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.","lang":"eng"}],"month":"01","publisher":"Neural Information Processing Systems","quality_controlled":0,"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01065586"}],"day":"01","year":"2014","publication_status":"published","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:55:26Z","_id":"2051","status":"public","type":"conference","conference":{"name":"NIPS: Neural Information Processing Systems"},"extern":1,"citation":{"mla":"Marchand, Mario, et al. Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. Neural Information Processing Systems, 2014.","short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Neural Information Processing Systems, 2014.","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.","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.","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.","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.","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."},"date_updated":"2021-01-12T06:54:59Z","title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks","publist_id":"4996","author":[{"last_name":"Marchand","full_name":"Marchand, Mario","first_name":"Mario"},{"first_name":"Su","full_name":"Hongyu, Su","last_name":"Hongyu"},{"first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8301-7240","full_name":"Emilie Morvant","last_name":"Morvant"},{"first_name":"Juho","full_name":"Rousu, Juho","last_name":"Rousu"},{"first_name":"John","full_name":"Shawe-Taylor, John","last_name":"Shawe Taylor"}]},{"oa":1,"publisher":"Springer","quality_controlled":"1","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.","date_created":"2018-12-11T11:55:29Z","date_published":"2014-02-20T00:00:00Z","doi":"10.1007/s00709-014-0616-1","page":"1077 - 1087","publication":"Protoplasma","day":"20","year":"2014","has_accepted_license":"1","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","publist_id":"4987","author":[{"first_name":"Ewa","last_name":"Dubas","full_name":"Dubas, Ewa"},{"last_name":"Moravčíková","full_name":"Moravčíková, Jana","first_name":"Jana"},{"first_name":"Jana","last_name":"Libantová","full_name":"Libantová, Jana"},{"first_name":"Ildikó","last_name":"Matušíková","full_name":"Matušíková, Ildikó"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Iwona","last_name":"Zur","full_name":"Zur, Iwona"},{"first_name":"Monika","full_name":"Krzewska, Monika","last_name":"Krzewska"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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.","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.","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","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","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.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","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."},"intvolume":" 251","month":"02","scopus_import":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":251,"issue":"5","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","date_created":"2018-12-12T10:18:31Z","file_size":6377990,"date_updated":"2020-07-14T12:45:27Z","creator":"system","file_id":"5353","checksum":"d570a6073765118fc0bb83c31d96fa53","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","pubrep_id":"394","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"2059","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:27Z","ddc":["580"],"date_updated":"2021-01-12T06:55:02Z"},{"issue":"6196","volume":345,"ec_funded":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5185","checksum":"a0036a589037d37e86364fa25cc0a82f","date_updated":"2020-07-14T12:45:27Z","file_size":215514,"creator":"system","date_created":"2018-12-12T10:16:00Z","file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf"},{"file_id":"5186","checksum":"e1f57d2713725449cb898fdcb8ef47b8","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:01Z","file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","creator":"system","date_updated":"2020-07-14T12:45:27Z","file_size":1732723}],"language":[{"iso":"eng"}],"publication_status":"published","month":"08","intvolume":" 345","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:27Z","department":[{"_id":"PeJo"}],"ddc":["570"],"date_updated":"2021-01-12T06:55:03Z","status":"public","pubrep_id":"821","type":"journal_article","_id":"2062","doi":"10.1126/science.1255263","date_published":"2014-08-01T00:00:00Z","date_created":"2018-12-11T11:55:29Z","day":"01","publication":"Science","has_accepted_license":"1","year":"2014","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","publist_id":"4984","author":[{"last_name":"Hu","full_name":"Hu, Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua"},{"first_name":"Jian","id":"3614E438-F248-11E8-B48F-1D18A9856A87","last_name":"Gan","full_name":"Gan, Jian"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).","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","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","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.","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.","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."},"project":[{"call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"article_number":"1255263"},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1752760a2e71e254537f31c0d10d9c6c","file_id":"4688","file_size":8387384,"date_updated":"2020-07-14T12:45:27Z","creator":"system","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","date_created":"2018-12-12T10:08:27Z"}],"publication_status":"published","issue":"4","volume":33,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 33","month":"07","scopus_import":"1","ddc":["000"],"date_updated":"2022-08-25T14:02:46Z","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:27Z","_id":"2058","pubrep_id":"606","status":"public","conference":{"name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","location":"Vancouver, Canada","end_date":"2014-08-14","start_date":"2014-08-10"},"type":"conference","publication":"ACM Transactions on Graphics","day":"01","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:55:28Z","date_published":"2014-07-01T00:00:00Z","doi":"10.1145/2601097.2601126","oa":1,"quality_controlled":"1","publisher":"ACM","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","mla":"Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics, vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126.","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","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","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4.","short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014."},"title":"Blending liquids","article_processing_charge":"No","author":[{"first_name":"Karthik","last_name":"Raveendran","full_name":"Raveendran, Karthik"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"last_name":"Türk","full_name":"Türk, Greg","first_name":"Greg"}],"publist_id":"4988","article_number":"137","project":[{"grant_number":"11-NSF-1070","name":"ROOTS Genome-wide Analysis of Root Traits","_id":"25636330-B435-11E9-9278-68D0E5697425"}]},{"year":"2014","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","page":"153 - 162","date_created":"2018-12-11T11:55:28Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-662-44415-3_16","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"ista":"Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.","chicago":"Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8621:153–62. Springer, 2014. https://doi.org/10.1007/978-3-662-44415-3_16.","short":"E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162.","ieee":"E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Joensuu, Finland, 2014, vol. 8621, pp. 153–162.","ama":"Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8621. Springer; 2014:153-162. doi:10.1007/978-3-662-44415-3_16","apa":"Morvant, E., Habrard, A., & Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. https://doi.org/10.1007/978-3-662-44415-3_16","mla":"Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8621, Springer, 2014, pp. 153–62, doi:10.1007/978-3-662-44415-3_16."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1404.7796"]},"author":[{"last_name":"Morvant","orcid":"0000-0002-8301-7240","full_name":"Morvant, Emilie","first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Habrard, Amaury","last_name":"Habrard","first_name":"Amaury"},{"last_name":"Ayache","full_name":"Ayache, Stéphane","first_name":"Stéphane"}],"publist_id":"4989","title":"Majority vote of diverse classifiers for late fusion","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":8621,"abstract":[{"lang":"eng","text":"In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark."}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1404.7796","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 8621","month":"01","date_updated":"2021-01-12T06:55:01Z","department":[{"_id":"ChLa"}],"_id":"2057","conference":{"location":"Joensuu, Finland","end_date":"2014-08-22","start_date":"2014-08-20","name":"IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition"},"type":"conference","status":"public"},{"citation":{"ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology. Springer, 2014. https://doi.org/10.1007/s00285-013-0738-7.","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.","ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” Journal of Mathematical Biology, vol. 69, no. 3. Springer, pp. 767–797, 2014.","apa":"Ganguly, A., Petrov, T., & Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-013-0738-7","ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 2014;69(3):767-797. doi:10.1007/s00285-013-0738-7","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:10.1007/s00285-013-0738-7."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ganguly, Arnab","last_name":"Ganguly","first_name":"Arnab"},{"first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"},{"last_name":"Koeppl","full_name":"Koeppl, Heinz","first_name":"Heinz"}],"publist_id":"4990","title":"Markov chain aggregation and its applications to combinatorial reaction networks","acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2014","publication":"Journal of Mathematical Biology","day":"20","page":"767 - 797","date_created":"2018-12-11T11:55:28Z","date_published":"2014-11-20T00:00:00Z","doi":"10.1007/s00285-013-0738-7","_id":"2056","type":"journal_article","status":"public","date_updated":"2021-01-12T06:55:01Z","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.4532"}],"scopus_import":1,"intvolume":" 69","month":"11","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":69},{"abstract":[{"lang":"eng","text":"Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis."}],"oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"Springer","month":"02","intvolume":" 251","publication_status":"published","year":"2014","day":"14","language":[{"iso":"eng"}],"publication":"Protoplasma","page":"1125 - 1139","issue":"5","volume":251,"date_published":"2014-02-14T00:00:00Z","doi":"10.1007/s00709-014-0620-5","date_created":"2018-12-11T11:55:29Z","_id":"2061","type":"journal_article","status":"public","date_updated":"2021-01-12T06:55:03Z","citation":{"chicago":"Mazur, Ewa, Ewa Kurczyñska, and Jiří Friml. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0620-5.","ista":"Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5), 1125–1139.","mla":"Mazur, Ewa, et al. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1125–39, doi:10.1007/s00709-014-0620-5.","apa":"Mazur, E., Kurczyñska, E., & Friml, J. (2014). Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0620-5","ama":"Mazur E, Kurczyñska E, Friml J. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 2014;251(5):1125-1139. doi:10.1007/s00709-014-0620-5","short":"E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139.","ieee":"E. Mazur, E. Kurczyñska, and J. Friml, “Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis,” Protoplasma, vol. 251, no. 5. Springer, pp. 1125–1139, 2014."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4985","author":[{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"},{"full_name":"Kurczyñska, Ewa","last_name":"Kurczyñska","first_name":"Ewa"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"department":[{"_id":"JiFr"}],"title":"Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis"},{"title":"Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus","author":[{"first_name":"Maía","last_name":"Rubio","full_name":"Rubio, Maía"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"full_name":"Clarkson, Cheryl","last_name":"Clarkson","first_name":"Cheryl"},{"first_name":"Elek","last_name":"Molnár","full_name":"Molnár, Elek"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"}],"publist_id":"4974","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., & Shigemoto, R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23654","ama":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 2014;522(18):4023-4042. doi:10.1002/cne.23654","ieee":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto, “Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus,” Journal of Comparative Neurology, vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014.","short":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042.","mla":"Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:10.1002/cne.23654.","ista":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18), 4023–4042.","chicago":"Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár, and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology. Wiley-Blackwell, 2014. https://doi.org/10.1002/cne.23654."},"oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","acknowledgement":"National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n","date_created":"2018-12-11T11:55:30Z","date_published":"2014-07-29T00:00:00Z","doi":"10.1002/cne.23654","page":"4023 - 4042","publication":"Journal of Comparative Neurology","day":"29","year":"2014","status":"public","type":"journal_article","_id":"2064","department":[{"_id":"RySh"}],"date_updated":"2021-01-12T06:55:05Z","intvolume":" 522","month":"07","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses.","lang":"eng"}],"issue":"18","volume":522,"language":[{"iso":"eng"}],"publication_status":"published"},{"acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF.","oa_version":"None","abstract":[{"text":"We propose an interactive, optimization-in-the-loop tool for designing inflatable structures. Given a target shape, the user draws a network of seams defining desired segment boundaries in 3D. Our method computes optimally-shaped flat panels for the segments, such that the inflated structure is as close as possible to the target while satisfying the desired seam positions. Our approach is underpinned by physics-based pattern optimization, accurate coarse-scale simulation using tension field theory, and a specialized constraint-optimization method. Our system is fast enough to warrant interactive exploration of different seam layouts, including internal connections, and their effects on the inflated shape. We demonstrate the resulting design process on a varied set of simulation examples, some of which we have fabricated, demonstrating excellent agreement with the design intent.","lang":"eng"}],"intvolume":" 33","month":"07","publisher":"ACM","language":[{"iso":"eng"}],"day":"01","year":"2014","publication_status":"published","date_created":"2018-12-11T11:55:36Z","date_published":"2014-07-01T00:00:00Z","issue":"4","doi":"10.1145/2601097.2601166","volume":33,"article_number":"63","_id":"2081","status":"public","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T06:55:11Z","citation":{"ista":"Skouras M, Thomaszewski B, Kaufmann P, Garg A, Bickel B, Grinspun E, Gross M. 2014. Designing inflatable structures. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 33, 63.","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Peter Kaufmann, Akash Garg, Bernd Bickel, Eitan Grinspun, and Markus Gross. “Designing Inflatable Structures,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601166.","short":"M. Skouras, B. Thomaszewski, P. Kaufmann, A. Garg, B. Bickel, E. Grinspun, M. Gross, in:, ACM, 2014.","ieee":"M. Skouras et al., “Designing inflatable structures,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.","apa":"Skouras, M., Thomaszewski, B., Kaufmann, P., Garg, A., Bickel, B., Grinspun, E., & Gross, M. (2014). Designing inflatable structures (Vol. 33). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601166","ama":"Skouras M, Thomaszewski B, Kaufmann P, et al. Designing inflatable structures. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601166","mla":"Skouras, Mélina, et al. Designing Inflatable Structures. Vol. 33, no. 4, 63, ACM, 2014, doi:10.1145/2601097.2601166."},"title":"Designing inflatable structures","author":[{"first_name":"Mélina","full_name":"Skouras, Mélina","last_name":"Skouras"},{"last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard","first_name":"Bernhard"},{"first_name":"Peter","last_name":"Kaufmann","full_name":"Kaufmann, Peter"},{"first_name":"Akash","last_name":"Garg","full_name":"Garg, Akash"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grinspun, Eitan","last_name":"Grinspun","first_name":"Eitan"},{"full_name":"Gross, Markus","last_name":"Gross","first_name":"Markus"}],"publist_id":"4957"},{"status":"public","conference":{"name":"SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques"},"type":"conference","_id":"2080","title":"Spin-It: Optimizing moment of inertia for spinnable objects","publist_id":"4958","author":[{"last_name":"Bac̈Her","full_name":"Bac̈her, Moritz","first_name":"Moritz"},{"last_name":"Whiting","full_name":"Whiting, Emily","first_name":"Emily"},{"orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","full_name":"Sorkine-Hornung, Olga","last_name":"Sorkine Hornung"}],"extern":1,"date_updated":"2019-04-26T07:22:07Z","citation":{"chicago":"Bac̈Her, Moritz, Emily Whiting, Bernd Bickel, and Olga Sorkine Hornung. “Spin-It: Optimizing Moment of Inertia for Spinnable Objects,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601157.","ista":"Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. 2014. Spin-It: Optimizing moment of inertia for spinnable objects. SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33.","mla":"Bac̈Her, Moritz, et al. Spin-It: Optimizing Moment of Inertia for Spinnable Objects. Vol. 33, no. 4, ACM, 2014, doi:10.1145/2601097.2601157.","ieee":"M. Bac̈Her, E. Whiting, B. Bickel, and O. Sorkine Hornung, “Spin-It: Optimizing moment of inertia for spinnable objects,” presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.","short":"M. Bac̈Her, E. Whiting, B. Bickel, O. Sorkine Hornung, in:, ACM, 2014.","ama":"Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. Spin-It: Optimizing moment of inertia for spinnable objects. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601157","apa":"Bac̈Her, M., Whiting, E., Bickel, B., & Sorkine Hornung, O. (2014). Spin-It: Optimizing moment of inertia for spinnable objects (Vol. 33). Presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601157"},"intvolume":" 33","month":"01","quality_controlled":0,"publisher":"ACM","acknowledgement":"This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting is supported by the ETH Zurich / Marie Curie COFUND Postdoctoral Fellowship.","abstract":[{"lang":"eng","text":"Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. We present an algorithm to generate designs for spinning objects by optimizing rotational dynamics properties. As input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. We augment the model by creating voids inside its volume, with interior fill represented by an adaptive multi-resolution vox-elization. The discrete voxel fill values are optimized using a continuous, nonlinear formulation. Further, we optimize for rotational stability by maximizing the dominant principal moment. We extend our technique to incorporate deformation and multiple materials for cases where internal voids alone are insufficient. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance. "}],"date_created":"2018-12-11T11:55:35Z","doi":"10.1145/2601097.2601157","date_published":"2014-01-01T00:00:00Z","volume":33,"issue":"4","day":"01","publication_status":"published","year":"2014"},{"publisher":"ACM","quality_controlled":0,"month":"03","intvolume":" 33","abstract":[{"text":"The facial performance of an individual is inherently rich in subtle deformation and timing details. Although these subtleties make the performance realistic and compelling, they often elude both motion capture and hand animation. We present a technique for adding fine-scale details and expressiveness to low-resolution art-directed facial performances, such as those created manually using a rig, via marker-based capture, by fitting a morphable model to a video, or through Kinect reconstruction using recent faceshift technology. We employ a high-resolution facial performance capture system to acquire a representative performance of an individual in which he or she explores the full range of facial expressiveness. From the captured data, our system extracts an expressiveness model that encodes subtle spatial and temporal deformation details specific to that particular individual. Once this model has been built, these details can be transferred to low-resolution art-directed performances. We demonstrate results on various forms of input; after our enhancement, the resulting animations exhibit the same nuances and fine spatial details as the captured performance, with optional temporal enhancement to match the dynamics of the actor. Finally, we show that our technique outperforms the current state-of-the-art in example-based facial animation.","lang":"eng"}],"volume":33,"issue":"2","date_published":"2014-03-01T00:00:00Z","doi":"10.1145/2546276","date_created":"2018-12-11T11:55:48Z","publication_status":"published","year":"2014","day":"01","publication":"ACM Transactions on Graphics","type":"journal_article","status":"public","_id":"2115","publist_id":"4919","author":[{"first_name":"Amit","full_name":"Bermano, Amit H","last_name":"Bermano"},{"last_name":"Bradley","full_name":"Bradley, Derek J","first_name":"Derek"},{"first_name":"Thabo","full_name":"Beeler, Thabo","last_name":"Beeler"},{"first_name":"Fabio","full_name":"Zund, Fabio","last_name":"Zund"},{"last_name":"Nowrouzezahrai","full_name":"Nowrouzezahrai, Derek","first_name":"Derek"},{"full_name":"Baran, Ilya","last_name":"Baran","first_name":"Ilya"},{"first_name":"Olga","full_name":"Sorkine-Hornung, Olga","last_name":"Sorkine Hornung"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"last_name":"Sumner","full_name":"Sumner, Robert W","first_name":"Robert"},{"full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","full_name":"Groß, Markus S","last_name":"Groß"}],"title":"Facial performance enhancement using dynamic shape space analysis","citation":{"ama":"Bermano A, Bradley D, Beeler T, et al. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2546276","apa":"Bermano, A., Bradley, D., Beeler, T., Zund, F., Nowrouzezahrai, D., Baran, I., … Groß, M. (2014). Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2546276","short":"A. Bermano, D. Bradley, T. Beeler, F. Zund, D. Nowrouzezahrai, I. Baran, O. Sorkine Hornung, H. Pfister, R. Sumner, B. Bickel, M. Groß, ACM Transactions on Graphics 33 (2014).","ieee":"A. Bermano et al., “Facial performance enhancement using dynamic shape space analysis,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014.","mla":"Bermano, Amit, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics, vol. 33, no. 2, ACM, 2014, doi:10.1145/2546276.","ista":"Bermano A, Bradley D, Beeler T, Zund F, Nowrouzezahrai D, Baran I, Sorkine Hornung O, Pfister H, Sumner R, Bickel B, Groß M. 2014. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 33(2).","chicago":"Bermano, Amit, Derek Bradley, Thabo Beeler, Fabio Zund, Derek Nowrouzezahrai, Ilya Baran, Olga Sorkine Hornung, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2546276."},"date_updated":"2021-01-12T06:55:24Z","extern":1},{"year":"2014","publication_status":"published","day":"01","publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"page":"887 - 926","volume":331,"date_published":"2014-11-01T00:00:00Z","issue":"3","doi":"10.1007/s00220-014-2124-8","date_created":"2018-12-11T11:55:54Z","abstract":[{"text":"Let ℭ denote the Clifford algebra over ℝ𝑛, which is the von Neumann algebra generated by n self-adjoint operators Q j , j = 1,…,n satisfying the canonical anticommutation relations, Q i Q j + Q j Q i = 2δ ij I, and let τ denote the normalized trace on ℭ. This algebra arises in quantum mechanics as the algebra of observables generated by n fermionic degrees of freedom. Let 𝔓 denote the set of all positive operators 𝜌∈ℭ such that τ(ρ) = 1; these are the non-commutative analogs of probability densities in the non-commutative probability space (ℭ,𝜏). The fermionic Fokker–Planck equation is a quantum-mechanical analog of the classical Fokker–Planck equation with which it has much in common, such as the same optimal hypercontractivity properties. In this paper we construct a Riemannian metric on 𝔓 that we show to be a natural analog of the classical 2-Wasserstein metric, and we show that, in analogy with the classical case, the fermionic Fokker–Planck equation is gradient flow in this metric for the relative entropy with respect to the ground state. We derive a number of consequences of this, such as a sharp Talagrand inequality for this metric, and we prove a number of results pertaining to this metric. Several open problems are raised.","lang":"eng"}],"oa_version":"Submitted Version","publisher":"Springer","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1203.5377 "}],"month":"11","intvolume":" 331","citation":{"mla":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics, vol. 331, no. 3, Springer, 2014, pp. 887–926, doi:10.1007/s00220-014-2124-8.","apa":"Carlen, E., & Maas, J. (2014). An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2124-8","ama":"Carlen E, Maas J. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 2014;331(3):887-926. doi:10.1007/s00220-014-2124-8","ieee":"E. Carlen and J. Maas, “An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy,” Communications in Mathematical Physics, vol. 331, no. 3. Springer, pp. 887–926, 2014.","short":"E. Carlen, J. Maas, Communications in Mathematical Physics 331 (2014) 887–926.","chicago":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2124-8.","ista":"Carlen E, Maas J. 2014. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 331(3), 887–926."},"date_updated":"2021-01-12T06:55:30Z","extern":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Carlen, Eric","last_name":"Carlen","first_name":"Eric"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas"}],"publist_id":"4901","title":"An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy","_id":"2133","type":"journal_article","status":"public"},{"extern":1,"date_updated":"2021-01-12T06:55:30Z","citation":{"mla":"Hairer, Martin, et al. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley-Blackwell, 2014, pp. 776–870, doi:10.1002/cpa.21495.","ama":"Hairer M, Maas J, Weber H. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 2014;67(5):776-870. doi:10.1002/cpa.21495","apa":"Hairer, M., Maas, J., & Weber, H. (2014). Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21495","short":"M. Hairer, J. Maas, H. Weber, Communications on Pure and Applied Mathematics 67 (2014) 776–870.","ieee":"M. Hairer, J. Maas, and H. Weber, “Approximating Rough Stochastic PDEs,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley-Blackwell, pp. 776–870, 2014.","chicago":"Hairer, Martin, Jan Maas, and Hendrik Weber. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2014. https://doi.org/10.1002/cpa.21495.","ista":"Hairer M, Maas J, Weber H. 2014. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 67(5), 776–870."},"title":"Approximating Rough Stochastic PDEs","author":[{"full_name":"Hairer, Martin M","last_name":"Hairer","first_name":"Martin"},{"last_name":"Maas","full_name":"Jan Maas","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weber, Hendrik","last_name":"Weber","first_name":"Hendrik"}],"publist_id":"4902","_id":"2131","status":"public","type":"journal_article","day":"01","publication":"Communications on Pure and Applied Mathematics","year":"2014","publication_status":"published","volume":67,"date_published":"2014-05-01T00:00:00Z","issue":"5","doi":"10.1002/cpa.21495","date_created":"2018-12-11T11:55:53Z","page":"776 - 870","acknowledgement":"JM is supported by Rubicon grant 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). MH is supported by EPSRC grant EP/D071593/1 and by the Royal Society through a Wolfson Research Merit Award. Both MH and HW are supported by the Le","abstract":[{"text":"We study approximations to a class of vector-valued equations of Burgers type driven by a multiplicative space-time white noise. A solution theory for this class of equations has been developed recently in Probability Theory Related Fields by Hairer and Weber. The key idea was to use the theory of controlled rough paths to give definitions of weak/mild solutions and to set up a Picard iteration argument. In this article the limiting behavior of a rather large class of (spatial) approximations to these equations is studied. These approximations are shown to converge and convergence rates are given, but the limit may depend on the particular choice of approximation. This effect is a spatial analogue to the Itô-Stratonovich correction in the theory of stochastic ordinary differential equations, where it is well known that different approximation schemes may converge to different solutions.","lang":"eng"}],"month":"05","intvolume":" 67","publisher":"Wiley-Blackwell","quality_controlled":0,"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.3094 "}]},{"_id":"2132","status":"public","type":"journal_article","extern":1,"citation":{"ista":"Erbar M, Maas J. 2014. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 34(4), 1355–1374.","chicago":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University, 2014. https://doi.org/10.3934/dcds.2014.34.1355 .","apa":"Erbar, M., & Maas, J. (2014). Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University. https://doi.org/10.3934/dcds.2014.34.1355 ","ama":"Erbar M, Maas J. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 2014;34(4):1355-1374. doi:10.3934/dcds.2014.34.1355 ","ieee":"M. Erbar and J. Maas, “Gradient flow structures for discrete porous medium equations,” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4. Southwest Missouri State University, pp. 1355–1374, 2014.","short":"M. Erbar, J. Maas, Discrete and Continuous Dynamical Systems- Series A 34 (2014) 1355–1374.","mla":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4, Southwest Missouri State University, 2014, pp. 1355–74, doi:10.3934/dcds.2014.34.1355 ."},"date_updated":"2021-01-12T06:55:30Z","title":"Gradient flow structures for discrete porous medium equations","publist_id":"4903","author":[{"first_name":"Matthias","last_name":"Erbar","full_name":"Erbar, Matthias"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Jan Maas","orcid":"0000-0002-0845-1338"}],"abstract":[{"text":"We consider discrete porous medium equations of the form ∂tρt=Δϕ(ρt), where Δ is the generator of a reversible continuous time Markov chain on a finite set χ, and ϕ is an increasing function. We show that these equations arise as gradient flows of certain entropy functionals with respect to suitable non-local transportation metrics. This may be seen as a discrete analogue of the Wasserstein gradient flow structure for porous medium equations in ℝn discovered by Otto. We present a one-dimensional counterexample to geodesic convexity and discuss Gromov-Hausdorff convergence to the Wasserstein metric.","lang":"eng"}],"month":"04","intvolume":" 34","publisher":"Southwest Missouri State University","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.1129"}],"oa":1,"day":"01","publication":"Discrete and Continuous Dynamical Systems- Series A","year":"2014","publication_status":"published","volume":34,"date_published":"2014-04-01T00:00:00Z","doi":"10.3934/dcds.2014.34.1355 ","issue":"4","date_created":"2018-12-11T11:55:54Z","page":"1355 - 1374"},{"date_published":"2014-08-11T00:00:00Z","doi":"10.1103/PhysRevLett.113.070401","issue":"7","volume":113,"date_created":"2018-12-11T11:55:56Z","year":"2014","publication_status":"published","day":"11","publication":"Physical Review Letters","language":[{"iso":"eng"}],"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.5905"}],"oa":1,"month":"08","intvolume":" 113","abstract":[{"lang":"eng","text":"We propose a technique for engineering momentum-dependent dissipation in Bose-Einstein condensates with non-local interactions. The scheme relies on the use of momentum-dependent dark-states in close analogy to velocity-selective coherent population trapping. During the short-time dissipative dynamics, the system is driven into a particular finite-momentum phonon mode, which in real space corresponds to an ordered structure with non-local density-density correlations. Dissipation-induced ordering can be observed and studied in present-day experiments using cold atoms with dipole-dipole or off-resonant Rydberg interactions. Due to its dissipative nature, the ordering does not require artificial breaking of translational symmetry by an opticallattice or harmonic trap. This opens up a perspective of direct cooling of quantum gases into strongly-interacting phases."}],"oa_version":"Submitted Version","acknowledgement":"This work was supported by NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory as well as the Harvard Quantum Optics Center.","publist_id":"4884","author":[{"first_name":"Johannes","full_name":"Otterbach, Johannes","last_name":"Otterbach"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"title":"Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates","date_updated":"2021-01-12T06:55:33Z","citation":{"mla":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters, vol. 113, no. 7, 070401, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.070401.","apa":"Otterbach, J., & Lemeshko, M. (2014). Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.070401","ama":"Otterbach J, Lemeshko M. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 2014;113(7). doi:10.1103/PhysRevLett.113.070401","short":"J. Otterbach, M. Lemeshko, Physical Review Letters 113 (2014).","ieee":"J. Otterbach and M. Lemeshko, “Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates,” Physical Review Letters, vol. 113, no. 7. American Physical Society, 2014.","chicago":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.070401.","ista":"Otterbach J, Lemeshko M. 2014. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 113(7), 070401."},"extern":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2140","article_number":"070401"},{"date_published":"2014-06-01T00:00:00Z","doi":"10.1145/2582112.2582168","date_created":"2018-12-11T11:56:01Z","ec_funded":1,"page":"355 - 364","day":"01","publication":"Proceedings of the Annual Symposium on Computational Geometry","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","month":"06","quality_controlled":"1","scopus_import":1,"publisher":"ACM","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1311.3681","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"We define a simple, explicit map sending a morphism f : M → N of pointwise finite dimensional persistence modules to a matching between the barcodes of M and N. Our main result is that, in a precise sense, the quality of this matching is tightly controlled by the lengths of the longest intervals in the barcodes of ker f and coker f . As an immediate corollary, we obtain a new proof of the algebraic stability theorem for persistence barcodes [5, 9], a fundamental result in the theory of persistent homology. In contrast to previous proofs, ours shows explicitly how a δ-interleaving morphism between two persistence modules induces a δ-matching between the barcodes of the two modules. Our main result also specializes to a structure theorem for submodules and quotients of persistence modules. Copyright is held by the owner/author(s).","lang":"eng"}],"department":[{"_id":"HeEd"}],"title":"Induced matchings of barcodes and the algebraic stability of persistence","author":[{"last_name":"Bauer","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"last_name":"Lesnick","full_name":"Lesnick, Michael","first_name":"Michael"}],"publist_id":"4853","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bauer U, Lesnick M. 2014. Induced matchings of barcodes and the algebraic stability of persistence. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 355–364.","chicago":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” In Proceedings of the Annual Symposium on Computational Geometry, 355–64. ACM, 2014. https://doi.org/10.1145/2582112.2582168.","apa":"Bauer, U., & Lesnick, M. (2014). Induced matchings of barcodes and the algebraic stability of persistence. In Proceedings of the Annual Symposium on Computational Geometry (pp. 355–364). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582168","ama":"Bauer U, Lesnick M. Induced matchings of barcodes and the algebraic stability of persistence. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:355-364. doi:10.1145/2582112.2582168","short":"U. Bauer, M. Lesnick, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–364.","ieee":"U. Bauer and M. Lesnick, “Induced matchings of barcodes and the algebraic stability of persistence,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 355–364.","mla":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–64, doi:10.1145/2582112.2582168."},"date_updated":"2021-01-12T06:55:38Z","status":"public","project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"type":"conference","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2014-06-08","end_date":"2014-06-11","location":"Kyoto, Japan"},"_id":"2153"},{"status":"public","type":"journal_article","_id":"2154","department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:55:38Z","month":"07","intvolume":" 52","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1102.3515"}],"oa_version":"Submitted Version","abstract":[{"text":"A result of Boros and Füredi (d = 2) and of Bárány (arbitrary d) asserts that for every d there exists cd > 0 such that for every n-point set P ⊂ ℝd, some point of ℝd is covered by at least (Formula presented.) of the d-simplices spanned by the points of P. The largest possible value of cd has been the subject of ongoing research. Recently Gromov improved the existing lower bounds considerably by introducing a new, topological proof method. We provide an exposition of the combinatorial component of Gromov's approach, in terms accessible to combinatorialists and discrete geometers, and we investigate the limits of his method. In particular, we give tighter bounds on the cofilling profiles for the (n - 1)-simplex. These bounds yield a minor improvement over Gromov's lower bounds on cd for large d, but they also show that the room for further improvement through the cofilling profiles alone is quite small. We also prove a slightly better lower bound for c3 by an approach using an additional structure besides the cofilling profiles. We formulate a combinatorial extremal problem whose solution might perhaps lead to a tight lower bound for cd.","lang":"eng"}],"issue":"1","volume":52,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425"}],"title":"On Gromov's method of selecting heavily covered points","author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"publist_id":"4852","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Matoušek J, Wagner U. 2014. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 52(1), 1–33.","chicago":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9584-7.","short":"J. Matoušek, U. Wagner, Discrete & Computational Geometry 52 (2014) 1–33.","ieee":"J. Matoušek and U. Wagner, “On Gromov’s method of selecting heavily covered points,” Discrete & Computational Geometry, vol. 52, no. 1. Springer, pp. 1–33, 2014.","apa":"Matoušek, J., & Wagner, U. (2014). On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9584-7","ama":"Matoušek J, Wagner U. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 2014;52(1):1-33. doi:10.1007/s00454-014-9584-7","mla":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry, vol. 52, no. 1, Springer, 2014, pp. 1–33, doi:10.1007/s00454-014-9584-7."},"quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Swiss National Science Foundation (SNF 200021-125309, 200020-138230, 200020-12507)","doi":"10.1007/s00454-014-9584-7","date_published":"2014-07-01T00:00:00Z","date_created":"2018-12-11T11:56:01Z","page":"1 - 33","day":"01","publication":"Discrete & Computational Geometry","year":"2014"},{"abstract":[{"lang":"eng","text":"We propose a metric for Reeb graphs, called the functional distortion distance. Under this distance, the Reeb graph is stable against small changes of input functions. At the same time, it remains discriminative at differentiating input functions. In particular, the main result is that the functional distortion distance between two Reeb graphs is bounded from below by the bottleneck distance between both the ordinary and extended persistence diagrams for appropriate dimensions. As an application of our results, we analyze a natural simplification scheme for Reeb graphs, and show that persistent features in Reeb graph remains persistent under simplification. Understanding the stability of important features of the Reeb graph under simplification is an interesting problem on its own right, and critical to the practical usage of Reeb graphs. Copyright is held by the owner/author(s)."}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1307.2839","open_access":"1"}],"scopus_import":1,"month":"06","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"_id":"2156","conference":{"start_date":"2014-06-08","end_date":"2014-06-11","location":"Kyoto, Japan","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","date_updated":"2021-01-12T06:55:39Z","department":[{"_id":"HeEd"}],"acknowledgement":"National Science Foundation under grants CCF-1319406, CCF-1116258.","oa":1,"publisher":"ACM","quality_controlled":"1","year":"2014","publication":"Proceedings of the Annual Symposium on Computational Geometry","day":"01","page":"464 - 473","date_created":"2018-12-11T11:56:02Z","date_published":"2014-06-01T00:00:00Z","doi":"10.1145/2582112.2582169","project":[{"grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"chicago":"Bauer, Ulrich, Xiaoyin Ge, and Yusu Wang. “Measuring Distance between Reeb Graphs.” In Proceedings of the Annual Symposium on Computational Geometry, 464–73. ACM, 2014. https://doi.org/10.1145/2582112.2582169.","ista":"Bauer U, Ge X, Wang Y. 2014. Measuring distance between Reeb graphs. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 464–473.","mla":"Bauer, Ulrich, et al. “Measuring Distance between Reeb Graphs.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–73, doi:10.1145/2582112.2582169.","short":"U. Bauer, X. Ge, Y. Wang, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–473.","ieee":"U. Bauer, X. Ge, and Y. Wang, “Measuring distance between Reeb graphs,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 464–473.","apa":"Bauer, U., Ge, X., & Wang, Y. (2014). Measuring distance between Reeb graphs. In Proceedings of the Annual Symposium on Computational Geometry (pp. 464–473). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582169","ama":"Bauer U, Ge X, Wang Y. Measuring distance between Reeb graphs. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:464-473. doi:10.1145/2582112.2582169"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bauer","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"last_name":"Ge","full_name":"Ge, Xiaoyin","first_name":"Xiaoyin"},{"last_name":"Wang","full_name":"Wang, Yusu","first_name":"Yusu"}],"publist_id":"4850","title":"Measuring distance between Reeb graphs"},{"page":"484 - 490","date_created":"2018-12-11T11:56:01Z","doi":"10.1145/2582112.2582167","date_published":"2014-06-01T00:00:00Z","year":"2014","publication":"Proceedings of the Annual Symposium on Computational Geometry","day":"01","oa":1,"publisher":"ACM","quality_controlled":"1","acknowledgement":"This research is partially supported by ESF under the ACAT Research Network Programme, and by the Russian Government under mega project 11.G34.31.0053","author":[{"last_name":"Bauer","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4851","title":"The morse theory of Čech and Delaunay filtrations","citation":{"chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” In Proceedings of the Annual Symposium on Computational Geometry, 484–90. ACM, 2014. https://doi.org/10.1145/2582112.2582167.","ista":"Bauer U, Edelsbrunner H. 2014. The morse theory of Čech and Delaunay filtrations. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 484–490.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–90, doi:10.1145/2582112.2582167.","ama":"Bauer U, Edelsbrunner H. The morse theory of Čech and Delaunay filtrations. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:484-490. doi:10.1145/2582112.2582167","apa":"Bauer, U., & Edelsbrunner, H. (2014). The morse theory of Čech and Delaunay filtrations. In Proceedings of the Annual Symposium on Computational Geometry (pp. 484–490). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582167","ieee":"U. Bauer and H. Edelsbrunner, “The morse theory of Čech and Delaunay filtrations,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 484–490.","short":"U. Bauer, H. Edelsbrunner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–490."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.1231"}],"scopus_import":1,"month":"06","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a positive radius, we study the Čech, Delaunay-Čech, alpha, and wrap complexes as instances of a generalized discrete Morse theory. We prove that the latter three complexes are simple-homotopy equivalent. Our results have applications in topological data analysis and in the reconstruction of shapes from sampled data. Copyright is held by the owner/author(s)."}],"oa_version":"Submitted Version","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:55:38Z","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2014-06-08","end_date":"2014-06-11","location":"Kyoto, Japan"},"type":"conference","status":"public","_id":"2155"},{"citation":{"ama":"Majumdar R, Sixt MK, Parent C. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 2014;30(1):33-40. doi:10.1016/j.ceb.2014.05.010","apa":"Majumdar, R., Sixt, M. K., & Parent, C. (2014). New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2014.05.010","short":"R. Majumdar, M.K. Sixt, C. Parent, Current Opinion in Cell Biology 30 (2014) 33–40.","ieee":"R. Majumdar, M. K. Sixt, and C. Parent, “New paradigms in the establishment and maintenance of gradients during directed cell migration,” Current Opinion in Cell Biology, vol. 30, no. 1. Elsevier, pp. 33–40, 2014.","mla":"Majumdar, Ritankar, et al. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology, vol. 30, no. 1, Elsevier, 2014, pp. 33–40, doi:10.1016/j.ceb.2014.05.010.","ista":"Majumdar R, Sixt MK, Parent C. 2014. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 30(1), 33–40.","chicago":"Majumdar, Ritankar, Michael K Sixt, and Carole Parent. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology. Elsevier, 2014. https://doi.org/10.1016/j.ceb.2014.05.010."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"4848","author":[{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"full_name":"Parent, Carole","last_name":"Parent","first_name":"Carole"}],"external_id":{"pmid":["24959970"]},"title":"New paradigms in the establishment and maintenance of gradients during directed cell migration","acknowledgement":"This effort was supported by the Intramural Research Program of the Center for Cancer Research, NCI, National Institutes of Health and the European Research Council (ERC).","publisher":"Elsevier","quality_controlled":"1","oa":1,"year":"2014","day":"01","publication":"Current Opinion in Cell Biology","page":"33 - 40","doi":"10.1016/j.ceb.2014.05.010","date_published":"2014-10-01T00:00:00Z","date_created":"2018-12-11T11:56:03Z","_id":"2158","type":"journal_article","status":"public","date_updated":"2021-01-12T06:55:40Z","department":[{"_id":"MiSi"}],"abstract":[{"text":"Directional guidance of migrating cells is relatively well explored in the reductionist setting of cell culture experiments. Here spatial gradients of chemical cues as well as gradients of mechanical substrate characteristics prove sufficient to attract single cells as well as their collectives. How such gradients present and act in the context of an organism is far less clear. Here we review recent advances in understanding how guidance cues emerge and operate in the physiological context.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177954/","open_access":"1"}],"month":"10","intvolume":" 30","publication_status":"published","language":[{"iso":"eng"}],"volume":30,"issue":"1"},{"title":"Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling","publist_id":"4819","author":[{"orcid":"0000-0002-8301-7240","full_name":"Morvant, Emilie","last_name":"Morvant","first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87"}],"extern":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Morvant E. 2014. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 51, 37–43.","chicago":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters. Elsevier, 2014. https://doi.org/10.1016/j.patrec.2014.08.013.","apa":"Morvant, E. (2014). Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2014.08.013","ama":"Morvant E. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 2014;51:37-43. doi:10.1016/j.patrec.2014.08.013","ieee":"E. Morvant, “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling,” Pattern Recognition Letters, vol. 51. Elsevier, pp. 37–43, 2014.","short":"E. Morvant, Pattern Recognition Letters 51 (2014) 37–43.","mla":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters, vol. 51, Elsevier, 2014, pp. 37–43, doi:10.1016/j.patrec.2014.08.013."},"date_updated":"2021-01-12T06:55:43Z","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"journal_article","_id":"2165","volume":51,"date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.patrec.2014.08.013","date_created":"2018-12-11T11:56:05Z","ec_funded":1,"page":"37-43","day":"01","language":[{"iso":"eng"}],"publication":"Pattern Recognition Letters","publication_status":"published","year":"2014","month":"10","intvolume":" 51","publisher":"Elsevier","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.0334","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In machine learning, the domain adaptation problem arrives when the test (tar-get) and the train (source) data are generated from different distributions. A key applied issue is thus the design of algorithms able to generalize on a new distribution, for which we have no label information. We focus on learning classification models defined as a weighted majority vote over a set of real-valued functions. In this context, Germain et al. (2013) have shown that a measure of disagreement between these functions is crucial to control. The core of this measure is a theoretical bound—the C-bound (Lacasse et al., 2007)—which involves the disagreement and leads to a well performing majority vote learn-ing algorithm in usual non-adaptative supervised setting: MinCq. In this work,we propose a framework to extend MinCq to a domain adaptation scenario.This procedure takes advantage of the recent perturbed variation divergence between distributions proposed by Harel and Mannor (2012). Justified by a theoretical bound on the target risk of the vote, we provide to MinCq a tar-get sample labeled thanks to a perturbed variation-based self-labeling focused on the regions where the source and target marginals appear similar. We also study the influence of our self-labeling, from which we deduce an original process for tuning the hyperparameters. Finally, our framework called PV-MinCq shows very promising results on a rotation and translation synthetic problem."}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chai, Xuejun, Gert Münzner, Shanting Zhao, Stefanie Tinnes, Janina Kowalski, Ute Häussler, Christina Young, Carola Haas, and Michael Frotscher. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex. Oxford University Press, 2014. https://doi.org/10.1093/cercor/bht067.","ista":"Chai X, Münzner G, Zhao S, Tinnes S, Kowalski J, Häussler U, Young C, Haas C, Frotscher M. 2014. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 24(8), 2130–2140.","mla":"Chai, Xuejun, et al. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex, vol. 24, no. 8, Oxford University Press, 2014, pp. 2130–40, doi:10.1093/cercor/bht067.","apa":"Chai, X., Münzner, G., Zhao, S., Tinnes, S., Kowalski, J., Häussler, U., … Frotscher, M. (2014). Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bht067","ama":"Chai X, Münzner G, Zhao S, et al. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 2014;24(8):2130-2140. doi:10.1093/cercor/bht067","ieee":"X. Chai et al., “Epilepsy-induced motility of differentiated neurons,” Cerebral Cortex, vol. 24, no. 8. Oxford University Press, pp. 2130–2140, 2014.","short":"X. Chai, G. Münzner, S. Zhao, S. Tinnes, J. Kowalski, U. Häussler, C. Young, C. Haas, M. Frotscher, Cerebral Cortex 24 (2014) 2130–2140."},"date_updated":"2021-01-12T06:55:43Z","department":[{"_id":"PeJo"}],"title":"Epilepsy-induced motility of differentiated neurons","author":[{"first_name":"Xuejun","last_name":"Chai","full_name":"Chai, Xuejun"},{"first_name":"Gert","last_name":"Münzner","full_name":"Münzner, Gert"},{"first_name":"Shanting","last_name":"Zhao","full_name":"Zhao, Shanting"},{"first_name":"Stefanie","last_name":"Tinnes","full_name":"Tinnes, Stefanie"},{"id":"3F3CA136-F248-11E8-B48F-1D18A9856A87","first_name":"Janina","last_name":"Kowalski","full_name":"Kowalski, Janina"},{"first_name":"Ute","full_name":"Häussler, Ute","last_name":"Häussler"},{"full_name":"Young, Christina","last_name":"Young","first_name":"Christina"},{"first_name":"Carola","full_name":"Haas, Carola","last_name":"Haas"},{"full_name":"Frotscher, Michael","last_name":"Frotscher","first_name":"Michael"}],"publist_id":"4820","_id":"2164","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication":"Cerebral Cortex","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:56:04Z","date_published":"2014-08-01T00:00:00Z","doi":"10.1093/cercor/bht067","issue":"8","volume":24,"page":"2130 - 2140","oa_version":"None","abstract":[{"lang":"eng","text":"Neuronal ectopia, such as granule cell dispersion (GCD) in temporal lobe epilepsy (TLE), has been assumed to result from a migration defect during development. Indeed, recent studies reported that aberrant migration of neonatal-generated dentate granule cells (GCs) increased the risk to develop epilepsy later in life. On the contrary, in the present study, we show that fully differentiated GCs become motile following the induction of epileptiform activity, resulting in GCD. Hippocampal slice cultures from transgenic mice expressing green fluorescent protein in differentiated, but not in newly generated GCs, were incubated with the glutamate receptor agonist kainate (KA), which induced GC burst activity and GCD. Using real-time microscopy, we observed that KA-exposed, differentiated GCs translocated their cell bodies and changed their dendritic organization. As found in human TLE, KA application was associated with decreased expression of the extracellular matrix protein Reelin, particularly in hilar interneurons. Together these findings suggest that KA-induced motility of differentiated GCs contributes to the development of GCD and establish slice cultures as a model to study neuronal changes induced by epileptiform activity. "}],"intvolume":" 24","month":"08","quality_controlled":"1","publisher":"Oxford University Press","scopus_import":1},{"intvolume":" 95","month":"08","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail."}],"ec_funded":1,"volume":95,"language":[{"iso":"eng"}],"file":[{"checksum":"979d7a8034e9df198f068f0d251f31bd","file_id":"4839","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:49Z","file_name":"IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf","date_updated":"2020-07-14T12:45:31Z","file_size":569005,"creator":"system"}],"publication_status":"published","pubrep_id":"391","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"2168","file_date_updated":"2020-07-14T12:45:31Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2021-01-12T06:55:44Z","oa":1,"quality_controlled":"1","publisher":"Academic Press","date_created":"2018-12-11T11:56:06Z","doi":"10.1016/j.tpb.2014.05.001","date_published":"2014-08-01T00:00:00Z","page":"13 - 23","publication":"Theoretical Population Biology","day":"01","year":"2014","has_accepted_license":"1","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"title":"Coalescent simulation in continuous space: Algorithms for large neighbourhood size","publist_id":"4816","author":[{"first_name":"Jerome","full_name":"Kelleher, Jerome","last_name":"Kelleher"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23.","ieee":"J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” Theoretical Population Biology, vol. 95. Academic Press, pp. 13–23, 2014.","apa":"Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001","ama":"Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 2014;95:13-23. doi:10.1016/j.tpb.2014.05.001","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95, Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001.","ista":"Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.","chicago":"Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001."}},{"oa_version":"Submitted Version","scopus_import":1,"publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/"}],"month":"07","intvolume":" 111","year":"2014","publication_status":"published","day":"22","language":[{"iso":"eng"}],"publication":"PNAS","page":"10398 - 10399","date_published":"2014-07-22T00:00:00Z","issue":"29","doi":"10.1073/pnas.1410107111","volume":111,"date_created":"2018-12-11T11:56:07Z","_id":"2169","type":"journal_article","status":"public","citation":{"chicago":"Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410107111.","ista":"Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.","mla":"Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111.","short":"N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.","ieee":"N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014.","apa":"Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1410107111","ama":"Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111"},"date_updated":"2021-01-12T06:55:45Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4815","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"department":[{"_id":"NiBa"}],"title":"Diverse forms of selection in evolution and computer science"},{"title":"Closed-form approximate CRF training for scalable image segmentation","editor":[{"last_name":"Fleet","full_name":"Fleet, David","first_name":"David"},{"last_name":"Pajdla","full_name":"Pajdla, Tomas","first_name":"Tomas"},{"full_name":"Schiele, Bernt","last_name":"Schiele","first_name":"Bernt"},{"last_name":"Tuytelaars","full_name":"Tuytelaars, Tinne","first_name":"Tinne"}],"publist_id":"4813","author":[{"full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander"},{"last_name":"Guillaumin","full_name":"Guillaumin, Matthieu","first_name":"Matthieu"},{"last_name":"Ferrari","full_name":"Ferrari, Vittorio","first_name":"Vittorio"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kolesnikov, Alexander, Matthieu Guillaumin, Vittorio Ferrari, and Christoph Lampert. “Closed-Form Approximate CRF Training for Scalable Image Segmentation.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by David Fleet, Tomas Pajdla, Bernt Schiele, and Tinne Tuytelaars, 8691:550–65. Springer, 2014. https://doi.org/10.1007/978-3-319-10578-9_36.","ista":"Kolesnikov A, Guillaumin M, Ferrari V, Lampert C. 2014. Closed-form approximate CRF training for scalable image segmentation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ECCV: European Conference on Computer Vision, LNCS, vol. 8691, 550–565.","mla":"Kolesnikov, Alexander, et al. “Closed-Form Approximate CRF Training for Scalable Image Segmentation.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by David Fleet et al., vol. 8691, no. PART 3, Springer, 2014, pp. 550–65, doi:10.1007/978-3-319-10578-9_36.","ieee":"A. Kolesnikov, M. Guillaumin, V. Ferrari, and C. Lampert, “Closed-form approximate CRF training for scalable image segmentation,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Zurich, Switzerland, 2014, vol. 8691, no. PART 3, pp. 550–565.","short":"A. Kolesnikov, M. Guillaumin, V. Ferrari, C. Lampert, in:, D. Fleet, T. Pajdla, B. Schiele, T. Tuytelaars (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 550–565.","ama":"Kolesnikov A, Guillaumin M, Ferrari V, Lampert C. Closed-form approximate CRF training for scalable image segmentation. In: Fleet D, Pajdla T, Schiele B, Tuytelaars T, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8691. Springer; 2014:550-565. doi:10.1007/978-3-319-10578-9_36","apa":"Kolesnikov, A., Guillaumin, M., Ferrari, V., & Lampert, C. (2014). Closed-form approximate CRF training for scalable image segmentation. In D. Fleet, T. Pajdla, B. Schiele, & T. Tuytelaars (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8691, pp. 550–565). Zurich, Switzerland: Springer. https://doi.org/10.1007/978-3-319-10578-9_36"},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"date_created":"2018-12-11T11:56:07Z","doi":"10.1007/978-3-319-10578-9_36","date_published":"2014-09-01T00:00:00Z","page":"550 - 565","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","year":"2014","oa":1,"quality_controlled":"1","publisher":"Springer","department":[{"_id":"ChLa"}],"date_updated":"2021-01-12T06:55:46Z","status":"public","conference":{"name":"ECCV: European Conference on Computer Vision","location":"Zurich, Switzerland","end_date":"2014-09-12","start_date":"2014-09-06"},"type":"conference","_id":"2171","ec_funded":1,"volume":8691,"issue":"PART 3","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 8691","month":"09","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1403.7057"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"We present LS-CRF, a new method for training cyclic Conditional Random Fields (CRFs) from large datasets that is inspired by classical closed-form expressions for the maximum likelihood parameters of a generative graphical model with tree topology. Training a CRF with LS-CRF requires only solving a set of independent regression problems, each of which can be solved efficiently in closed form or by an iterative solver. This makes LS-CRF orders of magnitude faster than classical CRF training based on probabilistic inference, and at the same time more flexible and easier to implement than other approximate techniques, such as pseudolikelihood or piecewise training. We apply LS-CRF to the task of semantic image segmentation, showing that it achieves on par accuracy to other training techniques at higher speed, thereby allowing efficient CRF training from very large training sets. For example, training a linearly parameterized pairwise CRF on 150,000 images requires less than one hour on a modern workstation.","lang":"eng"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this work we introduce a new approach to co-classification, i.e. the task of jointly classifying multiple, otherwise independent, data samples. The method we present, named CoConut, is based on the idea of adding a regularizer in the label space to encode certain priors on the resulting labelings. A regularizer that encourages labelings that are smooth across the test set, for instance, can be seen as a test-time variant of the cluster assumption, which has been proven useful at training time in semi-supervised learning. A regularizer that introduces a preference for certain class proportions can be regarded as a prior distribution on the class labels. CoConut can build on existing classifiers without making any assumptions on how they were obtained and without the need to re-train them. The use of a regularizer adds a new level of flexibility. It allows the integration of potentially new information at test time, even in other modalities than what the classifiers were trained on. We evaluate our framework on six datasets, reporting a clear performance gain in classification accuracy compared to the standard classification setup that predicts labels for each test sample separately.\r\n"}],"month":"09","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-490-v1+1_khamis-bmvc2014.pdf","date_created":"2018-12-12T10:08:23Z","creator":"system","file_size":408172,"date_updated":"2020-07-14T12:45:31Z","checksum":"c4c6d3efdb8ee648faf3e76849839ce2","file_id":"4683","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","ec_funded":1,"_id":"2173","pubrep_id":"490","status":"public","conference":{"name":"BMVC: British Machine Vision Conference","start_date":"2014-09-01","location":"Nottingham, UK","end_date":"2014-09-05"},"type":"conference","ddc":["000"],"date_updated":"2021-01-12T06:55:46Z","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:45:31Z","oa":1,"publisher":"BMVA Press","quality_controlled":"1","publication":"Proceedings of the British Machine Vision Conference 2014","day":"01","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:56:08Z","date_published":"2014-09-01T00:00:00Z","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Khamis S, Lampert C. 2014. CoConut: Co-classification with output space regularization. Proceedings of the British Machine Vision Conference 2014. BMVC: British Machine Vision Conference.","chicago":"Khamis, Sameh, and Christoph Lampert. “CoConut: Co-Classification with Output Space Regularization.” In Proceedings of the British Machine Vision Conference 2014. BMVA Press, 2014.","ama":"Khamis S, Lampert C. CoConut: Co-classification with output space regularization. In: Proceedings of the British Machine Vision Conference 2014. BMVA Press; 2014.","apa":"Khamis, S., & Lampert, C. (2014). CoConut: Co-classification with output space regularization. In Proceedings of the British Machine Vision Conference 2014. Nottingham, UK: BMVA Press.","short":"S. Khamis, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2014, BMVA Press, 2014.","ieee":"S. Khamis and C. Lampert, “CoConut: Co-classification with output space regularization,” in Proceedings of the British Machine Vision Conference 2014, Nottingham, UK, 2014.","mla":"Khamis, Sameh, and Christoph Lampert. “CoConut: Co-Classification with Output Space Regularization.” Proceedings of the British Machine Vision Conference 2014, BMVA Press, 2014."},"title":"CoConut: Co-classification with output space regularization","publist_id":"4811","author":[{"first_name":"Sameh","full_name":"Khamis, Sameh","last_name":"Khamis"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}]},{"abstract":[{"text":"Fisher Kernels and Deep Learning were two developments with significant impact on large-scale object categorization in the last years. Both approaches were shown to achieve state-of-the-art results on large-scale object categorization datasets, such as ImageNet. Conceptually, however, they are perceived as very different and it is not uncommon for heated debates to spring up when advocates of both paradigms meet at conferences or workshops. In this work, we emphasize the similarities between both architectures rather than their differences and we argue that such a unified view allows us to transfer ideas from one domain to the other. As a concrete example we introduce a method for learning a support vector machine classifier with Fisher kernel at the same time as a task-specific data representation. We reinterpret the setting as a multi-layer feed forward network. Its final layer is the classifier, parameterized by a weight vector, and the two previous layers compute Fisher vectors, parameterized by the coefficients of a Gaussian mixture model. We introduce a gradient descent based learning algorithm that, in contrast to other feature learning techniques, is not just derived from intuition or biological analogy, but has a theoretical justification in the framework of statistical learning theory. Our experiments show that the new training procedure leads to significant improvements in classification accuracy while preserving the modularity and geometric interpretability of a support vector machine setup.","lang":"eng"}],"oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"IEEE","month":"09","year":"2014","publication_status":"published","day":"24","language":[{"iso":"eng"}],"publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","page":"1402 - 1409","date_published":"2014-09-24T00:00:00Z","doi":"10.1109/CVPR.2014.182","date_created":"2018-12-11T11:56:08Z","ec_funded":1,"_id":"2172","type":"conference","conference":{"location":"Columbus, USA","end_date":"2014-06-28","start_date":"2014-06-23","name":"CVPR: Computer Vision and Pattern Recognition"},"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","date_updated":"2021-01-12T06:55:46Z","citation":{"ama":"Sydorov V, Sakurada M, Lampert C. Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE; 2014:1402-1409. doi:10.1109/CVPR.2014.182","apa":"Sydorov, V., Sakurada, M., & Lampert, C. (2014). Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (pp. 1402–1409). Columbus, USA: IEEE. https://doi.org/10.1109/CVPR.2014.182","short":"V. Sydorov, M. Sakurada, C. Lampert, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2014, pp. 1402–1409.","ieee":"V. Sydorov, M. Sakurada, and C. Lampert, “Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Columbus, USA, 2014, pp. 1402–1409.","mla":"Sydorov, Vladyslav, et al. “Deep Fisher Kernels – End to End Learning of the Fisher Kernel GMM Parameters.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2014, pp. 1402–09, doi:10.1109/CVPR.2014.182.","ista":"Sydorov V, Sakurada M, Lampert C. 2014. Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Computer Vision and Pattern Recognition, 1402–1409.","chicago":"Sydorov, Vladyslav, Mayu Sakurada, and Christoph Lampert. “Deep Fisher Kernels – End to End Learning of the Fisher Kernel GMM Parameters.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1402–9. IEEE, 2014. https://doi.org/10.1109/CVPR.2014.182."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4812","author":[{"full_name":"Sydorov, Vladyslav","last_name":"Sydorov","first_name":"Vladyslav"},{"last_name":"Sakurada","full_name":"Sakurada, Mayu","first_name":"Mayu"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"department":[{"_id":"ChLa"}],"title":"Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters"},{"volume":197,"issue":"2","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.1017"}],"month":"06","intvolume":" 197","abstract":[{"text":"When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The inpplayfi between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find p the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:55:47Z","type":"journal_article","status":"public","_id":"2174","page":"749 - 767","date_published":"2014-06-01T00:00:00Z","doi":"10.1534/genetics.113.159111","date_created":"2018-12-11T11:56:08Z","year":"2014","day":"01","publication":"Genetics","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"publist_id":"4809","author":[{"full_name":"De Vladar, Harold","last_name":"De Vladar","first_name":"Harold"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"title":"Stability and response of polygenic traits to stabilizing selection and mutation","citation":{"ieee":"H. De Vladar and N. H. Barton, “Stability and response of polygenic traits to stabilizing selection and mutation,” Genetics, vol. 197, no. 2. Genetics Society of America, pp. 749–767, 2014.","short":"H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.","apa":"De Vladar, H., & Barton, N. H. (2014). Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.159111","ama":"De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 2014;197(2):749-767. doi:10.1534/genetics.113.159111","mla":"De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics, vol. 197, no. 2, Genetics Society of America, 2014, pp. 749–67, doi:10.1534/genetics.113.159111.","ista":"De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 197(2), 749–767.","chicago":"De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.159111."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}]},{"oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","date_created":"2018-12-11T11:56:10Z","date_published":"2014-06-09T00:00:00Z","doi":"10.1214/ECP.v19-3121","publication":"Electronic Communications in Probability","day":"09","year":"2014","has_accepted_license":"1","title":"Local semicircle law with imprimitive variance matrix","author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4803","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local semicircle law with imprimitive variance matrix,” Electronic Communications in Probability, vol. 19. Institute of Mathematical Statistics, 2014.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Electronic Communications in Probability 19 (2014).","ama":"Ajanki OH, Erdös L, Krüger TH. Local semicircle law with imprimitive variance matrix. Electronic Communications in Probability. 2014;19. doi:10.1214/ECP.v19-3121","apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2014). Local semicircle law with imprimitive variance matrix. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v19-3121","mla":"Ajanki, Oskari H., et al. “Local Semicircle Law with Imprimitive Variance Matrix.” Electronic Communications in Probability, vol. 19, Institute of Mathematical Statistics, 2014, doi:10.1214/ECP.v19-3121.","ista":"Ajanki OH, Erdös L, Krüger TH. 2014. Local semicircle law with imprimitive variance matrix. Electronic Communications in Probability. 19.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Semicircle Law with Imprimitive Variance Matrix.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2014. https://doi.org/10.1214/ECP.v19-3121."},"intvolume":" 19","month":"06","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"We extend the proof of the local semicircle law for generalized Wigner matrices given in MR3068390 to the case when the matrix of variances has an eigenvalue -1. In particular, this result provides a short proof of the optimal local Marchenko-Pastur law at the hard edge (i.e. around zero) for sample covariance matrices X*X, where the variances of the entries of X may vary.","lang":"eng"}],"volume":19,"language":[{"iso":"eng"}],"file":[{"file_id":"4729","checksum":"bd8a041c76d62fe820bf73ff13ce7d1b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-426-v1+1_3121-17518-1-PB.pdf","date_created":"2018-12-12T10:09:06Z","creator":"system","file_size":327322,"date_updated":"2020-07-14T12:45:31Z"}],"publication_status":"published","pubrep_id":"426","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"2179","file_date_updated":"2020-07-14T12:45:31Z","department":[{"_id":"LaEr"}],"ddc":["570"],"date_updated":"2021-01-12T06:55:48Z"},{"_id":"2176","type":"journal_article","status":"public","project":[{"grant_number":"SFB-TR3-TP10B","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Studer, Daniel, et al. “Capture of Activity-Induced Ultrastructural Changes at Synapses by High-Pressure Freezing of Brain Tissue.” Nature Protocols, vol. 9, no. 6, Nature Publishing Group, 2014, pp. 1480–95, doi:10.1038/nprot.2014.099.","ieee":"D. Studer et al., “Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue,” Nature Protocols, vol. 9, no. 6. Nature Publishing Group, pp. 1480–1495, 2014.","short":"D. Studer, S. Zhao, X. Chai, P.M. Jonas, W. Graber, S. Nestel, M. Frotscher, Nature Protocols 9 (2014) 1480–1495.","ama":"Studer D, Zhao S, Chai X, et al. Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue. Nature Protocols. 2014;9(6):1480-1495. doi:10.1038/nprot.2014.099","apa":"Studer, D., Zhao, S., Chai, X., Jonas, P. M., Graber, W., Nestel, S., & Frotscher, M. (2014). Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2014.099","chicago":"Studer, Daniel, Shanting Zhao, Xuejun Chai, Peter M Jonas, Werner Graber, Sigrun Nestel, and Michael Frotscher. “Capture of Activity-Induced Ultrastructural Changes at Synapses by High-Pressure Freezing of Brain Tissue.” Nature Protocols. Nature Publishing Group, 2014. https://doi.org/10.1038/nprot.2014.099.","ista":"Studer D, Zhao S, Chai X, Jonas PM, Graber W, Nestel S, Frotscher M. 2014. Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue. Nature Protocols. 9(6), 1480–1495."},"date_updated":"2021-01-12T06:55:47Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4807","author":[{"full_name":"Studer, Daniel","last_name":"Studer","first_name":"Daniel"},{"full_name":"Zhao, Shanting","last_name":"Zhao","first_name":"Shanting"},{"last_name":"Chai","full_name":"Chai, Xuejun","first_name":"Xuejun"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Werner","full_name":"Graber, Werner","last_name":"Graber"},{"last_name":"Nestel","full_name":"Nestel, Sigrun","first_name":"Sigrun"},{"first_name":"Michael","last_name":"Frotscher","full_name":"Frotscher, Michael"}],"department":[{"_id":"PeJo"}],"title":"Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue","abstract":[{"lang":"eng","text":"Electron microscopy (EM) allows for the simultaneous visualization of all tissue components at high resolution. However, the extent to which conventional aldehyde fixation and ethanol dehydration of the tissue alter the fine structure of cells and organelles, thereby preventing detection of subtle structural changes induced by an experiment, has remained an issue. Attempts have been made to rapidly freeze tissue to preserve native ultrastructure. Shock-freezing of living tissue under high pressure (high-pressure freezing, HPF) followed by cryosubstitution of the tissue water avoids aldehyde fixation and dehydration in ethanol; the tissue water is immobilized in â ̂1/450 ms, and a close-to-native fine structure of cells, organelles and molecules is preserved. Here we describe a protocol for HPF that is useful to monitor ultrastructural changes associated with functional changes at synapses in the brain but can be applied to many other tissues as well. The procedure requires a high-pressure freezer and takes a minimum of 7 d but can be paused at several points."}],"oa_version":"None","quality_controlled":"1","publisher":"Nature Publishing Group","scopus_import":1,"intvolume":" 9","month":"05","publication_status":"published","year":"2014","publication":"Nature Protocols","language":[{"iso":"eng"}],"day":"29","page":"1480 - 1495","date_created":"2018-12-11T11:56:09Z","date_published":"2014-05-29T00:00:00Z","volume":9,"issue":"6","doi":"10.1038/nprot.2014.099"},{"intvolume":" 55","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1204.3070"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We consider the three-state toric homogeneous Markov chain model (THMC) without loops and initial parameters. At time T, the size of the design matrix is 6 × 3 · 2T-1 and the convex hull of its columns is the model polytope. We study the behavior of this polytope for T ≥ 3 and we show that it is defined by 24 facets for all T ≥ 5. Moreover, we give a complete description of these facets. From this, we deduce that the toric ideal associated with the design matrix is generated by binomials of degree at most 6. Our proof is based on a result due to Sturmfels, who gave a bound on the degree of the generators of a toric ideal, provided the normality of the corresponding toric variety. In our setting, we established the normality of the toric variety associated to the THMC model by studying the geometric properties of the model polytope."}],"volume":55,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"2178","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:55:48Z","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"Research of Martín del Campo supported in part by NSF Grant DMS-915211.","date_created":"2018-12-11T11:56:10Z","date_published":"2014-03-01T00:00:00Z","doi":"10.1007/s13366-013-0178-y","page":"161 - 188","publication":"Beitrage zur Algebra und Geometrie","day":"01","year":"2014","title":"Markov degree of the three-state toric homogeneous Markov chain model","publist_id":"4804","author":[{"first_name":"David","full_name":"Haws, David","last_name":"Haws"},{"id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez"},{"first_name":"Akimichi","last_name":"Takemura","full_name":"Takemura, Akimichi"},{"first_name":"Ruriko","full_name":"Yoshida, Ruriko","last_name":"Yoshida"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"D. Haws, A. Martin del Campo Sanchez, A. Takemura, R. Yoshida, Beitrage Zur Algebra Und Geometrie 55 (2014) 161–188.","ieee":"D. Haws, A. Martin del Campo Sanchez, A. Takemura, and R. Yoshida, “Markov degree of the three-state toric homogeneous Markov chain model,” Beitrage zur Algebra und Geometrie, vol. 55, no. 1. Springer, pp. 161–188, 2014.","ama":"Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. Markov degree of the three-state toric homogeneous Markov chain model. Beitrage zur Algebra und Geometrie. 2014;55(1):161-188. doi:10.1007/s13366-013-0178-y","apa":"Haws, D., Martin del Campo Sanchez, A., Takemura, A., & Yoshida, R. (2014). Markov degree of the three-state toric homogeneous Markov chain model. Beitrage Zur Algebra Und Geometrie. Springer. https://doi.org/10.1007/s13366-013-0178-y","mla":"Haws, David, et al. “Markov Degree of the Three-State Toric Homogeneous Markov Chain Model.” Beitrage Zur Algebra Und Geometrie, vol. 55, no. 1, Springer, 2014, pp. 161–88, doi:10.1007/s13366-013-0178-y.","ista":"Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. 2014. Markov degree of the three-state toric homogeneous Markov chain model. Beitrage zur Algebra und Geometrie. 55(1), 161–188.","chicago":"Haws, David, Abraham Martin del Campo Sanchez, Akimichi Takemura, and Ruriko Yoshida. “Markov Degree of the Three-State Toric Homogeneous Markov Chain Model.” Beitrage Zur Algebra Und Geometrie. Springer, 2014. https://doi.org/10.1007/s13366-013-0178-y."}},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:48Z","citation":{"mla":"Edelsbrunner, Herbert, and Salman Parsa. “On the Computational Complexity of Betti Numbers Reductions from Matrix Rank.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2014, pp. 152–60, doi:10.1137/1.9781611973402.11.","ama":"Edelsbrunner H, Parsa S. On the computational complexity of betti numbers reductions from matrix rank. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SIAM; 2014:152-160. doi:10.1137/1.9781611973402.11","apa":"Edelsbrunner, H., & Parsa, S. (2014). On the computational complexity of betti numbers reductions from matrix rank. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 152–160). Portland, USA: SIAM. https://doi.org/10.1137/1.9781611973402.11","short":"H. Edelsbrunner, S. Parsa, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2014, pp. 152–160.","ieee":"H. Edelsbrunner and S. Parsa, “On the computational complexity of betti numbers reductions from matrix rank,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Portland, USA, 2014, pp. 152–160.","chicago":"Edelsbrunner, Herbert, and Salman Parsa. “On the Computational Complexity of Betti Numbers Reductions from Matrix Rank.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 152–60. SIAM, 2014. https://doi.org/10.1137/1.9781611973402.11.","ista":"Edelsbrunner H, Parsa S. 2014. On the computational complexity of betti numbers reductions from matrix rank. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 152–160."},"title":"On the computational complexity of betti numbers reductions from matrix rank","department":[{"_id":"HeEd"}],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Parsa","full_name":"Parsa, Salman","first_name":"Salman","id":"4BDBD4F2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4805","_id":"2177","status":"public","conference":{"start_date":"2014-01-05","end_date":"2014-01-07","location":"Portland, USA","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","language":[{"iso":"eng"}],"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:56:09Z","doi":"10.1137/1.9781611973402.11","date_published":"2014-01-01T00:00:00Z","page":"152 - 160","oa_version":"None","abstract":[{"text":"We give evidence for the difficulty of computing Betti numbers of simplicial complexes over a finite field. We do this by reducing the rank computation for sparse matrices with to non-zero entries to computing Betti numbers of simplicial complexes consisting of at most a constant times to simplices. Together with the known reduction in the other direction, this implies that the two problems have the same computational complexity.","lang":"eng"}],"month":"01","publisher":"SIAM","quality_controlled":"1","scopus_import":1},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Dodis Y, Pietrzak KZ, Wichs D. 2014. Key derivation without entropy waste. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 8441, 93–110.","chicago":"Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Daniel Wichs. “Key Derivation without Entropy Waste.” edited by Phong Nguyen and Elisabeth Oswald, 8441:93–110. Springer, 2014. https://doi.org/10.1007/978-3-642-55220-5_6.","ieee":"Y. Dodis, K. Z. Pietrzak, and D. Wichs, “Key derivation without entropy waste,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Copenhagen, Denmark, 2014, vol. 8441, pp. 93–110.","short":"Y. Dodis, K.Z. Pietrzak, D. Wichs, in:, P. Nguyen, E. Oswald (Eds.), Springer, 2014, pp. 93–110.","ama":"Dodis Y, Pietrzak KZ, Wichs D. Key derivation without entropy waste. In: Nguyen P, Oswald E, eds. Vol 8441. Springer; 2014:93-110. doi:10.1007/978-3-642-55220-5_6","apa":"Dodis, Y., Pietrzak, K. Z., & Wichs, D. (2014). Key derivation without entropy waste. In P. Nguyen & E. Oswald (Eds.) (Vol. 8441, pp. 93–110). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Copenhagen, Denmark: Springer. https://doi.org/10.1007/978-3-642-55220-5_6","mla":"Dodis, Yevgeniy, et al. Key Derivation without Entropy Waste. Edited by Phong Nguyen and Elisabeth Oswald, vol. 8441, Springer, 2014, pp. 93–110, doi:10.1007/978-3-642-55220-5_6."},"editor":[{"first_name":"Phong","last_name":"Nguyen","full_name":"Nguyen, Phong"},{"last_name":"Oswald","full_name":"Oswald, Elisabeth","first_name":"Elisabeth"}],"title":"Key derivation without entropy waste","publist_id":"4795","author":[{"first_name":"Yevgeniy","last_name":"Dodis","full_name":"Dodis, Yevgeniy"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"day":"01","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:56:12Z","doi":"10.1007/978-3-642-55220-5_6","date_published":"2014-04-01T00:00:00Z","page":"93 - 110","oa":1,"quality_controlled":"1","publisher":"Springer","ddc":["000","004"],"date_updated":"2021-01-12T06:55:51Z","file_date_updated":"2020-07-14T12:45:31Z","department":[{"_id":"KrPi"}],"_id":"2185","pubrep_id":"680","status":"public","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","start_date":"2014-05-11","end_date":"2014-05-15","location":"Copenhagen, Denmark"},"type":"conference","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:08:43Z","file_name":"IST-2016-680-v1+1_708.pdf","date_updated":"2020-07-14T12:45:31Z","file_size":505389,"creator":"system","file_id":"4705","checksum":"da1aa01221086083b23c92e547b48ff4","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","volume":8441,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We revisit the classical problem of converting an imperfect source of randomness into a usable cryptographic key. Assume that we have some cryptographic application P that expects a uniformly random m-bit key R and ensures that the best attack (in some complexity class) against P(R) has success probability at most δ. Our goal is to design a key-derivation function (KDF) h that converts any random source X of min-entropy k into a sufficiently "good" key h(X), guaranteeing that P(h(X)) has comparable security δ′ which is 'close' to δ. Seeded randomness extractors provide a generic way to solve this problem for all applications P, with resulting security δ′ = O(δ), provided that we start with entropy k ≥ m + 2 log (1/δ) - O(1). By a result of Radhakrishnan and Ta-Shma, this bound on k (called the "RT-bound") is also known to be tight in general. Unfortunately, in many situations the loss of 2 log (1/δ) bits of entropy is unacceptable. This motivates the study KDFs with less entropy waste by placing some restrictions on the source X or the application P. In this work we obtain the following new positive and negative results in this regard: - Efficient samplability of the source X does not help beat the RT-bound for general applications. This resolves the SRT (samplable RT) conjecture of Dachman-Soled et al. [DGKM12] in the affirmative, and also shows that the existence of computationally-secure extractors beating the RT-bound implies the existence of one-way functions. - We continue in the line of work initiated by Barak et al. [BDK+11] and construct new information-theoretic KDFs which beat the RT-bound for large but restricted classes of applications. Specifically, we design efficient KDFs that work for all unpredictability applications P (e.g., signatures, MACs, one-way functions, etc.) and can either: (1) extract all of the entropy k = m with a very modest security loss δ′ = O(δ·log (1/δ)), or alternatively, (2) achieve essentially optimal security δ′ = O(δ) with a very modest entropy loss k ≥ m + loglog (1/δ). In comparison, the best prior results from [BDK+11] for this class of applications would only guarantee δ′ = O(√δ) when k = m, and would need k ≥ m + log (1/δ) to get δ′ = O(δ). - The weaker bounds of [BDK+11] hold for a larger class of so-called "square- friendly" applications (which includes all unpredictability, but also some important indistinguishability, applications). Unfortunately, we show that these weaker bounds are tight for the larger class of applications. - We abstract out a clean, information-theoretic notion of (k,δ,δ′)- unpredictability extractors, which guarantee "induced" security δ′ for any δ-secure unpredictability application P, and characterize the parameters achievable for such unpredictability extractors. Of independent interest, we also relate this notion to the previously-known notion of (min-entropy) condensers, and improve the state-of-the-art parameters for such condensers."}],"intvolume":" 8441","month":"04","alternative_title":["LNCS"],"scopus_import":1},{"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"citation":{"mla":"Bellet, Aurélien, et al. “Learning a Priori Constrained Weighted Majority Votes.” Machine Learning, vol. 97, no. 1–2, Springer, 2014, pp. 129–54, doi:10.1007/s10994-014-5462-z.","short":"A. Bellet, A. Habrard, E. Morvant, M. Sebban, Machine Learning 97 (2014) 129–154.","ieee":"A. Bellet, A. Habrard, E. Morvant, and M. Sebban, “Learning a priori constrained weighted majority votes,” Machine Learning, vol. 97, no. 1–2. Springer, pp. 129–154, 2014.","ama":"Bellet A, Habrard A, Morvant E, Sebban M. Learning a priori constrained weighted majority votes. Machine Learning. 2014;97(1-2):129-154. doi:10.1007/s10994-014-5462-z","apa":"Bellet, A., Habrard, A., Morvant, E., & Sebban, M. (2014). Learning a priori constrained weighted majority votes. Machine Learning. Springer. https://doi.org/10.1007/s10994-014-5462-z","chicago":"Bellet, Aurélien, Amaury Habrard, Emilie Morvant, and Marc Sebban. “Learning a Priori Constrained Weighted Majority Votes.” Machine Learning. Springer, 2014. https://doi.org/10.1007/s10994-014-5462-z.","ista":"Bellet A, Habrard A, Morvant E, Sebban M. 2014. Learning a priori constrained weighted majority votes. Machine Learning. 97(1–2), 129–154."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4802","author":[{"full_name":"Bellet, Aurélien","last_name":"Bellet","first_name":"Aurélien"},{"last_name":"Habrard","full_name":"Habrard, Amaury","first_name":"Amaury"},{"orcid":"0000-0002-8301-7240","full_name":"Morvant, Emilie","last_name":"Morvant","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie"},{"first_name":"Marc","full_name":"Sebban, Marc","last_name":"Sebban"}],"title":"Learning a priori constrained weighted majority votes","acknowledgement":"This work was funded by the French project SoLSTiCe ANR-13-BS02-01 of the ANR. ","quality_controlled":"1","publisher":"Springer","oa":1,"year":"2014","day":"01","publication":"Machine Learning","page":"129 - 154","date_published":"2014-10-01T00:00:00Z","doi":"10.1007/s10994-014-5462-z","date_created":"2018-12-11T11:56:10Z","_id":"2180","type":"journal_article","status":"public","date_updated":"2021-01-12T06:55:49Z","department":[{"_id":"ChLa"}],"abstract":[{"lang":"eng","text":"Weighted majority votes allow one to combine the output of several classifiers or voters. MinCq is a recent algorithm for optimizing the weight of each voter based on the minimization of a theoretical bound over the risk of the vote with elegant PAC-Bayesian generalization guarantees. However, while it has demonstrated good performance when combining weak classifiers, MinCq cannot make use of the useful a priori knowledge that one may have when using a mixture of weak and strong voters. In this paper, we propose P-MinCq, an extension of MinCq that can incorporate such knowledge in the form of a constraint over the distribution of the weights, along with general proofs of convergence that stand in the sample compression setting for data-dependent voters. The approach is applied to a vote of k-NN classifiers with a specific modeling of the voters' performance. P-MinCq significantly outperforms the classic k-NN classifier, a symmetric NN and MinCq using the same voters. We show that it is also competitive with LMNN, a popular metric learning algorithm, and that combining both approaches further reduces the error."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01009578/document"}],"month":"10","intvolume":" 97","publication_status":"published","language":[{"iso":"eng"}],"issue":"1-2","volume":97,"ec_funded":1},{"status":"public","type":"journal_article","_id":"2184","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"date_updated":"2021-01-12T06:55:50Z","intvolume":" 61","month":"05","main_file_link":[{"url":"http://arxiv.org/abs/1105.6257","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"Given topological spaces X,Y, a fundamental problem of algebraic topology is understanding the structure of all continuous maps X→ Y. We consider a computational version, where X,Y are given as finite simplicial complexes, and the goal is to compute [X,Y], that is, all homotopy classes of suchmaps.We solve this problem in the stable range, where for some d ≥ 2, we have dim X ≤ 2d-2 and Y is (d-1)-connected; in particular, Y can be the d-dimensional sphere Sd. The algorithm combines classical tools and ideas from homotopy theory (obstruction theory, Postnikov systems, and simplicial sets) with algorithmic tools from effective algebraic topology (locally effective simplicial sets and objects with effective homology). In contrast, [X,Y] is known to be uncomputable for general X,Y, since for X = S1 it includes a well known undecidable problem: testing triviality of the fundamental group of Y. In follow-up papers, the algorithm is shown to run in polynomial time for d fixed, and extended to other problems, such as the extension problem, where we are given a subspace A ⊂ X and a map A→ Y and ask whether it extends to a map X → Y, or computing the Z2-index-everything in the stable range. Outside the stable range, the extension problem is undecidable.","lang":"eng"}],"volume":61,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","article_number":"17 ","title":"Computing all maps into a sphere","publist_id":"4797","author":[{"last_name":"Čadek","full_name":"Čadek, Martin","first_name":"Martin"},{"full_name":"Krcál, Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"last_name":"Matoušek","full_name":"Matoušek, Jiří","first_name":"Jiří"},{"first_name":"Francis","full_name":"Sergeraert, Francis","last_name":"Sergeraert"},{"first_name":"Lukáš","full_name":"Vokřínek, Lukáš","last_name":"Vokřínek"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, and U. Wagner, “Computing all maps into a sphere,” Journal of the ACM, vol. 61, no. 3. ACM, 2014.","short":"M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, U. Wagner, Journal of the ACM 61 (2014).","apa":"Čadek, M., Krcál, M., Matoušek, J., Sergeraert, F., Vokřínek, L., & Wagner, U. (2014). Computing all maps into a sphere. Journal of the ACM. ACM. https://doi.org/10.1145/2597629","ama":"Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. Computing all maps into a sphere. Journal of the ACM. 2014;61(3). doi:10.1145/2597629","mla":"Čadek, Martin, et al. “Computing All Maps into a Sphere.” Journal of the ACM, vol. 61, no. 3, 17, ACM, 2014, doi:10.1145/2597629.","ista":"Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. 2014. Computing all maps into a sphere. Journal of the ACM. 61(3), 17.","chicago":"Čadek, Martin, Marek Krcál, Jiří Matoušek, Francis Sergeraert, Lukáš Vokřínek, and Uli Wagner. “Computing All Maps into a Sphere.” Journal of the ACM. ACM, 2014. https://doi.org/10.1145/2597629."},"oa":1,"publisher":"ACM","quality_controlled":"1","acknowledgement":"The research by M. K. was supported by project GAUK 49209. The research by M. K. was also supported by project 1M0545 by the Ministry of Education of the Czech Republic and by Center of Excellence { Inst. for Theor. Comput. Sci., Prague (project P202/12/G061 of GACR). The research by U. W. was supported by the Swiss National Science Foundation (SNF Projects 200021-125309, 200020-138230, and PP00P2-138948).","date_created":"2018-12-11T11:56:12Z","doi":"10.1145/2597629","date_published":"2014-05-01T00:00:00Z","publication":"Journal of the ACM","day":"01","year":"2014"},{"date_updated":"2022-08-25T14:04:45Z","department":[{"_id":"GaTk"}],"_id":"2183","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":89,"issue":"6","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"We describe a simple adaptive network of coupled chaotic maps. The network reaches a stationary state (frozen topology) for all values of the coupling parameter, although the dynamics of the maps at the nodes of the network can be nontrivial. The structure of the network shows interesting hierarchical properties and in certain parameter regions the dynamics is polysynchronous: Nodes can be divided in differently synchronized classes but, contrary to cluster synchronization, nodes in the same class need not be connected to each other. These complicated synchrony patterns have been conjectured to play roles in systems biology and circuits. The adaptive system we study describes ways whereby this behavior can evolve from undifferentiated nodes.","lang":"eng"}],"month":"06","intvolume":" 89","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1403.3209"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6, 062809, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.062809.","apa":"Botella Soler, V., & Glendinning, P. (2014). Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.062809","ama":"Botella Soler V, Glendinning P. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(6). doi:10.1103/PhysRevE.89.062809","ieee":"V. Botella Soler and P. Glendinning, “Hierarchy and polysynchrony in an adaptive network ,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6. American Institute of Physics, 2014.","short":"V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","chicago":"Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.062809.","ista":"Botella Soler V, Glendinning P. 2014. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(6), 062809."},"title":"Hierarchy and polysynchrony in an adaptive network ","author":[{"first_name":"Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","last_name":"Botella Soler","orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicente"},{"first_name":"Paul","last_name":"Glendinning","full_name":"Glendinning, Paul"}],"publist_id":"4798","article_processing_charge":"No","article_number":"062809","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"day":"16","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","year":"2014","doi":"10.1103/PhysRevE.89.062809","date_published":"2014-06-16T00:00:00Z","date_created":"2018-12-11T11:56:11Z","acknowledgement":"V.B.S. is partially supported by contract MEC (Grant No. AYA2010-22111-C03-02).\r\n","quality_controlled":"1","publisher":"American Institute of Physics","oa":1},{"year":"2014","day":"07","publication":"Letters in Mathematical Physics","page":"871 - 891","date_published":"2014-05-07T00:00:00Z","doi":"10.1007/s11005-014-0693-2","date_created":"2018-12-11T11:56:12Z","quality_controlled":"1","publisher":"Springer","oa":1,"citation":{"mla":"Chen, Thomas, et al. “On the Well-Posedness and Scattering for the Gross-Pitaevskii Hierarchy via Quantum de Finetti.” Letters in Mathematical Physics, vol. 104, no. 7, Springer, 2014, pp. 871–91, doi:10.1007/s11005-014-0693-2.","short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Letters in Mathematical Physics 104 (2014) 871–891.","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti,” Letters in Mathematical Physics, vol. 104, no. 7. Springer, pp. 871–891, 2014.","ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters in Mathematical Physics. 2014;104(7):871-891. doi:10.1007/s11005-014-0693-2","apa":"Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2014). On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-014-0693-2","chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “On the Well-Posedness and Scattering for the Gross-Pitaevskii Hierarchy via Quantum de Finetti.” Letters in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s11005-014-0693-2.","ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2014. On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters in Mathematical Physics. 104(7), 871–891."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4793","author":[{"first_name":"Thomas","full_name":"Chen, Thomas","last_name":"Chen"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"full_name":"Pavlović, Nataša","last_name":"Pavlović","first_name":"Nataša"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"publication_status":"published","language":[{"iso":"eng"}],"issue":"7","volume":104,"abstract":[{"lang":"eng","text":"We prove the existence of scattering states for the defocusing cubic Gross-Pitaevskii (GP) hierarchy in ℝ3. Moreover, we show that an exponential energy growth condition commonly used in the well-posedness theory of the GP hierarchy is, in a specific sense, necessary. In fact, we prove that without the latter, there exist initial data for the focusing cubic GP hierarchy for which instantaneous blowup occurs."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.2136"}],"month":"05","intvolume":" 104","date_updated":"2021-01-12T06:55:51Z","department":[{"_id":"RoSe"}],"_id":"2186","type":"journal_article","status":"public"},{"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"publist_id":"4787","author":[{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Karin","last_name":"Greimel","full_name":"Greimel, Karin"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Georg","last_name":"Hofferek","full_name":"Hofferek, Georg"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"},{"last_name":"Könighofer","full_name":"Könighofer, Bettina","first_name":"Bettina"},{"first_name":"Robert","last_name":"Könighofer","full_name":"Könighofer, Robert"}],"article_processing_charge":"No","title":"Synthesizing robust systems","citation":{"mla":"Bloem, Roderick, et al. “Synthesizing Robust Systems.” Acta Informatica, vol. 51, no. 3–4, Springer, 2014, pp. 193–220, doi:10.1007/s00236-013-0191-5.","apa":"Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., Hofferek, G., Jobstmann, B., … Könighofer, R. (2014). Synthesizing robust systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-013-0191-5","ama":"Bloem R, Chatterjee K, Greimel K, et al. Synthesizing robust systems. Acta Informatica. 2014;51(3-4):193-220. doi:10.1007/s00236-013-0191-5","ieee":"R. Bloem et al., “Synthesizing robust systems,” Acta Informatica, vol. 51, no. 3–4. Springer, pp. 193–220, 2014.","short":"R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, G. Hofferek, B. Jobstmann, B. Könighofer, R. Könighofer, Acta Informatica 51 (2014) 193–220.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, Georg Hofferek, Barbara Jobstmann, Bettina Könighofer, and Robert Könighofer. “Synthesizing Robust Systems.” Acta Informatica. Springer, 2014. https://doi.org/10.1007/s00236-013-0191-5.","ista":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Hofferek G, Jobstmann B, Könighofer B, Könighofer R. 2014. Synthesizing robust systems. Acta Informatica. 51(3–4), 193–220."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer","oa":1,"page":"193 - 220","doi":"10.1007/s00236-013-0191-5","date_published":"2014-06-01T00:00:00Z","date_created":"2018-12-11T11:56:13Z","has_accepted_license":"1","year":"2014","day":"01","publication":"Acta Informatica","article_type":"original","type":"journal_article","status":"public","pubrep_id":"71","_id":"2187","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:31Z","date_updated":"2021-01-12T06:55:51Z","ddc":["621"],"scopus_import":1,"month":"06","intvolume":" 51","abstract":[{"text":"Systems should not only be correct but also robust in the sense that they behave reasonably in unexpected situations. This article addresses synthesis of robust reactive systems from temporal specifications. Existing methods allow arbitrary behavior if assumptions in the specification are violated. To overcome this, we define two robustness notions, combine them, and show how to enforce them in synthesis. The first notion applies to safety properties: If safety assumptions are violated temporarily, we require that the system recovers to normal operation with as few errors as possible. The second notion requires that, if liveness assumptions are violated, as many guarantees as possible should be fulfilled nevertheless. We present a synthesis procedure achieving this for the important class of GR(1) specifications, and establish complexity bounds. We also present an implementation of a special case of robustness, and show experimental results.","lang":"eng"}],"oa_version":"Submitted Version","issue":"3-4","volume":51,"ec_funded":1,"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:45:31Z","file_size":169523,"date_created":"2018-12-12T10:16:44Z","file_name":"IST-2012-71-v1+1_Synthesizing_robust_systems.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5234","checksum":"d7f560f3d923f0f00aa10a0652f83273"}],"language":[{"iso":"eng"}]},{"has_accepted_license":"1","year":"2014","day":"16","publication":"Open Biology","date_published":"2014-04-16T00:00:00Z","doi":"10.1098/rsob.140017","date_created":"2018-12-11T11:56:13Z","acknowledgement":"This work was supported by a grant from the Research Foundation-Flanders (Odysseus).\r\n\r\n","quality_controlled":"1","publisher":"Royal Society","oa":1,"citation":{"ama":"Kania U, Fendrych M, Friml J. Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biology. 2014;4(APRIL). doi:10.1098/rsob.140017","apa":"Kania, U., Fendrych, M., & Friml, J. (2014). Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biology. Royal Society. https://doi.org/10.1098/rsob.140017","short":"U. Kania, M. Fendrych, J. Friml, Open Biology 4 (2014).","ieee":"U. Kania, M. Fendrych, and J. Friml, “Polar delivery in plants; commonalities and differences to animal epithelial cells,” Open Biology, vol. 4, no. APRIL. Royal Society, 2014.","mla":"Kania, Urszula, et al. “Polar Delivery in Plants; Commonalities and Differences to Animal Epithelial Cells.” Open Biology, vol. 4, no. APRIL, 140017, Royal Society, 2014, doi:10.1098/rsob.140017.","ista":"Kania U, Fendrych M, Friml J. 2014. Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biology. 4(APRIL), 140017.","chicago":"Kania, Urszula, Matyas Fendrych, and Jiří Friml. “Polar Delivery in Plants; Commonalities and Differences to Animal Epithelial Cells.” Open Biology. Royal Society, 2014. https://doi.org/10.1098/rsob.140017."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"4786","author":[{"full_name":"Kania, Urszula","last_name":"Kania","first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fendrych","full_name":"Fendrych, Matyas","first_name":"Matyas"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ"}],"title":"Polar delivery in plants; commonalities and differences to animal epithelial cells","article_number":"140017","publication_status":"published","file":[{"checksum":"2020627feff36cf0799167c84149fa75","file_id":"5025","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:13:40Z","file_name":"IST-2016-441-v1+1_140017.full.pdf","date_updated":"2020-07-14T12:45:31Z","file_size":682570,"creator":"system"}],"language":[{"iso":"eng"}],"volume":4,"issue":"APRIL","abstract":[{"text":"Although plant and animal cells use a similar core mechanism to deliver proteins to the plasma membrane, their different lifestyle, body organization and specific cell structures resulted in the acquisition of regulatory mechanisms that vary in the two kingdoms. In particular, cell polarity regulators do not seem to be conserved, because genes encoding key components are absent in plant genomes. In plants, the broad knowledge on polarity derives from the study of auxin transporters, the PIN-FORMED proteins, in the model plant Arabidopsis thaliana. In animals, much information is provided from the study of polarity in epithelial cells that exhibit basolateral and luminal apical polarities, separated by tight junctions. In this review, we summarize the similarities and differences of the polarization mechanisms between plants and animals and survey the main genetic approaches that have been used to characterize new genes involved in polarity establishment in plants, including the frequently used forward and reverse genetics screens as well as a novel chemical genetics approach that is expected to overcome the limitation of classical genetics methods.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"04","intvolume":" 4","date_updated":"2021-01-12T06:55:52Z","ddc":["570"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:31Z","_id":"2188","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"441"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01005776/"}],"publisher":"Elsevier","quality_controlled":"1","intvolume":" 1","month":"07","abstract":[{"lang":"fre","text":"En apprentissage automatique, nous parlons d'adaptation de domaine lorsque les données de test (cibles) et d'apprentissage (sources) sont générées selon différentes distributions. Nous devons donc développer des algorithmes de classification capables de s'adapter à une nouvelle distribution, pour laquelle aucune information sur les étiquettes n'est disponible. Nous attaquons cette problématique sous l'angle de l'approche PAC-Bayésienne qui se focalise sur l'apprentissage de modèles définis comme des votes de majorité sur un ensemble de fonctions. Dans ce contexte, nous introduisons PV-MinCq une version adaptative de l'algorithme (non adaptatif) MinCq. PV-MinCq suit le principe suivant. Nous transférons les étiquettes sources aux points cibles proches pour ensuite appliquer MinCq sur l'échantillon cible ``auto-étiqueté'' (justifié par une borne théorique). Plus précisément, nous définissons un auto-étiquetage non itératif qui se focalise dans les régions où les distributions marginales source et cible sont les plus similaires. Dans un second temps, nous étudions l'influence de notre auto-étiquetage pour en déduire une procédure de validation des hyperparamètres. Finalement, notre approche montre des résultats empiriques prometteurs."}],"oa_version":"Preprint","page":"49-58","date_created":"2018-12-11T11:56:13Z","date_published":"2014-07-01T00:00:00Z","volume":1,"publication_status":"published","year":"2014","language":[{"iso":"eng"}],"day":"01","conference":{"location":"Saint-Etienne, France","name":"CAP: Conférence Francophone sur l'Apprentissage Automatique (Machine Learning French Conference)"},"type":"conference","status":"public","_id":"2189","article_processing_charge":"No","publist_id":"4785","author":[{"last_name":"Morvant","orcid":"0000-0002-8301-7240","full_name":"Morvant, Emilie","first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87"}],"title":"Adaptation de domaine de vote de majorité par auto-étiquetage non itératif","department":[{"_id":"ChLa"}],"citation":{"chicago":"Morvant, Emilie. “Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage Non Itératif,” 1:49–58. Elsevier, 2014.","ista":"Morvant E. 2014. Adaptation de domaine de vote de majorité par auto-étiquetage non itératif. CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference) vol. 1, 49–58.","mla":"Morvant, Emilie. Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage Non Itératif. Vol. 1, Elsevier, 2014, pp. 49–58.","ieee":"E. Morvant, “Adaptation de domaine de vote de majorité par auto-étiquetage non itératif,” presented at the CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference), Saint-Etienne, France, 2014, vol. 1, pp. 49–58.","short":"E. Morvant, in:, Elsevier, 2014, pp. 49–58.","ama":"Morvant E. Adaptation de domaine de vote de majorité par auto-étiquetage non itératif. In: Vol 1. Elsevier; 2014:49-58.","apa":"Morvant, E. (2014). Adaptation de domaine de vote de majorité par auto-étiquetage non itératif (Vol. 1, pp. 49–58). Presented at the CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference), Saint-Etienne, France: Elsevier."},"date_updated":"2021-01-12T06:55:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2021-01-12T06:55:53Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"2190","conference":{"name":"CAV: Computer Aided Verification"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":8559,"abstract":[{"text":"We present a new algorithm to construct a (generalized) deterministic Rabin automaton for an LTL formula φ. The automaton is the product of a master automaton and an array of slave automata, one for each G-subformula of φ. The slave automaton for G ψ is in charge of recognizing whether FG ψ holds. As opposed to standard determinization procedures, the states of all our automata have a clear logical structure, which allows for various optimizations. Our construction subsumes former algorithms for fragments of LTL. Experimental results show improvement in the sizes of the resulting automata compared to existing methods.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1402.3388","open_access":"1"}],"alternative_title":["LNCS"],"intvolume":" 8559","month":"01","citation":{"chicago":"Esparza, Javier, and Jan Kretinsky. “From LTL to Deterministic Automata: A Safraless Compositional Approach,” 8559:192–208. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_13.","ista":"Esparza J, Kretinsky J. 2014. From LTL to deterministic automata: A safraless compositional approach. CAV: Computer Aided Verification, LNCS, vol. 8559, 192–208.","mla":"Esparza, Javier, and Jan Kretinsky. From LTL to Deterministic Automata: A Safraless Compositional Approach. Vol. 8559, Springer, 2014, pp. 192–208, doi:10.1007/978-3-319-08867-9_13.","ama":"Esparza J, Kretinsky J. From LTL to deterministic automata: A safraless compositional approach. In: Vol 8559. Springer; 2014:192-208. doi:10.1007/978-3-319-08867-9_13","apa":"Esparza, J., & Kretinsky, J. (2014). From LTL to deterministic automata: A safraless compositional approach (Vol. 8559, pp. 192–208). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/978-3-319-08867-9_13","ieee":"J. Esparza and J. Kretinsky, “From LTL to deterministic automata: A safraless compositional approach,” presented at the CAV: Computer Aided Verification, 2014, vol. 8559, pp. 192–208.","short":"J. Esparza, J. Kretinsky, in:, Springer, 2014, pp. 192–208."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Esparza, Javier","last_name":"Esparza","first_name":"Javier"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"}],"publist_id":"4784","title":"From LTL to deterministic automata: A safraless compositional approach","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"year":"2014","day":"01","page":"192 - 208","date_created":"2018-12-11T11:56:14Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-08867-9_13","acknowledgement":"The author is on leave from Faculty of Informatics, Masaryk University, Czech Republic, and partially supported by the Czech Science Foundation, grant No. P202/12/G061.","oa":1,"publisher":"Springer","quality_controlled":"1"},{"abstract":[{"text":"We propose to detect quadrupole interactions of neutral ultracold atoms via their induced mean-field shift. We consider a Mott insulator state of spin-polarized atoms in a two-dimensional optical square lattice. The quadrupole moments of the atoms are aligned by an external magnetic field. As the alignment angle is varied, the mean-field shift shows a characteristic angular dependence, which constitutes the defining signature of the quadrupole interaction. For the 3P2 states of Yb and Sr atoms, we find a frequency shift of the order of tens of Hertz, which can be realistically detected in experiment with current technology. We compare our results to the mean-field shift of a spin-polarized quasi-two-dimensional Fermi gas in continuum. ","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0873"}],"oa":1,"quality_controlled":"1","publisher":"American Physical Society","intvolume":" 89","month":"04","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","day":"23","date_created":"2018-12-11T11:56:20Z","issue":"4","doi":"10.1103/PhysRevA.89.043616","volume":89,"date_published":"2014-04-23T00:00:00Z","_id":"2208","article_number":"043616","type":"journal_article","status":"public","citation":{"short":"M. Lahrz, M. Lemeshko, K. Sengstock, C. Becker, L. Mathey, Physical Review A - Atomic, Molecular, and Optical Physics 89 (2014).","ieee":"M. Lahrz, M. Lemeshko, K. Sengstock, C. Becker, and L. Mathey, “Detecting quadrupole interactions in ultracold Fermi gases,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 89, no. 4. American Physical Society, 2014.","ama":"Lahrz M, Lemeshko M, Sengstock K, Becker C, Mathey L. Detecting quadrupole interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular, and Optical Physics. 2014;89(4). doi:10.1103/PhysRevA.89.043616","apa":"Lahrz, M., Lemeshko, M., Sengstock, K., Becker, C., & Mathey, L. (2014). Detecting quadrupole interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.89.043616","mla":"Lahrz, Martin, et al. “Detecting Quadrupole Interactions in Ultracold Fermi Gases.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 89, no. 4, 043616, American Physical Society, 2014, doi:10.1103/PhysRevA.89.043616.","ista":"Lahrz M, Lemeshko M, Sengstock K, Becker C, Mathey L. 2014. Detecting quadrupole interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular, and Optical Physics. 89(4), 043616.","chicago":"Lahrz, Martin, Mikhail Lemeshko, Klaus Sengstock, Christoph Becker, and Ludwig Mathey. “Detecting Quadrupole Interactions in Ultracold Fermi Gases.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevA.89.043616."},"date_updated":"2021-01-12T06:55:59Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","publist_id":"4764","author":[{"last_name":"Lahrz","full_name":"Lahrz, Martin","first_name":"Martin"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"full_name":"Sengstock, Klaus","last_name":"Sengstock","first_name":"Klaus"},{"first_name":"Christoph","full_name":"Becker, Christoph","last_name":"Becker"},{"full_name":"Mathey, Ludwig","last_name":"Mathey","first_name":"Ludwig"}],"title":"Detecting quadrupole interactions in ultracold Fermi gases"},{"acknowledgement":"Michael Sixt's research is supported by the European Research Council (ERC Starting grant).","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","year":"2014","has_accepted_license":"1","publication":"PLoS One","day":"22","date_created":"2018-12-11T11:56:22Z","doi":"10.1371/journal.pone.0085699","date_published":"2014-01-22T00:00:00Z","article_number":"e85699","project":[{"call_identifier":"FP7","_id":"25A76F58-B435-11E9-9278-68D0E5697425","name":"Stromal Cell-immune Cell Interactions in Health and Disease","grant_number":"289720"}],"citation":{"mla":"Stoler Barak, Liat, et al. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” PLoS One, vol. 9, no. 1, e85699, Public Library of Science, 2014, doi:10.1371/journal.pone.0085699.","ama":"Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085699","apa":"Stoler Barak, L., Moussion, C., Shezen, E., Hatzav, M., Sixt, M. K., & Alon, R. (2014). Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0085699","short":"L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M.K. Sixt, R. Alon, PLoS One 9 (2014).","ieee":"L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M. K. Sixt, and R. Alon, “Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects,” PLoS One, vol. 9, no. 1. Public Library of Science, 2014.","chicago":"Stoler Barak, Liat, Christine Moussion, Elias Shezen, Miki Hatzav, Michael K Sixt, and Ronen Alon. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0085699.","ista":"Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. 2014. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. 9(1), e85699."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4756","author":[{"last_name":"Stoler Barak","full_name":"Stoler Barak, Liat","first_name":"Liat"},{"last_name":"Moussion","full_name":"Moussion, Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87","first_name":"Christine"},{"first_name":"Elias","full_name":"Shezen, Elias","last_name":"Shezen"},{"first_name":"Miki","last_name":"Hatzav","full_name":"Hatzav, Miki"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alon, Ronen","last_name":"Alon","first_name":"Ronen"}],"title":"Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects","abstract":[{"text":"A hallmark of immune cell trafficking is directional guidance via gradients of soluble or surface bound chemokines. Vascular endothelial cells produce, transport and deposit either their own chemokines or chemokines produced by the underlying stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold for these chemokine pools, but it is unclear how steep chemokine gradients are sustained between the lumenal and ablumenal aspects of blood vessels. Addressing this question by semi-quantitative immunostaining of HS moieties around blood vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal lamina of resting and inflamed post capillary skin venules, as well as in high endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx probe further suggested that their lumenal glycocalyx contains much lower HS density than their basolateral extracellular matrix (ECM). This polarized HS pattern was observed also in isolated resting and inflamed microvascular dermal cells. Notably, progressive skin inflammation resulted in massive ECM deposition and in further HS enrichment around skin post capillary venules and their associated pericytes. Inflammation-dependent HS enrichment was not compromised in mice deficient in the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature patterns steep gradients of HS scaffolds between their lumenal and basolateral endothelial aspects, and that inflammatory processes can further enrich the HS content nearby inflamed vessels. We propose that chemokine gradients between the lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold gradients.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 9","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:33Z","file_size":12634775,"creator":"system","date_created":"2018-12-12T10:07:48Z","file_name":"IST-2016-433-v1+1_journal.pone.0085699.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"84a8033bda2e07e39405f5acc85f4eca","file_id":"4646"}],"ec_funded":1,"issue":"1","volume":9,"_id":"2214","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"433","status":"public","date_updated":"2021-01-12T06:56:03Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:33Z","department":[{"_id":"MiSi"}]},{"_id":"2215","type":"journal_article","status":"public","date_updated":"2021-01-12T06:56:03Z","citation":{"mla":"Renkawitz, Jörg, et al. “Mechanisms and Principles of Homology Search during Recombination.” Nature Reviews Molecular Cell Biology, vol. 15, no. 6, Nature Publishing Group, 2014, pp. 369–83, doi:10.1038/nrm3805.","short":"J. Renkawitz, C. Lademann, S. Jentsch, Nature Reviews Molecular Cell Biology 15 (2014) 369–383.","ieee":"J. Renkawitz, C. Lademann, and S. Jentsch, “Mechanisms and principles of homology search during recombination,” Nature Reviews Molecular Cell Biology, vol. 15, no. 6. Nature Publishing Group, pp. 369–383, 2014.","apa":"Renkawitz, J., Lademann, C., & Jentsch, S. (2014). Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3805","ama":"Renkawitz J, Lademann C, Jentsch S. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 2014;15(6):369-383. doi:10.1038/nrm3805","chicago":"Renkawitz, Jörg, Claudio Lademann, and Stefan Jentsch. “Mechanisms and Principles of Homology Search during Recombination.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/nrm3805.","ista":"Renkawitz J, Lademann C, Jentsch S. 2014. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 15(6), 369–383."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"4755","author":[{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lademann","full_name":"Lademann, Claudio","first_name":"Claudio"},{"first_name":"Stefan","full_name":"Jentsch, Stefan","last_name":"Jentsch"}],"department":[{"_id":"MiSi"}],"title":"Mechanisms and principles of homology search during recombination","abstract":[{"lang":"eng","text":"Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events."}],"oa_version":"None","acknowledgement":"J.R. was supported by a Boehringer Ingelheim Fonds PhD stipend.","quality_controlled":"1","publisher":"Nature Publishing Group","scopus_import":1,"month":"05","intvolume":" 15","year":"2014","publication_status":"published","day":"14","language":[{"iso":"eng"}],"publication":"Nature Reviews Molecular Cell Biology","page":"369 - 383","issue":"6","date_published":"2014-05-14T00:00:00Z","doi":"10.1038/nrm3805","volume":15,"date_created":"2018-12-11T11:56:22Z"},{"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","publication":"Plant and Cell Physiology","day":"01","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:56:25Z","doi":"10.1093/pcp/pct196","date_published":"2014-04-01T00:00:00Z","page":"737 - 749","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur","_id":"256BDAB0-B435-11E9-9278-68D0E5697425"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa, T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pct196","ama":"Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 2014;55(4):737-749. doi:10.1093/pcp/pct196","short":"H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa, J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749.","ieee":"H. Tanaka et al., “BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis,” Plant and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 737–749, 2014.","mla":"Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49, doi:10.1093/pcp/pct196.","ista":"Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 55(4), 737–749.","chicago":"Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pct196."},"title":"BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis","publist_id":"4741","author":[{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"last_name":"Kitakura","full_name":"Kitakura, Saeko","first_name":"Saeko"},{"first_name":"Mugurel","last_name":"Feraru","full_name":"Feraru, Mugurel"},{"last_name":"Sasabe","full_name":"Sasabe, Michiko","first_name":"Michiko"},{"full_name":"Ishikawa, Tomomi","last_name":"Ishikawa","first_name":"Tomomi"},{"last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen"},{"first_name":"Tatsuo","last_name":"Kakimoto","full_name":"Kakimoto, Tatsuo"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","abstract":[{"text":"Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes.","lang":"eng"}],"intvolume":" 55","month":"04","main_file_link":[{"url":"http://repository.ist.ac.at/id/eprint/431","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:25Z","file_name":"IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf","date_updated":"2020-07-14T12:45:34Z","file_size":2028111,"creator":"system","checksum":"b781a76b32ac35a520256453c3ba9433","file_id":"5076","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["00320781"]},"ec_funded":1,"volume":55,"issue":"4","_id":"2223","pubrep_id":"431","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:56:07Z","file_date_updated":"2020-07-14T12:45:34Z","department":[{"_id":"JiFr"}]},{"oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","year":"2014","has_accepted_license":"1","publication":"Electronic Journal of Probability","day":"15","date_created":"2018-12-11T11:56:25Z","date_published":"2014-03-15T00:00:00Z","doi":"10.1214/EJP.v19-3054","article_number":"33","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. 2014. Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. 19, 33.","chicago":"Bloemendal, Alex, László Erdös, Antti Knowles, Horng Yau, and Jun Yin. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2014. https://doi.org/10.1214/EJP.v19-3054.","short":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 19 (2014).","ieee":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, and J. Yin, “Isotropic local laws for sample covariance and generalized Wigner matrices,” Electronic Journal of Probability, vol. 19. Institute of Mathematical Statistics, 2014.","apa":"Bloemendal, A., Erdös, L., Knowles, A., Yau, H., & Yin, J. (2014). Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v19-3054","ama":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. 2014;19. doi:10.1214/EJP.v19-3054","mla":"Bloemendal, Alex, et al. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” Electronic Journal of Probability, vol. 19, 33, Institute of Mathematical Statistics, 2014, doi:10.1214/EJP.v19-3054."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4739","author":[{"first_name":"Alex","last_name":"Bloemendal","full_name":"Bloemendal, Alex"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antti","full_name":"Knowles, Antti","last_name":"Knowles"},{"first_name":"Horng","full_name":"Yau, Horng","last_name":"Yau"},{"last_name":"Yin","full_name":"Yin, Jun","first_name":"Jun"}],"title":"Isotropic local laws for sample covariance and generalized Wigner matrices","abstract":[{"text":"We consider sample covariance matrices of the form X∗X, where X is an M×N matrix with independent random entries. We prove the isotropic local Marchenko-Pastur law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the identity in the sense of quadratic forms. More precisely, we establish sharp high-probability bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout the entire spectrum away from 0. We also prove analogous results for generalized Wigner matrices.\r\n","lang":"eng"}],"oa_version":"Published Version","intvolume":" 19","month":"03","publication_status":"published","publication_identifier":{"issn":["10836489"]},"language":[{"iso":"eng"}],"file":[{"checksum":"7eb297ff367a2ee73b21b6dd1e1948e4","file_id":"5055","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:06Z","file_name":"IST-2016-427-v1+1_3054-16624-4-PB.pdf","date_updated":"2020-07-14T12:45:34Z","file_size":810150,"creator":"system"}],"ec_funded":1,"volume":19,"_id":"2225","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"427","status":"public","date_updated":"2021-01-12T06:56:07Z","ddc":["510"],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:45:34Z"},{"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Naramoto et al., “VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis,” Plant and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014.","short":"S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml, H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763.","ama":"Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 2014;55(4):750-763. doi:10.1093/pcp/pcu012","apa":"Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml, J., & Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcu012","mla":"Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:10.1093/pcp/pcu012.","ista":"Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763.","chicago":"Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka, Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pcu012."},"title":"VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis","publist_id":"4742","author":[{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Tomoko","last_name":"Dainobu","full_name":"Dainobu, Tomoko"},{"last_name":"Takatsuka","full_name":"Takatsuka, Hirotomo","first_name":"Hirotomo"},{"first_name":"Teruyo","last_name":"Okada","full_name":"Okada, Teruyo"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Hiroo","full_name":"Fukuda, Hiroo","last_name":"Fukuda"}],"quality_controlled":"1","publisher":"Oxford University Press","publication":"Plant and Cell Physiology","day":"01","year":"2014","date_created":"2018-12-11T11:56:24Z","date_published":"2014-04-01T00:00:00Z","doi":"10.1093/pcp/pcu012","page":"750 - 763","_id":"2222","status":"public","type":"journal_article","date_updated":"2021-01-12T06:56:06Z","department":[{"_id":"JiFr"}],"oa_version":"None","abstract":[{"text":"Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation.","lang":"eng"}],"intvolume":" 55","month":"04","scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00320781"]},"ec_funded":1,"issue":"4","volume":55},{"title":"On secondary instabilities generating footbridges between spiral vortex flow","department":[{"_id":"BjHo"}],"publist_id":"4740","author":[{"orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","last_name":"Altmeyer","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” Fluid Dynamics Research, vol. 46, no. 2, 025503, IOP Publishing Ltd., 2014, doi:10.1088/0169-5983/46/2/025503.","apa":"Altmeyer, S. (2014). On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. IOP Publishing Ltd. https://doi.org/10.1088/0169-5983/46/2/025503","ama":"Altmeyer S. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 2014;46(2). doi:10.1088/0169-5983/46/2/025503","short":"S. Altmeyer, Fluid Dynamics Research 46 (2014).","ieee":"S. Altmeyer, “On secondary instabilities generating footbridges between spiral vortex flow,” Fluid Dynamics Research, vol. 46, no. 2. IOP Publishing Ltd., 2014.","chicago":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” Fluid Dynamics Research. IOP Publishing Ltd., 2014. https://doi.org/10.1088/0169-5983/46/2/025503.","ista":"Altmeyer S. 2014. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 46(2), 025503."},"date_updated":"2021-01-12T06:56:07Z","status":"public","type":"journal_article","article_number":"025503","_id":"2224","doi":"10.1088/0169-5983/46/2/025503","date_published":"2014-04-01T00:00:00Z","issue":"2","volume":46,"date_created":"2018-12-11T11:56:25Z","day":"01","publication":"Fluid Dynamics Research","language":[{"iso":"eng"}],"publication_identifier":{"issn":["01695983"]},"publication_status":"published","year":"2014","month":"04","intvolume":" 46","scopus_import":1,"publisher":"IOP Publishing Ltd.","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet."}]},{"oa_version":"Submitted Version","abstract":[{"text":"Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext (IND-CCA) secure public-key encryption scheme from the learning parity with noise (LPN) assumption. In this work we give an alternative scheme which is conceptually simpler and more efficient. At the core of our construction is a trapdoor technique originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which we adapt to the LPN setting. The main technical tool is a new double-trapdoor mechanism, together with a trapdoor switching lemma based on a computational variant of the leftover hash lemma.","lang":"eng"}],"intvolume":" 8383","month":"03","main_file_link":[{"url":"https://eprint.iacr.org/2015/401","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-364254630-3"]},"volume":8383,"_id":"2219","status":"public","conference":{"name":"IACR: International Conference on Practice and Theory in Public-Key Cryptography"},"type":"conference","date_updated":"2021-01-12T06:56:05Z","department":[{"_id":"KrPi"}],"oa":1,"quality_controlled":"1","publisher":"Springer","day":"01","year":"2014","date_created":"2018-12-11T11:56:24Z","doi":"10.1007/978-3-642-54631-0_1","date_published":"2014-03-01T00:00:00Z","page":"1 - 18","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kiltz, Eike, Daniel Masny, and Krzysztof Z Pietrzak. “Simple Chosen-Ciphertext Security from Low Noise LPN,” 8383:1–18. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_1.","ista":"Kiltz E, Masny D, Pietrzak KZ. 2014. Simple chosen-ciphertext security from low noise LPN. IACR: International Conference on Practice and Theory in Public-Key Cryptography, LNCS, vol. 8383, 1–18.","mla":"Kiltz, Eike, et al. Simple Chosen-Ciphertext Security from Low Noise LPN. Vol. 8383, Springer, 2014, pp. 1–18, doi:10.1007/978-3-642-54631-0_1.","ieee":"E. Kiltz, D. Masny, and K. Z. Pietrzak, “Simple chosen-ciphertext security from low noise LPN,” presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, 2014, vol. 8383, pp. 1–18.","short":"E. Kiltz, D. Masny, K.Z. Pietrzak, in:, Springer, 2014, pp. 1–18.","apa":"Kiltz, E., Masny, D., & Pietrzak, K. Z. (2014). Simple chosen-ciphertext security from low noise LPN (Vol. 8383, pp. 1–18). Presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, Springer. https://doi.org/10.1007/978-3-642-54631-0_1","ama":"Kiltz E, Masny D, Pietrzak KZ. Simple chosen-ciphertext security from low noise LPN. In: Vol 8383. Springer; 2014:1-18. doi:10.1007/978-3-642-54631-0_1"},"title":"Simple chosen-ciphertext security from low noise LPN","author":[{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"last_name":"Masny","full_name":"Masny, Daniel","first_name":"Daniel"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"publist_id":"4748"},{"publist_id":"4747","author":[{"first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","full_name":"De Vos, Marjon"},{"first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"external_id":{"pmid":["24766845"]},"title":"Suppressive drug interactions between antifungals","citation":{"ama":"de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals. Chemistry and Biology. 2014;21(4):439-440. doi:10.1016/j.chembiol.2014.04.004","apa":"de Vos, M., & Bollenbach, M. T. (2014). Suppressive drug interactions between antifungals. Chemistry and Biology. Cell Press. https://doi.org/10.1016/j.chembiol.2014.04.004","short":"M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440.","ieee":"M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,” Chemistry and Biology, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.","mla":"de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology, vol. 21, no. 4, Cell Press, 2014, pp. 439–40, doi:10.1016/j.chembiol.2014.04.004.","ista":"de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals. Chemistry and Biology. 21(4), 439–440.","chicago":"Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology. Cell Press, 2014. https://doi.org/10.1016/j.chembiol.2014.04.004."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","quality_controlled":"1","oa":1,"page":"439 - 440","date_published":"2014-04-24T00:00:00Z","doi":"10.1016/j.chembiol.2014.04.004","date_created":"2018-12-11T11:56:24Z","year":"2014","day":"24","publication":"Chemistry and Biology","type":"journal_article","status":"public","_id":"2220","department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T06:56:06Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/24766845"}],"month":"04","intvolume":" 21","abstract":[{"text":"In this issue of Chemistry & Biology, Cokol and colleagues report a systematic study of drug interactions between antifungal compounds. Suppressive drug interactions occur more frequently than previously realized and come in different flavors with interesting implications.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":21,"issue":"4","publication_identifier":{"issn":["10745521"]},"publication_status":"published","language":[{"iso":"eng"}]},{"ec_funded":1,"issue":"1","volume":10,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9f6ea2e2d8d4a32ff0becc29d835bbf8","file_id":"4643","creator":"system","date_updated":"2020-07-14T12:45:34Z","file_size":550936,"date_created":"2018-12-12T10:07:45Z","file_name":"IST-2015-389-v1+1_1401.3957.pdf"}],"publication_status":"published","publication_identifier":{"issn":["18605974"]},"intvolume":" 10","month":"02","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":" A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, valuing a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by λi, where the discount factor λ is a fixed rational number greater than 1. The value of a word is the minimal value of the automaton runs on it. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, reflecting the assumption that earlier weights are more important than later weights. Unfortunately, determinization of NDAs, which is often essential in formal verification, is, in general, not possible. We provide positive news, showing that every NDA with an integral discount factor is determinizable. We complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: for every nonintegral rational discount factor λ, there is a nondeterminizable λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. For general NDAs, we look into approximate determinization, which is always possible as the influence of a word's suffix decays. We show that the naive approach, of unfolding the automaton computations up to a sufficient level, is doubly exponential in the discount factor. We provide an alternative construction for approximate determinization, which is singly exponential in the discount factor, in the precision, and in the number of states. We also prove matching lower bounds, showing that the exponential dependency on each of these three parameters cannot be avoided. All our results hold equally for automata over finite words and for automata over infinite words. "}],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:34Z","ddc":["000"],"date_updated":"2021-01-12T06:56:11Z","pubrep_id":"389","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"2233","date_created":"2018-12-11T11:56:28Z","doi":"10.2168/LMCS-10(1:10)2014","date_published":"2014-02-13T00:00:00Z","publication":"Logical Methods in Computer Science","day":"13","year":"2014","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"International Federation of Computational Logic","title":"Exact and approximate determinization of discounted-sum automata","publist_id":"4728","author":[{"full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"U. Boker, T.A. Henzinger, Logical Methods in Computer Science 10 (2014).","ieee":"U. Boker and T. A. Henzinger, “Exact and approximate determinization of discounted-sum automata,” Logical Methods in Computer Science, vol. 10, no. 1. International Federation of Computational Logic, 2014.","ama":"Boker U, Henzinger TA. Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. 2014;10(1). doi:10.2168/LMCS-10(1:10)2014","apa":"Boker, U., & Henzinger, T. A. (2014). Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-10(1:10)2014","mla":"Boker, Udi, and Thomas A. Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” Logical Methods in Computer Science, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:10)2014.","ista":"Boker U, Henzinger TA. 2014. Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. 10(1).","chicago":"Boker, Udi, and Thomas A Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2014. https://doi.org/10.2168/LMCS-10(1:10)2014."},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"}]},{"oa":1,"quality_controlled":"1","publisher":"Frontiers Research Foundation","date_created":"2018-12-11T11:56:27Z","doi":"10.3389/fninf.2014.00016","date_published":"2014-02-21T00:00:00Z","year":"2014","has_accepted_license":"1","publication":"Frontiers in Neuroinformatics","day":"21","article_number":"16","author":[{"first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","full_name":"Guzmán, José"},{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"first_name":"Christoph","last_name":"Schmidt Hieber","full_name":"Schmidt Hieber, Christoph"}],"publist_id":"4731","title":"Stimfit: Quantifying electrophysiological data with Python","citation":{"mla":"Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” Frontiers in Neuroinformatics, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:10.3389/fninf.2014.00016.","apa":"Guzmán, J., Schlögl, A., & Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. Frontiers Research Foundation. https://doi.org/10.3389/fninf.2014.00016","ama":"Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 2014;8(FEB). doi:10.3389/fninf.2014.00016","short":"J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014).","ieee":"J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” Frontiers in Neuroinformatics, vol. 8, no. FEB. Frontiers Research Foundation, 2014.","chicago":"Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” Frontiers in Neuroinformatics. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fninf.2014.00016.","ista":"Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 8","month":"02","abstract":[{"lang":"eng","text":"Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals."}],"oa_version":"Published Version","volume":8,"issue":"FEB","publication_status":"published","publication_identifier":{"issn":["16625196"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-425-v1+1_fninf-08-00016.pdf","date_created":"2018-12-12T10:12:17Z","creator":"system","file_size":2883372,"date_updated":"2020-07-14T12:45:34Z","file_id":"4935","checksum":"eeca00bba7232ff7d27db83321f6ea30","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"425","status":"public","_id":"2230","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:34Z","date_updated":"2021-01-12T06:56:09Z","ddc":["570"]},{"project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"},{"call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"}],"publist_id":"4733","author":[{"id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua","full_name":"Hu, Hua","last_name":"Hu"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"title":"A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons","citation":{"chicago":"Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience. Nature Publishing Group, 2014. https://doi.org/10.1038/nn.3678.","ista":"Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693.","mla":"Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:10.1038/nn.3678.","short":"H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.","ieee":"H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons,” Nature Neuroscience, vol. 17, no. 5. Nature Publishing Group, pp. 686–693, 2014.","apa":"Hu, H., & Jonas, P. M. (2014). A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3678","ama":"Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 2014;17(5):686-693. doi:10.1038/nn.3678"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","page":"686-693","date_created":"2018-12-11T11:56:26Z","doi":"10.1038/nn.3678","date_published":"2014-03-23T00:00:00Z","year":"2014","publication":"Nature Neuroscience","day":"23","type":"journal_article","status":"public","_id":"2228","department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:56:08Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/","open_access":"1"}],"scopus_import":1,"intvolume":" 17","month":"03","abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing."}],"oa_version":"Submitted Version","ec_funded":1,"volume":17,"issue":"5","publication_status":"published","publication_identifier":{"issn":["10976256"]},"language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","date_created":"2018-12-11T11:56:27Z","date_published":"2014-02-01T00:00:00Z","doi":"10.1126/science.1244811","page":"665 - 670","publication":"Science","day":"01","year":"2014","project":[{"grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"title":"Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse","publist_id":"4732","author":[{"first_name":"Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Nicholas","last_name":"Vyleta"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.","ieee":"N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse,” Science, vol. 343, no. 6171. American Association for the Advancement of Science, pp. 665–670, 2014.","apa":"Vyleta, N., & Jonas, P. M. (2014). Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1244811","ama":"Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 2014;343(6171):665-670. doi:10.1126/science.1244811","mla":"Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” Science, vol. 343, no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70, doi:10.1126/science.1244811.","ista":"Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.","chicago":"Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1244811."},"intvolume":" 343","month":"02","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose "microdomain" coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity."}],"ec_funded":1,"issue":"6171","volume":343,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00368075"]},"status":"public","type":"journal_article","_id":"2229","department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:56:09Z"}]