--- _id: '1791' abstract: - lang: eng text: Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways. acknowledgement: This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation author: - first_name: Seungtae full_name: Baek, SeungTae last_name: Baek - first_name: Géraldine full_name: Kerjan, Géraldine last_name: Kerjan - first_name: Stephanie full_name: Bielas, Stephanie L last_name: Bielas - first_name: Jieun full_name: Lee, Jieun last_name: Lee - first_name: Ali full_name: Fenstermaker, Ali G last_name: Fenstermaker - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036 apa: Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036 chicago: Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036. ieee: S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014. ista: Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262. mla: Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036. short: S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262. date_created: 2018-12-11T11:54:01Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T06:53:13Z day: '18' doi: 10.1016/j.neuron.2014.04.036 extern: 1 intvolume: ' 82' issue: '6' month: '06' page: 1255 - 1262 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5322' quality_controlled: 0 status: public title: Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation type: journal_article volume: 82 year: '2014' ... --- _id: '1806' abstract: - lang: eng text: The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants. author: - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8' apa: Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8 chicago: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8. ieee: P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170. ista: 'Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.' mla: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8. short: P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170. date_created: 2018-12-11T11:54:07Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:53:19Z day: '01' department: - _id: JiFr doi: 10.1007/978-3-7091-1526-8_8 editor: - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 language: - iso: eng month: '04' oa_version: None page: 143 - 170 publication: Auxin and Its Role in Plant Development publication_status: published publisher: Springer publist_id: '5304' quality_controlled: '1' scopus_import: 1 status: public title: Auxin on the road navigated by cellular PIN polarity type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1816' abstract: - lang: eng text: Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques. acknowledgement: 'Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.' author: - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Peter full_name: Meerwald, Peter last_name: Meerwald - first_name: Roland full_name: Kwitt, Roland last_name: Kwitt citation: ama: Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 2014;24(1):61-86. doi:10.1142/S0218195914500034 apa: Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034 chicago: Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034. ieee: S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” International Journal of Computational Geometry and Applications, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014. ista: Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86. mla: Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034. short: S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86. date_created: 2018-12-11T11:54:10Z date_published: 2014-03-16T00:00:00Z date_updated: 2021-01-12T06:53:23Z day: '16' ddc: - '000' department: - _id: HeEd doi: 10.1142/S0218195914500034 file: - access_level: open_access checksum: be45c133ab4d43351260e21beaa8f4b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:43Z date_updated: 2020-07-14T12:45:17Z file_id: '4704' file_name: IST-2016-443-v1+1_S0218195914500034.pdf file_size: 991734 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 24' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '03' oa: 1 oa_version: Published Version page: 61 - 86 publication: International Journal of Computational Geometry and Applications publication_status: published publisher: World Scientific Publishing publist_id: '5290' pubrep_id: '443' quality_controlled: '1' scopus_import: 1 status: public title: Topology-preserving watermarking of vector graphics 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1821' abstract: - lang: eng text: We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end. article_number: '1.4881536' author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536 apa: Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4881536 chicago: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4881536. ieee: R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014. ista: Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536. mla: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:10.1063/1.4881536. short: R. Seiringer, Journal of Mathematical Physics 55 (2014). date_created: 2018-12-11T11:54:11Z date_published: 2014-06-26T00:00:00Z date_updated: 2021-01-12T06:53:25Z day: '26' ddc: - '510' - '530' department: - _id: RoSe doi: 10.1063/1.4881536 file: - access_level: open_access checksum: ed0efc93c10f1341155f0316af617b82 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:49Z date_updated: 2020-07-14T12:45:17Z file_id: '5172' file_name: IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf file_size: 269171 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 55' issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5285' pubrep_id: '532' quality_controlled: '1' scopus_import: 1 status: public title: Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '1822' article_number: '075101' author: - first_name: Vojkan full_name: Jakšić, Vojkan last_name: Jakšić - first_name: Claude full_name: Pillet, Claude last_name: Pillet - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877 apa: Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877 chicago: Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877. ieee: V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014. ista: Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101. mla: Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877. short: V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014). date_created: 2018-12-11T11:54:12Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:53:25Z day: '01' department: - _id: RoSe doi: 10.1063/1.4884877 intvolume: ' 55' issue: '7' language: - iso: eng month: '07' oa_version: None publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5284' quality_controlled: '1' scopus_import: 1 status: public title: Introduction type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ...