--- _id: '1934' abstract: - lang: eng text: The plant hormones auxin and cytokinin mutually coordinate their activities to control various aspects of development [1-9], and their crosstalk occurs at multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate that cytokinin does not merely control the overall auxin flow capacity, but might also act as a polarizing cue and control the auxin stream directionality during plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter depletion at specific polar domains, thus rearranging the cellular PIN polarities and directly regulating the auxin flow direction. This selective cytokinin sensitivity correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking mutations, as well as enhanced phosphorylation in plants with modulated activities of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results reveal conceptually novel, cytokinin-driven polarization mechanism that operates in developmental processes involving rapid auxin stream redirection, such as lateral root organogenesis, in which a gradual PIN polarity switch defines the growth axis of the newly formed organ. author: - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Benjamin full_name: Weller, Benjamin last_name: Weller - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Claus full_name: Schwechheimer, Claus last_name: Schwechheimer - first_name: Angus full_name: Murphy, Angus last_name: Murphy - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: 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 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 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. 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. ista: Marhavý P, Duclercq J, Weller B, Feraru E, Bielach A, Offringa R, Friml J, Schwechheimer C, Murphy A, Benková E. 2014. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 24(9), 1031–1037. mla: Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology, vol. 24, no. 9, Cell Press, 2014, pp. 1031–37, doi:10.1016/j.cub.2014.04.002. short: P. Marhavý, J. Duclercq, B. Weller, E. Feraru, A. Bielach, R. Offringa, J. Friml, C. Schwechheimer, A. Murphy, E. Benková, Current Biology 24 (2014) 1031–1037. date_created: 2018-12-11T11:54:48Z date_published: 2014-05-05T00:00:00Z date_updated: 2021-01-12T06:54:10Z day: '05' department: - _id: EvBe - _id: JiFr doi: 10.1016/j.cub.2014.04.002 ec_funded: 1 intvolume: ' 24' issue: '9' language: - iso: eng month: '05' oa_version: None page: 1031 - 1037 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5160' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1932' abstract: - lang: eng text: The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. acknowledgement: "Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n" author: - first_name: Meredith full_name: Trotter, Meredith last_name: Trotter - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Grant full_name: Peterson, Grant last_name: Peterson - first_name: Kayla full_name: Peck, Kayla last_name: Peck - first_name: Joanna full_name: Masel, Joanna last_name: Masel citation: 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 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. 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. 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. date_created: 2018-12-11T11:54:47Z date_published: 2014-12-01T00:00:00Z date_updated: 2021-01-12T06:54:10Z day: '01' department: - _id: NiBa doi: 10.1111/evo.12517 ec_funded: 1 intvolume: ' 68' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.6077 month: '12' oa: 1 oa_version: Submitted Version page: 3357 - 3367 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '5162' quality_controlled: '1' scopus_import: 1 status: public title: Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2014' ... --- _id: '1930' abstract: - lang: eng text: (Figure Presented) Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications. acknowledgement: RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC author: - first_name: David full_name: Günther, David last_name: Günther - first_name: Alec full_name: Jacobson, Alec last_name: Jacobson - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Hans full_name: Seidel, Hans last_name: Seidel - first_name: Olga full_name: Sorkine Hornung, Olga last_name: Sorkine Hornung - first_name: Tino full_name: Weinkauf, Tino last_name: Weinkauf citation: 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 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. 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. ista: Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. 2014. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 20(12), 2585–2594. mla: Günther, David, et al. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12, IEEE, 2014, pp. 2585–94, doi:10.1109/TVCG.2014.2346432. short: D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, T. Weinkauf, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 2585–2594. date_created: 2018-12-11T11:54:46Z date_published: 2014-12-31T00:00:00Z date_updated: 2021-01-12T06:54:09Z day: '31' department: - _id: HeEd doi: 10.1109/TVCG.2014.2346432 intvolume: ' 20' issue: '12' language: - iso: eng month: '12' oa_version: None page: 2585 - 2594 publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '5164' quality_controlled: '1' scopus_import: 1 status: public title: Fast and memory-efficient topological denoising of 2D and 3D scalar fields type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2014' ... --- _id: '1933' abstract: - lang: eng text: The development of the vertebrate brain requires an exquisite balance between proliferation and differentiation of neural progenitors. Notch signaling plays a pivotal role in regulating this balance, yet the interaction between signaling and receiving cells remains poorly understood. We have found that numerous nascent neurons and/or intermediate neurogenic progenitors expressing the ligand of Notch retain apical endfeet transiently at the ventricular lumen that form adherens junctions (AJs) with the endfeet of progenitors. Forced detachment of the apical endfeet of those differentiating cells by disrupting AJs resulted in precocious neurogenesis that was preceded by the downregulation of Notch signaling. Both Notch1 and its ligand Dll1 are distributed around AJs in the apical endfeet, and these proteins physically interact with ZO-1, a constituent of the AJ. Furthermore, live imaging of a fluorescently tagged Notch1 demonstrated its trafficking from the apical endfoot to the nucleus upon cleavage. Our results identified the apical endfoot as the central site of active Notch signaling to securely prohibit inappropriate differentiation of neural progenitors. author: - first_name: Jun full_name: Hatakeyama, Jun last_name: Hatakeyama - first_name: Yoshio full_name: Wakamatsu, Yoshio last_name: Wakamatsu - first_name: Akira full_name: Nagafuchi, Akira last_name: Nagafuchi - first_name: Ryoichiro full_name: Kageyama, Ryoichiro last_name: Kageyama - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Kenji full_name: Shimamura, Kenji last_name: Shimamura citation: ama: Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. 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 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. ista: Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. 2014. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 141(8), 1671–1682. mla: Hatakeyama, Jun, et al. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development, vol. 141, no. 8, Company of Biologists, 2014, pp. 1671–82, doi:10.1242/dev.102988. short: J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682. date_created: 2018-12-11T11:54:47Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:54:10Z day: '01' department: - _id: RySh doi: 10.1242/dev.102988 intvolume: ' 141' issue: '8' language: - iso: eng month: '04' oa_version: None page: 1671 - 1682 publication: Development publication_status: published publisher: Company of Biologists publist_id: '5161' quality_controlled: '1' scopus_import: 1 status: public title: Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2014' ... --- _id: '1931' abstract: - lang: eng text: A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity. 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. article_number: '57' author: - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Jochen full_name: Triesch, Jochen last_name: Triesch citation: ama: Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057 apa: Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057 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. 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. 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. short: C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014). date_created: 2018-12-11T11:54:46Z date_published: 2014-05-28T00:00:00Z date_updated: 2021-01-12T06:54:09Z day: '28' department: - _id: GaTk doi: 10.3389/fncom.2014.00057 intvolume: ' 8' issue: MAY language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/ month: '05' oa: 1 oa_version: Submitted Version publication: Frontiers in Computational Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '5163' quality_controlled: '1' scopus_import: 1 status: public title: Emergence of task-dependent representations in working memory circuits type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2014' ... --- _id: '1937' abstract: - lang: eng 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. author: - first_name: Paul full_name: Bourgade, Paul last_name: Bourgade - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Horngtzer full_name: Yau, Horngtzer last_name: Yau citation: 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 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. 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. 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. short: P. Bourgade, L. Erdös, H. Yau, Communications in Mathematical Physics 332 (2014) 261–353. date_created: 2018-12-11T11:54:48Z date_published: 2014-11-01T00:00:00Z date_updated: 2021-01-12T06:54:12Z day: '01' department: - _id: LaEr doi: 10.1007/s00220-014-2120-z intvolume: ' 332' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1306.5728 month: '11' oa: 1 oa_version: Submitted Version page: 261 - 353 project: - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '5158' quality_controlled: '1' scopus_import: 1 status: public title: Edge universality of beta ensembles type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 332 year: '2014' ... --- _id: '1981' abstract: - lang: eng text: Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may provide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis. acknowledgement: Funded by University of Alaska Center for Global Change Student Research Cooperative Institute for Alaska Research and the Rasmuson Foundation author: - first_name: Michael full_name: Garvin, Michael R last_name: Garvin - first_name: Joseph full_name: Bielawski, Joseph P last_name: Bielawski - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Anthony full_name: Gharrett, Anthony J last_name: Gharrett citation: 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 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 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. 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. 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. short: M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2014) 1–17. date_created: 2018-12-11T11:55:02Z date_published: 2014-02-01T00:00:00Z date_updated: 2019-04-26T07:22:06Z day: '01' doi: 10.1111/jzs.12079 extern: 1 intvolume: ' 53' issue: '1' month: '02' page: 1 - 17 publication: Journal of Zoological Systematics and Evolutionary Research publication_status: published publisher: Wiley-Blackwell publist_id: '5102' quality_controlled: 0 status: public title: Review and meta-analysis of natural selection in mitochondrial complex I in metazoans type: review volume: 53 year: '2014' ... --- _id: '1980' abstract: - lang: eng text: Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors. acknowledgement: Funded by Health Research Council of New Zealand Royal Society of New Zealand University of Otago New Zealand Synchrotron Group author: - first_name: Adam full_name: 'Heikal, Adam ' last_name: Heikal - first_name: Yoshio full_name: Nakatani, Yoshio last_name: Nakatani - first_name: Elyse full_name: Dunn, Elyse A last_name: Dunn - first_name: Marion full_name: Weimar, Marion R last_name: Weimar - first_name: Catherine full_name: Day, Catherine last_name: Day - first_name: Edward full_name: Baker, Edward N last_name: Baker - first_name: Shaun full_name: Lott, Shaun J last_name: Lott - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Gregory full_name: Cook, Gregory last_name: Cook citation: 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' 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' 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.' 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.' 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.' mla: 'Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507.' short: A. Heikal, Y. Nakatani, E. Dunn, M. Weimar, C. Day, E. Baker, S. Lott, L.A. Sazanov, G. Cook, Molecular Microbiology 91 (2014) 950–964. date_created: 2018-12-11T11:55:01Z date_published: 2014-03-01T00:00:00Z date_updated: 2021-01-12T06:54:29Z day: '01' doi: 10.1111/mmi.12507 extern: 1 intvolume: ' 91' issue: '5' month: '03' page: 950 - 964 publication: Molecular Microbiology publication_status: published publisher: Wiley-Blackwell publist_id: '5103' quality_controlled: 0 status: public title: 'Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation' type: journal_article volume: 91 year: '2014' ... --- _id: '1979' 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. author: - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: 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 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. 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. 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. 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. short: L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253. date_created: 2018-12-11T11:55:01Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T06:54:28Z day: '01' doi: 10.1007/s10863-014-9554-z extern: 1 intvolume: ' 46' issue: '4' month: '08' page: 247 - 253 publication: Journal of Bioenergetics and Biomembranes publication_status: published publisher: Springer publist_id: '5104' quality_controlled: 0 status: public title: The mechanism of coupling between electron transfer and proton translocation in respiratory complex I type: journal_article volume: 46 year: '2014' ... --- _id: '1989' 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.). ' 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 full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Keisuke full_name: 'Ishihara, Keisuke ' last_name: Ishihara - first_name: Martin full_name: 'Wühr, Martin ' last_name: Wühr - first_name: Christine full_name: Field, Christine M last_name: Field - first_name: Timothy full_name: Mitchison, Timothy J last_name: Mitchison citation: 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 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 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. 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. 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. short: P. Nguyen, A. Groen, M. Loose, K. Ishihara, M. Wühr, C. Field, T. Mitchison, Science 346 (2014) 244–247. date_created: 2018-12-11T11:55:04Z date_published: 2014-10-10T00:00:00Z date_updated: 2021-01-12T06:54:32Z day: '10' doi: 10.1126/science.1256773 extern: 1 intvolume: ' 346' issue: '6206' month: '10' page: 244 - 247 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5093' quality_controlled: 0 status: public title: Spatial organization of cytokinesis signaling reconstituted in a cell-free system type: journal_article volume: 346 year: '2014' ... --- _id: '1990' 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. author: - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Timothy full_name: Mitchison, Timothy J last_name: Mitchison citation: ama: Loose M, Mitchison T. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 2014;16(1):38-46. doi:10.1038/ncb2885 apa: Loose, M., & Mitchison, T. (2014). The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2885 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. ieee: M. Loose and T. Mitchison, “The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns,” Nature Cell Biology, vol. 16, no. 1. Nature Publishing Group, pp. 38–46, 2014. ista: Loose M, Mitchison T. 2014. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 16(1), 38–46. 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. short: M. Loose, T. Mitchison, Nature Cell Biology 16 (2014) 38–46. date_created: 2018-12-11T11:55:05Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:33Z day: '01' doi: 10.1038/ncb2885 extern: 1 intvolume: ' 16' issue: '1' month: '01' page: 38 - 46 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5094' quality_controlled: 0 status: public title: The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns type: journal_article volume: 16 year: '2014' ... --- _id: '1996' abstract: - lang: eng 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. author: - first_name: Ora full_name: Hazak, Ora last_name: Hazak - first_name: Uri full_name: Obolski, Uri last_name: Obolski - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Lilach full_name: Hadany, Lilach last_name: Hadany - first_name: Shaul full_name: Yalovsky, Shaul last_name: Yalovsky citation: 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 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. 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. 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. date_created: 2018-12-11T11:55:07Z date_published: 2014-12-16T00:00:00Z date_updated: 2021-01-12T06:54:35Z day: '16' department: - _id: JiFr doi: 10.1073/pnas.1413918111 intvolume: ' 111' issue: '50' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/ month: '12' oa: 1 oa_version: Submitted Version page: E5471 - E5479 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5083' quality_controlled: '1' scopus_import: 1 status: public title: Bimodal regulation of ICR1 levels generates self-organizing auxin distribution type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1994' 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. author: - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Katarina full_name: Landberg, Katarina last_name: Landberg - first_name: Mattias full_name: Thelander, Mattias last_name: Thelander - first_name: Eva full_name: Medvecka, Eva last_name: Medvecka - first_name: Eric full_name: Pederson, Eric last_name: Pederson - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Endymion full_name: Cooper, Endymion last_name: Cooper - first_name: Mansour full_name: Karimi, Mansour last_name: Karimi - first_name: Charles full_name: Delwiche, Charles last_name: Delwiche - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Eva full_name: Sundberg, Eva last_name: Sundberg - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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. ieee: T. Viaene et al., “Directional auxin transport mechanisms in early diverging land plants,” Current Biology, vol. 24, no. 23. Cell Press, pp. 2786–2791, 2014. ista: Viaene T, Landberg K, Thelander M, Medvecka E, Pederson E, Feraru E, Cooper E, Karimi M, Delwiche C, Ljung K, Geisler M, Sundberg E, Friml J. 2014. Directional auxin transport mechanisms in early diverging land plants. Current Biology. 24(23), 2786–2791. 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. 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. date_created: 2018-12-11T11:55:06Z date_published: 2014-12-01T00:00:00Z date_updated: 2021-01-12T06:54:34Z day: '01' department: - _id: JiFr doi: 10.1016/j.cub.2014.09.056 ec_funded: 1 intvolume: ' 24' issue: '23' language: - iso: eng month: '12' oa_version: None page: 2786 - 2791 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5088' quality_controlled: '1' scopus_import: 1 status: public title: Directional auxin transport mechanisms in early diverging land plants type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1995' abstract: - lang: eng text: 'Optical transport represents a natural route towards fast communications, and it is currently used in large scale data transfer. The progressive miniaturization of devices for information processing calls for the microscopic tailoring of light transport and confinement at length scales appropriate for upcoming technologies. With this goal in mind, we present a theoretical analysis of a one-dimensional Fabry-Perot interferometer built with two highly saturable nonlinear mirrors: a pair of two-level systems. Our approach captures nonlinear and nonreciprocal effects of light transport that were not reported previously. Remarkably, we show that such an elementary device can operate as a microscopic integrated optical rectifier.' article_number: '243601' author: - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini - first_name: Eduardo full_name: Mascarenhas, Eduardo last_name: Mascarenhas - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: Jean full_name: Poizat, Jean last_name: Poizat - first_name: Daniel full_name: Valente, Daniel last_name: Valente - first_name: Alexia full_name: Auffèves, Alexia last_name: Auffèves - first_name: Dario full_name: Gerace, Dario last_name: Gerace - first_name: Marcelo full_name: Santos, Marcelo last_name: Santos citation: ama: 'Fratini F, Mascarenhas E, Safari L, et al. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. Physical Review Letters. 2014;113(24). doi:10.1103/PhysRevLett.113.243601' 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' 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.' 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.' 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.' short: F. Fratini, E. Mascarenhas, L. Safari, J. Poizat, D. Valente, A. Auffèves, D. Gerace, M. Santos, Physical Review Letters 113 (2014). date_created: 2018-12-11T11:55:06Z date_published: 2014-12-08T00:00:00Z date_updated: 2021-01-12T06:54:34Z day: '08' department: - _id: MiLe doi: 10.1103/PhysRevLett.113.243601 ec_funded: 1 intvolume: ' 113' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.5972 month: '12' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5085' quality_controlled: '1' scopus_import: 1 status: public title: 'Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2014' ... --- _id: '1998' abstract: - lang: eng text: Immune systems are able to protect the body against secondary infection with the same parasite. In insect colonies, this protection is not restricted to the level of the individual organism, but also occurs at the societal level. Here, we review recent evidence for and insights into the mechanisms underlying individual and social immunisation in insects. We disentangle general immune-protective effects from specific immune memory (priming), and examine immunisation in the context of the lifetime of an individual and that of a colony, and of transgenerational immunisation that benefits offspring. When appropriate, we discuss parallels with disease defence strategies in human societies. We propose that recurrent parasitic threats have shaped the evolution of both the individual immune systems and colony-level social immunity in insects. 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. " author: - first_name: Leila full_name: El Masri, Leila id: 349A6E66-F248-11E8-B48F-1D18A9856A87 last_name: El Masri - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: 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 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 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. ieee: L. El Masri and S. Cremer, “Individual and social immunisation in insects,” Trends in Immunology, vol. 35, no. 10. Elsevier, pp. 471–482, 2014. ista: El Masri L, Cremer S. 2014. Individual and social immunisation in insects. Trends in Immunology. 35(10), 471–482. 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. short: L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482. date_created: 2018-12-11T11:55:07Z date_published: 2014-10-01T00:00:00Z date_updated: 2021-01-12T06:54:35Z day: '01' department: - _id: SyCr doi: 10.1016/j.it.2014.08.005 intvolume: ' 35' issue: '10' language: - iso: eng month: '10' oa_version: None page: 471 - 482 publication: Trends in Immunology publication_status: published publisher: Elsevier publist_id: '5081' quality_controlled: '1' scopus_import: 1 status: public title: Individual and social immunisation in insects type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2014' ... --- _id: '2002' 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. article_number: '0113124' author: - first_name: Sooyun full_name: Kim, Sooyun id: 394AB1C8-F248-11E8-B48F-1D18A9856A87 last_name: Kim citation: 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 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 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. 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. 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. 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). date_created: 2018-12-11T11:55:09Z date_published: 2014-11-19T00:00:00Z date_updated: 2021-01-12T06:54:39Z day: '19' ddc: - '570' department: - _id: PeJo doi: 10.1371/journal.pone.0113124 ec_funded: 1 file: - access_level: open_access checksum: 85e4f4ea144f827272aaf376b2830564 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:52Z date_updated: 2020-07-14T12:45:24Z file_id: '5107' file_name: IST-2016-434-v1+1_journal.pone.0113124.pdf file_size: 5179993 relation: main_file file_date_updated: 2020-07-14T12:45:24Z has_accepted_license: '1' intvolume: ' 9' issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '11' oa: 1 oa_version: Published Version project: - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5074' pubrep_id: '434' quality_controlled: '1' scopus_import: 1 status: public title: Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus tmp: 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) short: CC BY-SA (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '2003' abstract: - lang: eng text: Learning can be facilitated by previous knowledge when it is organized into relational representations forming schemas. In this issue of Neuron, McKenzie et al. (2014) demonstrate that the hippocampus rapidly forms interrelated, hierarchical memory representations to support schema-based learning. author: - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: O’Neill J, Csicsvari JL. Learning by example in the hippocampus. Neuron. 2014;83(1):8-10. doi:10.1016/j.neuron.2014.06.013 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 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. ieee: J. O’Neill and J. L. Csicsvari, “Learning by example in the hippocampus,” Neuron, vol. 83, no. 1. Elsevier, pp. 8–10, 2014. ista: O’Neill J, Csicsvari JL. 2014. Learning by example in the hippocampus. Neuron. 83(1), 8–10. 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. date_created: 2018-12-11T11:55:09Z date_published: 2014-07-02T00:00:00Z date_updated: 2021-01-12T06:54:39Z day: '02' department: - _id: JoCs doi: 10.1016/j.neuron.2014.06.013 intvolume: ' 83' issue: '1' language: - iso: eng month: '07' oa_version: None page: 8 - 10 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5073' quality_controlled: '1' scopus_import: 1 status: public title: Learning by example in the hippocampus type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2014' ... --- _id: '2011' 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). 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. author: - first_name: Fei full_name: Yu, Fei last_name: Yu - first_name: Stephen full_name: Fienberg, Stephen last_name: Fienberg - first_name: Alexandra full_name: Slaković, Alexandra last_name: Slaković - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 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 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. ieee: F. Yu, S. Fienberg, A. Slaković, and C. Uhler, “Scalable privacy-preserving data sharing methodology for genome-wide association studies,” Journal of Biomedical Informatics, vol. 50. Elsevier, pp. 133–141, 2014. ista: Yu F, Fienberg S, Slaković A, Uhler C. 2014. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. 50, 133–141. 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. short: F. Yu, S. Fienberg, A. Slaković, C. Uhler, Journal of Biomedical Informatics 50 (2014) 133–141. date_created: 2018-12-11T11:55:12Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T06:54:42Z day: '01' department: - _id: CaUh doi: 10.1016/j.jbi.2014.01.008 intvolume: ' 50' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1401.5193 month: '08' oa: 1 oa_version: Submitted Version page: 133 - 141 publication: Journal of Biomedical Informatics publication_status: published publisher: Elsevier publist_id: '5065' quality_controlled: '1' scopus_import: 1 status: public title: Scalable privacy-preserving data sharing methodology for genome-wide association studies type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2014' ... --- _id: '2005' 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. author: - first_name: David full_name: Dupret, David last_name: Dupret - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: 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 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. 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. 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. date_created: 2018-12-11T11:55:09Z date_published: 2014-04-25T00:00:00Z date_updated: 2021-01-12T06:54:40Z day: '25' department: - _id: JoCs doi: 10.1038/nn.3700 intvolume: ' 17' issue: '5' language: - iso: eng month: '04' oa_version: None page: 643 - 644 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '5071' quality_controlled: '1' scopus_import: 1 status: public title: Turning heads to remember places type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2014' ... --- _id: '2007' abstract: - lang: eng text: Maximum likelihood estimation under relational models, with or without the overall effect. For more information see the reference manual article_processing_charge: No author: - first_name: Anna full_name: Klimova, Anna id: 31934120-F248-11E8-B48F-1D18A9856A87 last_name: Klimova - first_name: Tamás full_name: Rudas, Tamás last_name: Rudas 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.' chicago: 'Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional Fitting for Relational Models.” The Comprehensive R Archive Network, 2014.' ieee: 'A. Klimova and T. Rudas, “gIPFrm: Generalized iterative proportional fitting for relational models.” The Comprehensive R Archive Network, 2014.' ista: 'Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting for relational models, The Comprehensive R Archive Network.' mla: 'Klimova, Anna, and Tamás Rudas. GIPFrm: Generalized Iterative Proportional Fitting for Relational Models. The Comprehensive R Archive Network, 2014.' short: A. Klimova, T. Rudas, (2014). date_created: 2018-12-11T11:55:10Z date_published: 2014-03-20T00:00:00Z date_updated: 2022-08-26T08:12:12Z day: '20' department: - _id: CaUh main_file_link: - open_access: '1' url: 'https://CRAN.R-project.org/package=gIPFrm ' month: '03' oa: 1 oa_version: Published Version publisher: The Comprehensive R Archive Network publist_id: '5069' status: public title: 'gIPFrm: Generalized iterative proportional fitting for relational models' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2018' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Hiroshi full_name: Matsukawa, Hiroshi last_name: Matsukawa - first_name: Sachiko full_name: Akiyoshi Nishimura, Sachiko last_name: Akiyoshi Nishimura - first_name: Qi full_name: Zhang, Qi last_name: Zhang - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Kazuhiko full_name: Yamaguchi, Kazuhiko last_name: Yamaguchi - first_name: Hiromichi full_name: Goto, Hiromichi last_name: Goto - first_name: Kunio full_name: Yaguchi, Kunio last_name: Yaguchi - first_name: Tsutomu full_name: Hashikawa, Tsutomu last_name: Hashikawa - first_name: Chie full_name: Sano, Chie last_name: Sano - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Toshiaki full_name: Nakashiba, Toshiaki last_name: Nakashiba - first_name: Shigeyoshi full_name: Itohara, Shigeyoshi last_name: Itohara citation: 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 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 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. 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. 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. mla: Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:10.1523/JNEUROSCI.1141-14.2014. short: H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792. date_created: 2018-12-11T11:55:14Z date_published: 2014-11-19T00:00:00Z date_updated: 2022-05-24T08:54:54Z day: '19' ddc: - '570' department: - _id: RySh doi: 10.1523/JNEUROSCI.1141-14.2014 external_id: pmid: - '25411505' file: - access_level: open_access checksum: 6913e9bc26e9fc1c0441a739a4199229 content_type: application/pdf creator: dernst date_created: 2022-05-24T08:41:41Z date_updated: 2022-05-24T08:41:41Z file_id: '11410' file_name: 2014_JournNeuroscience_Matsukawa.pdf file_size: 3963728 relation: main_file success: 1 file_date_updated: 2022-05-24T08:41:41Z has_accepted_license: '1' intvolume: ' 34' issue: '47' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 15779 - 15792 pmid: 1 publication: Journal of Neuroscience publication_identifier: eissn: - 1529-2401 issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience publist_id: '5054' quality_controlled: '1' scopus_import: '1' status: public title: Netrin-G/NGL complexes encode functional synaptic diversification type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2014' ... --- _id: '2019' abstract: - lang: eng text: We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J last_name: Schröder citation: 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 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. 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. 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. mla: Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:10.1007/s11040-014-9164-3. short: L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464. date_created: 2018-12-11T11:55:15Z date_published: 2014-12-17T00:00:00Z date_updated: 2021-01-12T06:54:45Z day: '17' department: - _id: LaEr doi: 10.1007/s11040-014-9164-3 ec_funded: 1 intvolume: ' 17' issue: 3-4 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.1552 month: '12' oa: 1 oa_version: Submitted Version page: 441 - 464 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Mathematical Physics, Analysis and Geometry publication_status: published publisher: Springer publist_id: '5053' quality_controlled: '1' scopus_import: 1 status: public title: Phase transition in the density of states of quantum spin glasses type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2014' ... --- _id: '2013' abstract: - lang: eng text: "An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n" 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). author: - first_name: Shaowei full_name: Lin, Shaowei last_name: Lin - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Bernd full_name: Sturmfels, Bernd last_name: Sturmfels - first_name: Peter full_name: Bühlmann, Peter last_name: Bühlmann citation: ama: Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 2014;14(5):1079-1116. doi:10.1007/s10208-014-9205-0 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 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. 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. 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. mla: Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:10.1007/s10208-014-9205-0. short: S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116. date_created: 2018-12-11T11:55:12Z date_published: 2014-10-10T00:00:00Z date_updated: 2021-01-12T06:54:43Z day: '10' department: - _id: CaUh doi: 10.1007/s10208-014-9205-0 intvolume: ' 14' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.0285 month: '10' oa: 1 oa_version: Submitted Version page: 1079 - 1116 publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '5063' quality_controlled: '1' scopus_import: 1 status: public title: Hypersurfaces and their singularities in partial correlation testing type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '2017' 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. D.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. author: - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Alex full_name: Lenkoski, Alex last_name: Lenkoski - first_name: Donald full_name: Richards, Donald last_name: Richards citation: 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. chicago: Uhler, Caroline, Alex Lenkoski, and Donald Richards. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv. 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. ista: Uhler C, Lenkoski A, Richards D. 2014. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv, . mla: Uhler, Caroline, et al. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv, ArXiv, 2014. short: C. Uhler, A. Lenkoski, D. Richards, ArXiv (2014). date_created: 2018-12-11T11:55:14Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T06:54:44Z day: '18' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1406.4901 month: '06' oa: 1 publication: ArXiv publication_status: published publisher: ArXiv publist_id: '5058' quality_controlled: 0 status: public title: ' Exact formulas for the normalizing constants of Wishart distributions for graphical models' type: preprint year: '2014' ... --- _id: '2022' abstract: - lang: eng 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. author: - first_name: Peng full_name: Gao, Peng last_name: Gao - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Teresa full_name: Krieger, Teresa last_name: Krieger - first_name: Luisirene full_name: Hernandez, Luisirene last_name: Hernandez - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Zhi full_name: Han, Zhi last_name: Han - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Ekaterina full_name: Papusheva, Ekaterina id: 41DB591E-F248-11E8-B48F-1D18A9856A87 last_name: Papusheva - first_name: Ryan full_name: Insolera, Ryan last_name: Insolera - first_name: Kritika full_name: Chugh, Kritika last_name: Chugh - first_name: Oren full_name: Kodish, Oren last_name: Kodish - first_name: Kun full_name: Huang, Kun last_name: Huang - first_name: Benjamin full_name: Simons, Benjamin last_name: Simons - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Song full_name: Shi, Song last_name: Shi citation: ama: Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 2014;159(4):775-788. doi:10.1016/j.cell.2014.10.027 apa: Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.10.027 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. ieee: P. Gao et al., “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” Cell, vol. 159, no. 4. Cell Press, pp. 775–788, 2014. ista: Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788. 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. 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. date_created: 2018-12-11T11:55:16Z date_published: 2014-11-06T00:00:00Z date_updated: 2021-01-12T06:54:47Z day: '06' ddc: - '570' department: - _id: SiHi - _id: Bio doi: 10.1016/j.cell.2014.10.027 ec_funded: 1 file: - access_level: open_access checksum: 6c5de8329bb2ffa71cba9fda750f14ce content_type: application/pdf creator: system date_created: 2018-12-12T10:08:47Z date_updated: 2020-07-14T12:45:25Z file_id: '4709' file_name: IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf file_size: 4435787 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 159' issue: '4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 775 - 788 project: - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development - _id: 25D7962E-B435-11E9-9278-68D0E5697425 grant_number: RGP0053/2014 name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level publication: Cell publication_status: published publisher: Cell Press publist_id: '5050' pubrep_id: '423' quality_controlled: '1' scopus_import: 1 status: public title: Deterministic progenitor behavior and unitary production of neurons in the neocortex tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2014' ... --- _id: '2020' 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. author: - first_name: Shah full_name: Ali, Shah last_name: Ali - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Lily full_name: Saadat, Lily last_name: Saadat - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Irving full_name: Weissman, Irving last_name: Weissman - first_name: Reza full_name: Ardehali, Reza last_name: Ardehali 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 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. 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. 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. mla: Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:10.1073/pnas.1408233111. short: S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855. date_created: 2018-12-11T11:55:15Z date_published: 2014-06-17T00:00:00Z date_updated: 2021-01-12T06:54:46Z day: '17' department: - _id: SiHi doi: 10.1073/pnas.1408233111 intvolume: ' 111' issue: '24' language: - iso: eng month: '06' oa_version: None page: 8850 - 8855 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5052' quality_controlled: '1' scopus_import: 1 status: public title: Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '2021' 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. author: - first_name: Joo full_name: William, Joo last_name: William - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: 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 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 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. 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. 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. short: J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629. date_created: 2018-12-11T11:55:15Z date_published: 2014-10-31T00:00:00Z date_updated: 2021-01-12T06:54:47Z day: '31' department: - _id: SiHi doi: 10.1126/science.1258996 intvolume: ' 346' issue: '6209' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/ month: '10' oa: 1 oa_version: Submitted Version page: 626 - 629 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5051' quality_controlled: '1' scopus_import: 1 status: public title: Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 346 year: '2014' ... --- _id: '2027' 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. 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. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Marta full_name: Kwiatkowska, Marta last_name: Kwiatkowska - first_name: David full_name: Parker, David last_name: Parker - first_name: Mateusz full_name: Ujma, Mateusz last_name: Ujma 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' 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. 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. 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.' mla: Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:10.1007/978-3-319-11936-6_8. short: T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114. conference: end_date: 2014-11-07 location: Sydney, Australia name: 'ALENEX: Algorithm Engineering and Experiments' start_date: 2014-11-03 date_created: 2018-12-11T11:55:17Z date_published: 2014-11-01T00:00:00Z date_updated: 2021-01-12T06:54:49Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-11936-6_8 ec_funded: 1 editor: - first_name: Franck full_name: Cassez, Franck last_name: Cassez - first_name: Jean-François full_name: Raskin, Jean-François last_name: Raskin intvolume: ' 8837' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.2967 month: '11' oa: 1 oa_version: Submitted Version page: 98 - 114 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 26241A12-B435-11E9-9278-68D0E5697425 grant_number: '24696' name: LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ' Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)' publication_status: published publisher: Society of Industrial and Applied Mathematics publist_id: '5046' quality_controlled: '1' status: public title: Verification of markov decision processes using learning algorithms type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8837 year: '2014' ... --- _id: '2031' abstract: - lang: eng text: A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release. author: - first_name: Itaru full_name: Arai, Itaru id: 32A73F6C-F248-11E8-B48F-1D18A9856A87 last_name: Arai - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Arai itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 2014;3. doi:10.7554/eLife.04057 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. 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. ista: Arai itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3. mla: Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife, vol. 3, eLife Sciences Publications, 2014, doi:10.7554/eLife.04057. short: itaru Arai, P.M. Jonas, ELife 3 (2014). date_created: 2018-12-11T11:55:19Z date_published: 2014-12-09T00:00:00Z date_updated: 2021-01-12T06:54:51Z day: '09' ddc: - '570' department: - _id: PeJo doi: 10.7554/eLife.04057 ec_funded: 1 file: - access_level: open_access checksum: c240f915450d4ebe8f95043a2a8c7b1a content_type: application/pdf creator: system date_created: 2018-12-12T10:14:41Z date_updated: 2020-07-14T12:45:26Z file_id: '5094' file_name: IST-2016-421-v1+1_e04057.full.pdf file_size: 2239563 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 3' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF 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 publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5041' pubrep_id: '421' quality_controlled: '1' scopus_import: 1 status: public title: Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2014' ... --- _id: '2024' 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.' article_number: '3498' author: - first_name: Junko full_name: Toshima, Junko last_name: Toshima - first_name: Show full_name: Nishinoaki, Show last_name: Nishinoaki - first_name: Yoshifumi full_name: Sato, Yoshifumi last_name: Sato - first_name: Wataru full_name: Yamamoto, Wataru last_name: Yamamoto - first_name: Daiki full_name: Furukawa, Daiki last_name: Furukawa - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Akira full_name: Sawaguchi, Akira last_name: Sawaguchi - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: ama: Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 2014;5. doi:10.1038/ncomms4498 apa: Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4498 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. ieee: J. Toshima et al., “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498. 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. short: J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014). date_created: 2018-12-11T11:55:16Z date_published: 2014-03-25T00:00:00Z date_updated: 2021-01-12T06:54:48Z day: '25' ddc: - '570' department: - _id: DaSi doi: 10.1038/ncomms4498 file: - access_level: open_access checksum: 614fb6579c86d1f95bdd95eeb9ab01b0 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:11Z date_updated: 2020-07-14T12:45:25Z file_id: '4864' file_name: IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf file_size: 4803515 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5048' pubrep_id: '616' quality_controlled: '1' scopus_import: 1 status: public title: Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2014' ... --- _id: '2028' abstract: - lang: eng text: 'Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model.' 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. ' article_processing_charge: No author: - first_name: Katarina full_name: Bodova, Katarina id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bodova orcid: 0000-0002-7214-0171 - first_name: David full_name: Paydarfar, David last_name: Paydarfar - first_name: Daniel full_name: Forger, Daniel last_name: Forger citation: ama: Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041 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 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. 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. 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. date_created: 2018-12-11T11:55:18Z date_published: 2014-10-12T00:00:00Z date_updated: 2022-08-25T14:00:47Z day: '12' ddc: - '570' department: - _id: GaTk doi: 10.1016/j.jtbi.2014.09.041 file: - access_level: open_access checksum: a9dbae18d3233b3dab6944fd3f2cd49e content_type: application/pdf creator: system date_created: 2018-12-12T10:17:58Z date_updated: 2020-07-14T12:45:25Z file_id: '5316' file_name: IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf file_size: 2679222 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 365' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version page: 40 - 54 publication: ' Journal of Theoretical Biology' publication_status: published publisher: Academic Press publist_id: '5043' pubrep_id: '444' quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1016/j.jtbi.2015.03.013 scopus_import: '1' status: public title: Characterizing spiking in noisy type II neurons tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 365 year: '2014' ... --- _id: '2026' abstract: - lang: eng 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.' acknowledgement: "Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n" alternative_title: - LNCS author: - first_name: Zuzana full_name: Komárková, Zuzana last_name: Komárková - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: 'Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Springer; 2014:235-241. doi:10.1007/978-3-319-11936-6_17' apa: 'Komárková, Z., & Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_17' 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.' ieee: 'Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 235–241.' ista: 'Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.' 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.' 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. conference: end_date: 2014-11-07 location: Sydney, Australia name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2014-11-03 date_created: 2018-12-11T11:55:17Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:49Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-11936-6_17 ec_funded: 1 editor: - first_name: Franck full_name: Cassez, Franck last_name: Cassez - first_name: Jean-François full_name: Raskin, Jean-François last_name: Raskin intvolume: ' 8837' language: - iso: eng month: '01' oa_version: None page: 235 - 241 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5045' quality_controlled: '1' status: public title: 'Rabinizer 3: Safraless translation of ltl to small deterministic automata' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8837 year: '2014' ... --- _id: '2029' 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. acknowledgement: 239694; ERC; European Research Council article_number: '20003' author: - first_name: Michele full_name: Correggi, Michele last_name: Correggi - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 2014;108(2). doi:10.1209/0295-5075/108/20003 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 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. 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. ista: Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003. 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. short: M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014). date_created: 2018-12-11T11:55:18Z date_published: 2014-10-13T00:00:00Z date_updated: 2021-01-12T06:54:50Z day: '13' department: - _id: RoSe doi: 10.1209/0295-5075/108/20003 intvolume: ' 108' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.4717 month: '10' oa: 1 oa_version: Submitted Version publication: EPL publication_status: published publisher: IOP Publishing Ltd. publist_id: '5044' quality_controlled: '1' scopus_import: 1 status: public title: Validity of spin-wave theory for the quantum Heisenberg model type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2014' ... --- _id: '2033' 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.' author: - first_name: Daniel full_name: Hernandez Lobato, Daniel last_name: Hernandez Lobato - first_name: Viktoriia full_name: Sharmanska, Viktoriia id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87 last_name: Sharmanska orcid: 0000-0003-0192-9308 - first_name: Kristian full_name: Kersting, Kristian last_name: Kersting - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto citation: 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.' 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.' 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.' 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.' mla: 'Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” Advances in Neural Information Processing Systems, vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45.' short: D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems, 2014, pp. 837–845. conference: end_date: 2014-12-13 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2014-12-08 date_created: 2018-12-11T11:55:20Z date_published: 2014-12-08T00:00:00Z date_updated: 2023-02-23T10:25:24Z day: '08' department: - _id: ChLa intvolume: ' 1' issue: January language: - iso: eng main_file_link: - open_access: '1' url: https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise month: '12' oa: 1 oa_version: Submitted Version page: 837-845 publication: Advances in Neural Information Processing Systems publication_status: published publisher: Neural Information Processing Systems publist_id: '5038' quality_controlled: '1' scopus_import: 1 status: public title: 'Mind the nuisance: Gaussian process classification using privileged noise' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2014' ... --- _id: '2032' 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. article_number: e964045 author: - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 - first_name: Karin full_name: Schelch, Karin last_name: Schelch - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Michael full_name: Grusch, Michael last_name: Grusch citation: 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' 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' 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.' 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.' 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.' short: Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014). date_created: 2018-12-11T11:55:19Z date_published: 2014-12-31T00:00:00Z date_updated: 2021-01-12T06:54:51Z day: '31' ddc: - '570' department: - _id: HaJa doi: 10.4161/23723548.2014.964045 file: - access_level: open_access checksum: 44e17ad40577ab46eb602e88a8b0b8fd content_type: application/pdf creator: kschuh date_created: 2019-05-16T13:39:11Z date_updated: 2020-07-14T12:45:26Z file_id: '6464' file_name: 2014_Taylor_Alvaro.pdf file_size: 1765933 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 1' issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version publication: Molecular and Cellular Oncology publication_status: published publisher: Taylor & Francis publist_id: '5040' quality_controlled: '1' scopus_import: 1 status: public title: 'The optogenetic promise for oncology: Episode I' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2014' ... --- _id: '2045' abstract: - lang: eng text: 'We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest.' acknowledgement: The second author was supported by EPSRC grant EP/H043454/1. alternative_title: - LNCS author: - first_name: Dana full_name: Dachman Soled, Dana last_name: Dachman Soled - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Payman full_name: Mohassel, Payman last_name: Mohassel - first_name: Adam full_name: O’Neill, Adam last_name: O’Neill citation: 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' 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. 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. 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.' mla: Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:10.1007/978-3-642-54631-0_19. short: D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344. conference: end_date: 2014-03-28 location: Buenos Aires, Argentina name: 'PKC: Public Key Crypography' start_date: 2014-03-26 date_created: 2018-12-11T11:55:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:57Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-54631-0_19 ec_funded: 1 editor: - first_name: Hugo full_name: Krawczyk, Hugo last_name: Krawczyk intvolume: ' 8383' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2012/543 month: '01' oa: 1 oa_version: Submitted Version page: 329 - 344 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5006' quality_controlled: '1' scopus_import: 1 status: public title: Enhanced chosen-ciphertext security and applications type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8383 year: '2014' ... --- _id: '2042' 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.' article_number: '663' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663 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. 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. ista: Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663. mla: Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663. short: A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014). date_created: 2018-12-11T11:55:23Z date_published: 2014-08-08T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '08' ddc: - '570' department: - _id: JoBo doi: 10.1186/1471-2164-15-663 file: - access_level: open_access checksum: 3f6d2776b90a842a28359cc957d3d04b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:24Z date_updated: 2020-07-14T12:45:26Z file_id: '4878' file_name: IST-2015-396-v1+1_1471-2164-15-663.pdf file_size: 1489769 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 15' issue: '1' language: - iso: eng license: https://creativecommons.org/publicdomain/zero/1.0/ month: '08' oa: 1 oa_version: Published Version publication: BMC Genomics publication_status: published publisher: BioMed Central publist_id: '5009' pubrep_id: '396' quality_controlled: '1' scopus_import: 1 status: public title: Motif depletion in bacteriophages infecting hosts with CRISPR systems 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) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '2043' abstract: - lang: eng text: Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node. author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Michael full_name: Kerber, Michael last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus citation: 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' 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' 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. 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. 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.' mla: Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, Society of Industrial and Applied Mathematics, 2014, pp. 31–38, doi:10.1137/1.9781611973198.4. short: U. Bauer, M. Kerber, J. Reininghaus, in:, C. McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2014, pp. 31–38. conference: end_date: 2014-01-05 location: Portland, USA name: 'ALENEX: Algorithm Engineering and Experiments' start_date: 2014-01-05 date_created: 2018-12-11T11:55:23Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '01' department: - _id: HeEd doi: 10.1137/1.9781611973198.4 ec_funded: 1 editor: - first_name: Catherine full_name: ' McGeoch, Catherine' last_name: ' McGeoch' - first_name: Ulrich full_name: Meyer, Ulrich last_name: Meyer language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.0710 month: '01' oa: 1 oa_version: Submitted Version page: 31 - 38 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Proceedings of the Workshop on Algorithm Engineering and Experiments publication_status: published publisher: Society of Industrial and Applied Mathematics publist_id: '5008' quality_controlled: '1' scopus_import: 1 status: public title: Distributed computation of persistent homology type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2041' abstract: - lang: eng text: The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time. article_number: 2p author: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: John full_name: Lisman, John last_name: Lisman citation: ama: Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 2014;8. doi:10.3389/fncir.2014.00107 apa: Jonas, P. M., & Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. Frontiers Research Foundation. https://doi.org/10.3389/fncir.2014.00107 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. ieee: P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” Frontiers in Neural Circuits, vol. 8. Frontiers Research Foundation, 2014. ista: Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p. 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. short: P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014). date_created: 2018-12-11T11:55:22Z date_published: 2014-09-10T00:00:00Z date_updated: 2021-01-12T06:54:55Z day: '10' ddc: - '570' department: - _id: PeJo doi: 10.3389/fncir.2014.00107 file: - access_level: open_access checksum: 3ca57b164045523f876407e9f13a9fb8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:38Z date_updated: 2020-07-14T12:45:26Z file_id: '5294' file_name: IST-2016-424-v1+1_fncir-08-00107.pdf file_size: 201110 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Frontiers in Neural Circuits publication_status: published publisher: Frontiers Research Foundation publist_id: '5010' pubrep_id: '424' quality_controlled: '1' scopus_import: 1 status: public title: Structure, function and plasticity of hippocampal dentate gyrus microcircuits tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2014' ... --- _id: '2044' abstract: - lang: eng text: We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation. author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Michael full_name: Kerber, Michael last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus citation: ama: 'Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Springer; 2014:103-117. doi:10.1007/978-3-319-04099-8_7' apa: 'Bauer, U., Kerber, M., & Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (pp. 103–117). Springer. https://doi.org/10.1007/978-3-319-04099-8_7' 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.' ieee: 'U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in Topological Methods in Data Analysis and Visualization III, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.' ista: 'Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117.' 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.' 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. date_created: 2018-12-11T11:55:23Z date_published: 2014-03-19T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '19' department: - _id: HeEd doi: 10.1007/978-3-319-04099-8_7 ec_funded: 1 editor: - first_name: Peer-Timo full_name: Bremer, Peer-Timo last_name: Bremer - first_name: Ingrid full_name: Hotz, Ingrid last_name: Hotz - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci - first_name: Ronald full_name: Peikert, Ronald last_name: Peikert language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.0477 month: '03' oa: 1 oa_version: Submitted Version page: 103 - 117 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Topological Methods in Data Analysis and Visualization III publication_status: published publisher: Springer publist_id: '5007' quality_controlled: '1' scopus_import: 1 series_title: Mathematics and Visualization status: public title: 'Clear and Compress: Computing Persistent Homology in Chunks' type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2040' 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. ' article_number: '1254927' author: - first_name: Anna full_name: Kicheva, Anna last_name: Kicheva - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Ana full_name: Ribeiro, Ana last_name: Ribeiro - first_name: Helena full_name: Pérez Valle, Helena last_name: Pérez Valle - first_name: Robin full_name: Lovell Badge, Robin last_name: Lovell Badge - first_name: Vasso full_name: Episkopou, Vasso last_name: Episkopou - first_name: James full_name: Briscoe, James last_name: Briscoe citation: 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 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 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. 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. 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. mla: Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:10.1126/science.1254927. short: A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014). date_created: 2018-12-11T11:55:22Z date_published: 2014-09-26T00:00:00Z date_updated: 2021-01-12T06:54:55Z day: '26' department: - _id: ToBo doi: 10.1126/science.1254927 intvolume: ' 345' issue: '6204' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/ month: '09' oa: 1 oa_version: Submitted Version publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5011' quality_controlled: '1' scopus_import: 1 status: public title: Coordination of progenitor specification and growth in mouse and chick spinal cord type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 345 year: '2014' ... --- _id: '2047' 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. acknowledgement: This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University. alternative_title: - LNCS author: - first_name: Fei full_name: Yu, Fei last_name: Yu - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Stephen full_name: Fienberg, Stephen last_name: Fienberg citation: 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' 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' 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. 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. 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. 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. conference: end_date: 2014-09-19 location: Ibiza, Spain name: 'PSD: Privacy in Statistical Databases' start_date: 2014-09-17 date_created: 2018-12-11T11:55:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:57Z day: '01' department: - _id: KrPi - _id: CaUh doi: 10.1007/978-3-319-11257-2_14 editor: - first_name: Josep full_name: Domingo Ferrer, Josep last_name: Domingo Ferrer external_id: arxiv: - '1407.8067' intvolume: ' 8744' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.8067 month: '01' oa: 1 oa_version: Submitted Version page: 170 - 184 project: - _id: 25636330-B435-11E9-9278-68D0E5697425 grant_number: 11-NSF-1070 name: ROOTS Genome-wide Analysis of Root Traits publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5004' quality_controlled: '1' scopus_import: 1 status: public title: Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8744 year: '2014' ... --- _id: '2053' abstract: - lang: eng text: In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems. 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. alternative_title: - LNCS author: - first_name: Holger full_name: Hermanns, Holger last_name: Hermanns - first_name: Jan full_name: Krčál, Jan last_name: Krčál - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: 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' 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.' 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.' 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.' 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.' 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. conference: end_date: 2014-09-05 location: Rome, Italy name: 'CONCUR: Concurrency Theory' start_date: 2014-09-02 date_created: 2018-12-11T11:55:27Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:55:00Z day: '01' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-662-44584-6_18 ec_funded: 1 editor: - first_name: Paolo full_name: Baldan, Paolo last_name: Baldan - first_name: Daniele full_name: Gorla, Daniele last_name: Gorla intvolume: ' 8704' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.5084 month: '09' oa: 1 oa_version: Submitted Version page: 249 - 265 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4993' status: public title: 'Probabilistic bisimulation: Naturally on distributions' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8704 year: '2014' ... --- _id: '2052' 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. 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. alternative_title: - LNCS author: - first_name: Benjamin full_name: Aminof, Benjamin id: 4A55BD00-F248-11E8-B48F-1D18A9856A87 last_name: Aminof - first_name: Tomer full_name: Kotek, Tomer last_name: Kotek - first_name: Sacha full_name: Rubin, Sacha last_name: Rubin - first_name: Francesco full_name: Spegni, Francesco last_name: Spegni - first_name: Helmut full_name: Veith, Helmut last_name: Veith 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' 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. ieee: B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 109–124. ista: 'Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124.' 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. 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. conference: end_date: 2014-09-05 location: Rome, Italy name: 'CONCUR: Concurrency Theory' start_date: 2014-09-02 date_created: 2018-12-11T11:55:26Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:54:59Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-44584-6_9 editor: - first_name: Paolo full_name: Baldan, Paolo last_name: Baldan - first_name: Daniele full_name: Gorla, Daniele last_name: Gorla intvolume: ' 8704' language: - iso: eng month: '09' oa_version: None page: 109 - 124 publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4994' quality_controlled: '1' status: public title: Parameterized model checking of rendezvous systems type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8704 year: '2014' ... --- _id: '2046' abstract: - lang: eng 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.' acknowledgement: Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1. alternative_title: - LNCS author: - first_name: Mihir full_name: Bellare, Mihir last_name: Bellare - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer citation: ama: 'Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:520-537. doi:10.1007/978-3-642-54631-0_30' apa: 'Bellare, M., & Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_30' 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. ieee: M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537. ista: 'Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.' 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. 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. conference: end_date: 2014-05-28 location: Buenos Aires, Argentina name: 'PKC: Public Key Crypography' start_date: 2014-05-26 date_created: 2018-12-11T11:55:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:57Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-54631-0_30 ec_funded: 1 editor: - first_name: Hugo full_name: Krawczyk, Hugo last_name: Krawczyk intvolume: ' 8383' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2013/413 month: '01' oa: 1 oa_version: Submitted Version page: 520 - 537 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5005' quality_controlled: '1' scopus_import: 1 status: public title: Policy-based signatures type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8383 year: '2014' ... --- _id: '2050' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Markus full_name: Holzner, Markus last_name: Holzner - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Hendrik full_name: Kuhlmann, Hendrik last_name: Kuhlmann citation: 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 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 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. 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. 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. mla: Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:10.1017/jfm.2013.603. short: J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491. date_created: 2018-12-11T11:55:25Z date_published: 2014-01-10T00:00:00Z date_updated: 2021-01-12T06:54:59Z day: '10' department: - _id: BjHo doi: 10.1017/jfm.2013.603 external_id: arxiv: - '1508.06546' intvolume: ' 738' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.06546 month: '01' oa: 1 oa_version: Submitted Version page: 463 - 491 publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '5001' quality_controlled: '1' scopus_import: 1 status: public title: Experimental investigation of transitional flow in a toroidal pipe type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 738 year: '2014' ... --- _id: '2051' abstract: - lang: eng text: We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach. author: - first_name: Mario full_name: Marchand, Mario last_name: Marchand - first_name: Su full_name: Hongyu, Su last_name: Hongyu - first_name: Emilie full_name: Emilie Morvant id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87 last_name: Morvant orcid: 0000-0002-8301-7240 - first_name: Juho full_name: Rousu, Juho last_name: Rousu - first_name: John full_name: Shawe-Taylor, John last_name: Shawe Taylor citation: ama: 'Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: Neural Information Processing Systems; 2014.' apa: 'Marchand, M., Hongyu, S., Morvant, E., Rousu, J., & Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.' 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. ieee: 'M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” presented at the NIPS: Neural Information Processing Systems, 2014.' ista: 'Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. NIPS: Neural Information Processing Systems.' 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. conference: name: 'NIPS: Neural Information Processing Systems' date_created: 2018-12-11T11:55:26Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:59Z day: '01' extern: 1 main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01065586 month: '01' oa: 1 publication_status: published publisher: Neural Information Processing Systems publist_id: '4996' quality_controlled: 0 status: public title: Multilabel structured output learning with random spanning trees of max-margin Markov networks type: conference year: '2014' ... --- _id: '2059' abstract: - lang: eng text: Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant. 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. author: - first_name: Ewa full_name: Dubas, Ewa last_name: Dubas - first_name: Jana full_name: Moravčíková, Jana last_name: Moravčíková - first_name: Jana full_name: Libantová, Jana last_name: Libantová - first_name: Ildikó full_name: Matušíková, Ildikó last_name: Matušíková - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Iwona full_name: Zur, Iwona last_name: Zur - first_name: Monika full_name: Krzewska, Monika last_name: Krzewska citation: 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 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. 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. 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. mla: Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1. short: E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087. date_created: 2018-12-11T11:55:29Z date_published: 2014-02-20T00:00:00Z date_updated: 2021-01-12T06:55:02Z day: '20' ddc: - '580' department: - _id: EvBe doi: 10.1007/s00709-014-0616-1 file: - access_level: open_access checksum: d570a6073765118fc0bb83c31d96fa53 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:31Z date_updated: 2020-07-14T12:45:27Z file_id: '5353' file_name: IST-2015-394-v1+1_s00709-014-0616-1.pdf file_size: 6377990 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 251' issue: '5' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1077 - 1087 publication: Protoplasma publication_status: published publisher: Springer publist_id: '4987' pubrep_id: '394' quality_controlled: '1' scopus_import: 1 status: public title: The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 251 year: '2014' ... --- _id: '2062' abstract: - lang: eng text: The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes. article_number: '1255263' author: - first_name: Hua full_name: Hu, Hua id: 4AC0145C-F248-11E8-B48F-1D18A9856A87 last_name: Hu - first_name: Jian full_name: Gan, Jian id: 3614E438-F248-11E8-B48F-1D18A9856A87 last_name: Gan - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: 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' 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' 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.' 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.' ista: 'Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 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.' short: H. Hu, J. Gan, P.M. Jonas, Science 345 (2014). date_created: 2018-12-11T11:55:29Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T06:55:03Z day: '01' ddc: - '570' department: - _id: PeJo doi: 10.1126/science.1255263 ec_funded: 1 file: - access_level: open_access checksum: a0036a589037d37e86364fa25cc0a82f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:00Z date_updated: 2020-07-14T12:45:27Z file_id: '5185' file_name: IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf file_size: 215514 relation: main_file - access_level: open_access checksum: e1f57d2713725449cb898fdcb8ef47b8 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:01Z date_updated: 2020-07-14T12:45:27Z file_id: '5186' file_name: IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf file_size: 1732723 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 345' issue: '6196' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF 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 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '4984' pubrep_id: '821' quality_controlled: '1' scopus_import: 1 status: public title: 'Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 345 year: '2014' ... --- _id: '2058' abstract: - lang: eng text: We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations. article_number: '137' article_processing_charge: No author: - first_name: Karthik full_name: Raveendran, Karthik last_name: Raveendran - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Greg full_name: Türk, Greg last_name: Türk citation: ama: 'Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126' 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' 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. ieee: K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4. 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. short: K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014. conference: end_date: 2014-08-14 location: Vancouver, Canada name: 'SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques' start_date: 2014-08-10 date_created: 2018-12-11T11:55:28Z date_published: 2014-07-01T00:00:00Z date_updated: 2022-08-25T14:02:46Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2601097.2601126 file: - access_level: open_access checksum: 1752760a2e71e254537f31c0d10d9c6c content_type: application/pdf creator: system date_created: 2018-12-12T10:08:27Z date_updated: 2020-07-14T12:45:27Z file_id: '4688' file_name: IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf file_size: 8387384 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 33' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25636330-B435-11E9-9278-68D0E5697425 grant_number: 11-NSF-1070 name: ROOTS Genome-wide Analysis of Root Traits publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4988' pubrep_id: '606' quality_controlled: '1' scopus_import: '1' status: public title: Blending liquids type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2014' ...