--- _id: '1233' abstract: - lang: eng text: About three decades ago it was realized that implementing private channels between parties which can be adaptively corrupted requires an encryption scheme that is secure against selective opening attacks. Whether standard (IND-CPA) security implies security against selective opening attacks has been a major open question since. The only known reduction from selective opening to IND-CPA security loses an exponential factor. A polynomial reduction is only known for the very special case where the distribution considered in the selective opening security experiment is a product distribution, i.e., the messages are sampled independently from each other. In this paper we give a reduction whose loss is quantified via the dependence graph (where message dependencies correspond to edges) of the underlying message distribution. In particular, for some concrete distributions including Markov distributions, our reduction is polynomial. acknowledgement: G. Fuchsbauer and K. Pietrzak are supported by the European Research Council, ERC Starting Grant (259668-PSPC). F. Heuer is funded by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation and DFG SPP 1736, Algorithms for BIG DATA. E. Kiltz is supported by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation, the German Israel Foundation, and ERC Project ERCC (FP7/615074). alternative_title: - LNCS author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Felix full_name: Heuer, Felix last_name: Heuer - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. Standard security does imply security against selective opening for markov distributions. In: Vol 9562. Springer; 2016:282-305. doi:10.1007/978-3-662-49096-9_12' apa: 'Fuchsbauer, G., Heuer, F., Kiltz, E., & Pietrzak, K. Z. (2016). Standard security does imply security against selective opening for markov distributions (Vol. 9562, pp. 282–305). Presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-662-49096-9_12' chicago: Fuchsbauer, Georg, Felix Heuer, Eike Kiltz, and Krzysztof Z Pietrzak. “Standard Security Does Imply Security against Selective Opening for Markov Distributions,” 9562:282–305. Springer, 2016. https://doi.org/10.1007/978-3-662-49096-9_12. ieee: 'G. Fuchsbauer, F. Heuer, E. Kiltz, and K. Z. Pietrzak, “Standard security does imply security against selective opening for markov distributions,” presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel, 2016, vol. 9562, pp. 282–305.' ista: 'Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. 2016. Standard security does imply security against selective opening for markov distributions. TCC: Theory of Cryptography Conference, LNCS, vol. 9562, 282–305.' mla: Fuchsbauer, Georg, et al. Standard Security Does Imply Security against Selective Opening for Markov Distributions. Vol. 9562, Springer, 2016, pp. 282–305, doi:10.1007/978-3-662-49096-9_12. short: G. Fuchsbauer, F. Heuer, E. Kiltz, K.Z. Pietrzak, in:, Springer, 2016, pp. 282–305. conference: end_date: 2016-01-13 location: Tel Aviv, Israel name: 'TCC: Theory of Cryptography Conference' start_date: 2016-01-10 date_created: 2018-12-11T11:50:51Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T06:49:16Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-662-49096-9_12 ec_funded: 1 intvolume: ' 9562' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2015/853 month: '01' oa: 1 oa_version: Submitted Version page: 282 - 305 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '6100' quality_controlled: '1' scopus_import: 1 status: public title: Standard security does imply security against selective opening for markov distributions type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9562 year: '2016' ... --- _id: '1238' abstract: - lang: eng text: The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth. acknowledgement: "This work was supported by National Program for Sustainability I (grant no. LO1204) provided by the Czech Ministry of Education and by Institutional Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help with the statistics." article_number: '1262' author: - first_name: Daniel full_name: Von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Amparo full_name: Rosero, Amparo last_name: Rosero - first_name: George full_name: Komis, George last_name: Komis - first_name: Olga full_name: Šamajová, Olga last_name: Šamajová - first_name: Miroslav full_name: Ovečka, Miroslav last_name: Ovečka - first_name: Boris full_name: Voigt, Boris last_name: Voigt - first_name: Jozef full_name: Šamaj, Jozef last_name: Šamaj citation: ama: von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root hair growth. Frontiers in Plant Science. 2016;6(JAN2016). doi:10.3389/fpls.2015.01262 apa: von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt, B., & Šamaj, J. (2016). Endosomal interactions during root hair growth. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.01262 chicago: Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair Growth.” Frontiers in Plant Science. Frontiers Research Foundation, 2016. https://doi.org/10.3389/fpls.2015.01262. ieee: D. von Wangenheim et al., “Endosomal interactions during root hair growth,” Frontiers in Plant Science, vol. 6, no. JAN2016. Frontiers Research Foundation, 2016. ista: von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science. 6(JAN2016), 1262. mla: von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.” Frontiers in Plant Science, vol. 6, no. JAN2016, 1262, Frontiers Research Foundation, 2016, doi:10.3389/fpls.2015.01262. short: D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt, J. Šamaj, Frontiers in Plant Science 6 (2016). date_created: 2018-12-11T11:50:53Z date_published: 2016-01-29T00:00:00Z date_updated: 2021-01-12T06:49:18Z day: '29' ddc: - '581' department: - _id: JiFr doi: 10.3389/fpls.2015.01262 file: - access_level: open_access checksum: 3127eab844d53564bf47e2b6b42f1ca0 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:36Z date_updated: 2020-07-14T12:44:41Z file_id: '4760' file_name: IST-2016-710-v1+1_fpls-06-01262.pdf file_size: 1640550 relation: main_file file_date_updated: 2020-07-14T12:44:41Z has_accepted_license: '1' intvolume: ' 6' issue: JAN2016 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '6094' pubrep_id: '710' quality_controlled: '1' scopus_import: 1 status: public title: Endosomal interactions during root hair growth 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: 6 year: '2016' ... --- _id: '1237' abstract: - lang: eng text: 'Bitmap images of arbitrary dimension may be formally perceived as unions of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology and homology groups are well known topological invariants of such sets. Cohomological operations, such as the cup product, provide higher-order algebraic topological invariants, especially important for digital images of dimension higher than 3. If such an operation is determined at the level of simplicial chains [see e.g. González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively computable. However, decomposing a cubical complex into a simplicial one deleteriously affects the efficiency of such an approach. In order to avoid this overhead, a direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015, 253-275] for the cup product in cohomology, and implemented in the ChainCon software package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series, 1947, 290-320] directly at the level of cubical chains, and we prove the correctness of this formula. An implementation of this formula is programmed in C++ within the ChainCon software framework. We provide a few examples and discuss the effectiveness of this approach. One specific application follows from the fact that Steenrod squares yield tests for the topological extension problem: Can a given map A → Sd to a sphere Sd be extended to a given super-complex X of A? In particular, the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value r > 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the extension problem.' acknowledgement: The research conducted by both authors has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreements no. 291734 (for M. K.) and no. 622033 (for P. P.). alternative_title: - LNCS author: - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk citation: ama: 'Krcál M, Pilarczyk P. Computation of cubical Steenrod squares. In: Vol 9667. Springer; 2016:140-151. doi:10.1007/978-3-319-39441-1_13' apa: 'Krcál, M., & Pilarczyk, P. (2016). Computation of cubical Steenrod squares (Vol. 9667, pp. 140–151). Presented at the CTIC: Computational Topology in Image Context, Marseille, France: Springer. https://doi.org/10.1007/978-3-319-39441-1_13' chicago: Krcál, Marek, and Pawel Pilarczyk. “Computation of Cubical Steenrod Squares,” 9667:140–51. Springer, 2016. https://doi.org/10.1007/978-3-319-39441-1_13. ieee: 'M. Krcál and P. Pilarczyk, “Computation of cubical Steenrod squares,” presented at the CTIC: Computational Topology in Image Context, Marseille, France, 2016, vol. 9667, pp. 140–151.' ista: 'Krcál M, Pilarczyk P. 2016. Computation of cubical Steenrod squares. CTIC: Computational Topology in Image Context, LNCS, vol. 9667, 140–151.' mla: Krcál, Marek, and Pawel Pilarczyk. Computation of Cubical Steenrod Squares. Vol. 9667, Springer, 2016, pp. 140–51, doi:10.1007/978-3-319-39441-1_13. short: M. Krcál, P. Pilarczyk, in:, Springer, 2016, pp. 140–151. conference: end_date: 2016-06-17 location: Marseille, France name: 'CTIC: Computational Topology in Image Context' start_date: 2016-06-15 date_created: 2018-12-11T11:50:52Z date_published: 2016-06-02T00:00:00Z date_updated: 2021-01-12T06:49:18Z day: '02' department: - _id: UlWa - _id: HeEd doi: 10.1007/978-3-319-39441-1_13 ec_funded: 1 intvolume: ' 9667' language: - iso: eng month: '06' oa_version: None page: 140 - 151 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 255F06BE-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '622033' name: Persistent Homology - Images, Data and Maps publication_status: published publisher: Springer publist_id: '6096' quality_controlled: '1' scopus_import: 1 status: public title: Computation of cubical Steenrod squares type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9667 year: '2016' ... --- _id: '1240' abstract: - lang: eng text: 'Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers.' acknowledgement: "This study was partly funded by the Austrian Science Fund (FWF F43-B09, FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions, Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript." article_number: '14' author: - first_name: Aleksandra full_name: Kornienko, Aleksandra last_name: Kornienko - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter - first_name: Philipp full_name: Guenzl, Philipp last_name: Guenzl - first_name: Heinz full_name: Gisslinger, Heinz last_name: Gisslinger - first_name: Bettina full_name: Gisslinger, Bettina last_name: Gisslinger - first_name: Ciara full_name: Cleary, Ciara last_name: Cleary - first_name: Robert full_name: Kralovics, Robert last_name: Kralovics - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler - first_name: Denise full_name: Barlow, Denise last_name: Barlow citation: ama: Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 2016;17(1). doi:10.1186/s13059-016-0873-8 apa: Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary, C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-016-0873-8 chicago: Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger, Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” Genome Biology. BioMed Central, 2016. https://doi.org/10.1186/s13059-016-0873-8. ieee: A. Kornienko et al., “Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans,” Genome Biology, vol. 17, no. 1. BioMed Central, 2016. ista: Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 17(1), 14. mla: Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” Genome Biology, vol. 17, no. 1, 14, BioMed Central, 2016, doi:10.1186/s13059-016-0873-8. short: A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary, R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016). date_created: 2018-12-11T11:50:53Z date_published: 2016-01-29T00:00:00Z date_updated: 2021-01-12T06:49:20Z day: '29' ddc: - '576' department: - _id: GaNo doi: 10.1186/s13059-016-0873-8 file: - access_level: open_access checksum: a268beee1a690801c83ec6729f9ebc5b content_type: application/pdf creator: system date_created: 2018-12-12T10:10:05Z date_updated: 2020-07-14T12:44:41Z file_id: '4789' file_name: IST-2016-709-v1+1_s13059-016-0873-8.pdf file_size: 2914601 relation: main_file file_date_updated: 2020-07-14T12:44:41Z has_accepted_license: '1' intvolume: ' 17' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Genome Biology publication_status: published publisher: BioMed Central publist_id: '6093' pubrep_id: '709' quality_controlled: '1' scopus_import: 1 status: public title: Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans 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: 17 year: '2016' ... --- _id: '1239' abstract: - lang: eng text: Nonadherent polarized cells have been observed to have a pearlike, elongated shape. Using a minimal model that describes the cell cortex as a thin layer of contractile active gel, we show that the anisotropy of active stresses, controlled by cortical viscosity and filament ordering, can account for this morphology. The predicted shapes can be determined from the flow pattern only; they prove to be independent of the mechanism at the origin of the cortical flow, and are only weakly sensitive to the cytoplasmic rheology. In the case of actin flows resulting from a contractile instability, we propose a phase diagram of three-dimensional cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate shapes, all of which have been observed in experiment. acknowledgement: 'V. R. acknowledges support by the Austrian Science Fund (FWF): (Grant No. T560-B17).' article_number: '028102' author: - first_name: Andrew full_name: Callan Jones, Andrew last_name: Callan Jones - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez citation: ama: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 2016;116(2). doi:10.1103/PhysRevLett.116.028102 apa: Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez, R. (2016). Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.116.028102 chicago: Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Cortical Flow-Driven Shapes of Nonadherent Cells.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.116.028102. ieee: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Cortical flow-driven shapes of nonadherent cells,” Physical Review Letters, vol. 116, no. 2. American Physical Society, 2016. ista: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 116(2), 028102. mla: Callan Jones, Andrew, et al. “Cortical Flow-Driven Shapes of Nonadherent Cells.” Physical Review Letters, vol. 116, no. 2, 028102, American Physical Society, 2016, doi:10.1103/PhysRevLett.116.028102. short: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 116 (2016). date_created: 2018-12-11T11:50:53Z date_published: 2016-01-15T00:00:00Z date_updated: 2021-01-12T06:49:19Z day: '15' department: - _id: CaHe doi: 10.1103/PhysRevLett.116.028102 intvolume: ' 116' issue: '2' language: - iso: eng month: '01' oa_version: None project: - _id: 2529486C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T 560-B17 name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6095' quality_controlled: '1' scopus_import: 1 status: public title: Cortical flow-driven shapes of nonadherent cells type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 116 year: '2016' ... --- _id: '1242' abstract: - lang: eng text: A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression. acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S." article_number: '022404' author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Aleksandra full_name: Walczak, Aleksandra last_name: Walczak - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404 apa: Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404 chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404. ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics, 2016. ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404. mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022404. short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016). date_created: 2018-12-11T11:50:54Z date_published: 2016-02-04T00:00:00Z date_updated: 2021-01-12T06:49:20Z day: '04' department: - _id: GaTk doi: 10.1103/PhysRevE.93.022404 intvolume: ' 93' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.02562 month: '02' oa: 1 oa_version: Preprint project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '6088' quality_controlled: '1' scopus_import: 1 status: public title: Extending the dynamic range of transcription factor action by translational regulation type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2016' ... --- _id: '1241' abstract: - lang: eng text: 'How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.' acknowledgement: This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton). author: - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Joachim full_name: Hermisson, Joachim last_name: Hermisson citation: ama: Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299 apa: Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299 chicago: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299. ieee: H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016. ista: Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732. mla: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:10.1534/genetics.115.180299. short: H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732. date_created: 2018-12-11T11:50:54Z date_published: 2016-02-01T00:00:00Z date_updated: 2023-02-21T10:24:19Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.115.180299 ec_funded: 1 intvolume: ' 202' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://biorxiv.org/content/early/2015/07/06/022020.abstract month: '02' oa: 1 oa_version: Preprint page: 721 - 732 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 25B67606-B435-11E9-9278-68D0E5697425 name: L'OREAL Fellowship publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '6091' quality_controlled: '1' scopus_import: 1 status: public title: The role of recombination in evolutionary rescue type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1247' abstract: - lang: eng text: The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity. acknowledgement: "This work was supported by the Ghent University Special Research Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP) (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted to the Agency for Science and Technology for\r\na predoctoral fellowship." author: - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Pia full_name: Neyt, Pia last_name: Neyt - first_name: Steven full_name: De Groeve, Steven last_name: De Groeve - first_name: Stijn full_name: Aesaert, Stijn last_name: Aesaert - first_name: Griet full_name: Coussens, Griet last_name: Coussens - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Leonardo full_name: Bruno, Leonardo last_name: Bruno - first_name: Nancy full_name: De Winne, Nancy last_name: De Winne - first_name: Annemie full_name: Van Minnebruggen, Annemie last_name: Van Minnebruggen - first_name: Marc full_name: Van Montagu, Marc last_name: Van Montagu - first_name: Maria full_name: Ponce, Maria last_name: Ponce - first_name: José full_name: Micol, José last_name: Micol - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Mieke full_name: Van Lijsebettens, Mieke last_name: Van Lijsebettens citation: ama: Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 2016;113(10):2768-2773. doi:10.1073/pnas.1501343112 apa: Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík, J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1501343112 chicago: Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1501343112. ieee: M. Karampelias et al., “ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling,” PNAS, vol. 113, no. 10. National Academy of Sciences, pp. 2768–2773, 2016. ista: Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10), 2768–2773. mla: Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS, vol. 113, no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:10.1073/pnas.1501343112. short: M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík, L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol, J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773. date_created: 2018-12-11T11:50:56Z date_published: 2016-03-08T00:00:00Z date_updated: 2021-01-12T06:49:22Z day: '08' department: - _id: JiFr doi: 10.1073/pnas.1501343112 ec_funded: 1 intvolume: ' 113' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/ month: '03' oa: 1 oa_version: Submitted Version page: 2768 - 2773 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6081' quality_controlled: '1' scopus_import: 1 status: public title: ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2016' ... --- _id: '1246' abstract: - lang: eng text: Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire's evanescent field and the probe's response function. As a result, we find that the probe's sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments. acknowledgement: 'This work is supported part of the research program of the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO), and part of this work has been funded by the project ‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging Technologies (FET) program within the Seventh Framework Programme for Research of the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).' article_number: '22665' author: - first_name: Irina full_name: Kabakova, Irina last_name: Kabakova - first_name: Anouk full_name: De Hoogh, Anouk last_name: De Hoogh - first_name: Ruben full_name: Van Der Wel, Ruben last_name: Van Der Wel - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Boris full_name: Le Feber, Boris last_name: Le Feber - first_name: Laurens full_name: Kuipers, Laurens last_name: Kuipers citation: ama: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 2016;6. doi:10.1038/srep22665 apa: Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., & Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep22665 chicago: Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep22665. ieee: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers, “Imaging of electric and magnetic fields near plasmonic nanowires,” Scientific Reports, vol. 6. Nature Publishing Group, 2016. ista: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 6, 22665. mla: Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” Scientific Reports, vol. 6, 22665, Nature Publishing Group, 2016, doi:10.1038/srep22665. short: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers, Scientific Reports 6 (2016). date_created: 2018-12-11T11:50:55Z date_published: 2016-03-07T00:00:00Z date_updated: 2021-01-12T06:49:22Z day: '07' ddc: - '539' department: - _id: JoFi doi: 10.1038/srep22665 file: - access_level: open_access checksum: ca76236cb1aae22cb90c65313e2c5e98 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:11Z date_updated: 2020-07-14T12:44:41Z file_id: '5061' file_name: IST-2016-707-v1+1_srep22665.pdf file_size: 1425165 relation: main_file file_date_updated: 2020-07-14T12:44:41Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '6082' pubrep_id: '707' quality_controlled: '1' scopus_import: 1 status: public title: Imaging of electric and magnetic fields near plasmonic nanowires 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: 6 year: '2016' ... --- _id: '1245' abstract: - lang: eng text: 'To facilitate collaboration in massive online classrooms, instructors must make many decisions. For instance, the following parameters need to be decided when designing a peer-feedback system where students review each others'' essays: the number of students each student must provide feedback to, an algorithm to map feedback providers to receivers, constraints that ensure students do not become free-riders (receiving feedback but not providing it), the best times to receive feedback to improve learning etc. While instructors can answer these questions by running experiments or invoking past experience, game-theoretic models with data from online learning platforms can identify better initial designs for further improvements. As an example, we explore the design space of a peer feedback system by modeling it using game theory. Our simulations show that incentivizing students to provide feedback requires the value obtained from receiving a feedback to exceed the cost of providing it by a large factor (greater than 7). Furthermore, hiding feedback from low-effort students incentivizes them to provide more feedback.' acknowledgement: 'ERC Start Grant Graph Games 279307 supported this research. ' author: - first_name: Vineet full_name: Pandey, Vineet last_name: Pandey - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Pandey V, Chatterjee K. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In: Proceedings of the ACM Conference on Computer Supported Cooperative Work. Vol 26. ACM; 2016:365-368. doi:10.1145/2818052.2869122' apa: 'Pandey, V., & Chatterjee, K. (2016). Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In Proceedings of the ACM Conference on Computer Supported Cooperative Work (Vol. 26, pp. 365–368). San Francisco, CA, USA: ACM. https://doi.org/10.1145/2818052.2869122' chicago: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” In Proceedings of the ACM Conference on Computer Supported Cooperative Work, 26:365–68. ACM, 2016. https://doi.org/10.1145/2818052.2869122. ieee: V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles for peer collaboration in online learning platforms,” in Proceedings of the ACM Conference on Computer Supported Cooperative Work, San Francisco, CA, USA, 2016, vol. 26, no. Februar-2016, pp. 365–368. ista: 'Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. Proceedings of the ACM Conference on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work and Social Computing vol. 26, 365–368.' mla: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” Proceedings of the ACM Conference on Computer Supported Cooperative Work, vol. 26, no. Februar-2016, ACM, 2016, pp. 365–68, doi:10.1145/2818052.2869122. short: V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer Supported Cooperative Work, ACM, 2016, pp. 365–368. conference: end_date: 2016-03-02 location: San Francisco, CA, USA name: 'CSCW: Computer Supported Cooperative Work and Social Computing' start_date: 2016-02-26 date_created: 2018-12-11T11:50:55Z date_published: 2016-02-27T00:00:00Z date_updated: 2021-01-12T06:49:22Z day: '27' department: - _id: KrCh doi: 10.1145/2818052.2869122 ec_funded: 1 intvolume: ' 26' issue: Februar-2016 language: - iso: eng month: '02' oa_version: None page: 365 - 368 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the ACM Conference on Computer Supported Cooperative Work publication_status: published publisher: ACM publist_id: '6083' quality_controlled: '1' scopus_import: 1 status: public title: Game-theoretic models identify useful principles for peer collaboration in online learning platforms type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2016' ... --- _id: '1244' abstract: - lang: eng text: Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns. acknowledgement: "We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”" author: - first_name: Pierre full_name: Recouvreux, Pierre last_name: Recouvreux - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Aristea full_name: Grammoustianou, Aristea last_name: Grammoustianou - first_name: Pieter full_name: Tenwolde, Pieter last_name: Tenwolde - first_name: Marileen full_name: Dogterom, Marileen last_name: Dogterom citation: ama: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113 apa: Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., & Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1419248113 chicago: Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113. ieee: P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016. ista: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816. mla: Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113. short: P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816. date_created: 2018-12-11T11:50:55Z date_published: 2016-02-16T00:00:00Z date_updated: 2021-01-12T06:49:21Z day: '16' department: - _id: GaTk doi: 10.1073/pnas.1419248113 intvolume: ' 113' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/ month: '02' oa: 1 oa_version: Submitted Version page: 1811 - 1816 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6085' quality_controlled: '1' scopus_import: 1 status: public title: Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2016' ... --- _id: '1248' abstract: - lang: eng text: Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales. acknowledgement: "Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations." author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Tkačik G, Bialek W. Information processing in living systems. Annual Review of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803 apa: Tkačik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803 chicago: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803. ieee: G. Tkačik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016. ista: Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117. mla: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803. short: G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117. date_created: 2018-12-11T11:50:56Z date_published: 2016-03-10T00:00:00Z date_updated: 2021-01-12T06:49:23Z day: '10' department: - _id: GaTk doi: 10.1146/annurev-conmatphys-031214-014803 intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.8752 month: '03' oa: 1 oa_version: Preprint page: 89 - 117 project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: Annual Review of Condensed Matter Physics publication_status: published publisher: Annual Reviews publist_id: '6080' quality_controlled: '1' scopus_import: 1 status: public title: Information processing in living systems type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '1249' abstract: - lang: eng text: 'Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell- and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example, the characteristic time of stress relaxation (the Maxwell time τM) in the actomyosin sets the timescale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length λ) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer in vivo directly from laser ablation experiments. For this we investigate the cortical response to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained physical description of the cortex in terms of a two-dimensional thin film of an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated the response to laser ablation in two different ways: by quantifying flow and density fields as a function of space and time, and by determining the time evolution of the shape of the ablated region. Importantly, both methods provide best-fit physical parameters that are in close agreement with each other and that are similar to previous estimates in the two systems. Our method provides an accurate and robust means for measuring physical parameters of the actomyosin cortical layer. It can be useful for investigations of actomyosin mechanics at the cellular-scale, but also for providing insights into the active mechanics processes that govern tissue-scale morphogenesis.' acknowledgement: S.W.G. acknowledges support by grant no. 281903 from the European Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft. S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20). We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions. author: - first_name: Arnab full_name: Saha, Arnab last_name: Saha - first_name: Masatoshi full_name: Nishikawa, Masatoshi last_name: Nishikawa - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Stephan full_name: Grill, Stephan last_name: Grill citation: ama: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining physical properties of the cell cortex. Biophysical Journal. 2016;110(6):1421-1429. doi:10.1016/j.bpj.2016.02.013 apa: Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., & Grill, S. (2016). Determining physical properties of the cell cortex. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2016.02.013 chicago: Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg, Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell Cortex.” Biophysical Journal. Biophysical Society, 2016. https://doi.org/10.1016/j.bpj.2016.02.013. ieee: A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S. Grill, “Determining physical properties of the cell cortex,” Biophysical Journal, vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016. ista: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016. Determining physical properties of the cell cortex. Biophysical Journal. 110(6), 1421–1429. mla: Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” Biophysical Journal, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:10.1016/j.bpj.2016.02.013. short: A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill, Biophysical Journal 110 (2016) 1421–1429. date_created: 2018-12-11T11:50:56Z date_published: 2016-03-29T00:00:00Z date_updated: 2021-01-12T06:49:23Z day: '29' ddc: - '572' - '576' department: - _id: CaHe doi: 10.1016/j.bpj.2016.02.013 file: - access_level: open_access checksum: c408cf2e25a25c8d711cffea524bda55 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:54Z date_updated: 2020-07-14T12:44:41Z file_id: '4845' file_name: IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf file_size: 1965645 relation: main_file file_date_updated: 2020-07-14T12:44:41Z has_accepted_license: '1' intvolume: ' 110' issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '03' oa: 1 oa_version: Published Version page: 1421 - 1429 project: - _id: 252ABD0A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 930-B20 name: Control of Epithelial Cell Layer Spreading in Zebrafish publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '6079' pubrep_id: '706' quality_controlled: '1' scopus_import: 1 status: public title: Determining physical properties of the cell cortex 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: 110 year: '2016' ... --- _id: '1251' abstract: - lang: eng text: Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity. acknowledgement: ' This work was supported by grants from the European Social Fund (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F. and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all to M.G.). ' author: - first_name: Jinsheng full_name: Zhu, Jinsheng last_name: Zhu - first_name: Aurélien full_name: Bailly, Aurélien last_name: Bailly - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Valpuri full_name: Sovero, Valpuri last_name: Sovero - first_name: Martin full_name: Di Donato, Martin last_name: Di Donato - first_name: Pei full_name: Ge, Pei last_name: Ge - first_name: Jacqueline full_name: Oehri, Jacqueline last_name: Oehri - first_name: Bibek full_name: Aryal, Bibek last_name: Aryal - first_name: Pengchao full_name: Hao, Pengchao last_name: Hao - first_name: Miriam full_name: Linnert, Miriam last_name: Linnert - first_name: Noelia full_name: Burgardt, Noelia last_name: Burgardt - first_name: Christian full_name: Lücke, Christian last_name: Lücke - first_name: Matthias full_name: Weiwad, Matthias last_name: Weiwad - first_name: Max full_name: Michel, Max last_name: Michel - first_name: Oliver full_name: Weiergräber, Oliver last_name: Weiergräber - first_name: Stephan full_name: Pollmann, Stephan last_name: Pollmann - first_name: Elisa full_name: Azzarello, Elisa last_name: Azzarello - first_name: Stefano full_name: Mancuso, Stefano last_name: Mancuso - first_name: Noel full_name: Ferro, Noel last_name: Ferro - first_name: Yoichiro full_name: Fukao, Yoichiro last_name: Fukao - first_name: Céline full_name: Hoffmann, Céline last_name: Hoffmann - first_name: Roland full_name: Wedlich Söldner, Roland last_name: Wedlich Söldner - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Clément full_name: Thomas, Clément last_name: Thomas - first_name: Markus full_name: Geisler, Markus last_name: Geisler citation: ama: Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 2016;28(4):930-948. doi:10.1105/tpc.15.00726 apa: Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler, M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00726 chicago: Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00726. ieee: J. Zhu et al., “TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics,” Plant Cell, vol. 28, no. 4. American Society of Plant Biologists, pp. 930–948, 2016. ista: Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B, Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948. mla: Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell, vol. 28, no. 4, American Society of Plant Biologists, 2016, pp. 930–48, doi:10.1105/tpc.15.00726. short: J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri, B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O. Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann, R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948. date_created: 2018-12-11T11:50:57Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T06:49:24Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.15.00726 intvolume: ' 28' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/ month: '04' oa: 1 oa_version: Submitted Version page: 930 - 948 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '6078' quality_controlled: '1' scopus_import: 1 status: public title: TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2016' ... --- _id: '1252' abstract: - lang: eng text: We study the homomorphism induced in homology by a closed correspondence between topological spaces, using projections from the graph of the correspondence to its domain and codomain. We provide assumptions under which the homomorphism induced by an outer approximation of a continuous map coincides with the homomorphism induced in homology by the map. In contrast to more classical results we do not require that the projection to the domain have acyclic preimages. Moreover, we show that it is possible to retrieve correct homological information from a correspondence even if some data is missing or perturbed. Finally, we describe an application to combinatorial maps that are either outer approximations of continuous maps or reconstructions of such maps from a finite set of data points. acknowledgement: "The authors gratefully acknowledge the support of the Lorenz Center which\r\nprovided an opportunity for us to discuss in depth the work of this paper. Research leading to these results has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033 (supporting PP). The work of the first and third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019, 1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029), Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan." article_processing_charge: No article_type: original author: - first_name: Shaun full_name: Harker, Shaun last_name: Harker - first_name: Hiroshi full_name: Kokubu, Hiroshi last_name: Kokubu - first_name: Konstantin full_name: Mischaikow, Konstantin last_name: Mischaikow - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk citation: ama: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 2016;144(4):1787-1801. doi:10.1090/proc/12812 apa: Harker, S., Kokubu, H., Mischaikow, K., & Pilarczyk, P. (2016). Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12812 chicago: Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk. “Inducing a Map on Homology from a Correspondence.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12812. ieee: S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on homology from a correspondence,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016. ista: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 144(4), 1787–1801. mla: Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1787–801, doi:10.1090/proc/12812. short: S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American Mathematical Society 144 (2016) 1787–1801. date_created: 2018-12-11T11:50:57Z date_published: 2016-04-01T00:00:00Z date_updated: 2022-05-24T09:35:58Z day: '01' department: - _id: HeEd doi: 10.1090/proc/12812 ec_funded: 1 external_id: arxiv: - '1411.7563' intvolume: ' 144' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1411.7563 month: '04' oa: 1 oa_version: Preprint page: 1787 - 1801 project: - _id: 255F06BE-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '622033' name: Persistent Homology - Images, Data and Maps publication: Proceedings of the American Mathematical Society publication_identifier: issn: - 1088-6826 publication_status: published publisher: American Mathematical Society publist_id: '6075' quality_controlled: '1' scopus_import: '1' status: public title: Inducing a map on homology from a correspondence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 144 year: '2016' ... --- _id: '1254' abstract: - lang: eng text: We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/. acknowledgement: "AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics \ of Kyoto University for providing access\r\nto their server for conducting \ computations for this\r\nproject." author: - first_name: Ali full_name: Golmakani, Ali last_name: Golmakani - first_name: Stefano full_name: Luzzatto, Stefano last_name: Luzzatto - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk citation: ama: Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124. doi:10.1080/10586458.2015.1048011 apa: Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2015.1048011 chicago: Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics. Taylor and Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011. ieee: A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” Experimental Mathematics, vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016. ista: Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124. mla: Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor and Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011. short: A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124. date_created: 2018-12-11T11:50:58Z date_published: 2016-04-02T00:00:00Z date_updated: 2021-01-12T06:49:25Z day: '02' department: - _id: HeEd doi: 10.1080/10586458.2015.1048011 ec_funded: 1 intvolume: ' 25' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.00116 month: '04' oa: 1 oa_version: Preprint page: 116 - 124 project: - _id: 255F06BE-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '622033' name: Persistent Homology - Images, Data and Maps publication: Experimental Mathematics publication_status: published publisher: Taylor and Francis publist_id: '6071' quality_controlled: '1' scopus_import: 1 status: public title: Uniform expansivity outside a critical neighborhood in the quadratic family type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2016' ... --- _id: '1255' abstract: - lang: eng text: Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital neuronal functions although the role it plays in insect and crustacean immunity is less well understood. In this study, we combine different approaches to understand the roles that Dscam1 plays in fitness-related contexts in two model insect species. Contrary to our expectations, we found no short-term modulation of Dscam1 gene expression after haemocoelic or oral bacterial exposure in Tribolium castaneum, or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore, RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion defects, as well as dramatically reduced fecundity in males and females. We suggest that Dscam1 does not always play a straightforward role in immunity, but strongly influences behaviour and fecundity. This study takes a step towards understanding more about the role of this intriguing gene from different phenotypic perspectives. acknowledgement: "We thank Dietmar Schmucker for reading a draft of this manuscript and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert, Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions. We also thank two anonymous reviewers for their comments. This study was supported by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.) and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2 to R.P. and J.K.)." article_number: '160138' author: - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Kristina full_name: Wensing, Kristina last_name: Wensing - first_name: Luisa full_name: Woestmann, Luisa last_name: Woestmann - first_name: Hendrik full_name: Eggert, Hendrik last_name: Eggert - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Marlene full_name: Sroka, Marlene last_name: Sroka - first_name: Jörn full_name: Scharsack, Jörn last_name: Scharsack - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz - first_name: Sophie full_name: Armitage, Sophie last_name: Armitage citation: ama: 'Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 2016;3(4). doi:10.1098/rsos.160138' apa: 'Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka, M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160138' chicago: 'Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160138.' ieee: 'R. Peuß et al., “Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction,” Royal Society Open Science, vol. 3, no. 4. Royal Society, The, 2016.' ista: 'Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 3(4), 160138.' mla: 'Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open Science, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:10.1098/rsos.160138.' short: R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J. Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016). date_created: 2018-12-11T11:50:58Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T06:49:25Z day: '01' ddc: - '576' - '592' department: - _id: SyCr doi: 10.1098/rsos.160138 file: - access_level: open_access checksum: c3cd84666c8dc0ce6a784f1c82c1cf68 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:01Z date_updated: 2020-07-14T12:44:41Z file_id: '5049' file_name: IST-2016-704-v1+1_160138.full.pdf file_size: 627377 relation: main_file file_date_updated: 2020-07-14T12:44:41Z has_accepted_license: '1' intvolume: ' 3' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Royal Society Open Science publication_status: published publisher: Royal Society, The publist_id: '6070' pubrep_id: '704' quality_controlled: '1' scopus_import: 1 status: public title: 'Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction' 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: 3 year: '2016' ... --- _id: '1256' abstract: - lang: eng text: Simulink is widely used for model driven development (MDD) of industrial software systems. Typically, the Simulink based development is initiated from Stateflow modeling, followed by simulation, validation and code generation mapped to physical execution platforms. However, recent industrial trends have raised the demands of rigorous verification on safety-critical applications, which is unfortunately challenging for Simulink. In this paper, we present an approach to bridge the Stateflow based model driven development and a well- defined rigorous verification. First, we develop a self- contained toolkit to translate Stateflow model into timed automata, where major advanced modeling features in Stateflow are supported. Taking advantage of the strong verification capability of Uppaal, we can not only find bugs in Stateflow models which are missed by Simulink Design Verifier, but also check more important temporal properties. Next, we customize a runtime verifier for the generated nonintrusive VHDL and C code of Stateflow model for monitoring. The major strength of the customization is the flexibility to collect and analyze runtime properties with a pure software monitor, which opens more opportunities for engineers to achieve high reliability of the target system compared with the traditional act that only relies on Simulink Polyspace. We incorporate these two parts into original Stateflow based MDD seamlessly. In this way, safety-critical properties are both verified at the model level, and at the consistent system implementation level with physical execution environment in consideration. We apply our approach on a train controller design, and the verified implementation is tested and deployed on a real hardware platform. acknowledgement: This work is supported in part by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, NSFC 61303014, NSFC 61202010, and NSFC 91218302. article_number: '7461337' author: - first_name: Yu full_name: Jiang, Yu last_name: Jiang - first_name: Yixiao full_name: Yang, Yixiao last_name: Yang - first_name: Han full_name: Liu, Han last_name: Liu - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Ming full_name: Gu, Ming last_name: Gu - first_name: Jiaguang full_name: Sun, Jiaguang last_name: Sun - first_name: Lui full_name: Sha, Lui last_name: Sha citation: ama: 'Jiang Y, Yang Y, Liu H, et al. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. In: IEEE; 2016. doi:10.1109/RTAS.2016.7461337' apa: 'Jiang, Y., Yang, Y., Liu, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016). From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. Presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria: IEEE. https://doi.org/10.1109/RTAS.2016.7461337' chicago: 'Jiang, Yu, Yixiao Yang, Han Liu, Hui Kong, Ming Gu, Jiaguang Sun, and Lui Sha. “From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design.” IEEE, 2016. https://doi.org/10.1109/RTAS.2016.7461337.' ieee: 'Y. Jiang et al., “From stateflow simulation to verified implementation: A verification approach and a real-time train controller design,” presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria, 2016.' ista: 'Jiang Y, Yang Y, Liu H, Kong H, Gu M, Sun J, Sha L. 2016. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. RTAS: Real-time and Embedded Technology and Applications Symposium, 7461337.' mla: 'Jiang, Yu, et al. From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design. 7461337, IEEE, 2016, doi:10.1109/RTAS.2016.7461337.' short: Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 2016. conference: end_date: 2016-04-14 location: Vienna, Austria name: 'RTAS: Real-time and Embedded Technology and Applications Symposium' start_date: 2016-04-11 date_created: 2018-12-11T11:50:58Z date_published: 2016-04-27T00:00:00Z date_updated: 2021-01-12T06:49:26Z day: '27' ddc: - '005' department: - _id: ToHe doi: 10.1109/RTAS.2016.7461337 file: - access_level: open_access checksum: 42f0462911cc9957f2356b12fb33b4b6 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:31Z date_updated: 2020-07-14T12:44:41Z file_id: '4949' file_name: IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf file_size: 1293599 relation: main_file file_date_updated: 2020-07-14T12:44:41Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version publication_status: published publisher: IEEE publist_id: '6069' pubrep_id: '780' quality_controlled: '1' scopus_import: 1 status: public title: 'From stateflow simulation to verified implementation: A verification approach and a real-time train controller design' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1257' abstract: - lang: eng text: We consider products of random matrices that are small, independent identically distributed perturbations of a fixed matrix (Formula presented.). Focusing on the eigenvalues of (Formula presented.) of a particular size we obtain a limit to a SDE in a critical scaling. Previous results required (Formula presented.) to be a (conjugated) unitary matrix so it could not have eigenvalues of different modulus. From the result we can also obtain a limit SDE for the Markov process given by the action of the random products on the flag manifold. Applying the result to random Schrödinger operators we can improve some results by Valko and Virag showing GOE statistics for the rescaled eigenvalue process of a sequence of Anderson models on long boxes. In particular, we solve a problem posed in their work. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). The work of C. Sadel was supported by NSERC Discovery Grant 92997-2010 RGPIN and by the People Programme (Marie Curie Actions) of the EU 7th Framework Programme FP7/2007-2013, REA Grant 291734. article_processing_charge: Yes (via OA deal) author: - first_name: Christian full_name: Sadel, Christian id: 4760E9F8-F248-11E8-B48F-1D18A9856A87 last_name: Sadel orcid: 0000-0001-8255-3968 - first_name: Bálint full_name: Virág, Bálint last_name: Virág citation: ama: Sadel C, Virág B. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. 2016;343(3):881-919. doi:10.1007/s00220-016-2600-4 apa: Sadel, C., & Virág, B. (2016). A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2600-4 chicago: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2600-4. ieee: C. Sadel and B. Virág, “A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes,” Communications in Mathematical Physics, vol. 343, no. 3. Springer, pp. 881–919, 2016. ista: Sadel C, Virág B. 2016. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. 343(3), 881–919. mla: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications in Mathematical Physics, vol. 343, no. 3, Springer, 2016, pp. 881–919, doi:10.1007/s00220-016-2600-4. short: C. Sadel, B. Virág, Communications in Mathematical Physics 343 (2016) 881–919. date_created: 2018-12-11T11:50:59Z date_published: 2016-05-01T00:00:00Z date_updated: 2021-01-12T06:49:26Z day: '01' ddc: - '510' - '539' department: - _id: LaEr doi: 10.1007/s00220-016-2600-4 ec_funded: 1 file: - access_level: open_access checksum: 4fb2411d9c2f56676123165aad46c828 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:02Z date_updated: 2020-07-14T12:44:42Z file_id: '5119' file_name: IST-2016-703-v1+1_s00220-016-2600-4.pdf file_size: 800792 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 343' issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 881 - 919 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '6067' pubrep_id: '703' quality_controlled: '1' scopus_import: 1 status: public title: A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes 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: 343 year: '2016' ... --- _id: '1258' abstract: - lang: eng text: When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling. acknowledgement: M.G. received an FPI fellowship from the Spanish Ministerio de Economía y Competitividad (MINECO). A.G. and A.F.-A. received FPU fellowships from the Spanish Ministerio de Educación. S.P. received an FI fellowship from the Agència de Gestió D'ajuts Universitaris i de Recerca (AGAUR - Generalitat de Catalunya). C.T. received a Marie Curie IEF postdoctoral contract funded by the European Commission. I.R.-V. received initially an FPI fellowship from the Spanish MINECO and later a Beatriu de Pinós contract from AGAUR. Our research is supported by grants from the Spanish MINECO-FEDER [BIO2008-00169, BIO2011-23489 and BIO2014-59895-P] and Generalitat de Catalunya [2011-SGR447 and Xarba] to J.F.M.-G., and Generalitat Valenciana [PROMETEO/2009/112, PROMETEOII/2014/006] to M.R.P. and J.L.M. We acknowledge the support of the Spanish MINECO for the ‘Centro de Excelencia Severo Ochoa 2016-2019’ [award SEV-2015-0533]. We thank the CRAG greenhouse service for plant care; Chus Burillo for technical help; Sergi Portolés and Carles Rentero for assistance with mutagenesis; Mark Estelle (UCSD, USA) for providing sar1-4, sar3-1 and sar3-3 seeds; Juanjo López-Moya (CRAG, Barcelona; 35S:HcPro plasmid) and Dolors Ludevid (CRAG; C307 plasmid) for providing DNA plasmids; and Manuel Rodríguez-Concepción (CRAG) and Miguel Blázquez (IBMCP, Valencia, Spain) for comments on the manuscript. author: - first_name: Marcal full_name: Gallemi Rovira, Marcal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi Rovira - first_name: Anahit full_name: Galstyan, Anahit last_name: Galstyan - first_name: Sandi full_name: Paulišić, Sandi last_name: Paulišić - first_name: Christiane full_name: Then, Christiane last_name: Then - first_name: Almudena full_name: Ferrández Ayela, Almudena last_name: Ferrández Ayela - first_name: Laura full_name: Lorenzo Orts, Laura last_name: Lorenzo Orts - first_name: Irma full_name: Roig Villanova, Irma last_name: Roig Villanova - first_name: Xuewen full_name: Wang, Xuewen last_name: Wang - first_name: José full_name: Micol, José last_name: Micol - first_name: Maria full_name: Ponce, Maria last_name: Ponce - first_name: Paul full_name: Devlin, Paul last_name: Devlin - first_name: Jaime full_name: Martínez García, Jaime last_name: Martínez García citation: ama: Gallemi M, Galstyan A, Paulišić S, et al. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 2016;143(9):1623-1631. doi:10.1242/dev.130211 apa: Gallemi, M., Galstyan, A., Paulišić, S., Then, C., Ferrández Ayela, A., Lorenzo Orts, L., … Martínez García, J. (2016). DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. Company of Biologists. https://doi.org/10.1242/dev.130211 chicago: Gallemi, Marçal, Anahit Galstyan, Sandi Paulišić, Christiane Then, Almudena Ferrández Ayela, Laura Lorenzo Orts, Irma Roig Villanova, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.130211. ieee: M. Gallemi et al., “DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis,” Development, vol. 143, no. 9. Company of Biologists, pp. 1623–1631, 2016. ista: Gallemi M, Galstyan A, Paulišić S, Then C, Ferrández Ayela A, Lorenzo Orts L, Roig Villanova I, Wang X, Micol J, Ponce M, Devlin P, Martínez García J. 2016. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 143(9), 1623–1631. mla: Gallemi, Marçal, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development, vol. 143, no. 9, Company of Biologists, 2016, pp. 1623–31, doi:10.1242/dev.130211. short: M. Gallemi, A. Galstyan, S. Paulišić, C. Then, A. Ferrández Ayela, L. Lorenzo Orts, I. Roig Villanova, X. Wang, J. Micol, M. Ponce, P. Devlin, J. Martínez García, Development 143 (2016) 1623–1631. date_created: 2018-12-11T11:50:59Z date_published: 2016-05-03T00:00:00Z date_updated: 2021-01-12T06:49:27Z day: '03' department: - _id: EvBe doi: 10.1242/dev.130211 intvolume: ' 143' issue: '9' language: - iso: eng month: '05' oa_version: None page: 1623 - 1631 publication: Development publication_status: published publisher: Company of Biologists publist_id: '6068' quality_controlled: '1' scopus_import: 1 status: public title: DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 143 year: '2016' ... --- _id: '1259' abstract: - lang: eng text: We consider the Bogolubov–Hartree–Fock functional for a fermionic many-body system with two-body interactions. For suitable interaction potentials that have a strong enough attractive tail in order to allow for two-body bound states, but are otherwise sufficiently repulsive to guarantee stability of the system, we show that in the low-density limit the ground state of this model consists of a Bose–Einstein condensate of fermion pairs. The latter can be described by means of the Gross–Pitaevskii energy functional. acknowledgement: Partial financial support from the DFG grant GRK 1838, as well as the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R.S.), is gratefully acknowledged. article_number: '13' article_processing_charge: Yes (via OA deal) author: - first_name: Gerhard full_name: Bräunlich, Gerhard last_name: Bräunlich - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Bräunlich G, Hainzl C, Seiringer R. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. 2016;19(2). doi:10.1007/s11040-016-9209-x apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2016). Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9209-x chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9209-x. ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit,” Mathematical Physics, Analysis and Geometry, vol. 19, no. 2. Springer, 2016. ista: Bräunlich G, Hainzl C, Seiringer R. 2016. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. 19(2), 13. mla: Bräunlich, Gerhard, et al. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry, vol. 19, no. 2, 13, Springer, 2016, doi:10.1007/s11040-016-9209-x. short: G. Bräunlich, C. Hainzl, R. Seiringer, Mathematical Physics, Analysis and Geometry 19 (2016). date_created: 2018-12-11T11:50:59Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:49:27Z day: '01' ddc: - '510' - '539' department: - _id: RoSe doi: 10.1007/s11040-016-9209-x file: - access_level: open_access checksum: 9954f685cc25c58d7f1712c67b47ad8d content_type: application/pdf creator: system date_created: 2018-12-12T10:09:13Z date_updated: 2020-07-14T12:44:42Z file_id: '4736' file_name: IST-2016-702-v1+1_s11040-016-9209-x.pdf file_size: 506242 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 19' issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Mathematical Physics, Analysis and Geometry publication_status: published publisher: Springer publist_id: '6066' pubrep_id: '702' quality_controlled: '1' scopus_import: 1 status: public title: Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit 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: 19 year: '2016' ... --- _id: '1260' abstract: - lang: eng text: In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way. article_number: '1650067' article_processing_charge: No article_type: original author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: De Martino D. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674 apa: De Martino, D. (2016). The dual of the space of interactions in neural network models. International Journal of Modern Physics C. World Scientific Publishing. https://doi.org/10.1142/S0129183116500674 chicago: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C. World Scientific Publishing, 2016. https://doi.org/10.1142/S0129183116500674. ieee: D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6. World Scientific Publishing, 2016. ista: De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067. mla: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:10.1142/S0129183116500674. short: D. De Martino, International Journal of Modern Physics C 27 (2016). date_created: 2018-12-11T11:51:00Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:49:28Z day: '01' department: - _id: GaTk doi: 10.1142/S0129183116500674 external_id: arxiv: - '1505.02963' intvolume: ' 27' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1505.02963 month: '06' oa: 1 oa_version: Preprint publication: International Journal of Modern Physics C publication_status: published publisher: World Scientific Publishing publist_id: '6065' quality_controlled: '1' scopus_import: 1 status: public title: The dual of the space of interactions in neural network models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2016' ... --- _id: '1261' abstract: - lang: eng text: 'We consider a non-standard finite-volume discretization of a strongly non-linear fourth order diffusion equation on the d-dimensional cube, for arbitrary . The scheme preserves two important structural properties of the equation: the first is the interpretation as a gradient flow in a mass transportation metric, and the second is an intimate relation to a linear Fokker-Planck equation. Thanks to these structural properties, the scheme possesses two discrete Lyapunov functionals. These functionals approximate the entropy and the Fisher information, respectively, and their dissipation rates converge to the optimal ones in the discrete-to-continuous limit. Using the dissipation, we derive estimates on the long-time asymptotics of the discrete solutions. Finally, we present results from numerical experiments which indicate that our discretization is able to capture significant features of the complex original dynamics, even with a rather coarse spatial resolution.' acknowledgement: This research was supported by the DFG Collaborative Research Centers TRR 109, ‘ Discretization in Geometry and Dynamics ’ and 1060 ‘ The Mathematics of Emergent Effects ’ . author: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Daniel full_name: Matthes, Daniel last_name: Matthes citation: ama: Maas J, Matthes D. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 2016;29(7):1992-2023. doi:10.1088/0951-7715/29/7/1992 apa: Maas, J., & Matthes, D. (2016). Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. IOP Publishing Ltd. https://doi.org/10.1088/0951-7715/29/7/1992 chicago: Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity. IOP Publishing Ltd., 2016. https://doi.org/10.1088/0951-7715/29/7/1992. ieee: J. Maas and D. Matthes, “Long-time behavior of a finite volume discretization for a fourth order diffusion equation,” Nonlinearity, vol. 29, no. 7. IOP Publishing Ltd., pp. 1992–2023, 2016. ista: Maas J, Matthes D. 2016. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 29(7), 1992–2023. mla: Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity, vol. 29, no. 7, IOP Publishing Ltd., 2016, pp. 1992–2023, doi:10.1088/0951-7715/29/7/1992. short: J. Maas, D. Matthes, Nonlinearity 29 (2016) 1992–2023. date_created: 2018-12-11T11:51:00Z date_published: 2016-06-10T00:00:00Z date_updated: 2021-01-12T06:49:28Z day: '10' department: - _id: JaMa doi: 10.1088/0951-7715/29/7/1992 intvolume: ' 29' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1505.03178 month: '06' oa: 1 oa_version: Preprint page: 1992 - 2023 publication: Nonlinearity publication_status: published publisher: IOP Publishing Ltd. publist_id: '6062' quality_controlled: '1' scopus_import: 1 status: public title: Long-time behavior of a finite volume discretization for a fourth order diffusion equation type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2016' ... --- _id: '1264' abstract: - lang: eng text: n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively. acknowledgement: "We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis; Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance." author: - first_name: Gloria full_name: Sancho Andrés, Gloria last_name: Sancho Andrés - first_name: Esther full_name: Soriano Ortega, Esther last_name: Soriano Ortega - first_name: Caiji full_name: Gao, Caiji last_name: Gao - first_name: Joan full_name: Bernabé Orts, Joan last_name: Bernabé Orts - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Anna full_name: Müller, Anna id: 420AB15A-F248-11E8-B48F-1D18A9856A87 last_name: Müller - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Liwen full_name: Jiang, Liwen last_name: Jiang - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Fernando full_name: Aniento, Fernando last_name: Aniento - first_name: Maria full_name: Marcote, Maria last_name: Marcote citation: ama: Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 2016;171(3):1965-1982. doi:10.1104/pp.16.00373 apa: Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan, M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373 chicago: Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts, Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373. ieee: G. Sancho Andrés et al., “Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol. 171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016. ista: Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 171(3), 1965–1982. mla: Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol. 171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373. short: G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan, A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology 171 (2016) 1965–1982. date_created: 2018-12-11T11:51:01Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:49:29Z day: '01' department: - _id: JiFr - _id: EvBe doi: 10.1104/pp.16.00373 ec_funded: 1 intvolume: ' 171' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/ month: '07' oa: 1 oa_version: Submitted Version page: 1965 - 1982 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '6059' quality_controlled: '1' scopus_import: 1 status: public title: Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 171 year: '2016' ... --- _id: '1265' abstract: - lang: eng text: Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology. article_number: rs5 author: - first_name: Kareem full_name: Elsayad, Kareem last_name: Elsayad - first_name: Stephanie full_name: Werner, Stephanie last_name: Werner - first_name: Marcal full_name: Gallemi Rovira, Marcal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi Rovira - first_name: Jixiang full_name: Kong, Jixiang last_name: Kong - first_name: Edmundo full_name: Guajardo, Edmundo last_name: Guajardo - first_name: Lijuan full_name: Zhang, Lijuan last_name: Zhang - first_name: Yvon full_name: Jaillais, Yvon last_name: Jaillais - first_name: Thomas full_name: Greb, Thomas last_name: Greb - first_name: Youssef full_name: Belkhadir, Youssef last_name: Belkhadir citation: ama: Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 2016;9(435). doi:10.1126/scisignal.aaf6326 apa: Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., … Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.aaf6326 chicago: Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/scisignal.aaf6326. ieee: K. Elsayad et al., “Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging,” Science Signaling, vol. 9, no. 435. American Association for the Advancement of Science, 2016. ista: Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435), rs5. mla: Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling, vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016, doi:10.1126/scisignal.aaf6326. short: K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais, T. Greb, Y. Belkhadir, Science Signaling 9 (2016). date_created: 2018-12-11T11:51:02Z date_published: 2016-07-05T00:00:00Z date_updated: 2021-01-12T06:49:29Z day: '05' department: - _id: EvBe doi: 10.1126/scisignal.aaf6326 intvolume: ' 9' issue: '435' language: - iso: eng month: '07' oa_version: None publication: Science Signaling publication_status: published publisher: American Association for the Advancement of Science publist_id: '6057' quality_controlled: '1' scopus_import: 1 status: public title: Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2016' ... --- _id: '1266' abstract: - lang: eng text: 'Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code.' acknowledgement: Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’. article_number: e13824 author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Boris full_name: Gutkin, Boris last_name: Gutkin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824 apa: Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.13824 chicago: Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824. ieee: M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016. ista: Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824. mla: Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824. short: M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016). date_created: 2018-12-11T11:51:02Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:49:30Z day: '01' ddc: - '571' department: - _id: GaTk doi: 10.7554/eLife.13824 file: - access_level: open_access checksum: dc52d967dc76174477bb258d84be2899 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:20Z date_updated: 2020-07-14T12:44:42Z file_id: '4874' file_name: IST-2016-700-v1+1_e13824-download.pdf file_size: 2819055 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 5' issue: 2016JULY language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '6056' pubrep_id: '700' quality_controlled: '1' scopus_import: 1 status: public title: Neural oscillations as a signature of efficient coding in the presence of synaptic delays 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: 5 year: '2016' ... --- _id: '1269' abstract: - lang: eng text: Plants are continuously exposed to a myriad of external signals such as fluctuating nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks that can severely affect their development, growth, and fertility. As sessile organisms, plants must therefore be able to sense and rapidly react to these external inputs, activate efficient responses, and adjust development to changing conditions. In recent years, significant progress has been made towards understanding the molecular mechanisms underlying the intricate and complex communication between plants and the environment. It is now becoming increasingly evident that hormones have an important regulatory role in plant adaptation and defense mechanisms. author: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Benková E. Plant hormones in interactions with the environment. Plant Molecular Biology. 2016;91(6):597. doi:10.1007/s11103-016-0501-8 apa: Benková, E. (2016). Plant hormones in interactions with the environment. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-016-0501-8 chicago: Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology. Springer, 2016. https://doi.org/10.1007/s11103-016-0501-8. ieee: E. Benková, “Plant hormones in interactions with the environment,” Plant Molecular Biology, vol. 91, no. 6. Springer, p. 597, 2016. ista: Benková E. 2016. Plant hormones in interactions with the environment. Plant Molecular Biology. 91(6), 597. mla: Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology, vol. 91, no. 6, Springer, 2016, p. 597, doi:10.1007/s11103-016-0501-8. short: E. Benková, Plant Molecular Biology 91 (2016) 597. date_created: 2018-12-11T11:51:03Z date_published: 2016-08-01T00:00:00Z date_updated: 2021-01-12T06:49:31Z day: '01' ddc: - '581' department: - _id: EvBe doi: 10.1007/s11103-016-0501-8 file: - access_level: open_access checksum: 0ffb7a15c5336b3a55248cc67021a825 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:28Z date_updated: 2020-07-14T12:44:42Z file_id: '5349' file_name: IST-2016-697-v1+1_s11103-016-0501-8.pdf file_size: 297282 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 91' issue: '6' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '597' publication: Plant Molecular Biology publication_status: published publisher: Springer publist_id: '6052' pubrep_id: '697' quality_controlled: '1' scopus_import: 1 status: public title: Plant hormones in interactions with the environment 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: 91 year: '2016' ... --- _id: '1267' abstract: - lang: eng text: We give a simplified proof of the nonexistence of large nuclei in the liquid drop model and provide an explicit bound. Our bound is within a factor of 2.3 of the conjectured value and seems to be the first quantitative result. acknowledgement: "Open access funding provided by Institute of Science and Technology Austria.\r\n" author: - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Rowan full_name: Killip, Rowan last_name: Killip - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam citation: ama: Frank R, Killip R, Nam P. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 2016;106(8):1033-1036. doi:10.1007/s11005-016-0860-8 apa: Frank, R., Killip, R., & Nam, P. (2016). Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0860-8 chicago: Frank, Rupert, Rowan Killip, and Phan Nam. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0860-8. ieee: R. Frank, R. Killip, and P. Nam, “Nonexistence of large nuclei in the liquid drop model,” Letters in Mathematical Physics, vol. 106, no. 8. Springer, pp. 1033–1036, 2016. ista: Frank R, Killip R, Nam P. 2016. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 106(8), 1033–1036. mla: Frank, Rupert, et al. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics, vol. 106, no. 8, Springer, 2016, pp. 1033–36, doi:10.1007/s11005-016-0860-8. short: R. Frank, R. Killip, P. Nam, Letters in Mathematical Physics 106 (2016) 1033–1036. date_created: 2018-12-11T11:51:02Z date_published: 2016-08-01T00:00:00Z date_updated: 2021-01-12T06:49:30Z day: '01' ddc: - '510' - '539' department: - _id: RoSe doi: 10.1007/s11005-016-0860-8 file: - access_level: open_access checksum: d740a6a226e0f5f864f40e3e269d3cc0 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:09Z date_updated: 2020-07-14T12:44:42Z file_id: '4863' file_name: IST-2016-698-v1+1_s11005-016-0860-8.pdf file_size: 349464 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 106' issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 1033 - 1036 project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '6054' pubrep_id: '698' quality_controlled: '1' scopus_import: 1 status: public title: Nonexistence of large nuclei in the liquid drop model 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 106 year: '2016' ... --- _id: '1268' acknowledgement: We would like to thank Mihai Netea for inviting us to contribute to this Theme Issue. author: - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: Milutinovic B, Kurtz J. Immune memory in invertebrates. Seminars in Immunology. 2016;28(4):328-342. doi:10.1016/j.smim.2016.05.004 apa: Milutinovic, B., & Kurtz, J. (2016). Immune memory in invertebrates. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2016.05.004 chicago: Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” Seminars in Immunology. Academic Press, 2016. https://doi.org/10.1016/j.smim.2016.05.004. ieee: B. Milutinovic and J. Kurtz, “Immune memory in invertebrates,” Seminars in Immunology, vol. 28, no. 4. Academic Press, pp. 328–342, 2016. ista: Milutinovic B, Kurtz J. 2016. Immune memory in invertebrates. Seminars in Immunology. 28(4), 328–342. mla: Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” Seminars in Immunology, vol. 28, no. 4, Academic Press, 2016, pp. 328–42, doi:10.1016/j.smim.2016.05.004. short: B. Milutinovic, J. Kurtz, Seminars in Immunology 28 (2016) 328–342. date_created: 2018-12-11T11:51:03Z date_published: 2016-08-01T00:00:00Z date_updated: 2021-01-12T06:49:30Z day: '01' department: - _id: SyCr doi: 10.1016/j.smim.2016.05.004 intvolume: ' 28' issue: '4' language: - iso: eng month: '08' oa_version: None page: 328 - 342 publication: Seminars in Immunology publication_status: published publisher: Academic Press publist_id: '6053' quality_controlled: '1' scopus_import: 1 status: public title: Immune memory in invertebrates type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2016' ... --- _id: '1271' abstract: - lang: eng text: 'Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times.' acknowledged_ssus: - _id: LifeSc acknowledgement: "We thank K. Lee, C. Norden, A. Webb, and the members of the Paluch lab for\r\ncomments on the manuscript. We are grateful to P. Rørth and Peter Dieterich\r\nfor discussions, S. Ares, Y. Arboleda-Estudillo and S. Schneider for technical help,\r\nM. Biro for help with programming, and the BIOTEC/MPI-CBG and IST zebrafish\r\nand imaging facilities for help and advice at various stages of this project. This work was supported by the Max Planck Society, the Medical Research Council UK (core funding to the MRC LMCB), and by grants from the Polish Ministry of Science and Higher Education (454/N-MPG/2009/0) to EKP, the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EKP, a A*Star JCO career development award (12302FG010) to WY and a Damon Runyon fellowship award to ADM (DRG 2157-12). This work was also supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001317), the UK Medical Research Council (FC001317), and the Wellcome Trust (FC001317) to GS." article_number: '74' author: - first_name: Alba full_name: Diz Muñoz, Alba last_name: Diz Muñoz - first_name: Pawel full_name: Romanczuk, Pawel last_name: Romanczuk - first_name: Weimiao full_name: Yu, Weimiao last_name: Yu - first_name: Martin full_name: Bergert, Martin last_name: Bergert - first_name: Kenzo full_name: Ivanovitch, Kenzo last_name: Ivanovitch - first_name: Guillame full_name: Salbreux, Guillame last_name: Salbreux - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Ewa full_name: Paluch, Ewa last_name: Paluch citation: ama: Diz Muñoz A, Romanczuk P, Yu W, et al. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 2016;14(1). doi:10.1186/s12915-016-0294-x apa: Diz Muñoz, A., Romanczuk, P., Yu, W., Bergert, M., Ivanovitch, K., Salbreux, G., … Paluch, E. (2016). Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. BioMed Central. https://doi.org/10.1186/s12915-016-0294-x chicago: Diz Muñoz, Alba, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch, Guillame Salbreux, Carl-Philipp J Heisenberg, and Ewa Paluch. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology. BioMed Central, 2016. https://doi.org/10.1186/s12915-016-0294-x. ieee: A. Diz Muñoz et al., “Steering cell migration by alternating blebs and actin-rich protrusions,” BMC Biology, vol. 14, no. 1. BioMed Central, 2016. ista: Diz Muñoz A, Romanczuk P, Yu W, Bergert M, Ivanovitch K, Salbreux G, Heisenberg C-PJ, Paluch E. 2016. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 14(1), 74. mla: Diz Muñoz, Alba, et al. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology, vol. 14, no. 1, 74, BioMed Central, 2016, doi:10.1186/s12915-016-0294-x. short: A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux, C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016). date_created: 2018-12-11T11:51:04Z date_published: 2016-09-02T00:00:00Z date_updated: 2021-01-12T06:49:32Z day: '02' ddc: - '572' - '576' department: - _id: CaHe doi: 10.1186/s12915-016-0294-x file: - access_level: open_access checksum: 0bfa484ac69a0a560fb9a4589aeda7f6 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:20Z date_updated: 2020-07-14T12:44:42Z file_id: '5002' file_name: IST-2016-695-v1+1_s12915-016-0294-x.pdf file_size: 1875695 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 14' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 252064B8-B435-11E9-9278-68D0E5697425 grant_number: HE_3231/6-1 name: Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo publication: BMC Biology publication_status: published publisher: BioMed Central publist_id: '6049' pubrep_id: '695' quality_controlled: '1' scopus_import: 1 status: public title: Steering cell migration by alternating blebs and actin-rich protrusions 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: 14 year: '2016' ... --- _id: '1273' abstract: - lang: eng text: Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence. acknowledgement: "We acknowledge the support of glasshouse technicians at the University of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS) Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and a European Reintegration Grant under the 7th framework of the European Commission [ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.); The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan: Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research performed by S.M.B. and A.G. were provided by University of California, Davis startup funds." author: - first_name: Silvana full_name: Porco, Silvana last_name: Porco - first_name: Antoine full_name: Larrieu, Antoine last_name: Larrieu - first_name: Yujuan full_name: Du, Yujuan last_name: Du - first_name: Allison full_name: Gaudinier, Allison last_name: Gaudinier - first_name: Tatsuaki full_name: Goh, Tatsuaki last_name: Goh - first_name: Kamal full_name: Swarup, Kamal last_name: Swarup - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Britta full_name: Kuempers, Britta last_name: Kuempers - first_name: Anthony full_name: Bishopp, Anthony last_name: Bishopp - first_name: Julien full_name: Lavenus, Julien last_name: Lavenus - first_name: Ilda full_name: Casimiro, Ilda last_name: Casimiro - first_name: Kristine full_name: Hill, Kristine last_name: Hill - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Hidehiro full_name: Fukaki, Hidehiro last_name: Fukaki - first_name: Siobhan full_name: Brady, Siobhan last_name: Brady - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Benjamin full_name: Peéet, Benjamin last_name: Peéet - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett citation: ama: Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 2016;143(18):3340-3349. doi:10.1242/dev.136283 apa: Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett, M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. Company of Biologists. https://doi.org/10.1242/dev.136283 chicago: Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.136283. ieee: S. Porco et al., “Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3,” Development, vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016. ista: Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 143(18), 3340–3349. mla: Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development, vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:10.1242/dev.136283. short: S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup, B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki, S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349. date_created: 2018-12-11T11:51:04Z date_published: 2016-09-13T00:00:00Z date_updated: 2021-01-12T06:49:32Z day: '13' department: - _id: EvBe doi: 10.1242/dev.136283 intvolume: ' 143' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01595056/ month: '09' oa: 1 oa_version: Preprint page: 3340 - 3349 publication: Development publication_status: published publisher: Company of Biologists publist_id: '6044' quality_controlled: '1' scopus_import: 1 status: public title: Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3 type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 143 year: '2016' ... --- _id: '1272' abstract: - lang: eng text: We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams. acknowledgement: 'This work was supported by Austrian Science Fund (FWF): P25816-N15.' author: - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721. doi:10.1080/16864360.2016.1150718 apa: Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. Taylor and Francis. https://doi.org/10.1080/16864360.2016.1150718 chicago: Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications. Taylor and Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718. ieee: M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” Computer-Aided Design and Applications, vol. 13, no. 5. Taylor and Francis, pp. 712–721, 2016. ista: Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721. mla: Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications, vol. 13, no. 5, Taylor and Francis, 2016, pp. 712–21, doi:10.1080/16864360.2016.1150718. short: M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721. date_created: 2018-12-11T11:51:04Z date_published: 2016-09-02T00:00:00Z date_updated: 2021-01-12T06:49:32Z day: '02' ddc: - '004' - '516' department: - _id: HeEd doi: 10.1080/16864360.2016.1150718 file: - access_level: open_access checksum: c746f3a48edb62b588d92ea5d0fd2c0e content_type: application/pdf creator: system date_created: 2018-12-12T10:16:20Z date_updated: 2020-07-14T12:44:42Z file_id: '5206' file_name: IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf file_size: 1678369 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 13' issue: '5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 712 - 721 publication: Computer-Aided Design and Applications publication_status: published publisher: Taylor and Francis publist_id: '6048' pubrep_id: '694' quality_controlled: '1' scopus_import: 1 status: public title: Generalized offsetting of planar structures using skeletons 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: 13 year: '2016' ... --- _id: '1279' abstract: - lang: eng text: During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles. acknowledgement: 'The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union''s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] via the IST FELLOWSHIP awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant (acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We thank Lauri Viljanto for technical help in building the ripple detector.' article_number: e0164675 author: - first_name: Krisztián full_name: Kovács, Krisztián id: 2AB5821E-F248-11E8-B48F-1D18A9856A87 last_name: Kovács - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - first_name: Markku full_name: Penttonen, Markku last_name: Penttonen - first_name: Dámaris K full_name: Rangel Guerrero, Dámaris K id: 4871BCE6-F248-11E8-B48F-1D18A9856A87 last_name: Rangel Guerrero orcid: 0000-0002-8602-4374 - 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: Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164675 apa: Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero, D. K., & Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164675 chicago: Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen, Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164675. ieee: K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero, and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016. ista: Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 11(10), e0164675. mla: Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One, vol. 11, no. 10, e0164675, Public Library of Science, 2016, doi:10.1371/journal.pone.0164675. short: K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero, J.L. Csicsvari, PLoS One 11 (2016). date_created: 2018-12-11T11:51:06Z date_published: 2016-10-19T00:00:00Z date_updated: 2021-01-12T06:49:35Z day: '19' ddc: - '570' - '571' department: - _id: JoCs doi: 10.1371/journal.pone.0164675 ec_funded: 1 file: - access_level: open_access checksum: 395895ecb2216e9c39135abaa56b28b3 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:26Z date_updated: 2020-07-14T12:44:42Z file_id: '5009' file_name: IST-2016-690-v1+1_journal.pone.0164675.PDF file_size: 4353592 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 11' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6037' pubrep_id: '690' quality_controlled: '1' scopus_import: 1 status: public title: Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus 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: 11 year: '2016' ... --- _id: '1278' abstract: - lang: eng text: Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons. acknowledgement: This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112 to SN]. article_number: e0164037 article_processing_charge: No article_type: original author: - first_name: Hitomi full_name: Matsuno, Hitomi last_name: Matsuno - first_name: Moeko full_name: Kudoh, Moeko last_name: Kudoh - first_name: Akiya full_name: Watakabe, Akiya last_name: Watakabe - first_name: Tetsuo full_name: Yamamori, Tetsuo last_name: Yamamori - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Soichi full_name: Nagao, Soichi last_name: Nagao citation: ama: 'Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164037' apa: 'Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., & Nagao, S. (2016). Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164037' chicago: 'Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164037.' ieee: 'H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao, “Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.' ista: 'Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 11(10), e0164037.' mla: 'Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One, vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:10.1371/journal.pone.0164037.' short: H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS One 11 (2016). date_created: 2018-12-11T11:51:06Z date_published: 2016-10-06T00:00:00Z date_updated: 2021-01-12T06:49:34Z day: '06' ddc: - '570' - '571' department: - _id: RySh doi: 10.1371/journal.pone.0164037 file: - access_level: open_access checksum: 7c0ba0ca6d79844059158059d2a38d25 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:16Z date_updated: 2020-07-14T12:44:42Z file_id: '5269' file_name: IST-2016-689-v1+1_journal.pone.0164037.PDF file_size: 3657084 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 11' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6038' pubrep_id: '689' quality_controlled: '1' scopus_import: 1 status: public title: 'Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2016' ... --- _id: '1276' abstract: - lang: eng text: The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site. acknowledgement: We wish to thank CSC – IT Centre for Science (Espoo, Finland) for computational resources. For financial support, we wish to thank the Academy of Finland (TR, IV and PAP; Center of Excellence in Biomembrane Research (IV, TR)), the Finnish Doctoral Programme in Computational Sciences (KK), the Sigrid Juselius Foundation (IV), the Paulo Foundation (PAP), and the European Research Council (IV, TR; Advanced Grant project CROWDED-PRO-LIPIDS). AO acknowledges The Wellcome Trust International Senior Research Fellowship. article_number: '33607' author: - first_name: Pekka full_name: Postila, Pekka last_name: Postila - first_name: Karol full_name: Kaszuba, Karol id: 3FDF9472-F248-11E8-B48F-1D18A9856A87 last_name: Kaszuba - first_name: Patryk full_name: Kuleta, Patryk last_name: Kuleta - first_name: Ilpo full_name: Vattulainen, Ilpo last_name: Vattulainen - first_name: Marcin full_name: Sarewicz, Marcin last_name: Sarewicz - first_name: Artur full_name: Osyczka, Artur last_name: Osyczka - first_name: Tomasz full_name: Róg, Tomasz last_name: Róg citation: ama: Postila P, Kaszuba K, Kuleta P, et al. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 2016;6. doi:10.1038/srep33607 apa: Postila, P., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A., & Róg, T. (2016). Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33607 chicago: Postila, Pekka, Karol Kaszuba, Patryk Kuleta, Ilpo Vattulainen, Marcin Sarewicz, Artur Osyczka, and Tomasz Róg. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33607. ieee: P. Postila et al., “Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex,” Scientific Reports, vol. 6. Nature Publishing Group, 2016. ista: Postila P, Kaszuba K, Kuleta P, Vattulainen I, Sarewicz M, Osyczka A, Róg T. 2016. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 6, 33607. mla: Postila, Pekka, et al. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports, vol. 6, 33607, Nature Publishing Group, 2016, doi:10.1038/srep33607. short: P. Postila, K. Kaszuba, P. Kuleta, I. Vattulainen, M. Sarewicz, A. Osyczka, T. Róg, Scientific Reports 6 (2016). date_created: 2018-12-11T11:51:05Z date_published: 2016-09-26T00:00:00Z date_updated: 2021-01-12T06:49:34Z day: '26' ddc: - '576' department: - _id: LeSa doi: 10.1038/srep33607 file: - access_level: open_access checksum: 07c591c1250ebef266333cbc3228b4dd content_type: application/pdf creator: system date_created: 2018-12-12T10:17:09Z date_updated: 2020-07-14T12:44:42Z file_id: '5261' file_name: IST-2016-691-v1+1_srep33607.pdf file_size: 1960563 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '6040' pubrep_id: '691' quality_controlled: '1' scopus_import: 1 status: public title: Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex 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: 6 year: '2016' ... --- _id: '1277' abstract: - lang: eng text: "The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n" acknowledgement: "F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line." author: - first_name: Fausto full_name: Ortiz Morea, Fausto last_name: Ortiz Morea - first_name: Daniel full_name: Savatin, Daniel last_name: Savatin - first_name: Wim full_name: Dejonghe, Wim last_name: Dejonghe - first_name: Rahul full_name: Kumar, Rahul last_name: Kumar - first_name: Yu full_name: Luo, Yu last_name: Luo - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Jos full_name: Van Begin, Jos last_name: Van Begin - first_name: Keini full_name: Dressano, Keini last_name: Dressano - first_name: Guilherme full_name: De Oliveira, Guilherme last_name: De Oliveira - first_name: Xiuyang full_name: Zhao, Xiuyang last_name: Zhao - first_name: Qing full_name: Lu, Qing last_name: Lu - first_name: Annemieke full_name: Madder, Annemieke last_name: Madder - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Daniel full_name: De Moura, Daniel last_name: De Moura - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113 apa: Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113 chicago: Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1605588113. ieee: F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016. ista: Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033. mla: Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:10.1073/pnas.1605588113. short: F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033. date_created: 2018-12-11T11:51:06Z date_published: 2016-09-27T00:00:00Z date_updated: 2021-01-12T06:49:34Z day: '27' department: - _id: JiFr doi: 10.1073/pnas.1605588113 intvolume: ' 113' issue: '39' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/ month: '09' oa: 1 oa_version: Preprint page: 11028 - 11033 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6039' quality_controlled: '1' scopus_import: 1 status: public title: Danger-associated peptide signaling in Arabidopsis requires clathrin type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2016' ... --- _id: '1281' abstract: - lang: eng text: Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue. acknowledgement: "This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility." author: - first_name: Eléonore full_name: Bouguyon, Eléonore last_name: Bouguyon - first_name: Francine full_name: Perrine Walker, Francine last_name: Perrine Walker - first_name: Marjorie full_name: Pervent, Marjorie last_name: Pervent - first_name: Juliette full_name: Rochette, Juliette last_name: Rochette - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Alexandre full_name: Martinière, Alexandre last_name: Martinière - first_name: Lien full_name: Bach, Lien last_name: Bach - first_name: Gabriel full_name: Krouk, Gabriel last_name: Krouk - first_name: Alain full_name: Gojon, Alain last_name: Gojon - first_name: Philippe full_name: Nacry, Philippe last_name: Nacry citation: ama: Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 2016;172(2):1237-1248. doi:10.1104/pp.16.01047 apa: Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01047 chicago: Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.01047. ieee: E. Bouguyon et al., “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016. ista: Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248. mla: Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:10.1104/pp.16.01047. short: E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248. date_created: 2018-12-11T11:51:07Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:49:36Z day: '01' department: - _id: EvBe doi: 10.1104/pp.16.01047 intvolume: ' 172' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/ month: '10' oa: 1 oa_version: Preprint page: 1237 - 1248 publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '6035' quality_controlled: '1' scopus_import: 1 status: public title: Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 172 year: '2016' ... --- _id: '1282' abstract: - lang: eng text: 'We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k.' author: - first_name: Anna full_name: Gundert, Anna last_name: Gundert - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Gundert A, Wagner U. On eigenvalues of random complexes. Israel Journal of Mathematics. 2016;216(2):545-582. doi:10.1007/s11856-016-1419-1 apa: Gundert, A., & Wagner, U. (2016). On eigenvalues of random complexes. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1419-1 chicago: Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1419-1. ieee: A. Gundert and U. Wagner, “On eigenvalues of random complexes,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 545–582, 2016. ista: Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582. mla: Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:10.1007/s11856-016-1419-1. short: A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582. date_created: 2018-12-11T11:51:07Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:49:36Z day: '01' department: - _id: UlWa doi: 10.1007/s11856-016-1419-1 intvolume: ' 216' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1411.4906 month: '10' oa: 1 oa_version: Preprint page: 545 - 582 publication: Israel Journal of Mathematics publication_status: published publisher: Springer publist_id: '6034' quality_controlled: '1' scopus_import: 1 status: public title: On eigenvalues of random complexes type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 216 year: '2016' ... --- _id: '1280' abstract: - lang: eng text: We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics. acknowledgement: "The work of P.B. was partially supported by National Sci-\r\nence Foundation Grant DMS-1208859. The work of L.E. was partially supported\r\nby ERC Advanced Grant RANMAT 338804. The work of H.-T. Y. was partially\r\nsupported by National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award. \ The work of J.Y. was partially supported by National Science\r\nFoundation Grant DMS-1207961. The major part of this research was conducted\r\nwhen all authors were visiting IAS and were also supported by National Science\r\nFoundation Grant DMS-1128255." 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 - first_name: Jun full_name: Yin, Jun last_name: Yin citation: ama: Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 2016;69(10):1815-1881. doi:10.1002/cpa.21624 apa: Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2016). Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21624 chicago: Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2016. https://doi.org/10.1002/cpa.21624. ieee: P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for generalized wigner matrices,” Communications on Pure and Applied Mathematics, vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016. ista: Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881. mla: Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics, vol. 69, no. 10, Wiley-Blackwell, 2016, pp. 1815–81, doi:10.1002/cpa.21624. short: P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied Mathematics 69 (2016) 1815–1881. date_created: 2018-12-11T11:51:07Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:49:35Z day: '01' department: - _id: LaEr doi: 10.1002/cpa.21624 ec_funded: 1 intvolume: ' 69' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1407.5606 month: '10' oa: 1 oa_version: Preprint page: 1815 - 1881 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley-Blackwell publist_id: '6036' scopus_import: 1 status: public title: Fixed energy universality for generalized wigner matrices type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2016' ... --- _id: '1275' article_number: '139802' author: - first_name: Andrew full_name: Callan Jones, Andrew last_name: Callan Jones - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez citation: ama: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Callan-Jones et al. Reply. Physical Review Letters. 2016;117(13). doi:10.1103/PhysRevLett.117.139802 apa: Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez, R. (2016). Callan-Jones et al. Reply. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.117.139802 chicago: Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Callan-Jones et Al. Reply.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.117.139802. ieee: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Callan-Jones et al. Reply,” Physical Review Letters, vol. 117, no. 13. American Physical Society, 2016. ista: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Callan-Jones et al. Reply. Physical Review Letters. 117(13), 139802. mla: Callan Jones, Andrew, et al. “Callan-Jones et Al. Reply.” Physical Review Letters, vol. 117, no. 13, 139802, American Physical Society, 2016, doi:10.1103/PhysRevLett.117.139802. short: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 117 (2016). date_created: 2018-12-11T11:51:05Z date_published: 2016-09-22T00:00:00Z date_updated: 2021-01-12T06:49:33Z day: '22' department: - _id: CaHe doi: 10.1103/PhysRevLett.117.139802 intvolume: ' 117' issue: '13' language: - iso: eng month: '09' oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6041' quality_controlled: '1' scopus_import: 1 status: public title: Callan-Jones et al. Reply type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2016' ... --- _id: '1283' abstract: - lang: eng text: The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil. acknowledgement: "This work was supported by the Austrian Science Fund (FWF01_I1774S) to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript." article_type: original author: - first_name: Qiang full_name: Zhu, Qiang id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87 last_name: Zhu - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 2016;21(10):809-811. doi:10.1016/j.tplants.2016.08.003 apa: Zhu, Q., & Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2016.08.003 chicago: Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” Trends in Plant Science. Cell Press, 2016. https://doi.org/10.1016/j.tplants.2016.08.003. ieee: Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” Trends in Plant Science, vol. 21, no. 10. Cell Press, pp. 809–811, 2016. ista: Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 21(10), 809–811. mla: Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” Trends in Plant Science, vol. 21, no. 10, Cell Press, 2016, pp. 809–11, doi:10.1016/j.tplants.2016.08.003. short: Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811. date_created: 2018-12-11T11:51:08Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:49:36Z day: '01' ddc: - '575' department: - _id: EvBe doi: 10.1016/j.tplants.2016.08.003 file: - access_level: local checksum: 4d569977fad7a7f22b7e3424003d2ab1 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:19Z date_updated: 2020-07-14T12:44:42Z file_id: '4679' file_name: IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf file_size: 229094 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 21' issue: '10' language: - iso: eng month: '10' oa_version: Submitted Version page: 809 - 811 project: - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '6033' pubrep_id: '1018' quality_controlled: '1' scopus_import: 1 status: public title: Seedlings’ strategy to overcome a soil barrier 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2016' ... --- _id: '1286' abstract: - lang: eng text: We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models. acknowledgement: The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure. article_number: '041601' author: - first_name: Bikashkali full_name: Midya, Bikashkali id: 456187FC-F248-11E8-B48F-1D18A9856A87 last_name: Midya - first_name: Michał full_name: Tomza, Michał last_name: Tomza - first_name: Richard full_name: Schmidt, Richard last_name: Schmidt - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;94(4). doi:10.1103/PhysRevA.94.041601 apa: Midya, B., Tomza, M., Schmidt, R., & Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.94.041601 chicago: Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.94.041601. ieee: B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 94, no. 4. American Physical Society, 2016. ista: Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 94(4), 041601. mla: Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:10.1103/PhysRevA.94.041601. short: B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 94 (2016). date_created: 2018-12-11T11:51:09Z date_published: 2016-10-13T00:00:00Z date_updated: 2021-01-12T06:49:37Z day: '13' department: - _id: MiLe doi: 10.1103/PhysRevA.94.041601 ec_funded: 1 intvolume: ' 94' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.06092 month: '10' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '6030' quality_controlled: '1' scopus_import: 1 status: public title: Rotation of cold molecular ions inside a Bose-Einstein condensate type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 94 year: '2016' ... --- _id: '1285' abstract: - lang: eng text: Cell migration is central to a multitude of physiological processes, including embryonic development, immune surveillance, and wound healing, and deregulated migration is key to cancer dissemination. Decades of investigations have uncovered many of the molecular and physical mechanisms underlying cell migration. Together with protrusion extension and cell body retraction, adhesion to the substrate via specific focal adhesion points has long been considered an essential step in cell migration. Although this is true for cells moving on two-dimensional substrates, recent studies have demonstrated that focal adhesions are not required for cells moving in three dimensions, in which confinement is sufficient to maintain a cell in contact with its substrate. Here, we review the investigations that have led to challenging the requirement of specific adhesions for migration, discuss the physical mechanisms proposed for cell body translocation during focal adhesion-independent migration, and highlight the remaining open questions for the future. acknowledgement: We would like to thank Dani Bodor for critical comments on the manuscript and Guillaume Salbreux for discussions. The authors are supported by the United Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian Science Foundation (M.S.). author: - first_name: Ewa full_name: Paluch, Ewa last_name: Paluch - first_name: Irene full_name: Aspalter, Irene last_name: Aspalter - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 2016;32:469-490. doi:10.1146/annurev-cellbio-111315-125341 apa: Paluch, E., Aspalter, I., & Sixt, M. K. (2016). Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-111315-125341 chicago: Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent Cell Migration.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2016. https://doi.org/10.1146/annurev-cellbio-111315-125341. ieee: E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,” Annual Review of Cell and Developmental Biology, vol. 32. Annual Reviews, pp. 469–490, 2016. ista: Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 32, 469–490. mla: Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” Annual Review of Cell and Developmental Biology, vol. 32, Annual Reviews, 2016, pp. 469–90, doi:10.1146/annurev-cellbio-111315-125341. short: E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental Biology 32 (2016) 469–490. date_created: 2018-12-11T11:51:08Z date_published: 2016-10-06T00:00:00Z date_updated: 2021-01-12T06:49:37Z day: '06' department: - _id: MiSi doi: 10.1146/annurev-cellbio-111315-125341 ec_funded: 1 intvolume: ' 32' language: - iso: eng month: '10' oa_version: None page: 469 - 490 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) publication: Annual Review of Cell and Developmental Biology publication_status: published publisher: Annual Reviews publist_id: '6031' quality_controlled: '1' scopus_import: 1 status: public title: Focal adhesion-independent cell migration type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2016' ... --- _id: '1288' abstract: - lang: eng text: Respiratory complex I transfers electrons from NADH to quinone, utilizing the reaction energy to translocate protons across the membrane. It is a key enzyme of the respiratory chain of many prokaryotic and most eukaryotic organisms. The reversible NADH oxidation reaction is facilitated in complex I by non-covalently bound flavin mononucleotide (FMN). Here we report that the catalytic activity of E. coli complex I with artificial electron acceptors potassium ferricyanide (FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar range in oxidized complex I to the nanomolar range in the NADH reduced enzyme, with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex I, rather than that of FMN, proved critical to the dissociation. Such dissociation is not observed with the T. thermophilus enzyme and our analysis suggests that the difference may be due to the unusually high redox potential of Fe-S cluster N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo by releasing FMN under highly reducing conditions. acknowledgement: This work was funded by the UK Medical Research Council. author: - first_name: Peter full_name: Holt, Peter last_name: Holt - first_name: Rouslan full_name: Efremov, Rouslan last_name: Efremov - first_name: Eiko full_name: Nakamaru Ogiso, Eiko last_name: Nakamaru Ogiso - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 2016;1857(11):1777-1785. doi:10.1016/j.bbabio.2016.08.008 apa: Holt, P., Efremov, R., Nakamaru Ogiso, E., & Sazanov, L. A. (2016). Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2016.08.008 chicago: Holt, Peter, Rouslan Efremov, Eiko Nakamaru Ogiso, and Leonid A Sazanov. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2016. https://doi.org/10.1016/j.bbabio.2016.08.008. ieee: P. Holt, R. Efremov, E. Nakamaru Ogiso, and L. A. Sazanov, “Reversible FMN dissociation from Escherichia coli respiratory complex I,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 11. Elsevier, pp. 1777–1785, 2016. ista: Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. 2016. Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(11), 1777–1785. mla: Holt, Peter, et al. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 11, Elsevier, 2016, pp. 1777–85, doi:10.1016/j.bbabio.2016.08.008. short: P. Holt, R. Efremov, E. Nakamaru Ogiso, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 1777–1785. date_created: 2018-12-11T11:51:09Z date_published: 2016-11-01T00:00:00Z date_updated: 2021-01-12T06:49:38Z day: '01' department: - _id: LeSa doi: 10.1016/j.bbabio.2016.08.008 intvolume: ' 1857' issue: '11' language: - iso: eng month: '11' oa_version: None page: 1777 - 1785 publication: Biochimica et Biophysica Acta - Bioenergetics publication_status: published publisher: Elsevier publist_id: '6028' quality_controlled: '1' scopus_import: 1 status: public title: Reversible FMN dissociation from Escherichia coli respiratory complex I type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1857 year: '2016' ... --- _id: '1291' abstract: - lang: eng text: We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p > 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity. acknowledgement: "Open access funding provided by Institute of Science and Technology (IST Austria). The\r\nresearch leading to these results has received funding from the European Research Council under the European\r\nUnion’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN National Grant Geometric and analytic theory of Hamiltonian systems in finite and infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27. Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems, random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully acknowledged." author: - 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: Giuliani A, Seiringer R. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 2016;347(3):983-1007. doi:10.1007/s00220-016-2665-0 apa: Giuliani, A., & Seiringer, R. (2016). Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2665-0 chicago: Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2665-0. ieee: A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models with competing interactions,” Communications in Mathematical Physics, vol. 347, no. 3. Springer, pp. 983–1007, 2016. ista: Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007. mla: Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” Communications in Mathematical Physics, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:10.1007/s00220-016-2665-0. short: A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016) 983–1007. date_created: 2018-12-11T11:51:11Z date_published: 2016-11-01T00:00:00Z date_updated: 2021-01-12T06:49:40Z day: '01' ddc: - '510' - '530' department: - _id: RoSe doi: 10.1007/s00220-016-2665-0 file: - access_level: open_access checksum: 3c6e08c048fc462e312788be72874bb1 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:02Z date_updated: 2020-07-14T12:44:42Z file_id: '4725' file_name: IST-2016-688-v1+1_s00220-016-2665-0.pdf file_size: 794983 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 347' issue: '3' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 983 - 1007 project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '6025' pubrep_id: '688' quality_controlled: '1' scopus_import: 1 status: public title: Periodic striped ground states in Ising models with competing interactions 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 347 year: '2016' ... --- _id: '1293' abstract: - lang: eng text: For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry. acknowledgement: We wish to thank Alexander Engström and Bernd Sturmfels for various valuable discussions and insights. We also thank the two anonymous referees for their thoughtful feedback on the paper. CU was partially supported by the Austrian Science Fund (FWF) Y 903-N35. author: - first_name: Liam T full_name: Solus, Liam T id: 2AADA620-F248-11E8-B48F-1D18A9856A87 last_name: Solus - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Ruriko full_name: Yoshida, Ruriko last_name: Yoshida citation: ama: Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 2016;509:247-275. doi:10.1016/j.laa.2016.07.026 apa: Solus, L. T., Uhler, C., & Yoshida, R. (2016). Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2016.07.026 chicago: Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications. Elsevier, 2016. https://doi.org/10.1016/j.laa.2016.07.026. ieee: L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors,” Linear Algebra and Its Applications, vol. 509. Elsevier, pp. 247–275, 2016. ista: Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 509, 247–275. mla: Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications, vol. 509, Elsevier, 2016, pp. 247–75, doi:10.1016/j.laa.2016.07.026. short: L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509 (2016) 247–275. date_created: 2018-12-11T11:51:11Z date_published: 2016-11-15T00:00:00Z date_updated: 2021-01-12T06:49:40Z day: '15' department: - _id: CaUh doi: 10.1016/j.laa.2016.07.026 intvolume: ' 509' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/pdf/1506.06702.pdf month: '11' oa: 1 oa_version: Preprint page: 247 - 275 project: - _id: 2530CA10-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 903-N35 name: 'Gaussian Graphical Models: Theory and Applications' publication: Linear Algebra and Its Applications publication_status: published publisher: Elsevier publist_id: '6024' quality_controlled: '1' scopus_import: 1 status: public title: Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 509 year: '2016' ... --- _id: '1290' abstract: - lang: eng text: We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline. acknowledgement: "This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n" author: - first_name: Laura full_name: Stone, Laura last_name: Stone - first_name: Michael full_name: Baym, Michael last_name: Baym - first_name: Tami full_name: Lieberman, Tami last_name: Lieberman - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Jon full_name: Clardy, Jon last_name: Clardy - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 2016;12(11):902-904. doi:10.1038/nchembio.2176 apa: Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176 chicago: Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176. ieee: L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016. ista: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904. mla: Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176. short: L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904. date_created: 2018-12-11T11:51:10Z date_published: 2016-11-01T00:00:00Z date_updated: 2021-01-12T06:49:39Z day: '01' department: - _id: CaGu - _id: GaTk doi: 10.1038/nchembio.2176 intvolume: ' 12' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/ month: '11' oa: 1 oa_version: Preprint page: 902 - 904 publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '6026' quality_controlled: '1' scopus_import: 1 status: public title: Compounds that select against the tetracycline-resistance efflux pump type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2016' ... --- _id: '1295' abstract: - lang: eng text: Voronoi diagrams and Delaunay triangulations have been extensively used to represent and compute geometric features of point configurations. We introduce a generalization to poset diagrams and poset complexes, which contain order-k and degree-k Voronoi diagrams and their duals as special cases. Extending a result of Aurenhammer from 1990, we show how to construct poset diagrams as weighted Voronoi diagrams of average balls. acknowledgement: This work is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: ama: 'Edelsbrunner H, Iglesias Ham M. Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. 2016;54:169-174. doi:10.1016/j.endm.2016.09.030' apa: 'Edelsbrunner, H., & Iglesias Ham, M. (2016). Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2016.09.030' chicago: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” Electronic Notes in Discrete Mathematics. Elsevier, 2016. https://doi.org/10.1016/j.endm.2016.09.030.' ieee: 'H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls II: Weighted averages,” Electronic Notes in Discrete Mathematics, vol. 54. Elsevier, pp. 169–174, 2016.' ista: 'Edelsbrunner H, Iglesias Ham M. 2016. Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. 54, 169–174.' mla: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” Electronic Notes in Discrete Mathematics, vol. 54, Elsevier, 2016, pp. 169–74, doi:10.1016/j.endm.2016.09.030.' short: H. Edelsbrunner, M. Iglesias Ham, Electronic Notes in Discrete Mathematics 54 (2016) 169–174. date_created: 2018-12-11T11:51:12Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:49:41Z day: '01' department: - _id: HeEd doi: 10.1016/j.endm.2016.09.030 ec_funded: 1 intvolume: ' 54' language: - iso: eng month: '10' oa_version: None page: 169 - 174 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Electronic Notes in Discrete Mathematics publication_status: published publisher: Elsevier publist_id: '5976' quality_controlled: '1' scopus_import: 1 status: public title: 'Multiple covers with balls II: Weighted averages' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2016' ... --- _id: '1292' abstract: - lang: eng text: We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds. acknowledgement: "The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful discussions and advice and Christian Evers for helpful remarks on a draft version." author: - first_name: Sebastian full_name: Durst, Sebastian last_name: Durst - first_name: Marc full_name: Kegel, Marc last_name: Kegel - first_name: Mirko D full_name: Klukas, Mirko D id: 34927512-F248-11E8-B48F-1D18A9856A87 last_name: Klukas citation: ama: Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 2016;150(2):441-455. doi:10.1007/s10474-016-0648-4 apa: Durst, S., Kegel, M., & Klukas, M. D. (2016). Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. Springer. https://doi.org/10.1007/s10474-016-0648-4 chicago: Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin Invariant in Open Books.” Acta Mathematica Hungarica. Springer, 2016. https://doi.org/10.1007/s10474-016-0648-4. ieee: S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant in open books,” Acta Mathematica Hungarica, vol. 150, no. 2. Springer, pp. 441–455, 2016. ista: Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 150(2), 441–455. mla: Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open Books.” Acta Mathematica Hungarica, vol. 150, no. 2, Springer, 2016, pp. 441–55, doi:10.1007/s10474-016-0648-4. short: S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455. date_created: 2018-12-11T11:51:11Z date_published: 2016-12-01T00:00:00Z date_updated: 2021-01-12T06:49:40Z day: '01' department: - _id: HeEd doi: 10.1007/s10474-016-0648-4 intvolume: ' 150' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1605.00794 month: '12' oa: 1 oa_version: Preprint page: 441 - 455 publication: Acta Mathematica Hungarica publication_status: published publisher: Springer publist_id: '6023' quality_controlled: '1' scopus_import: 1 status: public title: Computing the Thurston–Bennequin invariant in open books type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 150 year: '2016' ... --- _id: '1319' abstract: - lang: eng text: We present a novel optimization-based algorithm for the design and fabrication of customized, deformable input devices, capable of continuously sensing their deformation. We propose to embed piezoresistive sensing elements into flexible 3D printed objects. These sensing elements are then utilized to recover rich and natural user interactions at runtime. Designing such objects is a challenging and hard problem if attempted manually for all but the simplest geometries and deformations. Our method simultaneously optimizes the internal routing of the sensing elements and computes a mapping from low-level sensor readings to user-specified outputs in order to minimize reconstruction error. We demonstrate the power and flexibility of the approach by designing and fabricating a set of flexible input devices. Our results indicate that the optimization-based design greatly outperforms manual routings in terms of reconstruction accuracy and thus interaction fidelity. acknowledgement: "We thank Damian Karrer, Rocco Ghielmini and Jemin\r\nHwangbo for their help in our initial explorations. We would\r\nlike to thank Christian Schumacher for creating the video and\r\nC\r\n ́\r\necile Edwards-Rietmann for providing the voiceover. Mau-\r\nrizio Nitti helped us in designing our 3D characters. We thank\r\nChiara Daraio for insightful discussions on material proper-\r\nties and 3D printing. We also thank the CHI reviewers for\r\ntheir feedback and guidance. Fabrizio Pece was supported by\r\nan ETH/Marie Curie fellowship (FEL-3314-1)." author: - first_name: Moritz full_name: Bächer, Moritz last_name: Bächer - first_name: Benjamin full_name: Hepp, Benjamin last_name: Hepp - first_name: Fabrizio full_name: Pece, Fabrizio last_name: Pece - first_name: Paul full_name: Kry, Paul last_name: Kry - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Otmar full_name: Hilliges, Otmar last_name: Hilliges citation: ama: 'Bächer M, Hepp B, Pece F, et al. DefSense: computational design of customized deformable input devices. In: ACM; 2016:3806-3816. doi:10.1145/2858036.2858354' apa: 'Bächer, M., Hepp, B., Pece, F., Kry, P., Bickel, B., Thomaszewski, B., & Hilliges, O. (2016). DefSense: computational design of customized deformable input devices (pp. 3806–3816). Presented at the CHI: Conference on Human Factors in Computing Systems, San Jose, California, USA: ACM. https://doi.org/10.1145/2858036.2858354' chicago: 'Bächer, Moritz, Benjamin Hepp, Fabrizio Pece, Paul Kry, Bernd Bickel, Bernhard Thomaszewski, and Otmar Hilliges. “DefSense: Computational Design of Customized Deformable Input Devices,” 3806–16. ACM, 2016. https://doi.org/10.1145/2858036.2858354.' ieee: 'M. Bächer et al., “DefSense: computational design of customized deformable input devices,” presented at the CHI: Conference on Human Factors in Computing Systems, San Jose, California, USA, 2016, pp. 3806–3816.' ista: 'Bächer M, Hepp B, Pece F, Kry P, Bickel B, Thomaszewski B, Hilliges O. 2016. DefSense: computational design of customized deformable input devices. CHI: Conference on Human Factors in Computing Systems, 3806–3816.' mla: 'Bächer, Moritz, et al. DefSense: Computational Design of Customized Deformable Input Devices. ACM, 2016, pp. 3806–16, doi:10.1145/2858036.2858354.' short: M. Bächer, B. Hepp, F. Pece, P. Kry, B. Bickel, B. Thomaszewski, O. Hilliges, in:, ACM, 2016, pp. 3806–3816. conference: end_date: 2016-05-12 location: San Jose, California, USA name: 'CHI: Conference on Human Factors in Computing Systems' start_date: 2016-05-07 date_created: 2018-12-11T11:51:21Z date_published: 2016-05-07T00:00:00Z date_updated: 2021-01-12T06:49:51Z day: '07' department: - _id: BeBi doi: 10.1145/2858036.2858354 language: - iso: eng month: '05' oa_version: None page: 3806 - 3816 publication_status: published publisher: ACM publist_id: '5951' quality_controlled: '1' scopus_import: 1 status: public title: 'DefSense: computational design of customized deformable input devices' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1323' abstract: - lang: eng text: Mossy fiber synapses on CA3 pyramidal cells are 'conditional detonators' that reliably discharge postsynaptic targets. The 'conditional' nature implies that burst activity in dentate gyrus granule cells is required for detonation. Whether single unitary excitatory postsynaptic potentials (EPSPs) trigger spikes in CA3 neurons remains unknown. Mossy fiber synapses exhibit both pronounced short-term facilitation and uniquely large post-tetanic potentiation (PTP). We tested whether PTP could convert mossy fiber synapses from subdetonator into detonator mode, using a recently developed method to selectively and noninvasively stimulate individual presynaptic terminals in rat brain slices. Unitary EPSPs failed to initiate a spike in CA3 neurons under control conditions, but reliably discharged them after induction of presynaptic short-term plasticity. Remarkably, PTP switched mossy fiber synapses into full detonators for tens of seconds. Plasticity-dependent detonation may be critical for efficient coding, storage, and recall of information in the granule cell–CA3 cell network. acknowledged_ssus: - _id: M-Shop - _id: PreCl article_number: e17977 author: - first_name: Nicholas full_name: Vyleta, Nicholas id: 36C4978E-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - 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: Vyleta N, Borges Merjane C, Jonas PM. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 2016;5. doi:10.7554/eLife.17977 apa: Vyleta, N., Borges Merjane, C., & Jonas, P. M. (2016). Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.17977 chicago: Vyleta, Nicholas, Carolina Borges Merjane, and Peter M Jonas. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.17977. ieee: N. Vyleta, C. Borges Merjane, and P. M. Jonas, “Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses,” eLife, vol. 5. eLife Sciences Publications, 2016. ista: Vyleta N, Borges Merjane C, Jonas PM. 2016. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 5, e17977. mla: Vyleta, Nicholas, et al. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife, vol. 5, e17977, eLife Sciences Publications, 2016, doi:10.7554/eLife.17977. short: N. Vyleta, C. Borges Merjane, P.M. Jonas, ELife 5 (2016). date_created: 2018-12-11T11:51:22Z date_published: 2016-10-25T00:00:00Z date_updated: 2023-02-21T10:34:24Z day: '25' ddc: - '571' - '572' department: - _id: PeJo doi: 10.7554/eLife.17977 ec_funded: 1 file: - access_level: open_access checksum: a7201280c571bed88ebd459ce5ce6a47 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:05Z date_updated: 2020-07-14T12:44:44Z file_id: '5257' file_name: IST-2016-715-v1+1_e17977-download.pdf file_size: 1477891 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '10' 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 - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5947' pubrep_id: '715' quality_controlled: '1' scopus_import: 1 status: public title: Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses 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: 5 year: '2016' ... --- _id: '1325' abstract: - lang: eng text: We study graphs and two-player games in which rewards are assigned to states, and the goal of the players is to satisfy or dissatisfy certain property of the generated outcome, given as a mean payoff property. Since the notion of mean-payoff does not reflect possible fluctuations from the mean-payoff along a run, we propose definitions and algorithms for capturing the stability of the system, and give algorithms for deciding if a given mean payoff and stability objective can be ensured in the system. acknowledgement: "The work has been supported by the Czech Science Foundation, grant No. 15-17564S, by EPSRC grant\r\nEP/M023656/1, and by the People Programme (Marie Curie Actions) of the European Union’s Seventh\r\nFramework Programme (FP7/2007-2013) under REA grant agreement no [291734]" alternative_title: - LIPIcs article_number: '10' author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil T, Forejt V, Kučera A, Novotný P. Stability in graphs and games. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.10' apa: 'Brázdil, T., Forejt, V., Kučera, A., & Novotný, P. (2016). Stability in graphs and games (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10' chicago: Brázdil, Tomáš, Vojtěch Forejt, Antonín Kučera, and Petr Novotný. “Stability in Graphs and Games,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10. ieee: 'T. Brázdil, V. Forejt, A. Kučera, and P. Novotný, “Stability in graphs and games,” presented at the CONCUR: Concurrency Theory, Quebec City, Canada, 2016, vol. 59.' ista: 'Brázdil T, Forejt V, Kučera A, Novotný P. 2016. Stability in graphs and games. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 10.' mla: Brázdil, Tomáš, et al. Stability in Graphs and Games. Vol. 59, 10, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.10. short: T. Brázdil, V. Forejt, A. Kučera, P. Novotný, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. conference: end_date: 2016-08-26 location: Quebec City, Canada name: 'CONCUR: Concurrency Theory' start_date: 2016-08-23 date_created: 2018-12-11T11:51:23Z date_published: 2016-08-01T00:00:00Z date_updated: 2021-01-12T06:49:53Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2016.10 ec_funded: 1 file: - access_level: open_access checksum: 3c2dc6ab0358f8aa8f7aa7d6c1293159 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:40Z date_updated: 2020-07-14T12:44:44Z file_id: '5229' file_name: IST-2016-665-v1+1_Forejt_et_al__Stability_in_graphs_and_games.pdf file_size: 553648 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 59' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5944' pubrep_id: '665' quality_controlled: '1' scopus_import: 1 status: public title: Stability in graphs and games 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 59 year: '2016' ... --- _id: '1320' abstract: - lang: eng text: 'In recent years, several biomolecular systems have been shown to be scale-invariant (SI), i.e. to show the same output dynamics when exposed to geometrically scaled input signals (u → pu, p > 0) after pre-adaptation to accordingly scaled constant inputs. In this article, we show that SI systems-as well as systems invariant with respect to other input transformations-can realize nonlinear differential operators: when excited by inputs obeying functional forms characteristic for a given class of invariant systems, the systems'' outputs converge to constant values directly quantifying the speed of the input.' acknowledgement: The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734]. Work supported in part by grants AFOSR FA9550-14-1-0060 and NIH 1R01GM100473. article_number: '7526722' author: - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Eduardo full_name: Sontag, Eduardo last_name: Sontag citation: ama: 'Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722' apa: 'Lang, M., & Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE. https://doi.org/10.1109/ACC.2016.7526722' chicago: Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722. ieee: 'M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.' ista: 'Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.' mla: Lang, Moritz, and Eduardo Sontag. Scale-Invariant Systems Realize Nonlinear Differential Operators. Vol. 2016–July, 7526722, IEEE, 2016, doi:10.1109/ACC.2016.7526722. short: M. Lang, E. Sontag, in:, IEEE, 2016. conference: end_date: 2016-07-08 location: Boston, MA, USA name: 'ACC: American Control Conference' start_date: 2016-07-06 date_created: 2018-12-11T11:51:21Z date_published: 2016-07-28T00:00:00Z date_updated: 2021-01-12T06:49:51Z day: '28' ddc: - '003' - '621' department: - _id: CaGu - _id: GaTk doi: 10.1109/ACC.2016.7526722 ec_funded: 1 file: - access_level: local checksum: 7219432b43defc62a0d45f48d4ce6a19 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:17Z date_updated: 2020-07-14T12:44:43Z file_id: '5203' file_name: IST-2017-810-v1+1_root.pdf file_size: 539166 relation: main_file file_date_updated: 2020-07-14T12:44:43Z has_accepted_license: '1' language: - iso: eng month: '07' oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: IEEE publist_id: '5950' pubrep_id: '810' quality_controlled: '1' scopus_import: 1 status: public title: Scale-invariant systems realize nonlinear differential operators type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016-July year: '2016' ... --- _id: '1324' abstract: - lang: eng text: 'DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. DEC-POMDPs have been studied with finite-horizon and infinite-horizon discounted-sum objectives, and there exist solvers both for exact and approximate solutions. In this work we consider Goal-DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the RTDP-Bel approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. Copyright ' author: - 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 citation: ama: 'Chatterjee K, Chmelik M. Indefinite-horizon reachability in Goal-DEC-POMDPs. In: Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling. Vol 2016-January. AAAI Press; 2016:88-96.' apa: 'Chatterjee, K., & Chmelik, M. (2016). Indefinite-horizon reachability in Goal-DEC-POMDPs. In Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling (Vol. 2016–January, pp. 88–96). London, United Kingdom: AAAI Press.' chicago: Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” In Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, 2016–January:88–96. AAAI Press, 2016. ieee: K. Chatterjee and M. Chmelik, “Indefinite-horizon reachability in Goal-DEC-POMDPs,” in Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, London, United Kingdom, 2016, vol. 2016–January, pp. 88–96. ista: 'Chatterjee K, Chmelik M. 2016. Indefinite-horizon reachability in Goal-DEC-POMDPs. Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 2016–January, 88–96.' mla: Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, vol. 2016–January, AAAI Press, 2016, pp. 88–96. short: K. Chatterjee, M. Chmelik, in:, Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, AAAI Press, 2016, pp. 88–96. conference: end_date: 2016-06-17 location: London, United Kingdom name: 'ICAPS: International Conference on Automated Planning and Scheduling' start_date: 2016-06-12 date_created: 2018-12-11T11:51:22Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T06:49:53Z day: '01' department: - _id: KrCh ec_funded: 1 language: - iso: eng main_file_link: - url: http://www.aaai.org/ocs/index.php/ICAPS/ICAPS16/paper/view/12999 month: '01' oa_version: None page: 88 - 96 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling publication_status: published publisher: AAAI Press publist_id: '5946' quality_controlled: '1' scopus_import: 1 status: public title: Indefinite-horizon reachability in Goal-DEC-POMDPs type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016-January year: '2016' ... --- _id: '1329' abstract: - lang: eng text: Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species. acknowledgement: This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L. Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and K. Otte for providing the necessary resources and help for maintaining Daphnia cultures in the laboratory. H. Lainer supported us for the molecular laboratory work. D. Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and L. Hardulak did the orthology mapping including more insect species. This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium. author: - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Alberto full_name: López Ezquerra, Alberto last_name: López Ezquerra - first_name: John full_name: Parsch, John last_name: Parsch - first_name: Mathilde full_name: Cordellier, Mathilde last_name: Cordellier citation: ama: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 2016;8(10):3120-3139. doi:10.1093/gbe/evw221 apa: Huylmans, A. K., López Ezquerra, A., Parsch, J., & Cordellier, M. (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evw221 chicago: Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/gbe/evw221. ieee: A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata,” Genome Biology and Evolution, vol. 8, no. 10. Oxford University Press, pp. 3120–3139, 2016. ista: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 8(10), 3120–3139. mla: Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:10.1093/gbe/evw221. short: A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology and Evolution 8 (2016) 3120–3139. date_created: 2018-12-11T11:51:24Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:49:55Z day: '01' ddc: - '576' department: - _id: BeVi doi: 10.1093/gbe/evw221 file: - access_level: open_access checksum: 25c7adcb452d39d3b6343ff4b57a652d content_type: application/pdf creator: system date_created: 2018-12-12T10:12:06Z date_updated: 2020-07-14T12:44:44Z file_id: '4924' file_name: IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf file_size: 1406265 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 8' issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '10' oa: 1 oa_version: Published Version page: 3120 - 3139 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5940' pubrep_id: '663' quality_controlled: '1' scopus_import: 1 status: public title: De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata 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: 8 year: '2016' ... --- _id: '1327' abstract: - lang: eng text: 'We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. ' 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: Anchit full_name: Gupta, Anchit last_name: Gupta - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. Stochastic shortest path with energy constraints in POMDPs. In: Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. ACM; 2016:1465-1466.' apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., & Novotný, P. (2016). Stochastic shortest path with energy constraints in POMDPs. In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems (pp. 1465–1466). Singapore: ACM.' chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, 1465–66. ACM, 2016. ieee: T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, and P. Novotný, “Stochastic shortest path with energy constraints in POMDPs,” in Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, Singapore, 2016, pp. 1465–1466. ista: 'Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. 2016. Stochastic shortest path with energy constraints in POMDPs. Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. AAMAS: Autonomous Agents & Multiagent Systems, 1465–1466.' mla: Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in POMDPs.” Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–66. short: T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, P. Novotný, in:, Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–1466. conference: end_date: 2016-05-13 location: Singapore name: 'AAMAS: Autonomous Agents & Multiagent Systems' start_date: 2016-05-09 date_created: 2018-12-11T11:51:23Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T06:49:54Z day: '01' department: - _id: KrCh ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.07565 month: '01' oa: 1 oa_version: Preprint page: 1465 - 1466 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems publication_status: published publisher: ACM publist_id: '5942' quality_controlled: '1' scopus_import: 1 status: public title: Stochastic shortest path with energy constraints in POMDPs type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1326' abstract: - lang: eng text: 'Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. ' acknowledgement: The research was funded by the Czech Science Foundation Grant No. P202/12/G061 and by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734]. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil T, Kučera A, Novotný P. Optimizing the expected mean payoff in Energy Markov Decision Processes. In: Vol 9938. Springer; 2016:32-49. doi:10.1007/978-3-319-46520-3_3' apa: 'Brázdil, T., Kučera, A., & Novotný, P. (2016). Optimizing the expected mean payoff in Energy Markov Decision Processes (Vol. 9938, pp. 32–49). Presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan: Springer. https://doi.org/10.1007/978-3-319-46520-3_3' chicago: Brázdil, Tomáš, Antonín Kučera, and Petr Novotný. “Optimizing the Expected Mean Payoff in Energy Markov Decision Processes,” 9938:32–49. Springer, 2016. https://doi.org/10.1007/978-3-319-46520-3_3. ieee: 'T. Brázdil, A. Kučera, and P. Novotný, “Optimizing the expected mean payoff in Energy Markov Decision Processes,” presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan, 2016, vol. 9938, pp. 32–49.' ista: 'Brázdil T, Kučera A, Novotný P. 2016. Optimizing the expected mean payoff in Energy Markov Decision Processes. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 9938, 32–49.' mla: Brázdil, Tomáš, et al. Optimizing the Expected Mean Payoff in Energy Markov Decision Processes. Vol. 9938, Springer, 2016, pp. 32–49, doi:10.1007/978-3-319-46520-3_3. short: T. Brázdil, A. Kučera, P. Novotný, in:, Springer, 2016, pp. 32–49. conference: end_date: 2016-10-20 location: Chiba, Japan name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2016-10-17 date_created: 2018-12-11T11:51:23Z date_published: 2016-09-22T00:00:00Z date_updated: 2021-01-12T06:49:53Z day: '22' department: - _id: KrCh doi: 10.1007/978-3-319-46520-3_3 ec_funded: 1 intvolume: ' 9938' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.00678 month: '09' oa: 1 oa_version: Preprint page: 32 - 49 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5943' quality_controlled: '1' scopus_import: 1 status: public title: Optimizing the expected mean payoff in Energy Markov Decision Processes type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9938 year: '2016' ... --- _id: '1330' abstract: - lang: eng text: In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K. acknowledgement: Supported by People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n°[291734]. Supported by the Russian Foundation for Basic Research grant 15-31-20403 (mol a ved), by the Russian Foundation for Basic Research grant 15-01-99563 A, in part by the Moebius Contest Foundation for Young Scientists, and in part by the Simons Foundation. author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Alexey full_name: Balitskiy, Alexey last_name: Balitskiy citation: ama: Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 2016;216(2):833-845. doi:10.1007/s11856-016-1429-z apa: Akopyan, A., & Balitskiy, A. (2016). Billiards in convex bodies with acute angles. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1429-z chicago: Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1429-z. ieee: A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 833–845, 2016. ista: Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 216(2), 833–845. mla: Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 833–45, doi:10.1007/s11856-016-1429-z. short: A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845. date_created: 2018-12-11T11:51:24Z date_published: 2016-10-15T00:00:00Z date_updated: 2021-01-12T06:49:56Z day: '15' department: - _id: HeEd doi: 10.1007/s11856-016-1429-z ec_funded: 1 intvolume: ' 216' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1506.06014 month: '10' oa: 1 oa_version: Preprint page: 833 - 845 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Israel Journal of Mathematics publication_status: published publisher: Springer publist_id: '5938' quality_controlled: '1' scopus_import: 1 status: public title: Billiards in convex bodies with acute angles type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 216 year: '2016' ... --- _id: '1334' abstract: - lang: eng text: Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping. article_number: '11824' author: - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - 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: Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of hippocampal place maps. Nature Communications. 2016;7. doi:10.1038/ncomms11824 apa: Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2016). Activity dependent plasticity of hippocampal place maps. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11824 chicago: Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11824. ieee: P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity of hippocampal place maps,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Schönenberger P, O’Neill J, Csicsvari JL. 2016. Activity dependent plasticity of hippocampal place maps. Nature Communications. 7, 11824. mla: Schönenberger, Philipp, et al. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications, vol. 7, 11824, Nature Publishing Group, 2016, doi:10.1038/ncomms11824. short: P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:26Z date_published: 2016-06-10T00:00:00Z date_updated: 2021-01-12T06:49:57Z day: '10' ddc: - '570' department: - _id: JoCs doi: 10.1038/ncomms11824 ec_funded: 1 file: - access_level: open_access checksum: e43307754abe65b840a21939fe163618 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:10Z date_updated: 2020-07-14T12:44:44Z file_id: '5196' file_name: IST-2016-660-v1+1_ncomms11824.pdf file_size: 1793846 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex - _id: 257D4372-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I2072-B27 name: Interneuron plasticity during spatial learning publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5934' pubrep_id: '660' quality_controlled: '1' scopus_import: 1 status: public title: Activity dependent plasticity of hippocampal place maps 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: 7 year: '2016' ... --- _id: '1331' abstract: - lang: eng text: 'Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response.' acknowledgement: "This work was financially supported by the following: The Alabama Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055 for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported by an Auburn University Cellular and Molecular Biosciences Research Fellowship. I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043) and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W)." article_processing_charge: No article_type: original author: - first_name: Paul full_name: Zwack, Paul last_name: Zwack - first_name: Inge full_name: De Clercq, Inge last_name: De Clercq - first_name: Timothy full_name: Howton, Timothy last_name: Howton - first_name: H Tucker full_name: Hallmark, H Tucker last_name: Hallmark - first_name: Andrej full_name: Hurny, Andrej id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87 last_name: Hurny - first_name: Erika full_name: Keshishian, Erika last_name: Keshishian - first_name: Alyssa full_name: Parish, Alyssa last_name: Parish - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: M Shahid full_name: Mukhtar, M Shahid last_name: Mukhtar - first_name: Frank full_name: Van Breusegem, Frank last_name: Van Breusegem - first_name: Aaron full_name: Rashotte, Aaron last_name: Rashotte citation: ama: Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 2016;172(2):1249-1258. doi:10.1104/pp.16.00415 apa: Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian, E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00415 chicago: Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00415. ieee: P. Zwack et al., “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016. ista: Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 172(2), 1249–1258. mla: Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:10.1104/pp.16.00415. short: P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian, A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology 172 (2016) 1249–1258. date_created: 2018-12-11T11:51:25Z date_published: 2016-10-02T00:00:00Z date_updated: 2022-05-24T09:26:03Z day: '02' department: - _id: EvBe doi: 10.1104/pp.16.00415 intvolume: ' 172' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1104/pp.16.00415 month: '10' oa: 1 oa_version: Published Version page: 1249 - 1258 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists publist_id: '5937' quality_controlled: '1' scopus_import: '1' status: public title: Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 172 year: '2016' ... --- _id: '1333' abstract: - lang: eng text: Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most. acknowledgement: We thank the students for participation; H.-J. Krambeck for writing the software for the game; H. Arndt, T. Bakker, L. Becks, H. Brendelberger, S. Dobler and T. Reusch for support; and the Max Planck Society for the Advancement of Science for funding. article_number: '10915' author: - first_name: Manfred full_name: Milinski, Manfred last_name: Milinski - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Dirk full_name: Semmann, Dirk last_name: Semmann - first_name: Ralf full_name: Sommerfeld, Ralf last_name: Sommerfeld - first_name: Jochem full_name: Marotzke, Jochem last_name: Marotzke citation: ama: Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 2016;7. doi:10.1038/ncomms10915 apa: Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., & Marotzke, J. (2016). Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10915 chicago: Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10915. ieee: M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans choose representatives who enforce cooperation in social dilemmas through extortion,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. 2016. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 7, 10915. mla: Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications, vol. 7, 10915, Nature Publishing Group, 2016, doi:10.1038/ncomms10915. short: M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:25Z date_published: 2016-03-07T00:00:00Z date_updated: 2021-01-12T06:49:57Z day: '07' ddc: - '519' - '530' - '599' department: - _id: KrCh doi: 10.1038/ncomms10915 file: - access_level: open_access checksum: 9ea0d7ce59a555a1cb8353d5559407cb content_type: application/pdf creator: system date_created: 2018-12-12T10:10:44Z date_updated: 2020-07-14T12:44:44Z file_id: '4834' file_name: IST-2016-661-v1+1_ncomms10915.pdf file_size: 1432577 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5935' pubrep_id: '661' quality_controlled: '1' scopus_import: 1 status: public title: Humans choose representatives who enforce cooperation in social dilemmas through extortion 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: 7 year: '2016' ... --- _id: '1332' abstract: - lang: eng text: Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance. acknowledgement: This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891. article_number: '10333' author: - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Adam full_name: Palmer, Adam last_name: Palmer - first_name: Idan full_name: Yelin, Idan last_name: Yelin - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333 apa: Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333 chicago: Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333. ieee: R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333. mla: Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333. short: R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:25Z date_published: 2016-01-20T00:00:00Z date_updated: 2021-01-12T06:49:57Z day: '20' ddc: - '570' - '579' department: - _id: CaGu - _id: GaTk doi: 10.1038/ncomms10333 file: - access_level: open_access checksum: ef147bcbb8bd37e9079cf3ce06f5815d content_type: application/pdf creator: system date_created: 2018-12-12T10:13:52Z date_updated: 2020-07-14T12:44:44Z file_id: '5039' file_name: IST-2016-662-v1+1_ncomms10333.pdf file_size: 1844107 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5936' pubrep_id: '662' quality_controlled: '1' scopus_import: 1 status: public title: Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments 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: 7 year: '2016' ... --- _id: '1335' abstract: - lang: eng text: In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: 'Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol 9837. Springer; 2016:23-38. doi:10.1007/978-3-662-53413-7_2' apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative monitor automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53413-7_2' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Monitor Automata,” 9837:23–38. Springer, 2016. https://doi.org/10.1007/978-3-662-53413-7_2. ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative monitor automata,” presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom, 2016, vol. 9837, pp. 23–38.' ista: 'Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata. SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38.' mla: Chatterjee, Krishnendu, et al. Quantitative Monitor Automata. Vol. 9837, Springer, 2016, pp. 23–38, doi:10.1007/978-3-662-53413-7_2. short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38. conference: end_date: 2016-09-10 location: Edinburgh, United Kingdom name: 'SAS: Static Analysis Symposium' start_date: 2016-09-08 date_created: 2018-12-11T11:51:26Z date_published: 2016-08-31T00:00:00Z date_updated: 2021-01-12T06:49:58Z day: '31' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-662-53413-7_2 ec_funded: 1 intvolume: ' 9837' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.06764 month: '08' oa: 1 oa_version: Preprint page: 23 - 38 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_status: published publisher: Springer publist_id: '5932' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative monitor automata type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9837 year: '2016' ... --- _id: '1344' abstract: - lang: eng text: Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms. acknowledgement: "The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP)." article_number: e19048 author: - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jeffrey full_name: Leung, Jeffrey last_name: Leung - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5. doi:10.7554/eLife.19048 apa: Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.19048 chicago: Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048. ieee: M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife, vol. 5. eLife Sciences Publications, 2016. ista: Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048. mla: Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife, vol. 5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048. short: M. Fendrych, J. Leung, J. Friml, ELife 5 (2016). date_created: 2018-12-11T11:51:29Z date_published: 2016-09-14T00:00:00Z date_updated: 2021-01-12T06:50:01Z day: '14' ddc: - '581' department: - _id: JiFr doi: 10.7554/eLife.19048 ec_funded: 1 file: - access_level: open_access checksum: 9209541fbba00f24daad21a5d568540d content_type: application/pdf creator: system date_created: 2018-12-12T10:09:24Z date_updated: 2020-07-14T12:44:45Z file_id: '4748' file_name: IST-2016-693-v1+1_e19048-download.pdf file_size: 5666343 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5908' pubrep_id: '654' quality_controlled: '1' scopus_import: 1 status: public title: TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls 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: 5 year: '2016' ... --- _id: '1343' abstract: - lang: eng text: "The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a\r\n\r\npotential for explaining the mystery of high-temperature superconductivity. Recent progress in\r\n\r\nultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using\r\n\r\nthe tools of quantum simulation, which emerged as a promising alternative to the numerical\r\n\r\ncalculations plagued by the infamous sign problem. However, the temperatures achieved using\r\n\r\nelaborate laser cooling protocols so far have been too high to show the appearance of\r\n\r\nantiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate\r\n\r\nthat using the machinery of dissipative quantum state engineering, one can observe the emergence of\r\n\r\nthe AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach\r\n\r\nis to add incoherent laser scattering in such a way that the AF state emerges as the dark state of\r\n\r\nthe driven-dissipative dynamics. The proposed controlled dissipation channels described in this work\r\n\r\nare straightforward to add to already existing experimental setups." acknowledgement: "We acknowledge stimulating discussions with Ken Brown, Tommaso Calarco, Andrew Daley, Suzanne\r\nMcEndoo, Tobias Osborne, Cindy Regal, Luis Santos, Micha\r\nł\r\nTomza, and Martin Zwierlein. The work was supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734], by the Volkswagen Foundation, and by DFG within SFB 1227 (DQ-mat)." article_number: '093042' author: - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Hendrik full_name: Weimer, Hendrik last_name: Weimer - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Kaczmarczyk J, Weimer H, Lemeshko M. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 2016;18(9). doi:10.1088/1367-2630/18/9/093042 apa: Kaczmarczyk, J., Weimer, H., & Lemeshko, M. (2016). Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/9/093042 chicago: Kaczmarczyk, Jan, Hendrik Weimer, and Mikhail Lemeshko. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/9/093042. ieee: J. Kaczmarczyk, H. Weimer, and M. Lemeshko, “Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model,” New Journal of Physics, vol. 18, no. 9. IOP Publishing Ltd., 2016. ista: Kaczmarczyk J, Weimer H, Lemeshko M. 2016. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 18(9), 093042. mla: Kaczmarczyk, Jan, et al. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics, vol. 18, no. 9, 093042, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/9/093042. short: J. Kaczmarczyk, H. Weimer, M. Lemeshko, New Journal of Physics 18 (2016). date_created: 2018-12-11T11:51:29Z date_published: 2016-09-22T00:00:00Z date_updated: 2021-01-12T06:50:01Z day: '22' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/18/9/093042 ec_funded: 1 file: - access_level: open_access checksum: 2a43e235222755e31ffbd369882c61de content_type: application/pdf creator: system date_created: 2018-12-12T10:17:52Z date_updated: 2020-07-14T12:44:45Z file_id: '5309' file_name: IST-2016-655-v1+1_njp_18_9_093042.pdf file_size: 1076029 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 18' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '5909' pubrep_id: '655' quality_controlled: '1' scopus_import: 1 status: public title: Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model 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: 18 year: '2016' ... --- _id: '1340' abstract: - lang: eng text: We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11]. alternative_title: - LNCS author: - first_name: Kristoffer full_name: Hansen, Kristoffer last_name: Hansen - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Michal full_name: Koucký, Michal last_name: Koucký citation: ama: 'Hansen K, Ibsen-Jensen R, Koucký M. The big match in small space. In: Vol 9928. Springer; 2016:64-76. doi:10.1007/978-3-662-53354-3_6' apa: 'Hansen, K., Ibsen-Jensen, R., & Koucký, M. (2016). The big match in small space (Vol. 9928, pp. 64–76). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_6' chicago: Hansen, Kristoffer, Rasmus Ibsen-Jensen, and Michal Koucký. “The Big Match in Small Space,” 9928:64–76. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_6. ieee: 'K. Hansen, R. Ibsen-Jensen, and M. Koucký, “The big match in small space,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 64–76.' ista: 'Hansen K, Ibsen-Jensen R, Koucký M. 2016. The big match in small space. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 64–76.' mla: Hansen, Kristoffer, et al. The Big Match in Small Space. Vol. 9928, Springer, 2016, pp. 64–76, doi:10.1007/978-3-662-53354-3_6. short: K. Hansen, R. Ibsen-Jensen, M. Koucký, in:, Springer, 2016, pp. 64–76. conference: end_date: 2016-09-21 location: Liverpool, United Kingdom name: 'SAGT: Symposium on Algorithmic Game Theory' start_date: 2016-09-19 date_created: 2018-12-11T11:51:28Z date_published: 2016-09-01T00:00:00Z date_updated: 2021-01-12T06:50:00Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-53354-3_6 ec_funded: 1 intvolume: ' 9928' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.07634 month: '09' oa: 1 oa_version: Preprint page: 64 - 76 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '5927' quality_controlled: '1' scopus_import: 1 status: public title: The big match in small space type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9928 year: '2016' ... --- _id: '1345' abstract: - lang: eng text: The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components. article_number: '16102' author: - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature Plants. 2016;2. doi:10.1038/nplants.2016.102' apa: 'Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102' chicago: 'Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102.' ieee: 'G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” Nature Plants, vol. 2. Nature Publishing Group, 2016.' ista: 'Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.' mla: 'Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.' short: G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016). date_created: 2018-12-11T11:51:30Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:02Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1038/nplants.2016.102 file: - access_level: open_access checksum: 9ba65f558563b287f875f48fa9f30fb2 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:36Z date_updated: 2020-07-14T12:44:45Z file_id: '4954' file_name: IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf file_size: 127781 relation: main_file - access_level: open_access checksum: 550d252be808d8ca2b43e83dddb4212f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:37Z date_updated: 2020-07-14T12:44:45Z file_id: '4955' file_name: IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf file_size: 430556 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 2' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '5907' pubrep_id: '1007' quality_controlled: '1' scopus_import: 1 status: public title: 'Plasma membrane: Negative attraction' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2016' ... --- _id: '1342' abstract: - lang: eng text: A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics. author: - first_name: Michael full_name: Baym, Michael last_name: Baym - first_name: Tami full_name: Lieberman, Tami last_name: Lieberman - first_name: Eric full_name: Kelsic, Eric last_name: Kelsic - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Rotem full_name: Gross, Rotem last_name: Gross - first_name: Idan full_name: Yelin, Idan last_name: Yelin - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822 apa: Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., & Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag0822 chicago: Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aag0822. ieee: M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016. ista: Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151. mla: Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822. short: M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151. date_created: 2018-12-11T11:51:29Z date_published: 2016-09-09T00:00:00Z date_updated: 2021-01-12T06:50:01Z day: '09' department: - _id: CaGu - _id: GaTk doi: 10.1126/science.aag0822 intvolume: ' 353' issue: '6304' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/ month: '09' oa: 1 oa_version: Preprint page: 1147 - 1151 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5911' quality_controlled: '1' scopus_import: 1 status: public title: Spatiotemporal microbial evolution on antibiotic landscapes type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 353 year: '2016' ... --- _id: '1339' abstract: - lang: eng text: "We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n" acknowledgement: We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140). article_number: '143507' author: - first_name: Gerard full_name: Verbiest, Gerard last_name: Verbiest - first_name: Duo full_name: Xu, Duo id: 3454D55E-F248-11E8-B48F-1D18A9856A87 last_name: Xu - first_name: Matthias full_name: Goldsche, Matthias last_name: Goldsche - first_name: Timofiy full_name: Khodkov, Timofiy last_name: Khodkov - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Nils full_name: Von Den Driesch, Nils last_name: Von Den Driesch - first_name: Dan full_name: Buca, Dan last_name: Buca - first_name: Christoph full_name: Stampfer, Christoph last_name: Stampfer citation: ama: Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. Applied  Physics Letter. 2016;109. doi:10.1063/1.4964122 apa: Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. Applied  Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122 chicago: Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied  Physics Letter. American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122. ieee: G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical resonators,” Applied  Physics Letter, vol. 109. American Institute of Physics, 2016. ista: Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied  Physics Letter. 109, 143507. mla: Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied  Physics Letter, vol. 109, 143507, American Institute of Physics, 2016, doi:10.1063/1.4964122. short: G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied  Physics Letter 109 (2016). date_created: 2018-12-11T11:51:28Z date_published: 2016-10-04T00:00:00Z date_updated: 2023-02-21T10:35:06Z day: '04' department: - _id: JoFi doi: 10.1063/1.4964122 intvolume: ' 109' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.04406 month: '10' oa: 1 oa_version: Preprint publication: Applied Physics Letter publication_status: published publisher: American Institute of Physics publist_id: '5928' quality_controlled: '1' scopus_import: 1 status: public title: Tunable mechanical coupling between driven microelectromechanical resonators type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2016' ... --- _id: '1349' abstract: - lang: eng text: Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys. author: - first_name: Pietro full_name: Oliveto, Pietro last_name: Oliveto - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Jorge full_name: Heredia, Jorge last_name: Heredia - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909' apa: 'Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909' chicago: Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909. ieee: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170. ista: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.' mla: Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909. short: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170. conference: end_date: 2016-07-24 location: Denver, CO, USA name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2016-07-20 date_created: 2018-12-11T11:51:31Z date_published: 2016-07-20T00:00:00Z date_updated: 2021-01-12T06:50:03Z day: '20' ddc: - '576' department: - _id: NiBa - _id: CaGu doi: 10.1145/2908812.2908909 ec_funded: 1 file: - access_level: open_access checksum: a1896e39e4113f2711e46b435d5f3e69 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:27Z date_updated: 2020-07-14T12:44:45Z file_id: '5214' file_name: IST-2016-650-v1+1_p1163-oliveto.pdf file_size: 979026 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1163 - 1170 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: 'Proceedings of the Genetic and Evolutionary Computation Conference 2016 ' publication_status: published publisher: ACM publist_id: '5900' pubrep_id: '650' quality_controlled: '1' scopus_import: 1 status: public title: When non-elitism outperforms elitism for crossing fitness valleys 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1350' abstract: - lang: eng text: "The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion. However, the\r\nsynaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient\r\nmemory storage and retrieval in hippocampal networks." acknowledged_ssus: - _id: ScienComp author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - 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: Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 2016;353(6304):1117-1123. doi:10.1126/science.aaf1836 apa: Guzmán, J., Schlögl, A., Frotscher, M., & Jonas, P. M. (2016). Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf1836 chicago: Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf1836. ieee: J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms of pattern completion in the hippocampal CA3 network,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1117–1123, 2016. ista: Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123. mla: Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1117–23, doi:10.1126/science.aaf1836. short: J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123. date_created: 2018-12-11T11:51:31Z date_published: 2016-09-09T00:00:00Z date_updated: 2021-01-12T06:50:04Z day: '09' ddc: - '570' department: - _id: ScienComp - _id: PeJo doi: 10.1126/science.aaf1836 ec_funded: 1 file: - access_level: open_access checksum: 89caefa4e181424cbf0aecc835fcc5ec content_type: application/pdf creator: system date_created: 2018-12-12T10:12:27Z date_updated: 2020-07-14T12:44:46Z file_id: '4945' file_name: IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf file_size: 19408143 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 353' issue: '6304' language: - iso: eng month: '09' oa: 1 oa_version: Preprint page: 1117 - 1123 project: - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5899' pubrep_id: '823' quality_controlled: '1' scopus_import: 1 status: public title: Synaptic mechanisms of pattern completion in the hippocampal CA3 network type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 353 year: '2016' ... --- _id: '1347' abstract: - lang: eng text: 'During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem''s constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.' acknowledgement: We are grateful to Eugene Demler, Jan Kaczmarczyk, Laleh Safari, and Hendrik Weimer for insightful discussions. The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory. article_number: '011012' author: - first_name: Richard full_name: Schmidt, Richard last_name: Schmidt - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Schmidt R, Lemeshko M. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 2016;6(1). doi:10.1103/PhysRevX.6.011012 apa: Schmidt, R., & Lemeshko, M. (2016). Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.011012 chicago: Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X. American Physical Society, 2016. https://doi.org/10.1103/PhysRevX.6.011012. ieee: R. Schmidt and M. Lemeshko, “Deformation of a quantum many-particle system by a rotating impurity,” Physical Review X, vol. 6, no. 1. American Physical Society, 2016. ista: Schmidt R, Lemeshko M. 2016. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 6(1), 011012. mla: Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X, vol. 6, no. 1, 011012, American Physical Society, 2016, doi:10.1103/PhysRevX.6.011012. short: R. Schmidt, M. Lemeshko, Physical Review X 6 (2016). date_created: 2018-12-11T11:51:30Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T06:50:03Z day: '01' ddc: - '530' department: - _id: MiLe doi: 10.1103/PhysRevX.6.011012 file: - access_level: open_access checksum: 6757a164d3c38905e05b2b5a188cb8ff content_type: application/pdf creator: system date_created: 2018-12-12T10:15:59Z date_updated: 2020-07-14T12:44:45Z file_id: '5183' file_name: IST-2016-652-v1+1_PhysRevX.6.011012.pdf file_size: 1165869 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Physical Review X publication_status: published publisher: American Physical Society publist_id: '5902' pubrep_id: '652' quality_controlled: '1' scopus_import: 1 status: public title: Deformation of a quantum many-particle system by a rotating impurity 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: 6 year: '2016' ... --- _id: '1348' abstract: - lang: eng text: 'A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest.' alternative_title: - LNCS author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 citation: ama: 'Fulek R. Bounded embeddings of graphs in the plane. In: Vol 9843. Springer; 2016:31-42. doi:10.1007/978-3-319-44543-4_3' apa: 'Fulek, R. (2016). Bounded embeddings of graphs in the plane (Vol. 9843, pp. 31–42). Presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-319-44543-4_3' chicago: Fulek, Radoslav. “Bounded Embeddings of Graphs in the Plane,” 9843:31–42. Springer, 2016. https://doi.org/10.1007/978-3-319-44543-4_3. ieee: 'R. Fulek, “Bounded embeddings of graphs in the plane,” presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland, 2016, vol. 9843, pp. 31–42.' ista: 'Fulek R. 2016. Bounded embeddings of graphs in the plane. IWOCA: International Workshop on Combinatorial Algorithms, LNCS, vol. 9843, 31–42.' mla: Fulek, Radoslav. Bounded Embeddings of Graphs in the Plane. Vol. 9843, Springer, 2016, pp. 31–42, doi:10.1007/978-3-319-44543-4_3. short: R. Fulek, in:, Springer, 2016, pp. 31–42. conference: end_date: 2018-08-19 location: Helsinki, Finland name: 'IWOCA: International Workshop on Combinatorial Algorithms' start_date: 2016-08-17 date_created: 2018-12-11T11:51:31Z date_published: 2016-08-09T00:00:00Z date_updated: 2021-01-12T06:50:03Z day: '09' department: - _id: UlWa doi: 10.1007/978-3-319-44543-4_3 ec_funded: 1 intvolume: ' 9843' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.07144 month: '08' oa: 1 oa_version: Preprint page: 31 - 42 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5901' quality_controlled: '1' scopus_import: 1 status: public title: Bounded embeddings of graphs in the plane type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9843 year: '2016' ... --- _id: '1355' abstract: - lang: eng text: Radiation pressure has recently been used to effectively couple the quantum motion of mechanical elements to the fields of optical or microwave light. Integration of all three degrees of freedom—mechanical, optical and microwave—would enable a quantum interconnect between microwave and optical quantum systems. We present a platform based on silicon nitride nanomembranes for integrating superconducting microwave circuits with planar acoustic and optical devices such as phononic and photonic crystals. Using planar capacitors with vacuum gaps of 60 nm and spiral inductor coils of micron pitch we realize microwave resonant circuits with large electromechanical coupling to planar acoustic structures of nanoscale dimensions and femtoFarad motional capacitance. Using this enhanced coupling, we demonstrate microwave backaction cooling of the 4.48 MHz mechanical resonance of a nanobeam to an occupancy as low as 0.32. These results indicate the viability of silicon nitride nanomembranes as an all-in-one substrate for quantum electro-opto-mechanical experiments. acknowledgement: This work was supported by the DARPA MESO programme, the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.P. was supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme, NEMO (GA 298861). Certain commercial equipment and software are identified in this documentation to describe the subject adequately. Such identification does not imply recommendation or endorsement by the NIST, nor does it imply that the equipment identified is necessarily the best available for the purpose. article_number: '12396' author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Mahmoud full_name: Kalaee, Mahmoud last_name: Kalaee - first_name: Alessandro full_name: Pitanti, Alessandro last_name: Pitanti - first_name: Richard full_name: Norte, Richard last_name: Norte - first_name: Lukas full_name: Heinzle, Lukas last_name: Heinzle - first_name: Marcelo full_name: Davanço, Marcelo last_name: Davanço - first_name: Kartik full_name: Srinivasan, Kartik last_name: Srinivasan - first_name: Oskar full_name: Painter, Oskar last_name: Painter citation: ama: Fink JM, Kalaee M, Pitanti A, et al. Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. 2016;7. doi:10.1038/ncomms12396 apa: Fink, J. M., Kalaee, M., Pitanti, A., Norte, R., Heinzle, L., Davanço, M., … Painter, O. (2016). Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12396 chicago: Fink, Johannes M, Mahmoud Kalaee, Alessandro Pitanti, Richard Norte, Lukas Heinzle, Marcelo Davanço, Kartik Srinivasan, and Oskar Painter. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12396. ieee: J. M. Fink et al., “Quantum electromechanics on silicon nitride nanomembranes,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Fink JM, Kalaee M, Pitanti A, Norte R, Heinzle L, Davanço M, Srinivasan K, Painter O. 2016. Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. 7, 12396. mla: Fink, Johannes M., et al. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” Nature Communications, vol. 7, 12396, Nature Publishing Group, 2016, doi:10.1038/ncomms12396. short: J.M. Fink, M. Kalaee, A. Pitanti, R. Norte, L. Heinzle, M. Davanço, K. Srinivasan, O. Painter, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:33Z date_published: 2016-08-03T00:00:00Z date_updated: 2021-01-12T06:50:06Z day: '03' ddc: - '530' department: - _id: JoFi doi: 10.1038/ncomms12396 file: - access_level: open_access checksum: 25513bd59d5bda495efa8f5920e91b22 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:30Z date_updated: 2020-07-14T12:44:46Z file_id: '5014' file_name: IST-2016-629-v1+1_ncomms12396.pdf file_size: 2139802 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5891' pubrep_id: '629' quality_controlled: '1' scopus_import: 1 status: public title: Quantum electromechanics on silicon nitride nanomembranes 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: 7 year: '2016' ... --- _id: '1359' abstract: - lang: eng text: "The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population." article_processing_charge: No article_type: original author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113 apa: Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1518830113 chicago: Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1518830113. ieee: T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016. ista: Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427. mla: Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113. short: T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427. date_created: 2018-12-11T11:51:34Z date_published: 2016-04-19T00:00:00Z date_updated: 2021-01-12T06:50:08Z day: '19' department: - _id: NiBa - _id: CaGu doi: 10.1073/pnas.1518830113 ec_funded: 1 external_id: pmid: - '27044080' intvolume: ' 113' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/ month: '04' oa: 1 oa_version: Published Version page: 4422 - 4427 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5886' quality_controlled: '1' scopus_import: 1 status: public title: The effect of gene interactions on the long-term response to selection type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2016' ... --- _id: '1352' abstract: - lang: eng text: We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking. acknowledgement: The authors are grateful to Florian Gebhard and Mikhail Lemeshko for discussions and critical reading of the manuscript. The work was supported by the Ministry of Science and Higher Education in Poland through the Iuventus Plus Grant No. IP2012 017172, as well as by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. 291734. J.K. acknowledges hospitality of the Leibniz Universität in Hannover where a large part of the work was performed. article_number: '085152' author: - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Tobias full_name: Schickling, Tobias last_name: Schickling - first_name: Jörg full_name: Bünemann, Jörg last_name: Bünemann citation: ama: Kaczmarczyk J, Schickling T, Bünemann J. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 2016;94(8). doi:10.1103/PhysRevB.94.085152 apa: Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2016). Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.085152 chicago: Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.085152. ieee: J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Coexistence of nematic order and superconductivity in the Hubbard model,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8. American Physical Society, 2016. ista: Kaczmarczyk J, Schickling T, Bünemann J. 2016. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 94(8), 085152. mla: Kaczmarczyk, Jan, et al. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8, 085152, American Physical Society, 2016, doi:10.1103/PhysRevB.94.085152. short: J. Kaczmarczyk, T. Schickling, J. Bünemann, Physical Review B - Condensed Matter and Materials Physics 94 (2016). date_created: 2018-12-11T11:51:32Z date_published: 2016-08-30T00:00:00Z date_updated: 2021-01-12T06:50:05Z day: '30' department: - _id: MiLe doi: 10.1103/PhysRevB.94.085152 ec_funded: 1 intvolume: ' 94' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1512.06688 month: '08' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '5897' quality_controlled: '1' scopus_import: 1 status: public title: Coexistence of nematic order and superconductivity in the Hubbard model type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 94 year: '2016' ... --- _id: '1354' abstract: - lang: eng text: Fabrication processes involving anhydrous hydrofluoric vapor etching are developed to create high-Q aluminum superconducting microwave resonators on free-standing silicon membranes formed from a silicon-on-insulator wafer. Using this fabrication process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave spectroscopy and radiation pressure backaction are used to characterize the coupled system in a dilution refrigerator down to temperatures of Tf=11  mK, yielding a measured electromechanical vacuum coupling rate of g0/2π=24.6  Hz and a mechanical resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being realized at an elevated fridge temperature of Tf=211  mK. article_number: '014013' author: - first_name: Paul full_name: Dieterle, Paul last_name: Dieterle - first_name: Mahmoud full_name: Kalaee, Mahmoud last_name: Kalaee - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Oskar full_name: Painter, Oskar last_name: Painter citation: ama: Dieterle P, Kalaee M, Fink JM, Painter O. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 2016;6(1). doi:10.1103/PhysRevApplied.6.014013 apa: Dieterle, P., Kalaee, M., Fink, J. M., & Painter, O. (2016). Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.6.014013 chicago: Dieterle, Paul, Mahmoud Kalaee, Johannes M Fink, and Oskar Painter. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied. American Physical Society, 2016. https://doi.org/10.1103/PhysRevApplied.6.014013. ieee: P. Dieterle, M. Kalaee, J. M. Fink, and O. Painter, “Superconducting cavity electromechanics on a silicon-on-insulator platform,” Physical Review Applied, vol. 6, no. 1. American Physical Society, 2016. ista: Dieterle P, Kalaee M, Fink JM, Painter O. 2016. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 6(1), 014013. mla: Dieterle, Paul, et al. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied, vol. 6, no. 1, 014013, American Physical Society, 2016, doi:10.1103/PhysRevApplied.6.014013. short: P. Dieterle, M. Kalaee, J.M. Fink, O. Painter, Physical Review Applied 6 (2016). date_created: 2018-12-11T11:51:32Z date_published: 2016-07-22T00:00:00Z date_updated: 2021-01-12T06:50:06Z day: '22' department: - _id: JoFi doi: 10.1103/PhysRevApplied.6.014013 intvolume: ' 6' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1601.04019 month: '07' oa: 1 oa_version: Preprint publication: Physical Review Applied publication_status: published publisher: American Physical Society publist_id: '5892' quality_controlled: '1' scopus_import: 1 status: public title: Superconducting cavity electromechanics on a silicon-on-insulator platform type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2016' ... --- _id: '1356' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796 apa: Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796 chicago: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184796. ieee: N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016. ista: Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4. mla: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796. short: N.H. Barton, Genetics 202 (2016) 3–4. date_created: 2018-12-11T11:51:33Z date_published: 2016-01-05T00:00:00Z date_updated: 2021-01-12T06:50:07Z day: '05' ddc: - '570' department: - _id: NiBa doi: 10.1534/genetics.115.184796 file: - access_level: open_access checksum: 3562b89c821a4be84edf2b6ebd870cf5 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:26Z date_updated: 2020-07-14T12:44:46Z file_id: '4687' file_name: IST-2017-769-v1+1_SewallWright1931.pdf file_size: 112674 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 202' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 3 - 4 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5889' pubrep_id: '769' quality_controlled: '1' scopus_import: 1 status: public title: Sewall Wright on evolution in Mendelian populations and the “Shifting Balance” type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1357' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542 apa: Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542 chicago: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542. ieee: N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016. ista: Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866. mla: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:10.1534/genetics.116.187542. short: N.H. Barton, Genetics 202 (2016) 865–866. date_created: 2018-12-11T11:51:33Z date_published: 2016-03-01T00:00:00Z date_updated: 2021-01-12T06:50:07Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1534/genetics.116.187542 file: - access_level: open_access checksum: b2174bab2de1d1142900062a150f35c9 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:09Z date_updated: 2020-07-14T12:44:46Z file_id: '5127' file_name: IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf file_size: 130779 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 202' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 865 - 866 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5888' pubrep_id: '768' quality_controlled: '1' scopus_import: 1 status: public title: Richard Hudson and Norman Kaplan on the coalescent process type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1353' abstract: - lang: eng text: We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations. acknowledgement: 'Libor Barto and Alexandr Kazda were supported by the the Grant Agency of the Czech Republic, grant GACR 13-01832S. ' author: - first_name: Libor full_name: Barto, Libor last_name: Barto - first_name: Alexandr full_name: Kazda, Alexandr id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87 last_name: Kazda citation: ama: Barto L, Kazda A. Deciding absorption. International Journal of Algebra and Computation. 2016;26(5):1033-1060. doi:10.1142/S0218196716500430 apa: Barto, L., & Kazda, A. (2016). Deciding absorption. International Journal of Algebra and Computation. World Scientific Publishing. https://doi.org/10.1142/S0218196716500430 chicago: Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation. World Scientific Publishing, 2016. https://doi.org/10.1142/S0218196716500430. ieee: L. Barto and A. Kazda, “Deciding absorption,” International Journal of Algebra and Computation, vol. 26, no. 5. World Scientific Publishing, pp. 1033–1060, 2016. ista: Barto L, Kazda A. 2016. Deciding absorption. International Journal of Algebra and Computation. 26(5), 1033–1060. mla: Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation, vol. 26, no. 5, World Scientific Publishing, 2016, pp. 1033–60, doi:10.1142/S0218196716500430. short: L. Barto, A. Kazda, International Journal of Algebra and Computation 26 (2016) 1033–1060. date_created: 2018-12-11T11:51:32Z date_published: 2016-07-20T00:00:00Z date_updated: 2021-01-12T06:50:06Z day: '20' department: - _id: VlKo doi: 10.1142/S0218196716500430 intvolume: ' 26' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1512.07009 month: '07' oa: 1 oa_version: Preprint page: 1033 - 1060 publication: International Journal of Algebra and Computation publication_status: published publisher: World Scientific Publishing publist_id: '5893' quality_controlled: '1' scopus_import: 1 status: public title: Deciding absorption type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2016' ... --- _id: '1363' abstract: - lang: eng text: When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special "non-reflecting" boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation. acknowledged_ssus: - _id: ScienComp acknowledgement: 'We thank the IST Austria Visual Computing group for helpful feedback throughout the project. ' alternative_title: - ACM Transactions on Graphics article_number: '96' author: - first_name: Morten full_name: Bojsen-Hansen, Morten id: 439F0C8C-F248-11E8-B48F-1D18A9856A87 last_name: Bojsen-Hansen orcid: 0000-0002-4417-3224 - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid re-simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925963' apa: 'Bojsen-Hansen, M., & Wojtan, C. (2016). Generalized non-reflecting boundaries for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925963' chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925963. ieee: M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4. ista: Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96. mla: Bojsen-Hansen, Morten, and Chris Wojtan. Generalized Non-Reflecting Boundaries for Fluid Re-Simulation. Vol. 35, no. 4, 96, ACM, 2016, doi:10.1145/2897824.2925963. short: M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016. conference: end_date: 2016-07-28 location: Anaheim, CA, USA name: ACM SIGGRAPH start_date: 2016-07-24 date_created: 2018-12-11T11:51:35Z date_published: 2016-07-11T00:00:00Z date_updated: 2023-02-21T10:36:12Z day: '11' ddc: - '000' department: - _id: ChWo doi: 10.1145/2897824.2925963 ec_funded: 1 file: - access_level: open_access checksum: 140b5532f0a2a006a0149cab7c73c17c content_type: application/pdf creator: system date_created: 2018-12-12T10:13:00Z date_updated: 2020-07-14T12:44:47Z file_id: '4981' file_name: IST-2016-631-v1+2_a96-bojsen-hansen.pdf file_size: 12422760 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 35' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication_status: published publisher: ACM publist_id: '5879' pubrep_id: '631' quality_controlled: '1' status: public title: Generalized non-reflecting boundaries for fluid re-simulation 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: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1364' abstract: - lang: eng text: We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated. acknowledgement: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 645599. alternative_title: - ACM Transactions on Graphics article_number: '86' author: - first_name: Eder full_name: Miguel Villalba, Eder id: 3FB91342-F248-11E8-B48F-1D18A9856A87 last_name: Miguel Villalba - first_name: Mathias full_name: Lepoutre, Mathias last_name: Lepoutre - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod structures. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925978' apa: 'Miguel Villalba, E., Lepoutre, M., & Bickel, B. (2016). Computational design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925978' chicago: Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925978. ieee: E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4. ista: Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86. mla: Miguel Villalba, Eder, et al. Computational Design of Stable Planar-Rod Structures. Vol. 35, no. 4, 86, ACM, 2016, doi:10.1145/2897824.2925978. short: E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016. conference: end_date: 2016-07-28 location: Anaheim, CA, USA name: ACM SIGGRAPH start_date: 2016-07-24 date_created: 2018-12-11T11:51:36Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:10Z day: '01' ddc: - '006' department: - _id: BeBi doi: 10.1145/2897824.2925978 ec_funded: 1 file: - access_level: open_access checksum: d00c2664a43d945df8876ea0193734e3 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:01Z date_updated: 2020-07-14T12:44:47Z file_id: '4853' file_name: IST-2017-763-v1+1_wirebending.pdf file_size: 44766392 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 35' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Preprint project: - _id: 25082902-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '645599' name: Soft-bodied intelligence for Manipulation publication_status: published publisher: ACM publist_id: '5878' pubrep_id: '763' quality_controlled: '1' scopus_import: 1 status: public title: Computational design of stable planar-rod structures type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1361' abstract: - lang: eng text: We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes. alternative_title: - ACM Transactions on Graphics article_number: a78 author: - first_name: Fang full_name: Da, Fang last_name: Da - first_name: David full_name: Hahn, David id: 357A6A66-F248-11E8-B48F-1D18A9856A87 last_name: Hahn - first_name: Christopher full_name: Batty, Christopher last_name: Batty - 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: Eitan full_name: Grinspun, Eitan last_name: Grinspun citation: ama: 'Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925899' apa: 'Da, F., Hahn, D., Batty, C., Wojtan, C., & Grinspun, E. (2016). Surface only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925899' chicago: Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Surface Only Liquids,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925899. ieee: F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4. ista: Da F, Hahn D, Batty C, Wojtan C, Grinspun E. 2016. Surface only liquids. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78. mla: Da, Fang, et al. Surface Only Liquids. Vol. 35, no. 4, a78, ACM, 2016, doi:10.1145/2897824.2925899. short: F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016. conference: end_date: 2016-07-28 location: Anaheim, CA, USA name: ACM SIGGRAPH start_date: 2016-07-24 date_created: 2018-12-11T11:51:35Z date_published: 2016-07-11T00:00:00Z date_updated: 2023-02-21T10:36:07Z day: '11' ddc: - '000' department: - _id: ChWo doi: 10.1145/2897824.2925899 ec_funded: 1 file: - access_level: open_access checksum: 6d662893bd447d4f575b4961a2247811 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:01Z date_updated: 2020-07-14T12:44:46Z file_id: '4660' file_name: IST-2016-637-v1+1_2016_Da_SOL.pdf file_size: 10561865 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 35' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication_status: published publisher: ACM publist_id: '5881' pubrep_id: '637' quality_controlled: '1' scopus_import: 1 status: public title: Surface only liquids type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1365' abstract: - lang: eng text: A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest. alternative_title: - LNCS author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Jeremiah full_name: Blocki, Jeremiah last_name: Blocki citation: ama: 'Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions. In: Vol 9815. Springer; 2016:241-271. doi:10.1007/978-3-662-53008-5_9' apa: 'Alwen, J. F., & Blocki, J. (2016). Efficiently computing data-independent memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-53008-5_9' chicago: Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent Memory-Hard Functions,” 9815:241–71. Springer, 2016. https://doi.org/10.1007/978-3-662-53008-5_9. ieee: 'J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard functions,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.' ista: 'Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.' mla: Alwen, Joel F., and Jeremiah Blocki. Efficiently Computing Data-Independent Memory-Hard Functions. Vol. 9815, Springer, 2016, pp. 241–71, doi:10.1007/978-3-662-53008-5_9. short: J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271. conference: end_date: 2016-08-18 location: Santa Barbara, CA, USA name: 'CRYPTO: International Cryptology Conference' start_date: 2016-08-14 date_created: 2018-12-11T11:51:36Z date_published: 2016-08-01T00:00:00Z date_updated: 2021-01-12T06:50:11Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-662-53008-5_9 intvolume: ' 9815' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2016/115 month: '08' oa: 1 oa_version: Preprint page: 241 - 271 publication_status: published publisher: Springer publist_id: '5876' quality_controlled: '1' scopus_import: 1 status: public title: Efficiently computing data-independent memory-hard functions type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9815 year: '2016' ... --- _id: '1366' abstract: - lang: eng text: 'We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions.' alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: 'Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665. Springer; 2016:87-116. doi:10.1007/978-3-662-49890-3_4' apa: 'Gazi, P., & Tessaro, S. (2016). Provably robust sponge-based PRNGs and KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-662-49890-3_4' chicago: Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and KDFs,” 9665:87–116. Springer, 2016. https://doi.org/10.1007/978-3-662-49890-3_4. ieee: 'P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9665, pp. 87–116.' ista: 'Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.' mla: Gazi, Peter, and Stefano Tessaro. Provably Robust Sponge-Based PRNGs and KDFs. Vol. 9665, Springer, 2016, pp. 87–116, doi:10.1007/978-3-662-49890-3_4. short: P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116. conference: end_date: 2016-05-12 location: Vienna, Austria name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2016-05-08 date_created: 2018-12-11T11:51:36Z date_published: 2016-05-01T00:00:00Z date_updated: 2021-01-12T06:50:11Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-662-49890-3_4 ec_funded: 1 intvolume: ' 9665' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/169/20160219:201940 month: '05' oa: 1 oa_version: Preprint page: 87 - 116 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5872' quality_controlled: '1' scopus_import: 1 status: public title: Provably robust sponge-based PRNGs and KDFs type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9665 year: '2016' ... --- _id: '1360' abstract: - lang: eng text: 'We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. ' acknowledgement: The first and third authors were supported by the Dynasty Foundation. The first, second and third authors were supported by the Russian Foundation for Basic Re- search grant 15-31-20403 (mol a ved). article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Alexey full_name: Balitskiy, Alexey last_name: Balitskiy - first_name: Roman full_name: Karasev, Roman last_name: Karasev - first_name: Anastasia full_name: Sharipova, Anastasia last_name: Sharipova citation: ama: Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 2016;144(10):4501-4513. doi:10.1090/proc/13062 apa: Akopyan, A., Balitskiy, A., Karasev, R., & Sharipova, A. (2016). Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13062 chicago: Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/13062. ieee: A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach to closed billiard trajectories in asymmetric normed spaces,” Proceedings of the American Mathematical Society, vol. 144, no. 10. American Mathematical Society, pp. 4501–4513, 2016. ista: Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 144(10), 4501–4513. mla: Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society, vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:10.1090/proc/13062. short: A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American Mathematical Society 144 (2016) 4501–4513. date_created: 2018-12-11T11:51:34Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:50:09Z day: '01' department: - _id: HeEd doi: 10.1090/proc/13062 ec_funded: 1 intvolume: ' 144' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1401.0442 month: '10' oa: 1 oa_version: Preprint page: 4501 - 4513 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Proceedings of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '5885' quality_controlled: '1' scopus_import: 1 status: public title: Elementary approach to closed billiard trajectories in asymmetric normed spaces type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 144 year: '2016' ... --- _id: '1372' abstract: - lang: eng text: Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism. acknowledgement: 'Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P' author: - first_name: Markéta full_name: Pernisová, Markéta last_name: Pernisová - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Danka full_name: Haruštiaková, Danka last_name: Haruštiaková - first_name: Martina full_name: Matonohova, Martina last_name: Matonohova - first_name: Lukáš full_name: Spíchal, Lukáš last_name: Spíchal - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko citation: ama: Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049 apa: Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049 chicago: Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14049. ieee: M. Pernisová et al., “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” New Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016. ista: Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509. mla: Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049. short: M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509. date_created: 2018-12-11T11:51:38Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:50:13Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1111/nph.14049 file: - access_level: open_access checksum: 27fd841ceaf0403559d7048ef51500f9 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:53Z date_updated: 2020-07-14T12:44:47Z file_id: '5108' file_name: IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf file_size: 972763 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 212' issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 497 - 509 publication: New Phytologist publication_status: published publisher: Wiley-Blackwell publist_id: '5839' pubrep_id: '1006' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 212 year: '2016' ... --- _id: '1369' abstract: - lang: eng text: 'We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations.' alternative_title: - LNCS author: - first_name: Alexander full_name: Kolesnikov, Alexander id: 2D157DB6-F248-11E8-B48F-1D18A9856A87 last_name: Kolesnikov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:10.1007/978-3-319-46493-0_42' apa: 'Kolesnikov, A., & Lampert, C. (2016). Seed, expand and constrain: Three principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711). Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands: Springer. https://doi.org/10.1007/978-3-319-46493-0_42' chicago: 'Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer, 2016. https://doi.org/10.1007/978-3-319-46493-0_42.' ieee: 'A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles for weakly-supervised image segmentation,” presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.' ista: 'Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 9908, 695–711.' mla: 'Kolesnikov, Alexander, and Christoph Lampert. Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation. Vol. 9908, Springer, 2016, pp. 695–711, doi:10.1007/978-3-319-46493-0_42.' short: A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711. conference: end_date: 2016-10-14 location: Amsterdam, The Netherlands name: 'ECCV: European Conference on Computer Vision' start_date: 2016-10-11 date_created: 2018-12-11T11:51:37Z date_published: 2016-09-15T00:00:00Z date_updated: 2021-01-12T06:50:12Z day: '15' department: - _id: ChLa doi: 10.1007/978-3-319-46493-0_42 ec_funded: 1 intvolume: ' 9908' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1603.06098 month: '09' oa: 1 oa_version: Preprint page: 695 - 711 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: Springer publist_id: '5842' quality_controlled: '1' scopus_import: 1 status: public title: 'Seed, expand and constrain: Three principles for weakly-supervised image segmentation' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9908 year: '2016' ... --- _id: '1368' abstract: - lang: eng text: Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5. acknowledgement: "The work has been supported by the National Science Center \ (NCN) under the Grant MAESTRO, No.\r\nDEC-2012/04/A/ST3/00342. " article_number: '024517' author: - first_name: Marcin full_name: Wysokiński, Marcin last_name: Wysokiński - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Jozef full_name: Spałek, Jozef last_name: Spałek citation: ama: 'Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 2016;94(2). doi:10.1103/PhysRevB.94.024517' apa: 'Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.024517' chicago: 'Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.024517.' ieee: 'M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2. American Physical Society, 2016.' ista: 'Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 94(2), 024517.' mla: 'Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:10.1103/PhysRevB.94.024517.' short: M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter and Materials Physics 94 (2016). date_created: 2018-12-11T11:51:37Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:12Z day: '01' department: - _id: MiLe doi: 10.1103/PhysRevB.94.024517 ec_funded: 1 intvolume: ' 94' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.00224 month: '07' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '5844' quality_controlled: '1' scopus_import: 1 status: public title: 'Correlation driven d wave superconductivity in Anderson lattice model: Two gaps' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 94 year: '2016' ... --- _id: '1371' abstract: - lang: eng text: Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure. acknowledgement: 'MZ has been supported by Polish National Science Centre Grant No. DEC-2012/07/N/NZ2/00107 and by Foundation of Polish Science award START. ' author: - first_name: Olivier full_name: Martin, Olivier last_name: Martin - first_name: André full_name: Krzywicki, André last_name: Krzywicki - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 citation: ama: 'Martin O, Krzywicki A, Zagórski MP. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 2016;17:124-158. doi:10.1016/j.plrev.2016.06.002' apa: 'Martin, O., Krzywicki, A., & Zagórski, M. P. (2016). Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.002' chicago: 'Martin, Olivier, André Krzywicki, and Marcin P Zagórski. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.002.' ieee: 'O. Martin, A. Krzywicki, and M. P. Zagórski, “Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function,” Physics of Life Reviews, vol. 17. Elsevier, pp. 124–158, 2016.' ista: 'Martin O, Krzywicki A, Zagórski MP. 2016. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 17, 124–158.' mla: 'Martin, Olivier, et al. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 124–58, doi:10.1016/j.plrev.2016.06.002.' short: O. Martin, A. Krzywicki, M.P. Zagórski, Physics of Life Reviews 17 (2016) 124–158. date_created: 2018-12-11T11:51:38Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:13Z day: '01' department: - _id: AnKi doi: 10.1016/j.plrev.2016.06.002 ec_funded: 1 intvolume: ' 17' language: - iso: eng month: '07' oa_version: None page: 124 - 158 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physics of Life Reviews publication_status: published publisher: Elsevier publist_id: '5840' quality_controlled: '1' scopus_import: 1 status: public title: 'Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2016' ... --- _id: '1370' abstract: - lang: eng text: 'We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction.' acknowledgement: 'The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation. ' article_number: '033846' author: - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: David full_name: Vitali, David last_name: Vitali citation: ama: Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3). doi:10.1103/PhysRevA.93.033846 apa: Barzanjeh, S., & Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.93.033846 chicago: Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.033846. ieee: S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3. American Physical Society, 2016. ista: Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 033846. mla: Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:10.1103/PhysRevA.93.033846. short: S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016). date_created: 2018-12-11T11:51:38Z date_published: 2016-03-28T00:00:00Z date_updated: 2023-02-21T10:36:32Z day: '28' department: - _id: JoFi doi: 10.1103/PhysRevA.93.033846 intvolume: ' 93' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1601.01818 month: '03' oa: 1 oa_version: Preprint publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '5841' quality_controlled: '1' scopus_import: 1 status: public title: Phonon Josephson junction with nanomechanical resonators type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2016' ... --- _id: '1373' article_processing_charge: No author: - first_name: Olivier full_name: Martin, Olivier last_name: Martin - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 citation: ama: 'Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot; Physics of Life Reviews. 2016;17:168-171. doi:10.1016/j.plrev.2016.06.006' apa: 'Martin, O., & Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot; Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.006' chicago: 'Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&quot;” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.006.' ieee: 'O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot;,” Physics of Life Reviews, vol. 17. Elsevier, pp. 168–171, 2016.' ista: 'Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot; Physics of Life Reviews. 17, 168–171.' mla: 'Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&quot;” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 168–71, doi:10.1016/j.plrev.2016.06.006.' short: O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171. date_created: 2018-12-11T11:51:39Z date_published: 2016-07-01T00:00:00Z date_updated: 2022-08-26T09:39:27Z day: '01' department: - _id: AnKi doi: 10.1016/j.plrev.2016.06.006 intvolume: ' 17' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01531698 month: '07' oa: 1 oa_version: Preprint page: 168 - 171 publication: Physics of Life Reviews publication_status: published publisher: Elsevier publist_id: '5838' quality_controlled: '1' scopus_import: '1' status: public title: 'Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2016' ... --- _id: '1377' abstract: - lang: eng text: We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Thomas full_name: Pock, Thomas last_name: Pock - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257 apa: Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M1010257 chicago: Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M1010257. ieee: V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016. ista: Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636. mla: Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:10.1137/15M1010257. short: V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636. date_created: 2018-12-11T11:51:40Z date_published: 2016-05-03T00:00:00Z date_updated: 2021-01-12T06:50:15Z day: '03' department: - _id: VlKo doi: 10.1137/15M1010257 ec_funded: 1 intvolume: ' 9' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.07770 month: '05' oa: 1 oa_version: Preprint page: 605 - 636 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: SIAM Journal on Imaging Sciences publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '5834' quality_controlled: '1' scopus_import: 1 status: public title: Total variation on a tree type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2016' ... --- _id: '1381' abstract: - lang: eng text: 'Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.' alternative_title: - LIPIcs author: - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:10.4230/LIPIcs.SoCG.2016.51' apa: 'Mabillard, I., & Wagner, U. (2016). Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. https://doi.org/10.4230/LIPIcs.SoCG.2016.51' chicago: Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.51. ieee: 'I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 51.1-51.12.' ista: 'Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.' mla: Mabillard, Isaac, and Uli Wagner. Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:10.4230/LIPIcs.SoCG.2016.51. short: I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12. conference: end_date: 2016-06-17 location: Medford, MA, USA name: 'SoCG: Symposium on Computational Geometry' start_date: 2016-06-14 date_created: 2018-12-11T11:51:41Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:50:17Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2016.51 file: - access_level: open_access checksum: 92c0c3735fe908f8ded6e484005cb3b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:06Z date_updated: 2020-07-14T12:44:47Z file_id: '4791' file_name: IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf file_size: 622969 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 51' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 51.1 - 51.12 project: - _id: 25FA3206-B435-11E9-9278-68D0E5697425 grant_number: PP00P2_138948 name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics' publication_status: published publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH publist_id: '5830' pubrep_id: '621' quality_controlled: '1' scopus_import: 1 status: public title: Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2016' ... --- _id: '1380' abstract: - lang: eng text: We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP. article_number: '23' author: - first_name: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev - first_name: Joël full_name: Ouaknine, Joël last_name: Ouaknine - first_name: James full_name: Worrell, James last_name: Worrell citation: ama: Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. Journal of the ACM. 2016;63(3). doi:10.1145/2857050 apa: Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the complexity of the orbit problem. Journal of the ACM. ACM. https://doi.org/10.1145/2857050 chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2857050. ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” Journal of the ACM, vol. 63, no. 3. ACM, 2016. ista: Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23. mla: Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” Journal of the ACM, vol. 63, no. 3, 23, ACM, 2016, doi:10.1145/2857050. short: V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016). date_created: 2018-12-11T11:51:41Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:50:17Z day: '01' department: - _id: KrCh doi: 10.1145/2857050 intvolume: ' 63' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.2981 month: '06' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '5831' quality_controlled: '1' scopus_import: 1 status: public title: On the complexity of the orbit problem type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2016' ... --- _id: '1389' abstract: - lang: eng text: "The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear\r\ndifferential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision." author: - first_name: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev - first_name: Joël full_name: Ouaknine, Joël last_name: Ouaknine - first_name: James full_name: Worrell, James last_name: Worrell citation: ama: 'Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous linear dynamical systems. In: LICS ’16. IEEE; 2016:515-524. doi:10.1145/2933575.2934548' apa: 'Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On recurrent reachability for continuous linear dynamical systems. In LICS ’16 (pp. 515–524). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934548' chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” In LICS ’16, 515–24. IEEE, 2016. https://doi.org/10.1145/2933575.2934548. ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for continuous linear dynamical systems,” in LICS ’16, New York, NY, USA, 2016, pp. 515–524. ista: 'Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.' mla: Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” LICS ’16, IEEE, 2016, pp. 515–24, doi:10.1145/2933575.2934548. short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524. conference: end_date: 2018-07-08 location: New York, NY, USA name: 'LICS: Logic in Computer Science' start_date: 2018-07-05 date_created: 2018-12-11T11:51:44Z date_published: 2016-07-05T00:00:00Z date_updated: 2021-01-12T06:50:20Z day: '05' department: - _id: KrCh doi: 10.1145/2933575.2934548 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.03632 month: '07' oa: 1 oa_version: Preprint page: 515 - 524 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: LICS '16 publication_status: published publisher: IEEE publist_id: '5820' quality_controlled: '1' scopus_import: 1 status: public title: On recurrent reachability for continuous linear dynamical systems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1390' abstract: - lang: eng text: "The goal of automatic program repair is to identify a set of syntactic changes that can turn a program that is incorrect with respect\r\nto a given specification into a correct one. Existing program repair techniques typically aim to find any program that meets the given specification. Such “best-effort” strategies can end up generating a program that is quite different from the original one. Novel techniques have been proposed to compute syntactically minimal program fixes, but the smallest syntactic fix to a program can still significantly alter the original program’s behaviour. We propose a new approach to program repair based on program distances, which can quantify changes not only to the program syntax but also to the program semantics. We call this the quantitative program repair problem where the “optimal” repair is derived using multiple distances. We implement a solution to the quantitative repair\r\nproblem in a prototype tool called Qlose\r\n(Quantitatively close), using the program synthesizer Sketch. We evaluate the effectiveness of different distances in obtaining desirable repairs by evaluating\r\nQlose on programs taken from educational tools such as CodeHunt and edX." alternative_title: - LNCS author: - first_name: Loris full_name: D'Antoni, Loris last_name: D'Antoni - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Rishabh full_name: Singh, Rishabh last_name: Singh citation: ama: 'D’Antoni L, Samanta R, Singh R. QLOSE: Program repair with quantitative objectives. In: Vol 9780. Springer; 2016:383-401. doi:10.1007/978-3-319-41540-6_21' apa: 'D’Antoni, L., Samanta, R., & Singh, R. (2016). QLOSE: Program repair with quantitative objectives (Vol. 9780, pp. 383–401). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_21' chicago: 'D’Antoni, Loris, Roopsha Samanta, and Rishabh Singh. “QLOSE: Program Repair with Quantitative Objectives,” 9780:383–401. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_21.' ieee: 'L. D’Antoni, R. Samanta, and R. Singh, “QLOSE: Program repair with quantitative objectives,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 383–401.' ista: 'D’Antoni L, Samanta R, Singh R. 2016. QLOSE: Program repair with quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 9780, 383–401.' mla: 'D’Antoni, Loris, et al. QLOSE: Program Repair with Quantitative Objectives. Vol. 9780, Springer, 2016, pp. 383–401, doi:10.1007/978-3-319-41540-6_21.' short: L. D’Antoni, R. Samanta, R. Singh, in:, Springer, 2016, pp. 383–401. conference: end_date: 2016-07-23 location: Toronto, Canada name: 'CAV: Computer Aided Verification' start_date: 2016-07-17 date_created: 2018-12-11T11:51:45Z date_published: 2016-07-13T00:00:00Z date_updated: 2021-01-12T06:50:21Z day: '13' department: - _id: ToHe doi: 10.1007/978-3-319-41540-6_21 ec_funded: 1 intvolume: ' 9780' language: - iso: eng month: '07' oa_version: None page: 383 - 401 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '5819' quality_controlled: '1' scopus_import: 1 status: public title: 'QLOSE: Program repair with quantitative objectives' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9780 year: '2016' ... --- _id: '1394' abstract: - lang: eng text: "The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity." acknowledgement: "The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038." article_number: '036005' author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Fabrizio full_name: Capuani, Fabrizio last_name: Capuani - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino citation: ama: 'De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005' apa: 'De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005' chicago: 'De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005.' ieee: 'D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.' ista: 'De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.' mla: 'De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.' short: D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016). date_created: 2018-12-11T11:51:46Z date_published: 2016-05-27T00:00:00Z date_updated: 2021-01-12T06:50:23Z day: '27' department: - _id: GaTk doi: 10.1088/1478-3975/13/3/036005 ec_funded: 1 intvolume: ' 13' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1601.03243 month: '05' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Biology publication_status: published publisher: IOP Publishing Ltd. publist_id: '5815' quality_controlled: '1' scopus_import: 1 status: public title: 'Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2016' ... --- _id: '1412' abstract: - lang: eng text: Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods. acknowledgement: 'This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ' author: - first_name: Ryan full_name: Goldade, Ryan last_name: Goldade - first_name: Christopher full_name: Batty, Christopher last_name: Batty - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826 apa: Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826 chicago: Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826. ieee: R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 233–242, 2016. ista: Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242. mla: Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 233–42, doi:10.1111/cgf.12826. short: R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242. date_created: 2018-12-11T11:51:52Z date_published: 2016-05-27T00:00:00Z date_updated: 2023-02-21T10:38:30Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12826 ec_funded: 1 file: - access_level: open_access checksum: 8e61387ee2e3bd0e776fbe301629bfd9 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:18Z date_updated: 2020-07-14T12:44:53Z file_id: '5000' file_name: IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf file_size: 15873858 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 35' issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 233 - 242 project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5795' pubrep_id: '612' quality_controlled: '1' scopus_import: 1 status: public title: A practical method for high-resolution embedded liquid surfaces type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1410' abstract: - lang: eng text: The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis. acknowledgement: the Odysseus Program of the Research Foundation-Flanders [G091608] to JF. author: - first_name: José full_name: Ugalde, José last_name: Ugalde - first_name: Cecilia full_name: Rodríguez Furlán, Cecilia last_name: Rodríguez Furlán - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Lorena full_name: Norambuena, Lorena last_name: Norambuena - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Gabriel full_name: León, Gabriel last_name: León - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos citation: ama: Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014 apa: Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014 chicago: Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014. ieee: J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016. ista: Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19. mla: Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014. short: J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19. date_created: 2018-12-11T11:51:51Z date_published: 2016-09-01T00:00:00Z date_updated: 2021-01-12T06:50:33Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1016/j.plantsci.2016.05.014 external_id: pmid: - '27457979' file: - access_level: open_access checksum: ca08de036e6ddc81e6f760e0ccdebd3f content_type: application/pdf creator: dernst date_created: 2019-04-17T07:41:57Z date_updated: 2020-07-14T12:44:53Z file_id: '6331' file_name: 2016_PlantScience_Ugalde.pdf file_size: 4338545 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 250' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 10 - 19 pmid: 1 publication: Plant Science publication_status: published publisher: Elsevier publist_id: '5797' pubrep_id: '1005' quality_controlled: '1' scopus_import: 1 status: public title: Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 250 year: '2016' ...