--- _id: '2018' abstract: - lang: eng text: Synaptic cell adhesion molecules are increasingly gaining attention for conferring specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic adhesion molecules that distribute on distinct axons, and their presence restricts the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific subdendritic segments of target neurons. However, the neural circuits and functional roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify excitatory synapses in independent hippocampal pathways. In the hippocampal CA1 area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G mutant synapses displayed opposing phenotypes in long-term and short-term plasticity through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic membranes. Our findings show that netrin-G/NGL interactions differentially control synaptic plasticity in distinct circuits via retrograde signaling mechanisms and explain how synaptic inputs are diversified to control neuronal activity. acknowledgement: This work was supported by “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)” initiated by the Council for Science and Technology Policy. article_processing_charge: No article_type: original author: - first_name: Hiroshi full_name: Matsukawa, Hiroshi last_name: Matsukawa - first_name: Sachiko full_name: Akiyoshi Nishimura, Sachiko last_name: Akiyoshi Nishimura - first_name: Qi full_name: Zhang, Qi last_name: Zhang - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Kazuhiko full_name: Yamaguchi, Kazuhiko last_name: Yamaguchi - first_name: Hiromichi full_name: Goto, Hiromichi last_name: Goto - first_name: Kunio full_name: Yaguchi, Kunio last_name: Yaguchi - first_name: Tsutomu full_name: Hashikawa, Tsutomu last_name: Hashikawa - first_name: Chie full_name: Sano, Chie last_name: Sano - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Toshiaki full_name: Nakashiba, Toshiaki last_name: Nakashiba - first_name: Shigeyoshi full_name: Itohara, Shigeyoshi last_name: Itohara citation: ama: Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 2014;34(47):15779-15792. doi:10.1523/JNEUROSCI.1141-14.2014 apa: Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K., Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1141-14.2014 chicago: Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján, Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience. Society for Neuroscience, 2014. https://doi.org/10.1523/JNEUROSCI.1141-14.2014. ieee: H. Matsukawa et al., “Netrin-G/NGL complexes encode functional synaptic diversification,” Journal of Neuroscience, vol. 34, no. 47. Society for Neuroscience, pp. 15779–15792, 2014. ista: Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H, Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 34(47), 15779–15792. mla: Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:10.1523/JNEUROSCI.1141-14.2014. short: H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792. date_created: 2018-12-11T11:55:14Z date_published: 2014-11-19T00:00:00Z date_updated: 2022-05-24T08:54:54Z day: '19' ddc: - '570' department: - _id: RySh doi: 10.1523/JNEUROSCI.1141-14.2014 external_id: pmid: - '25411505' file: - access_level: open_access checksum: 6913e9bc26e9fc1c0441a739a4199229 content_type: application/pdf creator: dernst date_created: 2022-05-24T08:41:41Z date_updated: 2022-05-24T08:41:41Z file_id: '11410' file_name: 2014_JournNeuroscience_Matsukawa.pdf file_size: 3963728 relation: main_file success: 1 file_date_updated: 2022-05-24T08:41:41Z has_accepted_license: '1' intvolume: ' 34' issue: '47' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 15779 - 15792 pmid: 1 publication: Journal of Neuroscience publication_identifier: eissn: - 1529-2401 issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience publist_id: '5054' quality_controlled: '1' scopus_import: '1' status: public title: Netrin-G/NGL complexes encode functional synaptic diversification type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2014' ... --- _id: '2019' abstract: - lang: eng text: We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J last_name: Schröder citation: ama: Erdös L, Schröder DJ. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):441-464. doi:10.1007/s11040-014-9164-3 apa: Erdös, L., & Schröder, D. J. (2014). Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9164-3 chicago: Erdös, László, and Dominik J Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9164-3. ieee: L. Erdös and D. J. Schröder, “Phase transition in the density of states of quantum spin glasses,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 441–464, 2014. ista: Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464. mla: Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:10.1007/s11040-014-9164-3. short: L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464. date_created: 2018-12-11T11:55:15Z date_published: 2014-12-17T00:00:00Z date_updated: 2021-01-12T06:54:45Z day: '17' department: - _id: LaEr doi: 10.1007/s11040-014-9164-3 ec_funded: 1 intvolume: ' 17' issue: 3-4 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.1552 month: '12' oa: 1 oa_version: Submitted Version page: 441 - 464 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Mathematical Physics, Analysis and Geometry publication_status: published publisher: Springer publist_id: '5053' quality_controlled: '1' scopus_import: 1 status: public title: Phase transition in the density of states of quantum spin glasses type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2014' ... --- _id: '2013' abstract: - lang: eng text: "An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n" acknowledgement: This work was supported in part by the US National Science Foundation (DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning program (FA8650-10-C-7020). author: - first_name: Shaowei full_name: Lin, Shaowei last_name: Lin - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Bernd full_name: Sturmfels, Bernd last_name: Sturmfels - first_name: Peter full_name: Bühlmann, Peter last_name: Bühlmann citation: ama: Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 2014;14(5):1079-1116. doi:10.1007/s10208-014-9205-0 apa: Lin, S., Uhler, C., Sturmfels, B., & Bühlmann, P. (2014). Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9205-0 chicago: Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics. Springer, 2014. https://doi.org/10.1007/s10208-014-9205-0. ieee: S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their singularities in partial correlation testing,” Foundations of Computational Mathematics, vol. 14, no. 5. Springer, pp. 1079–1116, 2014. ista: Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 14(5), 1079–1116. mla: Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:10.1007/s10208-014-9205-0. short: S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116. date_created: 2018-12-11T11:55:12Z date_published: 2014-10-10T00:00:00Z date_updated: 2021-01-12T06:54:43Z day: '10' department: - _id: CaUh doi: 10.1007/s10208-014-9205-0 intvolume: ' 14' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.0285 month: '10' oa: 1 oa_version: Submitted Version page: 1079 - 1116 publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '5063' quality_controlled: '1' scopus_import: 1 status: public title: Hypersurfaces and their singularities in partial correlation testing type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '2017' abstract: - lang: eng text: ' Gaussian graphical models have received considerable attention during the past four decades from the statistical and machine learning communities. In Bayesian treatments of this model, the G-Wishart distribution serves as the conjugate prior for inverse covariance matrices satisfying graphical constraints. While it is straightforward to posit the unnormalized densities, the normalizing constants of these distributions have been known only for graphs that are chordal, or decomposable. Up until now, it was unknown whether the normalizing constant for a general graph could be represented explicitly, and a considerable body of computational literature emerged that attempted to avoid this apparent intractability. We close this question by providing an explicit representation of the G-Wishart normalizing constant for general graphs.' acknowledgement: |- A.L.'s research was supported by Statistics for Innovation sfi2 in Oslo. D.R.'s research was partially supported by the U.S. National Science Foun-dation grant DMS-1309808; and by a Romberg Guest Professorship at the Heidelberg University Graduate School for Mathematical and Computational Methods in the Sciences, funded by German Universities Excellence Initiative grant GSC 220/2. author: - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Alex full_name: Lenkoski, Alex last_name: Lenkoski - first_name: Donald full_name: Richards, Donald last_name: Richards citation: ama: Uhler C, Lenkoski A, Richards D. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. 2014. apa: Uhler, C., Lenkoski, A., & Richards, D. (2014). Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. ArXiv. chicago: Uhler, Caroline, Alex Lenkoski, and Donald Richards. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv. ArXiv, 2014. ieee: C. Uhler, A. Lenkoski, and D. Richards, “ Exact formulas for the normalizing constants of Wishart distributions for graphical models,” ArXiv. ArXiv, 2014. ista: Uhler C, Lenkoski A, Richards D. 2014. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv, . mla: Uhler, Caroline, et al. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv, ArXiv, 2014. short: C. Uhler, A. Lenkoski, D. Richards, ArXiv (2014). date_created: 2018-12-11T11:55:14Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T06:54:44Z day: '18' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1406.4901 month: '06' oa: 1 publication: ArXiv publication_status: published publisher: ArXiv publist_id: '5058' quality_controlled: 0 status: public title: ' Exact formulas for the normalizing constants of Wishart distributions for graphical models' type: preprint year: '2014' ... --- _id: '2022' abstract: - lang: eng text: Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program. author: - first_name: Peng full_name: Gao, Peng last_name: Gao - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Teresa full_name: Krieger, Teresa last_name: Krieger - first_name: Luisirene full_name: Hernandez, Luisirene last_name: Hernandez - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Zhi full_name: Han, Zhi last_name: Han - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Ekaterina full_name: Papusheva, Ekaterina id: 41DB591E-F248-11E8-B48F-1D18A9856A87 last_name: Papusheva - first_name: Ryan full_name: Insolera, Ryan last_name: Insolera - first_name: Kritika full_name: Chugh, Kritika last_name: Chugh - first_name: Oren full_name: Kodish, Oren last_name: Kodish - first_name: Kun full_name: Huang, Kun last_name: Huang - first_name: Benjamin full_name: Simons, Benjamin last_name: Simons - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Song full_name: Shi, Song last_name: Shi citation: ama: Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 2014;159(4):775-788. doi:10.1016/j.cell.2014.10.027 apa: Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.10.027 chicago: Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell. Cell Press, 2014. https://doi.org/10.1016/j.cell.2014.10.027. ieee: P. Gao et al., “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” Cell, vol. 159, no. 4. Cell Press, pp. 775–788, 2014. ista: Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788. mla: Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell, vol. 159, no. 4, Cell Press, 2014, pp. 775–88, doi:10.1016/j.cell.2014.10.027. short: P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher, E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S. Hippenmeyer, S. Shi, Cell 159 (2014) 775–788. date_created: 2018-12-11T11:55:16Z date_published: 2014-11-06T00:00:00Z date_updated: 2021-01-12T06:54:47Z day: '06' ddc: - '570' department: - _id: SiHi - _id: Bio doi: 10.1016/j.cell.2014.10.027 ec_funded: 1 file: - access_level: open_access checksum: 6c5de8329bb2ffa71cba9fda750f14ce content_type: application/pdf creator: system date_created: 2018-12-12T10:08:47Z date_updated: 2020-07-14T12:45:25Z file_id: '4709' file_name: IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf file_size: 4435787 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 159' issue: '4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 775 - 788 project: - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development - _id: 25D7962E-B435-11E9-9278-68D0E5697425 grant_number: RGP0053/2014 name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level publication: Cell publication_status: published publisher: Cell Press publist_id: '5050' pubrep_id: '423' quality_controlled: '1' scopus_import: 1 status: public title: Deterministic progenitor behavior and unitary production of neurons in the neocortex tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2014' ... --- _id: '2020' abstract: - lang: eng text: The mammalian heart has long been considered a postmitotic organ, implying that the total number of cardiomyocytes is set at birth. Analysis of cell division in the mammalian heart is complicated by cardiomyocyte binucleation shortly after birth, which makes it challenging to interpret traditional assays of cell turnover [Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009) Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry technique recently calculated the low, discrete rate of cardiomyocyte generation in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level understanding of postnatal cardiomyogenesis remains limited. Herein, we provide a new line of evidence for the differentiated α-myosin heavy chain-expressing cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic analysis with double markers” mouse model. We show limited, life-long, symmetric division of cardiomyocytes as a rare event that is evident in utero but significantly diminishes after the first month of life in mice; daughter cardiomyocytes divide very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore, ligation of the left anterior descending coronary artery, which causes a myocardial infarction in the mosaic analysis with double-marker mice, did not increase the rate of cardiomyocyte division above the basal level for up to 4 wk after the injury. The clonal analysis described here provides direct evidence of postnatal mammalian cardiomyogenesis. author: - first_name: Shah full_name: Ali, Shah last_name: Ali - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Lily full_name: Saadat, Lily last_name: Saadat - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Irving full_name: Weissman, Irving last_name: Weissman - first_name: Reza full_name: Ardehali, Reza last_name: Ardehali citation: ama: Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 2014;111(24):8850-8855. doi:10.1073/pnas.1408233111 apa: Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., & Ardehali, R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1408233111 chicago: Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman, and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1408233111. ieee: S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” PNAS, vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014. ista: Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 111(24), 8850–8855. mla: Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:10.1073/pnas.1408233111. short: S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855. date_created: 2018-12-11T11:55:15Z date_published: 2014-06-17T00:00:00Z date_updated: 2021-01-12T06:54:46Z day: '17' department: - _id: SiHi doi: 10.1073/pnas.1408233111 intvolume: ' 111' issue: '24' language: - iso: eng month: '06' oa_version: None page: 8850 - 8855 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5052' quality_controlled: '1' scopus_import: 1 status: public title: Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '2021' abstract: - lang: eng text: Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development. author: - first_name: Joo full_name: William, Joo last_name: William - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: ama: William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 2014;346(6209):626-629. doi:10.1126/science.1258996 apa: William, J., Hippenmeyer, S., & Luo, L. (2014). Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1258996 chicago: William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1258996. ieee: J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling,” Science, vol. 346, no. 6209. American Association for the Advancement of Science, pp. 626–629, 2014. ista: William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629. mla: William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science, vol. 346, no. 6209, American Association for the Advancement of Science, 2014, pp. 626–29, doi:10.1126/science.1258996. short: J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629. date_created: 2018-12-11T11:55:15Z date_published: 2014-10-31T00:00:00Z date_updated: 2021-01-12T06:54:47Z day: '31' department: - _id: SiHi doi: 10.1126/science.1258996 intvolume: ' 346' issue: '6209' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/ month: '10' oa: 1 oa_version: Submitted Version page: 626 - 629 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5051' quality_controlled: '1' scopus_import: 1 status: public title: Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 346 year: '2014' ... --- _id: '2027' abstract: - lang: eng text: We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples. acknowledgement: This research was funded in part by the European Research Council (ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Marta full_name: Kwiatkowska, Marta last_name: Kwiatkowska - first_name: David full_name: Parker, David last_name: Parker - first_name: Mateusz full_name: Ujma, Mateusz last_name: Ujma citation: ama: 'Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision processes using learning algorithms. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Society of Industrial and Applied Mathematics; 2014:98-114. doi:10.1007/978-3-319-11936-6_8' apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska, M., … Ujma, M. (2014). Verification of markov decision processes using learning algorithms. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 98–114). Sydney, Australia: Society of Industrial and Applied Mathematics. https://doi.org/10.1007/978-3-319-11936-6_8' chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt, Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification of Markov Decision Processes Using Learning Algorithms.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1007/978-3-319-11936-6_8. ieee: T. Brázdil et al., “Verification of markov decision processes using learning algorithms,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 98–114. ista: 'Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M, Parker D, Ujma M. 2014. Verification of markov decision processes using learning algorithms. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm Engineering and Experiments, LNCS, vol. 8837, 98–114.' mla: Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:10.1007/978-3-319-11936-6_8. short: T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114. conference: end_date: 2014-11-07 location: Sydney, Australia name: 'ALENEX: Algorithm Engineering and Experiments' start_date: 2014-11-03 date_created: 2018-12-11T11:55:17Z date_published: 2014-11-01T00:00:00Z date_updated: 2021-01-12T06:54:49Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-11936-6_8 ec_funded: 1 editor: - first_name: Franck full_name: Cassez, Franck last_name: Cassez - first_name: Jean-François full_name: Raskin, Jean-François last_name: Raskin intvolume: ' 8837' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.2967 month: '11' oa: 1 oa_version: Submitted Version page: 98 - 114 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 26241A12-B435-11E9-9278-68D0E5697425 grant_number: '24696' name: LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ' Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)' publication_status: published publisher: Society of Industrial and Applied Mathematics publist_id: '5046' quality_controlled: '1' status: public title: Verification of markov decision processes using learning algorithms type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8837 year: '2014' ... --- _id: '2031' abstract: - lang: eng text: A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release. author: - first_name: Itaru full_name: Arai, Itaru id: 32A73F6C-F248-11E8-B48F-1D18A9856A87 last_name: Arai - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Arai itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 2014;3. doi:10.7554/eLife.04057 apa: Arai, itaru, & Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.04057 chicago: Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.04057. ieee: itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse,” eLife, vol. 3. eLife Sciences Publications, 2014. ista: Arai itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3. mla: Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife, vol. 3, eLife Sciences Publications, 2014, doi:10.7554/eLife.04057. short: itaru Arai, P.M. Jonas, ELife 3 (2014). date_created: 2018-12-11T11:55:19Z date_published: 2014-12-09T00:00:00Z date_updated: 2021-01-12T06:54:51Z day: '09' ddc: - '570' department: - _id: PeJo doi: 10.7554/eLife.04057 ec_funded: 1 file: - access_level: open_access checksum: c240f915450d4ebe8f95043a2a8c7b1a content_type: application/pdf creator: system date_created: 2018-12-12T10:14:41Z date_updated: 2020-07-14T12:45:26Z file_id: '5094' file_name: IST-2016-421-v1+1_e04057.full.pdf file_size: 2239563 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 3' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5041' pubrep_id: '421' quality_controlled: '1' scopus_import: 1 status: public title: Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2014' ... --- _id: '2024' abstract: - lang: eng text: 'The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and in the endocytic pathway from the plasma membrane to the vacuole. However, the intracellular location at which these two pathways converge remains unclear. In addition, the endocytic pathway is not completely blocked in yeast cells lacking all Rab5 genes, suggesting the existence of an unidentified route that bypasses the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic and VPS pathways occurs upstream of the requirement for Vps21p in these pathways. We also identify a previously unidentified endocytic pathway mediated by the AP-3 complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted cells, and thus works as an alternative route to the vacuole/lysosome. We propose that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent VPS pathway and a Rab5-independent AP-3-mediated pathway.' article_number: '3498' author: - first_name: Junko full_name: Toshima, Junko last_name: Toshima - first_name: Show full_name: Nishinoaki, Show last_name: Nishinoaki - first_name: Yoshifumi full_name: Sato, Yoshifumi last_name: Sato - first_name: Wataru full_name: Yamamoto, Wataru last_name: Yamamoto - first_name: Daiki full_name: Furukawa, Daiki last_name: Furukawa - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Akira full_name: Sawaguchi, Akira last_name: Sawaguchi - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: ama: Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 2014;5. doi:10.1038/ncomms4498 apa: Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4498 chicago: Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4498. ieee: J. Toshima et al., “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498. mla: Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications, vol. 5, 3498, Nature Publishing Group, 2014, doi:10.1038/ncomms4498. short: J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014). date_created: 2018-12-11T11:55:16Z date_published: 2014-03-25T00:00:00Z date_updated: 2021-01-12T06:54:48Z day: '25' ddc: - '570' department: - _id: DaSi doi: 10.1038/ncomms4498 file: - access_level: open_access checksum: 614fb6579c86d1f95bdd95eeb9ab01b0 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:11Z date_updated: 2020-07-14T12:45:25Z file_id: '4864' file_name: IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf file_size: 4803515 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5048' pubrep_id: '616' quality_controlled: '1' scopus_import: 1 status: public title: Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2014' ... --- _id: '2028' abstract: - lang: eng text: 'Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model.' acknowledgement: 'This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ' article_processing_charge: No author: - first_name: Katarina full_name: Bodova, Katarina id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bodova orcid: 0000-0002-7214-0171 - first_name: David full_name: Paydarfar, David last_name: Paydarfar - first_name: Daniel full_name: Forger, Daniel last_name: Forger citation: ama: Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041 apa: Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. Academic Press. https://doi.org/10.1016/j.jtbi.2014.09.041 chicago: Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press, 2014. https://doi.org/10.1016/j.jtbi.2014.09.041. ieee: K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press, pp. 40–54, 2014. ista: Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 365, 40–54. mla: Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54, doi:10.1016/j.jtbi.2014.09.041. short: K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54. date_created: 2018-12-11T11:55:18Z date_published: 2014-10-12T00:00:00Z date_updated: 2022-08-25T14:00:47Z day: '12' ddc: - '570' department: - _id: GaTk doi: 10.1016/j.jtbi.2014.09.041 file: - access_level: open_access checksum: a9dbae18d3233b3dab6944fd3f2cd49e content_type: application/pdf creator: system date_created: 2018-12-12T10:17:58Z date_updated: 2020-07-14T12:45:25Z file_id: '5316' file_name: IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf file_size: 2679222 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 365' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 40 - 54 publication: ' Journal of Theoretical Biology' publication_status: published publisher: Academic Press publist_id: '5043' pubrep_id: '444' quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1016/j.jtbi.2015.03.013 scopus_import: '1' status: public title: Characterizing spiking in noisy type II neurons tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 365 year: '2014' ... --- _id: '2026' abstract: - lang: eng text: 'We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata.' acknowledgement: "Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n" alternative_title: - LNCS author: - first_name: Zuzana full_name: Komárková, Zuzana last_name: Komárková - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: 'Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Springer; 2014:235-241. doi:10.1007/978-3-319-11936-6_17' apa: 'Komárková, Z., & Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_17' chicago: 'Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_17.' ieee: 'Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 235–241.' ista: 'Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.' mla: 'Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:10.1007/978-3-319-11936-6_17.' short: Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241. conference: end_date: 2014-11-07 location: Sydney, Australia name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2014-11-03 date_created: 2018-12-11T11:55:17Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:49Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-11936-6_17 ec_funded: 1 editor: - first_name: Franck full_name: Cassez, Franck last_name: Cassez - first_name: Jean-François full_name: Raskin, Jean-François last_name: Raskin intvolume: ' 8837' language: - iso: eng month: '01' oa_version: None page: 235 - 241 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5045' quality_controlled: '1' status: public title: 'Rabinizer 3: Safraless translation of ltl to small deterministic automata' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8837 year: '2014' ... --- _id: '2029' abstract: - lang: eng text: Spin-wave theory is a key ingredient in our comprehension of quantum spin systems, and is used successfully for understanding a wide range of magnetic phenomena, including magnon condensation and stability of patterns in dipolar systems. Nevertheless, several decades of research failed to establish the validity of spin-wave theory rigorously, even for the simplest models of quantum spins. A rigorous justification of the method for the three-dimensional quantum Heisenberg ferromagnet at low temperatures is presented here. We derive sharp bounds on its free energy by combining a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic estimates and operator inequalities. acknowledgement: 239694; ERC; European Research Council article_number: '20003' author: - first_name: Michele full_name: Correggi, Michele last_name: Correggi - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 2014;108(2). doi:10.1209/0295-5075/108/20003 apa: Correggi, M., Giuliani, A., & Seiringer, R. (2014). Validity of spin-wave theory for the quantum Heisenberg model. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/108/20003 chicago: Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL. IOP Publishing Ltd., 2014. https://doi.org/10.1209/0295-5075/108/20003. ieee: M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory for the quantum Heisenberg model,” EPL, vol. 108, no. 2. IOP Publishing Ltd., 2014. ista: Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003. mla: Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL, vol. 108, no. 2, 20003, IOP Publishing Ltd., 2014, doi:10.1209/0295-5075/108/20003. short: M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014). date_created: 2018-12-11T11:55:18Z date_published: 2014-10-13T00:00:00Z date_updated: 2021-01-12T06:54:50Z day: '13' department: - _id: RoSe doi: 10.1209/0295-5075/108/20003 intvolume: ' 108' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.4717 month: '10' oa: 1 oa_version: Submitted Version publication: EPL publication_status: published publisher: IOP Publishing Ltd. publist_id: '5044' quality_controlled: '1' scopus_import: 1 status: public title: Validity of spin-wave theory for the quantum Heisenberg model type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2014' ... --- _id: '2033' abstract: - lang: eng text: 'The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information.' author: - first_name: Daniel full_name: Hernandez Lobato, Daniel last_name: Hernandez Lobato - first_name: Viktoriia full_name: Sharmanska, Viktoriia id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87 last_name: Sharmanska orcid: 0000-0003-0192-9308 - first_name: Kristian full_name: Kersting, Kristian last_name: Kersting - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto citation: ama: 'Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind the nuisance: Gaussian process classification using privileged noise. In: Advances in Neural Information Processing Systems. Vol 1. Neural Information Processing Systems; 2014:837-845.' apa: 'Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., & Quadrianto, N. (2014). Mind the nuisance: Gaussian process classification using privileged noise. In Advances in Neural Information Processing Systems (Vol. 1, pp. 837–845). Montreal, Canada: Neural Information Processing Systems.' chicago: 'Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” In Advances in Neural Information Processing Systems, 1:837–45. Neural Information Processing Systems, 2014.' ieee: 'D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto, “Mind the nuisance: Gaussian process classification using privileged noise,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2014, vol. 1, no. January, pp. 837–845.' ista: 'Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014. Mind the nuisance: Gaussian process classification using privileged noise. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 1, 837–845.' mla: 'Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” Advances in Neural Information Processing Systems, vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45.' short: D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems, 2014, pp. 837–845. conference: end_date: 2014-12-13 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2014-12-08 date_created: 2018-12-11T11:55:20Z date_published: 2014-12-08T00:00:00Z date_updated: 2023-02-23T10:25:24Z day: '08' department: - _id: ChLa intvolume: ' 1' issue: January language: - iso: eng main_file_link: - open_access: '1' url: https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise month: '12' oa: 1 oa_version: Submitted Version page: 837-845 publication: Advances in Neural Information Processing Systems publication_status: published publisher: Neural Information Processing Systems publist_id: '5038' quality_controlled: '1' scopus_import: 1 status: public title: 'Mind the nuisance: Gaussian process classification using privileged noise' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2014' ... --- _id: '2032' abstract: - lang: eng text: As light-based control of fundamental signaling pathways is becoming a reality, the field of optogenetics is rapidly moving beyond neuroscience. We have recently developed receptor tyrosine kinases that are activated by light and control cell proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell behaviors central to cancer progression. article_number: e964045 author: - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 - first_name: Karin full_name: Schelch, Karin last_name: Schelch - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Michael full_name: Grusch, Michael last_name: Grusch citation: ama: 'Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 2014;1(4). doi:10.4161/23723548.2014.964045' apa: 'Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L., & Grusch, M. (2014). The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. Taylor & Francis. https://doi.org/10.4161/23723548.2014.964045' chicago: 'Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology. Taylor & Francis, 2014. https://doi.org/10.4161/23723548.2014.964045.' ieee: 'Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and M. Grusch, “The optogenetic promise for oncology: Episode I,” Molecular and Cellular Oncology, vol. 1, no. 4. Taylor & Francis, 2014.' ista: 'Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. 2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 1(4), e964045.' mla: 'Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology, vol. 1, no. 4, e964045, Taylor & Francis, 2014, doi:10.4161/23723548.2014.964045.' short: Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014). date_created: 2018-12-11T11:55:19Z date_published: 2014-12-31T00:00:00Z date_updated: 2021-01-12T06:54:51Z day: '31' ddc: - '570' department: - _id: HaJa doi: 10.4161/23723548.2014.964045 file: - access_level: open_access checksum: 44e17ad40577ab46eb602e88a8b0b8fd content_type: application/pdf creator: kschuh date_created: 2019-05-16T13:39:11Z date_updated: 2020-07-14T12:45:26Z file_id: '6464' file_name: 2014_Taylor_Alvaro.pdf file_size: 1765933 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 1' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Molecular and Cellular Oncology publication_status: published publisher: Taylor & Francis publist_id: '5040' quality_controlled: '1' scopus_import: 1 status: public title: 'The optogenetic promise for oncology: Episode I' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2014' ... --- _id: '2045' abstract: - lang: eng text: 'We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest.' acknowledgement: The second author was supported by EPSRC grant EP/H043454/1. alternative_title: - LNCS author: - first_name: Dana full_name: Dachman Soled, Dana last_name: Dachman Soled - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Payman full_name: Mohassel, Payman last_name: Mohassel - first_name: Adam full_name: O’Neill, Adam last_name: O’Neill citation: ama: 'Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:329-344. doi:10.1007/978-3-642-54631-0_19' apa: 'Dachman Soled, D., Fuchsbauer, G., Mohassel, P., & O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_19' chicago: Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_19. ieee: D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344. ista: 'Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344.' mla: Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:10.1007/978-3-642-54631-0_19. short: D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344. conference: end_date: 2014-03-28 location: Buenos Aires, Argentina name: 'PKC: Public Key Crypography' start_date: 2014-03-26 date_created: 2018-12-11T11:55:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:57Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-54631-0_19 ec_funded: 1 editor: - first_name: Hugo full_name: Krawczyk, Hugo last_name: Krawczyk intvolume: ' 8383' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2012/543 month: '01' oa: 1 oa_version: Submitted Version page: 329 - 344 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5006' quality_controlled: '1' scopus_import: 1 status: public title: Enhanced chosen-ciphertext security and applications type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8383 year: '2014' ... --- _id: '2042' abstract: - lang: eng text: 'Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.' article_number: '663' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663 apa: Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663 chicago: Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014. https://doi.org/10.1186/1471-2164-15-663. ieee: A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014. ista: Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663. mla: Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663. short: A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014). date_created: 2018-12-11T11:55:23Z date_published: 2014-08-08T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '08' ddc: - '570' department: - _id: JoBo doi: 10.1186/1471-2164-15-663 file: - access_level: open_access checksum: 3f6d2776b90a842a28359cc957d3d04b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:24Z date_updated: 2020-07-14T12:45:26Z file_id: '4878' file_name: IST-2015-396-v1+1_1471-2164-15-663.pdf file_size: 1489769 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 15' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: BMC Genomics publication_status: published publisher: BioMed Central publist_id: '5009' pubrep_id: '396' quality_controlled: '1' scopus_import: 1 status: public title: Motif depletion in bacteriophages infecting hosts with CRISPR systems tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '2043' abstract: - lang: eng text: Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node. author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Michael full_name: Kerber, Michael last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus citation: ama: 'Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In: McGeoch C, Meyer U, eds. Proceedings of the Workshop on Algorithm Engineering and Experiments. Society of Industrial and Applied Mathematics; 2014:31-38. doi:10.1137/1.9781611973198.4' apa: 'Bauer, U., Kerber, M., & Reininghaus, J. (2014). Distributed computation of persistent homology. In C. McGeoch & U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments (pp. 31–38). Portland, USA: Society of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973198.4' chicago: Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, 31–38. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973198.4. ieee: U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in Proceedings of the Workshop on Algorithm Engineering and Experiments, Portland, USA, 2014, pp. 31–38. ista: 'Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38.' mla: Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, Society of Industrial and Applied Mathematics, 2014, pp. 31–38, doi:10.1137/1.9781611973198.4. short: U. Bauer, M. Kerber, J. Reininghaus, in:, C. McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2014, pp. 31–38. conference: end_date: 2014-01-05 location: Portland, USA name: 'ALENEX: Algorithm Engineering and Experiments' start_date: 2014-01-05 date_created: 2018-12-11T11:55:23Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '01' department: - _id: HeEd doi: 10.1137/1.9781611973198.4 ec_funded: 1 editor: - first_name: Catherine full_name: ' McGeoch, Catherine' last_name: ' McGeoch' - first_name: Ulrich full_name: Meyer, Ulrich last_name: Meyer language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.0710 month: '01' oa: 1 oa_version: Submitted Version page: 31 - 38 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Proceedings of the Workshop on Algorithm Engineering and Experiments publication_status: published publisher: Society of Industrial and Applied Mathematics publist_id: '5008' quality_controlled: '1' scopus_import: 1 status: public title: Distributed computation of persistent homology type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2041' abstract: - lang: eng text: The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time. article_number: 2p author: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: John full_name: Lisman, John last_name: Lisman citation: ama: Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 2014;8. doi:10.3389/fncir.2014.00107 apa: Jonas, P. M., & Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. Frontiers Research Foundation. https://doi.org/10.3389/fncir.2014.00107 chicago: Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncir.2014.00107. ieee: P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” Frontiers in Neural Circuits, vol. 8. Frontiers Research Foundation, 2014. ista: Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p. mla: Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:10.3389/fncir.2014.00107. short: P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014). date_created: 2018-12-11T11:55:22Z date_published: 2014-09-10T00:00:00Z date_updated: 2021-01-12T06:54:55Z day: '10' ddc: - '570' department: - _id: PeJo doi: 10.3389/fncir.2014.00107 file: - access_level: open_access checksum: 3ca57b164045523f876407e9f13a9fb8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:38Z date_updated: 2020-07-14T12:45:26Z file_id: '5294' file_name: IST-2016-424-v1+1_fncir-08-00107.pdf file_size: 201110 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Frontiers in Neural Circuits publication_status: published publisher: Frontiers Research Foundation publist_id: '5010' pubrep_id: '424' quality_controlled: '1' scopus_import: 1 status: public title: Structure, function and plasticity of hippocampal dentate gyrus microcircuits tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2014' ... --- _id: '2044' abstract: - lang: eng text: We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation. author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Michael full_name: Kerber, Michael last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus citation: ama: 'Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Springer; 2014:103-117. doi:10.1007/978-3-319-04099-8_7' apa: 'Bauer, U., Kerber, M., & Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (pp. 103–117). Springer. https://doi.org/10.1007/978-3-319-04099-8_7' chicago: 'Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_7.' ieee: 'U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in Topological Methods in Data Analysis and Visualization III, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.' ista: 'Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117.' mla: 'Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:10.1007/978-3-319-04099-8_7.' short: U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117. date_created: 2018-12-11T11:55:23Z date_published: 2014-03-19T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '19' department: - _id: HeEd doi: 10.1007/978-3-319-04099-8_7 ec_funded: 1 editor: - first_name: Peer-Timo full_name: Bremer, Peer-Timo last_name: Bremer - first_name: Ingrid full_name: Hotz, Ingrid last_name: Hotz - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci - first_name: Ronald full_name: Peikert, Ronald last_name: Peikert language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.0477 month: '03' oa: 1 oa_version: Submitted Version page: 103 - 117 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Topological Methods in Data Analysis and Visualization III publication_status: published publisher: Springer publist_id: '5007' quality_controlled: '1' scopus_import: 1 series_title: Mathematics and Visualization status: public title: 'Clear and Compress: Computing Persistent Homology in Chunks' type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2040' abstract: - lang: eng text: 'Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. ' article_number: '1254927' author: - first_name: Anna full_name: Kicheva, Anna last_name: Kicheva - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Ana full_name: Ribeiro, Ana last_name: Ribeiro - first_name: Helena full_name: Pérez Valle, Helena last_name: Pérez Valle - first_name: Robin full_name: Lovell Badge, Robin last_name: Lovell Badge - first_name: Vasso full_name: Episkopou, Vasso last_name: Episkopou - first_name: James full_name: Briscoe, James last_name: Briscoe citation: ama: Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 2014;345(6204). doi:10.1126/science.1254927 apa: Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., & Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254927 chicago: Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1254927. ieee: A. Kicheva et al., “Coordination of progenitor specification and growth in mouse and chick spinal cord,” Science, vol. 345, no. 6204. American Association for the Advancement of Science, 2014. ista: Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927. mla: Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:10.1126/science.1254927. short: A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014). date_created: 2018-12-11T11:55:22Z date_published: 2014-09-26T00:00:00Z date_updated: 2021-01-12T06:54:55Z day: '26' department: - _id: ToBo doi: 10.1126/science.1254927 intvolume: ' 345' issue: '6204' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/ month: '09' oa: 1 oa_version: Submitted Version publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5011' quality_controlled: '1' scopus_import: 1 status: public title: Coordination of progenitor specification and growth in mouse and chick spinal cord type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 345 year: '2014' ... --- _id: '2047' abstract: - lang: eng text: Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance. acknowledgement: This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University. alternative_title: - LNCS author: - first_name: Fei full_name: Yu, Fei last_name: Yu - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Stephen full_name: Fienberg, Stephen last_name: Fienberg citation: ama: 'Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8744. Springer; 2014:170-184. doi:10.1007/978-3-319-11257-2_14' apa: 'Yu, F., Rybar, M., Uhler, C., & Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. https://doi.org/10.1007/978-3-319-11257-2_14' chicago: Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. https://doi.org/10.1007/978-3-319-11257-2_14. ieee: F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Ibiza, Spain, 2014, vol. 8744, pp. 170–184. ista: 'Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.' mla: Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:10.1007/978-3-319-11257-2_14. short: F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184. conference: end_date: 2014-09-19 location: Ibiza, Spain name: 'PSD: Privacy in Statistical Databases' start_date: 2014-09-17 date_created: 2018-12-11T11:55:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:57Z day: '01' department: - _id: KrPi - _id: CaUh doi: 10.1007/978-3-319-11257-2_14 editor: - first_name: Josep full_name: Domingo Ferrer, Josep last_name: Domingo Ferrer external_id: arxiv: - '1407.8067' intvolume: ' 8744' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.8067 month: '01' oa: 1 oa_version: Submitted Version page: 170 - 184 project: - _id: 25636330-B435-11E9-9278-68D0E5697425 grant_number: 11-NSF-1070 name: ROOTS Genome-wide Analysis of Root Traits publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5004' quality_controlled: '1' scopus_import: 1 status: public title: Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8744 year: '2014' ... --- _id: '2053' abstract: - lang: eng text: In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems. acknowledgement: This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams. alternative_title: - LNCS author: - first_name: Holger full_name: Hermanns, Holger last_name: Hermanns - first_name: Jan full_name: Krčál, Jan last_name: Krčál - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: 'Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:10.1007/978-3-662-44584-6_18' apa: 'Hermanns, H., Krčál, J., & Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_18' chicago: 'Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_18.' ieee: 'H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 249–265.' ista: 'Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265.' mla: 'Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:10.1007/978-3-662-44584-6_18.' short: H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265. conference: end_date: 2014-09-05 location: Rome, Italy name: 'CONCUR: Concurrency Theory' start_date: 2014-09-02 date_created: 2018-12-11T11:55:27Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:55:00Z day: '01' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-662-44584-6_18 ec_funded: 1 editor: - first_name: Paolo full_name: Baldan, Paolo last_name: Baldan - first_name: Daniele full_name: Gorla, Daniele last_name: Gorla intvolume: ' 8704' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.5084 month: '09' oa: 1 oa_version: Submitted Version page: 249 - 265 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4993' status: public title: 'Probabilistic bisimulation: Naturally on distributions' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8704 year: '2014' ... --- _id: '2052' abstract: - lang: eng text: A standard technique for solving the parameterized model checking problem is to reduce it to the classic model checking problem of finitely many finite-state systems. This work considers some of the theoretical power and limitations of this technique. We focus on concurrent systems in which processes communicate via pairwise rendezvous, as well as the special cases of disjunctive guards and token passing; specifications are expressed in indexed temporal logic without the next operator; and the underlying network topologies are generated by suitable Monadic Second Order Logic formulas and graph operations. First, we settle the exact computational complexity of the parameterized model checking problem for some of our concurrent systems, and establish new decidability results for others. Second, we consider the cases that model checking the parameterized system can be reduced to model checking some fixed number of processes, the number is known as a cutoff. We provide many cases for when such cutoffs can be computed, establish lower bounds on the size of such cutoffs, and identify cases where no cutoff exists. Third, we consider cases for which the parameterized system is equivalent to a single finite-state system (more precisely a Büchi word automaton), and establish tight bounds on the sizes of such automata. acknowledgement: The second, third, fourth and fifth authors were supported by the Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund (FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED, ICT12-059, and VRG11-005. alternative_title: - LNCS author: - first_name: Benjamin full_name: Aminof, Benjamin id: 4A55BD00-F248-11E8-B48F-1D18A9856A87 last_name: Aminof - first_name: Tomer full_name: Kotek, Tomer last_name: Kotek - first_name: Sacha full_name: Rubin, Sacha last_name: Rubin - first_name: Francesco full_name: Spegni, Francesco last_name: Spegni - first_name: Helmut full_name: Veith, Helmut last_name: Veith citation: ama: 'Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking of rendezvous systems. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:109-124. doi:10.1007/978-3-662-44584-6_9' apa: 'Aminof, B., Kotek, T., Rubin, S., Spegni, F., & Veith, H. (2014). Parameterized model checking of rendezvous systems. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 109–124). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_9' chicago: Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut Veith. “Parameterized Model Checking of Rendezvous Systems.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_9. ieee: B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 109–124. ista: 'Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124.' mla: Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–24, doi:10.1007/978-3-662-44584-6_9. short: B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–124. conference: end_date: 2014-09-05 location: Rome, Italy name: 'CONCUR: Concurrency Theory' start_date: 2014-09-02 date_created: 2018-12-11T11:55:26Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:54:59Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-44584-6_9 editor: - first_name: Paolo full_name: Baldan, Paolo last_name: Baldan - first_name: Daniele full_name: Gorla, Daniele last_name: Gorla intvolume: ' 8704' language: - iso: eng month: '09' oa_version: None page: 109 - 124 publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4994' quality_controlled: '1' status: public title: Parameterized model checking of rendezvous systems type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8704 year: '2014' ... --- _id: '2046' abstract: - lang: eng text: 'We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications.' acknowledgement: Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1. alternative_title: - LNCS author: - first_name: Mihir full_name: Bellare, Mihir last_name: Bellare - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer citation: ama: 'Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:520-537. doi:10.1007/978-3-642-54631-0_30' apa: 'Bellare, M., & Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_30' chicago: Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_30. ieee: M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537. ista: 'Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.' mla: Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:10.1007/978-3-642-54631-0_30. short: M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537. conference: end_date: 2014-05-28 location: Buenos Aires, Argentina name: 'PKC: Public Key Crypography' start_date: 2014-05-26 date_created: 2018-12-11T11:55:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:57Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-54631-0_30 ec_funded: 1 editor: - first_name: Hugo full_name: Krawczyk, Hugo last_name: Krawczyk intvolume: ' 8383' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2013/413 month: '01' oa: 1 oa_version: Submitted Version page: 520 - 537 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '5005' quality_controlled: '1' scopus_import: 1 status: public title: Policy-based signatures type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8383 year: '2014' ... --- _id: '2050' abstract: - lang: eng text: The flow instability and further transition to turbulence in a toroidal pipe (torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated experimentally. The flow inside the toroidal pipe is driven by a steel sphere fitted to the inner pipe diameter. The sphere is moved with constant azimuthal velocity from outside the torus by a moving magnet. The experiment is designed to investigate curved pipe flow by optical measurement techniques. Using stereoscopic particle image velocimetry, laser Doppler velocimetry and pressure drop measurements, the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and space-resolved velocity fields are obtained and analysed. The steady axisymmetric basic flow is strongly influenced by centrifugal effects. On an increase of the Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical bifurcation to an oscillatory flow is found in which waves travel in the streamwise direction with a phase velocity slightly faster than the mean flow. The oscillatory flow is superseded by a presumably quasi-periodic flow at a further increase of the Reynolds number before turbulence sets in. The results are found to be compatible, in general, with earlier experimental and numerical investigations on transition to turbulence in helical and curved pipes. However, important aspects of the bifurcation scenario differ considerably. article_processing_charge: No author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Markus full_name: Holzner, Markus last_name: Holzner - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Hendrik full_name: Kuhlmann, Hendrik last_name: Kuhlmann citation: ama: Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 2014;738:463-491. doi:10.1017/jfm.2013.603 apa: Kühnen, J., Holzner, M., Hof, B., & Kuhlmann, H. (2014). Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.603 chicago: Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2014. https://doi.org/10.1017/jfm.2013.603. ieee: J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation of transitional flow in a toroidal pipe,” Journal of Fluid Mechanics, vol. 738. Cambridge University Press, pp. 463–491, 2014. ista: Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491. mla: Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:10.1017/jfm.2013.603. short: J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491. date_created: 2018-12-11T11:55:25Z date_published: 2014-01-10T00:00:00Z date_updated: 2021-01-12T06:54:59Z day: '10' department: - _id: BjHo doi: 10.1017/jfm.2013.603 external_id: arxiv: - '1508.06546' intvolume: ' 738' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.06546 month: '01' oa: 1 oa_version: Submitted Version page: 463 - 491 publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '5001' quality_controlled: '1' scopus_import: 1 status: public title: Experimental investigation of transitional flow in a toroidal pipe type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 738 year: '2014' ... --- _id: '2051' abstract: - lang: eng text: We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach. author: - first_name: Mario full_name: Marchand, Mario last_name: Marchand - first_name: Su full_name: Hongyu, Su last_name: Hongyu - first_name: Emilie full_name: Emilie Morvant id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87 last_name: Morvant orcid: 0000-0002-8301-7240 - first_name: Juho full_name: Rousu, Juho last_name: Rousu - first_name: John full_name: Shawe-Taylor, John last_name: Shawe Taylor citation: ama: 'Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: Neural Information Processing Systems; 2014.' apa: 'Marchand, M., Hongyu, S., Morvant, E., Rousu, J., & Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.' chicago: Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” Neural Information Processing Systems, 2014. ieee: 'M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” presented at the NIPS: Neural Information Processing Systems, 2014.' ista: 'Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. NIPS: Neural Information Processing Systems.' mla: Marchand, Mario, et al. Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. Neural Information Processing Systems, 2014. short: M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Neural Information Processing Systems, 2014. conference: name: 'NIPS: Neural Information Processing Systems' date_created: 2018-12-11T11:55:26Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:59Z day: '01' extern: 1 main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01065586 month: '01' oa: 1 publication_status: published publisher: Neural Information Processing Systems publist_id: '4996' quality_controlled: 0 status: public title: Multilabel structured output learning with random spanning trees of max-margin Markov networks type: conference year: '2014' ... --- _id: '2059' abstract: - lang: eng text: Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant. acknowledgement: The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14. author: - first_name: Ewa full_name: Dubas, Ewa last_name: Dubas - first_name: Jana full_name: Moravčíková, Jana last_name: Moravčíková - first_name: Jana full_name: Libantová, Jana last_name: Libantová - first_name: Ildikó full_name: Matušíková, Ildikó last_name: Matušíková - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Iwona full_name: Zur, Iwona last_name: Zur - first_name: Monika full_name: Krzewska, Monika last_name: Krzewska citation: ama: Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 2014;251(5):1077-1087. doi:10.1007/s00709-014-0616-1 apa: Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., & Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0616-1 chicago: Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0616-1. ieee: E. Dubas et al., “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” Protoplasma, vol. 251, no. 5. Springer, pp. 1077–1087, 2014. ista: Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087. mla: Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1. short: E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087. date_created: 2018-12-11T11:55:29Z date_published: 2014-02-20T00:00:00Z date_updated: 2021-01-12T06:55:02Z day: '20' ddc: - '580' department: - _id: EvBe doi: 10.1007/s00709-014-0616-1 file: - access_level: open_access checksum: d570a6073765118fc0bb83c31d96fa53 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:31Z date_updated: 2020-07-14T12:45:27Z file_id: '5353' file_name: IST-2015-394-v1+1_s00709-014-0616-1.pdf file_size: 6377990 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 251' issue: '5' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1077 - 1087 publication: Protoplasma publication_status: published publisher: Springer publist_id: '4987' pubrep_id: '394' quality_controlled: '1' scopus_import: 1 status: public title: The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 251 year: '2014' ... --- _id: '2062' abstract: - lang: eng text: The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes. article_number: '1255263' author: - first_name: Hua full_name: Hu, Hua id: 4AC0145C-F248-11E8-B48F-1D18A9856A87 last_name: Hu - first_name: Jian full_name: Gan, Jian id: 3614E438-F248-11E8-B48F-1D18A9856A87 last_name: Gan - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 2014;345(6196). doi:10.1126/science.1255263' apa: 'Hu, H., Gan, J., & Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1255263' chicago: 'Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1255263.' ieee: 'H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function,” Science, vol. 345, no. 6196. American Association for the Advancement of Science, 2014.' ista: 'Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.' mla: 'Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science, vol. 345, no. 6196, 1255263, American Association for the Advancement of Science, 2014, doi:10.1126/science.1255263.' short: H. Hu, J. Gan, P.M. Jonas, Science 345 (2014). date_created: 2018-12-11T11:55:29Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T06:55:03Z day: '01' ddc: - '570' department: - _id: PeJo doi: 10.1126/science.1255263 ec_funded: 1 file: - access_level: open_access checksum: a0036a589037d37e86364fa25cc0a82f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:00Z date_updated: 2020-07-14T12:45:27Z file_id: '5185' file_name: IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf file_size: 215514 relation: main_file - access_level: open_access checksum: e1f57d2713725449cb898fdcb8ef47b8 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:01Z date_updated: 2020-07-14T12:45:27Z file_id: '5186' file_name: IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf file_size: 1732723 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 345' issue: '6196' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '4984' pubrep_id: '821' quality_controlled: '1' scopus_import: 1 status: public title: 'Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 345 year: '2014' ... --- _id: '2058' abstract: - lang: eng text: We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations. article_number: '137' article_processing_charge: No author: - first_name: Karthik full_name: Raveendran, Karthik last_name: Raveendran - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Greg full_name: Türk, Greg last_name: Türk citation: ama: 'Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126' apa: 'Raveendran, K., Wojtan, C., Thuerey, N., & Türk, G. (2014). Blending liquids. In ACM Transactions on Graphics (Vol. 33). Vancouver, Canada: ACM. https://doi.org/10.1145/2601097.2601126' chicago: Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In ACM Transactions on Graphics, Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601126. ieee: K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4. ista: 'Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137.' mla: Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics, vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126. short: K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014. conference: end_date: 2014-08-14 location: Vancouver, Canada name: 'SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques' start_date: 2014-08-10 date_created: 2018-12-11T11:55:28Z date_published: 2014-07-01T00:00:00Z date_updated: 2022-08-25T14:02:46Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2601097.2601126 file: - access_level: open_access checksum: 1752760a2e71e254537f31c0d10d9c6c content_type: application/pdf creator: system date_created: 2018-12-12T10:08:27Z date_updated: 2020-07-14T12:45:27Z file_id: '4688' file_name: IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf file_size: 8387384 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 33' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25636330-B435-11E9-9278-68D0E5697425 grant_number: 11-NSF-1070 name: ROOTS Genome-wide Analysis of Root Traits publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4988' pubrep_id: '606' quality_controlled: '1' scopus_import: '1' status: public title: Blending liquids type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2014' ... --- _id: '2057' abstract: - lang: eng text: 'In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark.' alternative_title: - LNCS author: - first_name: Emilie full_name: Morvant, Emilie id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87 last_name: Morvant orcid: 0000-0002-8301-7240 - first_name: Amaury full_name: Habrard, Amaury last_name: Habrard - first_name: Stéphane full_name: Ayache, Stéphane last_name: Ayache citation: ama: 'Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8621. Springer; 2014:153-162. doi:10.1007/978-3-662-44415-3_16' apa: 'Morvant, E., Habrard, A., & Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. https://doi.org/10.1007/978-3-662-44415-3_16' chicago: Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8621:153–62. Springer, 2014. https://doi.org/10.1007/978-3-662-44415-3_16. ieee: E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Joensuu, Finland, 2014, vol. 8621, pp. 153–162. ista: 'Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.' mla: Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8621, Springer, 2014, pp. 153–62, doi:10.1007/978-3-662-44415-3_16. short: E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162. conference: end_date: 2014-08-22 location: Joensuu, Finland name: 'IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition' start_date: 2014-08-20 date_created: 2018-12-11T11:55:28Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:55:01Z day: '01' department: - _id: ChLa doi: 10.1007/978-3-662-44415-3_16 ec_funded: 1 external_id: arxiv: - '1404.7796' intvolume: ' 8621' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.7796 month: '01' oa: 1 oa_version: Preprint page: 153 - 162 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '4989' quality_controlled: '1' scopus_import: 1 status: public title: Majority vote of diverse classifiers for late fusion type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8621 year: '2014' ... --- _id: '2056' abstract: - lang: eng text: 'We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk.' acknowledgement: T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology. author: - first_name: Arnab full_name: Ganguly, Arnab last_name: Ganguly - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 - first_name: Heinz full_name: Koeppl, Heinz last_name: Koeppl citation: ama: Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 2014;69(3):767-797. doi:10.1007/s00285-013-0738-7 apa: Ganguly, A., Petrov, T., & Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-013-0738-7 chicago: Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology. Springer, 2014. https://doi.org/10.1007/s00285-013-0738-7. ieee: A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” Journal of Mathematical Biology, vol. 69, no. 3. Springer, pp. 767–797, 2014. ista: Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797. mla: Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:10.1007/s00285-013-0738-7. short: A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797. date_created: 2018-12-11T11:55:28Z date_published: 2014-11-20T00:00:00Z date_updated: 2021-01-12T06:55:01Z day: '20' department: - _id: CaGu - _id: ToHe doi: 10.1007/s00285-013-0738-7 intvolume: ' 69' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.4532 month: '11' oa: 1 oa_version: Submitted Version page: 767 - 797 publication: Journal of Mathematical Biology publication_status: published publisher: Springer publist_id: '4990' quality_controlled: '1' scopus_import: 1 status: public title: Markov chain aggregation and its applications to combinatorial reaction networks type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2014' ... --- _id: '2061' abstract: - lang: eng text: 'Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis.' author: - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur - first_name: Ewa full_name: Kurczyñska, Ewa last_name: Kurczyñska - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Mazur E, Kurczyñska E, Friml J. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 2014;251(5):1125-1139. doi:10.1007/s00709-014-0620-5 apa: Mazur, E., Kurczyñska, E., & Friml, J. (2014). Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0620-5 chicago: Mazur, Ewa, Ewa Kurczyñska, and Jiří Friml. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0620-5. ieee: E. Mazur, E. Kurczyñska, and J. Friml, “Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis,” Protoplasma, vol. 251, no. 5. Springer, pp. 1125–1139, 2014. ista: Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5), 1125–1139. mla: Mazur, Ewa, et al. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1125–39, doi:10.1007/s00709-014-0620-5. short: E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139. date_created: 2018-12-11T11:55:29Z date_published: 2014-02-14T00:00:00Z date_updated: 2021-01-12T06:55:03Z day: '14' department: - _id: JiFr doi: 10.1007/s00709-014-0620-5 intvolume: ' 251' issue: '5' language: - iso: eng month: '02' oa_version: None page: 1125 - 1139 publication: Protoplasma publication_status: published publisher: Springer publist_id: '4985' quality_controlled: '1' scopus_import: 1 status: public title: Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 251 year: '2014' ... --- _id: '2064' abstract: - lang: eng text: We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses. acknowledgement: "National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n" author: - first_name: Maía full_name: Rubio, Maía last_name: Rubio - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Naomi full_name: Kamasawa, Naomi last_name: Kamasawa - first_name: Cheryl full_name: Clarkson, Cheryl last_name: Clarkson - first_name: Elek full_name: Molnár, Elek last_name: Molnár - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 2014;522(18):4023-4042. doi:10.1002/cne.23654 apa: Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., & Shigemoto, R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23654 chicago: Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár, and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology. Wiley-Blackwell, 2014. https://doi.org/10.1002/cne.23654. ieee: M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto, “Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus,” Journal of Comparative Neurology, vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014. ista: Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18), 4023–4042. mla: Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:10.1002/cne.23654. short: M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042. date_created: 2018-12-11T11:55:30Z date_published: 2014-07-29T00:00:00Z date_updated: 2021-01-12T06:55:05Z day: '29' department: - _id: RySh doi: 10.1002/cne.23654 intvolume: ' 522' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/ month: '07' oa: 1 oa_version: Submitted Version page: 4023 - 4042 publication: Journal of Comparative Neurology publication_status: published publisher: Wiley-Blackwell publist_id: '4974' quality_controlled: '1' scopus_import: 1 status: public title: Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 522 year: '2014' ... --- _id: '2081' abstract: - lang: eng text: We propose an interactive, optimization-in-the-loop tool for designing inflatable structures. Given a target shape, the user draws a network of seams defining desired segment boundaries in 3D. Our method computes optimally-shaped flat panels for the segments, such that the inflated structure is as close as possible to the target while satisfying the desired seam positions. Our approach is underpinned by physics-based pattern optimization, accurate coarse-scale simulation using tension field theory, and a specialized constraint-optimization method. Our system is fast enough to warrant interactive exploration of different seam layouts, including internal connections, and their effects on the inflated shape. We demonstrate the resulting design process on a varied set of simulation examples, some of which we have fabricated, demonstrating excellent agreement with the design intent. acknowledgement: This work was partly funded by the NCCR Co-Me of the Swiss NSF. article_number: '63' author: - first_name: Mélina full_name: Skouras, Mélina last_name: Skouras - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Peter full_name: Kaufmann, Peter last_name: Kaufmann - first_name: Akash full_name: Garg, Akash last_name: Garg - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Eitan full_name: Grinspun, Eitan last_name: Grinspun - first_name: Markus full_name: Gross, Markus last_name: Gross citation: ama: 'Skouras M, Thomaszewski B, Kaufmann P, et al. Designing inflatable structures. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601166' apa: 'Skouras, M., Thomaszewski, B., Kaufmann, P., Garg, A., Bickel, B., Grinspun, E., & Gross, M. (2014). Designing inflatable structures (Vol. 33). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601166' chicago: Skouras, Mélina, Bernhard Thomaszewski, Peter Kaufmann, Akash Garg, Bernd Bickel, Eitan Grinspun, and Markus Gross. “Designing Inflatable Structures,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601166. ieee: 'M. Skouras et al., “Designing inflatable structures,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.' ista: 'Skouras M, Thomaszewski B, Kaufmann P, Garg A, Bickel B, Grinspun E, Gross M. 2014. Designing inflatable structures. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 33, 63.' mla: Skouras, Mélina, et al. Designing Inflatable Structures. Vol. 33, no. 4, 63, ACM, 2014, doi:10.1145/2601097.2601166. short: M. Skouras, B. Thomaszewski, P. Kaufmann, A. Garg, B. Bickel, E. Grinspun, M. Gross, in:, ACM, 2014. conference: name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' date_created: 2018-12-11T11:55:36Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:55:11Z day: '01' doi: 10.1145/2601097.2601166 extern: '1' intvolume: ' 33' issue: '4' language: - iso: eng month: '07' oa_version: None publication_status: published publisher: ACM publist_id: '4957' status: public title: Designing inflatable structures type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2014' ... --- _id: '2080' abstract: - lang: eng text: 'Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. We present an algorithm to generate designs for spinning objects by optimizing rotational dynamics properties. As input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. We augment the model by creating voids inside its volume, with interior fill represented by an adaptive multi-resolution vox-elization. The discrete voxel fill values are optimized using a continuous, nonlinear formulation. Further, we optimize for rotational stability by maximizing the dominant principal moment. We extend our technique to incorporate deformation and multiple materials for cases where internal voids alone are insufficient. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance. ' acknowledgement: This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting is supported by the ETH Zurich / Marie Curie COFUND Postdoctoral Fellowship. author: - first_name: Moritz full_name: Bac̈her, Moritz last_name: Bac̈Her - first_name: Emily full_name: Whiting, Emily last_name: Whiting - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Olga full_name: Sorkine-Hornung, Olga last_name: Sorkine Hornung citation: ama: 'Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. Spin-It: Optimizing moment of inertia for spinnable objects. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601157' apa: 'Bac̈Her, M., Whiting, E., Bickel, B., & Sorkine Hornung, O. (2014). Spin-It: Optimizing moment of inertia for spinnable objects (Vol. 33). Presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601157' chicago: 'Bac̈Her, Moritz, Emily Whiting, Bernd Bickel, and Olga Sorkine Hornung. “Spin-It: Optimizing Moment of Inertia for Spinnable Objects,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601157.' ieee: 'M. Bac̈Her, E. Whiting, B. Bickel, and O. Sorkine Hornung, “Spin-It: Optimizing moment of inertia for spinnable objects,” presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.' ista: 'Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. 2014. Spin-It: Optimizing moment of inertia for spinnable objects. SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33.' mla: 'Bac̈Her, Moritz, et al. Spin-It: Optimizing Moment of Inertia for Spinnable Objects. Vol. 33, no. 4, ACM, 2014, doi:10.1145/2601097.2601157.' short: M. Bac̈Her, E. Whiting, B. Bickel, O. Sorkine Hornung, in:, ACM, 2014. conference: name: 'SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques' date_created: 2018-12-11T11:55:35Z date_published: 2014-01-01T00:00:00Z date_updated: 2019-04-26T07:22:07Z day: '01' doi: 10.1145/2601097.2601157 extern: 1 intvolume: ' 33' issue: '4' month: '01' publication_status: published publisher: ACM publist_id: '4958' quality_controlled: 0 status: public title: 'Spin-It: Optimizing moment of inertia for spinnable objects' type: conference volume: 33 year: '2014' ... --- _id: '2115' abstract: - lang: eng text: The facial performance of an individual is inherently rich in subtle deformation and timing details. Although these subtleties make the performance realistic and compelling, they often elude both motion capture and hand animation. We present a technique for adding fine-scale details and expressiveness to low-resolution art-directed facial performances, such as those created manually using a rig, via marker-based capture, by fitting a morphable model to a video, or through Kinect reconstruction using recent faceshift technology. We employ a high-resolution facial performance capture system to acquire a representative performance of an individual in which he or she explores the full range of facial expressiveness. From the captured data, our system extracts an expressiveness model that encodes subtle spatial and temporal deformation details specific to that particular individual. Once this model has been built, these details can be transferred to low-resolution art-directed performances. We demonstrate results on various forms of input; after our enhancement, the resulting animations exhibit the same nuances and fine spatial details as the captured performance, with optional temporal enhancement to match the dynamics of the actor. Finally, we show that our technique outperforms the current state-of-the-art in example-based facial animation. author: - first_name: Amit full_name: Bermano, Amit H last_name: Bermano - first_name: Derek full_name: Bradley, Derek J last_name: Bradley - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler - first_name: Fabio full_name: Zund, Fabio last_name: Zund - first_name: Derek full_name: Nowrouzezahrai, Derek last_name: Nowrouzezahrai - first_name: Ilya full_name: Baran, Ilya last_name: Baran - first_name: Olga full_name: Sorkine-Hornung, Olga last_name: Sorkine Hornung - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Robert full_name: Sumner, Robert W last_name: Sumner - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Bermano A, Bradley D, Beeler T, et al. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2546276 apa: Bermano, A., Bradley, D., Beeler, T., Zund, F., Nowrouzezahrai, D., Baran, I., … Groß, M. (2014). Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2546276 chicago: Bermano, Amit, Derek Bradley, Thabo Beeler, Fabio Zund, Derek Nowrouzezahrai, Ilya Baran, Olga Sorkine Hornung, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2546276. ieee: A. Bermano et al., “Facial performance enhancement using dynamic shape space analysis,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014. ista: Bermano A, Bradley D, Beeler T, Zund F, Nowrouzezahrai D, Baran I, Sorkine Hornung O, Pfister H, Sumner R, Bickel B, Groß M. 2014. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 33(2). mla: Bermano, Amit, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics, vol. 33, no. 2, ACM, 2014, doi:10.1145/2546276. short: A. Bermano, D. Bradley, T. Beeler, F. Zund, D. Nowrouzezahrai, I. Baran, O. Sorkine Hornung, H. Pfister, R. Sumner, B. Bickel, M. Groß, ACM Transactions on Graphics 33 (2014). date_created: 2018-12-11T11:55:48Z date_published: 2014-03-01T00:00:00Z date_updated: 2021-01-12T06:55:24Z day: '01' doi: 10.1145/2546276 extern: 1 intvolume: ' 33' issue: '2' month: '03' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4919' quality_controlled: 0 status: public title: Facial performance enhancement using dynamic shape space analysis type: journal_article volume: 33 year: '2014' ... --- _id: '2133' abstract: - lang: eng text: "Let ℭ denote the Clifford algebra over ℝ\U0001D45B, which is the von Neumann algebra generated by n self-adjoint operators Q j , j = 1,…,n satisfying the canonical anticommutation relations, Q i Q j + Q j Q i = 2δ ij I, and let τ denote the normalized trace on ℭ. This algebra arises in quantum mechanics as the algebra of observables generated by n fermionic degrees of freedom. Let \U0001D513 denote the set of all positive operators \U0001D70C∈ℭ such that τ(ρ) = 1; these are the non-commutative analogs of probability densities in the non-commutative probability space (ℭ,\U0001D70F). The fermionic Fokker–Planck equation is a quantum-mechanical analog of the classical Fokker–Planck equation with which it has much in common, such as the same optimal hypercontractivity properties. In this paper we construct a Riemannian metric on \U0001D513 that we show to be a natural analog of the classical 2-Wasserstein metric, and we show that, in analogy with the classical case, the fermionic Fokker–Planck equation is gradient flow in this metric for the relative entropy with respect to the ground state. We derive a number of consequences of this, such as a sharp Talagrand inequality for this metric, and we prove a number of results pertaining to this metric. Several open problems are raised." author: - first_name: Eric full_name: Carlen, Eric last_name: Carlen - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Carlen E, Maas J. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 2014;331(3):887-926. doi:10.1007/s00220-014-2124-8 apa: Carlen, E., & Maas, J. (2014). An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2124-8 chicago: Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2124-8. ieee: E. Carlen and J. Maas, “An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy,” Communications in Mathematical Physics, vol. 331, no. 3. Springer, pp. 887–926, 2014. ista: Carlen E, Maas J. 2014. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 331(3), 887–926. mla: Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics, vol. 331, no. 3, Springer, 2014, pp. 887–926, doi:10.1007/s00220-014-2124-8. short: E. Carlen, J. Maas, Communications in Mathematical Physics 331 (2014) 887–926. date_created: 2018-12-11T11:55:54Z date_published: 2014-11-01T00:00:00Z date_updated: 2021-01-12T06:55:30Z day: '01' doi: 10.1007/s00220-014-2124-8 extern: '1' intvolume: ' 331' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: 'http://arxiv.org/abs/1203.5377 ' month: '11' oa: 1 oa_version: Submitted Version page: 887 - 926 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4901' quality_controlled: '1' status: public title: An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 331 year: '2014' ... --- _id: '2131' abstract: - lang: eng text: We study approximations to a class of vector-valued equations of Burgers type driven by a multiplicative space-time white noise. A solution theory for this class of equations has been developed recently in Probability Theory Related Fields by Hairer and Weber. The key idea was to use the theory of controlled rough paths to give definitions of weak/mild solutions and to set up a Picard iteration argument. In this article the limiting behavior of a rather large class of (spatial) approximations to these equations is studied. These approximations are shown to converge and convergence rates are given, but the limit may depend on the particular choice of approximation. This effect is a spatial analogue to the Itô-Stratonovich correction in the theory of stochastic ordinary differential equations, where it is well known that different approximation schemes may converge to different solutions. acknowledgement: JM is supported by Rubicon grant 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). MH is supported by EPSRC grant EP/D071593/1 and by the Royal Society through a Wolfson Research Merit Award. Both MH and HW are supported by the Le author: - first_name: Martin full_name: Hairer, Martin M last_name: Hairer - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Hendrik full_name: Weber, Hendrik last_name: Weber citation: ama: Hairer M, Maas J, Weber H. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 2014;67(5):776-870. doi:10.1002/cpa.21495 apa: Hairer, M., Maas, J., & Weber, H. (2014). Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21495 chicago: Hairer, Martin, Jan Maas, and Hendrik Weber. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2014. https://doi.org/10.1002/cpa.21495. ieee: M. Hairer, J. Maas, and H. Weber, “Approximating Rough Stochastic PDEs,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley-Blackwell, pp. 776–870, 2014. ista: Hairer M, Maas J, Weber H. 2014. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 67(5), 776–870. mla: Hairer, Martin, et al. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley-Blackwell, 2014, pp. 776–870, doi:10.1002/cpa.21495. short: M. Hairer, J. Maas, H. Weber, Communications on Pure and Applied Mathematics 67 (2014) 776–870. date_created: 2018-12-11T11:55:53Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T06:55:30Z day: '01' doi: 10.1002/cpa.21495 extern: 1 intvolume: ' 67' issue: '5' main_file_link: - open_access: '1' url: 'http://arxiv.org/abs/1202.3094 ' month: '05' oa: 1 page: 776 - 870 publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley-Blackwell publist_id: '4902' quality_controlled: 0 status: public title: Approximating Rough Stochastic PDEs type: journal_article volume: 67 year: '2014' ... --- _id: '2132' abstract: - lang: eng text: We consider discrete porous medium equations of the form ∂tρt=Δϕ(ρt), where Δ is the generator of a reversible continuous time Markov chain on a finite set χ, and ϕ is an increasing function. We show that these equations arise as gradient flows of certain entropy functionals with respect to suitable non-local transportation metrics. This may be seen as a discrete analogue of the Wasserstein gradient flow structure for porous medium equations in ℝn discovered by Otto. We present a one-dimensional counterexample to geodesic convexity and discuss Gromov-Hausdorff convergence to the Wasserstein metric. author: - first_name: Matthias full_name: Erbar, Matthias last_name: Erbar - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Erbar M, Maas J. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 2014;34(4):1355-1374. doi:10.3934/dcds.2014.34.1355  apa: Erbar, M., & Maas, J. (2014). Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University. https://doi.org/10.3934/dcds.2014.34.1355  chicago: Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University, 2014. https://doi.org/10.3934/dcds.2014.34.1355  . ieee: M. Erbar and J. Maas, “Gradient flow structures for discrete porous medium equations,” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4. Southwest Missouri State University, pp. 1355–1374, 2014. ista: Erbar M, Maas J. 2014. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 34(4), 1355–1374. mla: Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4, Southwest Missouri State University, 2014, pp. 1355–74, doi:10.3934/dcds.2014.34.1355  . short: M. Erbar, J. Maas, Discrete and Continuous Dynamical Systems- Series A 34 (2014) 1355–1374. date_created: 2018-12-11T11:55:54Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:55:30Z day: '01' doi: '10.3934/dcds.2014.34.1355 ' extern: 1 intvolume: ' 34' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1212.1129 month: '04' oa: 1 page: 1355 - 1374 publication: Discrete and Continuous Dynamical Systems- Series A publication_status: published publisher: Southwest Missouri State University publist_id: '4903' quality_controlled: 0 status: public title: Gradient flow structures for discrete porous medium equations type: journal_article volume: 34 year: '2014' ... --- _id: '2140' abstract: - lang: eng text: We propose a technique for engineering momentum-dependent dissipation in Bose-Einstein condensates with non-local interactions. The scheme relies on the use of momentum-dependent dark-states in close analogy to velocity-selective coherent population trapping. During the short-time dissipative dynamics, the system is driven into a particular finite-momentum phonon mode, which in real space corresponds to an ordered structure with non-local density-density correlations. Dissipation-induced ordering can be observed and studied in present-day experiments using cold atoms with dipole-dipole or off-resonant Rydberg interactions. Due to its dissipative nature, the ordering does not require artificial breaking of translational symmetry by an opticallattice or harmonic trap. This opens up a perspective of direct cooling of quantum gases into strongly-interacting phases. acknowledgement: This work was supported by NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory as well as the Harvard Quantum Optics Center. article_number: '070401' author: - first_name: Johannes full_name: Otterbach, Johannes last_name: Otterbach - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Otterbach J, Lemeshko M. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 2014;113(7). doi:10.1103/PhysRevLett.113.070401 apa: Otterbach, J., & Lemeshko, M. (2014). Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.070401 chicago: Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.070401. ieee: J. Otterbach and M. Lemeshko, “Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates,” Physical Review Letters, vol. 113, no. 7. American Physical Society, 2014. ista: Otterbach J, Lemeshko M. 2014. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 113(7), 070401. mla: Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters, vol. 113, no. 7, 070401, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.070401. short: J. Otterbach, M. Lemeshko, Physical Review Letters 113 (2014). date_created: 2018-12-11T11:55:56Z date_published: 2014-08-11T00:00:00Z date_updated: 2021-01-12T06:55:33Z day: '11' doi: 10.1103/PhysRevLett.113.070401 extern: '1' intvolume: ' 113' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1308.5905 month: '08' oa: 1 oa_version: Submitted Version publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '4884' status: public title: Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2014' ... --- _id: '2153' abstract: - lang: eng text: 'We define a simple, explicit map sending a morphism f : M → N of pointwise finite dimensional persistence modules to a matching between the barcodes of M and N. Our main result is that, in a precise sense, the quality of this matching is tightly controlled by the lengths of the longest intervals in the barcodes of ker f and coker f . As an immediate corollary, we obtain a new proof of the algebraic stability theorem for persistence barcodes [5, 9], a fundamental result in the theory of persistent homology. In contrast to previous proofs, ours shows explicitly how a δ-interleaving morphism between two persistence modules induces a δ-matching between the barcodes of the two modules. Our main result also specializes to a structure theorem for submodules and quotients of persistence modules. Copyright is held by the owner/author(s).' author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Michael full_name: Lesnick, Michael last_name: Lesnick citation: ama: 'Bauer U, Lesnick M. Induced matchings of barcodes and the algebraic stability of persistence. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:355-364. doi:10.1145/2582112.2582168' apa: 'Bauer, U., & Lesnick, M. (2014). Induced matchings of barcodes and the algebraic stability of persistence. In Proceedings of the Annual Symposium on Computational Geometry (pp. 355–364). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582168' chicago: Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” In Proceedings of the Annual Symposium on Computational Geometry, 355–64. ACM, 2014. https://doi.org/10.1145/2582112.2582168. ieee: U. Bauer and M. Lesnick, “Induced matchings of barcodes and the algebraic stability of persistence,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 355–364. ista: 'Bauer U, Lesnick M. 2014. Induced matchings of barcodes and the algebraic stability of persistence. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 355–364.' mla: Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–64, doi:10.1145/2582112.2582168. short: U. Bauer, M. Lesnick, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–364. conference: end_date: 2014-06-11 location: Kyoto, Japan name: 'SoCG: Symposium on Computational Geometry' start_date: 2014-06-08 date_created: 2018-12-11T11:56:01Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:55:38Z day: '01' department: - _id: HeEd doi: 10.1145/2582112.2582168 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1311.3681 month: '06' oa: 1 oa_version: Submitted Version page: 355 - 364 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Proceedings of the Annual Symposium on Computational Geometry publication_status: published publisher: ACM publist_id: '4853' quality_controlled: '1' scopus_import: 1 status: public title: Induced matchings of barcodes and the algebraic stability of persistence type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2154' abstract: - lang: eng text: A result of Boros and Füredi (d = 2) and of Bárány (arbitrary d) asserts that for every d there exists cd > 0 such that for every n-point set P ⊂ ℝd, some point of ℝd is covered by at least (Formula presented.) of the d-simplices spanned by the points of P. The largest possible value of cd has been the subject of ongoing research. Recently Gromov improved the existing lower bounds considerably by introducing a new, topological proof method. We provide an exposition of the combinatorial component of Gromov's approach, in terms accessible to combinatorialists and discrete geometers, and we investigate the limits of his method. In particular, we give tighter bounds on the cofilling profiles for the (n - 1)-simplex. These bounds yield a minor improvement over Gromov's lower bounds on cd for large d, but they also show that the room for further improvement through the cofilling profiles alone is quite small. We also prove a slightly better lower bound for c3 by an approach using an additional structure besides the cofilling profiles. We formulate a combinatorial extremal problem whose solution might perhaps lead to a tight lower bound for cd. acknowledgement: Swiss National Science Foundation (SNF 200021-125309, 200020-138230, 200020-12507) author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Matoušek J, Wagner U. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 2014;52(1):1-33. doi:10.1007/s00454-014-9584-7 apa: Matoušek, J., & Wagner, U. (2014). On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9584-7 chicago: Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9584-7. ieee: J. Matoušek and U. Wagner, “On Gromov’s method of selecting heavily covered points,” Discrete & Computational Geometry, vol. 52, no. 1. Springer, pp. 1–33, 2014. ista: Matoušek J, Wagner U. 2014. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 52(1), 1–33. mla: Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry, vol. 52, no. 1, Springer, 2014, pp. 1–33, doi:10.1007/s00454-014-9584-7. short: J. Matoušek, U. Wagner, Discrete & Computational Geometry 52 (2014) 1–33. date_created: 2018-12-11T11:56:01Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:55:38Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-014-9584-7 intvolume: ' 52' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1102.3515 month: '07' oa: 1 oa_version: Submitted Version page: 1 - 33 project: - _id: 25FA3206-B435-11E9-9278-68D0E5697425 grant_number: PP00P2_138948 name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics' publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '4852' quality_controlled: '1' scopus_import: 1 status: public title: On Gromov's method of selecting heavily covered points type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2014' ... --- _id: '2156' abstract: - lang: eng text: We propose a metric for Reeb graphs, called the functional distortion distance. Under this distance, the Reeb graph is stable against small changes of input functions. At the same time, it remains discriminative at differentiating input functions. In particular, the main result is that the functional distortion distance between two Reeb graphs is bounded from below by the bottleneck distance between both the ordinary and extended persistence diagrams for appropriate dimensions. As an application of our results, we analyze a natural simplification scheme for Reeb graphs, and show that persistent features in Reeb graph remains persistent under simplification. Understanding the stability of important features of the Reeb graph under simplification is an interesting problem on its own right, and critical to the practical usage of Reeb graphs. Copyright is held by the owner/author(s). acknowledgement: National Science Foundation under grants CCF-1319406, CCF-1116258. author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Xiaoyin full_name: Ge, Xiaoyin last_name: Ge - first_name: Yusu full_name: Wang, Yusu last_name: Wang citation: ama: 'Bauer U, Ge X, Wang Y. Measuring distance between Reeb graphs. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:464-473. doi:10.1145/2582112.2582169' apa: 'Bauer, U., Ge, X., & Wang, Y. (2014). Measuring distance between Reeb graphs. In Proceedings of the Annual Symposium on Computational Geometry (pp. 464–473). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582169' chicago: Bauer, Ulrich, Xiaoyin Ge, and Yusu Wang. “Measuring Distance between Reeb Graphs.” In Proceedings of the Annual Symposium on Computational Geometry, 464–73. ACM, 2014. https://doi.org/10.1145/2582112.2582169. ieee: U. Bauer, X. Ge, and Y. Wang, “Measuring distance between Reeb graphs,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 464–473. ista: 'Bauer U, Ge X, Wang Y. 2014. Measuring distance between Reeb graphs. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 464–473.' mla: Bauer, Ulrich, et al. “Measuring Distance between Reeb Graphs.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–73, doi:10.1145/2582112.2582169. short: U. Bauer, X. Ge, Y. Wang, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–473. conference: end_date: 2014-06-11 location: Kyoto, Japan name: 'SoCG: Symposium on Computational Geometry' start_date: 2014-06-08 date_created: 2018-12-11T11:56:02Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:55:39Z day: '01' department: - _id: HeEd doi: 10.1145/2582112.2582169 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.2839 month: '06' oa: 1 oa_version: Submitted Version page: 464 - 473 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Proceedings of the Annual Symposium on Computational Geometry publication_status: published publisher: ACM publist_id: '4850' quality_controlled: '1' scopus_import: 1 status: public title: Measuring distance between Reeb graphs type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2155' abstract: - lang: eng text: Given a finite set of points in Rn and a positive radius, we study the Čech, Delaunay-Čech, alpha, and wrap complexes as instances of a generalized discrete Morse theory. We prove that the latter three complexes are simple-homotopy equivalent. Our results have applications in topological data analysis and in the reconstruction of shapes from sampled data. Copyright is held by the owner/author(s). acknowledgement: This research is partially supported by ESF under the ACAT Research Network Programme, and by the Russian Government under mega project 11.G34.31.0053 author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Bauer U, Edelsbrunner H. The morse theory of Čech and Delaunay filtrations. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:484-490. doi:10.1145/2582112.2582167' apa: 'Bauer, U., & Edelsbrunner, H. (2014). The morse theory of Čech and Delaunay filtrations. In Proceedings of the Annual Symposium on Computational Geometry (pp. 484–490). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582167' chicago: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” In Proceedings of the Annual Symposium on Computational Geometry, 484–90. ACM, 2014. https://doi.org/10.1145/2582112.2582167. ieee: U. Bauer and H. Edelsbrunner, “The morse theory of Čech and Delaunay filtrations,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 484–490. ista: 'Bauer U, Edelsbrunner H. 2014. The morse theory of Čech and Delaunay filtrations. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 484–490.' mla: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–90, doi:10.1145/2582112.2582167. short: U. Bauer, H. Edelsbrunner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–490. conference: end_date: 2014-06-11 location: Kyoto, Japan name: 'SoCG: Symposium on Computational Geometry' start_date: 2014-06-08 date_created: 2018-12-11T11:56:01Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:55:38Z day: '01' department: - _id: HeEd doi: 10.1145/2582112.2582167 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1312.1231 month: '06' oa: 1 oa_version: Submitted Version page: 484 - 490 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Proceedings of the Annual Symposium on Computational Geometry publication_status: published publisher: ACM publist_id: '4851' quality_controlled: '1' scopus_import: 1 status: public title: The morse theory of Čech and Delaunay filtrations type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2158' abstract: - lang: eng text: Directional guidance of migrating cells is relatively well explored in the reductionist setting of cell culture experiments. Here spatial gradients of chemical cues as well as gradients of mechanical substrate characteristics prove sufficient to attract single cells as well as their collectives. How such gradients present and act in the context of an organism is far less clear. Here we review recent advances in understanding how guidance cues emerge and operate in the physiological context. acknowledgement: This effort was supported by the Intramural Research Program of the Center for Cancer Research, NCI, National Institutes of Health and the European Research Council (ERC). author: - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Carole full_name: Parent, Carole last_name: Parent citation: ama: Majumdar R, Sixt MK, Parent C. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 2014;30(1):33-40. doi:10.1016/j.ceb.2014.05.010 apa: Majumdar, R., Sixt, M. K., & Parent, C. (2014). New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2014.05.010 chicago: Majumdar, Ritankar, Michael K Sixt, and Carole Parent. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology. Elsevier, 2014. https://doi.org/10.1016/j.ceb.2014.05.010. ieee: R. Majumdar, M. K. Sixt, and C. Parent, “New paradigms in the establishment and maintenance of gradients during directed cell migration,” Current Opinion in Cell Biology, vol. 30, no. 1. Elsevier, pp. 33–40, 2014. ista: Majumdar R, Sixt MK, Parent C. 2014. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 30(1), 33–40. mla: Majumdar, Ritankar, et al. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology, vol. 30, no. 1, Elsevier, 2014, pp. 33–40, doi:10.1016/j.ceb.2014.05.010. short: R. Majumdar, M.K. Sixt, C. Parent, Current Opinion in Cell Biology 30 (2014) 33–40. date_created: 2018-12-11T11:56:03Z date_published: 2014-10-01T00:00:00Z date_updated: 2021-01-12T06:55:40Z day: '01' department: - _id: MiSi doi: 10.1016/j.ceb.2014.05.010 external_id: pmid: - '24959970' intvolume: ' 30' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177954/ month: '10' oa: 1 oa_version: Submitted Version page: 33 - 40 pmid: 1 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '4848' quality_controlled: '1' scopus_import: 1 status: public title: New paradigms in the establishment and maintenance of gradients during directed cell migration type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2014' ... --- _id: '2165' abstract: - lang: eng text: 'In machine learning, the domain adaptation problem arrives when the test (tar-get) and the train (source) data are generated from different distributions. A key applied issue is thus the design of algorithms able to generalize on a new distribution, for which we have no label information. We focus on learning classification models defined as a weighted majority vote over a set of real-valued functions. In this context, Germain et al. (2013) have shown that a measure of disagreement between these functions is crucial to control. The core of this measure is a theoretical bound—the C-bound (Lacasse et al., 2007)—which involves the disagreement and leads to a well performing majority vote learn-ing algorithm in usual non-adaptative supervised setting: MinCq. In this work,we propose a framework to extend MinCq to a domain adaptation scenario.This procedure takes advantage of the recent perturbed variation divergence between distributions proposed by Harel and Mannor (2012). Justified by a theoretical bound on the target risk of the vote, we provide to MinCq a tar-get sample labeled thanks to a perturbed variation-based self-labeling focused on the regions where the source and target marginals appear similar. We also study the influence of our self-labeling, from which we deduce an original process for tuning the hyperparameters. Finally, our framework called PV-MinCq shows very promising results on a rotation and translation synthetic problem.' author: - first_name: Emilie full_name: Morvant, Emilie id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87 last_name: Morvant orcid: 0000-0002-8301-7240 citation: ama: Morvant E. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 2014;51:37-43. doi:10.1016/j.patrec.2014.08.013 apa: Morvant, E. (2014). Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2014.08.013 chicago: Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters. Elsevier, 2014. https://doi.org/10.1016/j.patrec.2014.08.013. ieee: E. Morvant, “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling,” Pattern Recognition Letters, vol. 51. Elsevier, pp. 37–43, 2014. ista: Morvant E. 2014. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 51, 37–43. mla: Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters, vol. 51, Elsevier, 2014, pp. 37–43, doi:10.1016/j.patrec.2014.08.013. short: E. Morvant, Pattern Recognition Letters 51 (2014) 37–43. date_created: 2018-12-11T11:56:05Z date_published: 2014-10-01T00:00:00Z date_updated: 2021-01-12T06:55:43Z day: '01' doi: 10.1016/j.patrec.2014.08.013 ec_funded: 1 extern: '1' intvolume: ' 51' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.0334 month: '10' oa: 1 oa_version: Submitted Version page: 37-43 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: Pattern Recognition Letters publication_status: published publisher: Elsevier publist_id: '4819' quality_controlled: '1' status: public title: Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2014' ... --- _id: '2164' abstract: - lang: eng text: 'Neuronal ectopia, such as granule cell dispersion (GCD) in temporal lobe epilepsy (TLE), has been assumed to result from a migration defect during development. Indeed, recent studies reported that aberrant migration of neonatal-generated dentate granule cells (GCs) increased the risk to develop epilepsy later in life. On the contrary, in the present study, we show that fully differentiated GCs become motile following the induction of epileptiform activity, resulting in GCD. Hippocampal slice cultures from transgenic mice expressing green fluorescent protein in differentiated, but not in newly generated GCs, were incubated with the glutamate receptor agonist kainate (KA), which induced GC burst activity and GCD. Using real-time microscopy, we observed that KA-exposed, differentiated GCs translocated their cell bodies and changed their dendritic organization. As found in human TLE, KA application was associated with decreased expression of the extracellular matrix protein Reelin, particularly in hilar interneurons. Together these findings suggest that KA-induced motility of differentiated GCs contributes to the development of GCD and establish slice cultures as a model to study neuronal changes induced by epileptiform activity. ' author: - first_name: Xuejun full_name: Chai, Xuejun last_name: Chai - first_name: Gert full_name: Münzner, Gert last_name: Münzner - first_name: Shanting full_name: Zhao, Shanting last_name: Zhao - first_name: Stefanie full_name: Tinnes, Stefanie last_name: Tinnes - first_name: Janina full_name: Kowalski, Janina id: 3F3CA136-F248-11E8-B48F-1D18A9856A87 last_name: Kowalski - first_name: Ute full_name: Häussler, Ute last_name: Häussler - first_name: Christina full_name: Young, Christina last_name: Young - first_name: Carola full_name: Haas, Carola last_name: Haas - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher citation: ama: Chai X, Münzner G, Zhao S, et al. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 2014;24(8):2130-2140. doi:10.1093/cercor/bht067 apa: Chai, X., Münzner, G., Zhao, S., Tinnes, S., Kowalski, J., Häussler, U., … Frotscher, M. (2014). Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bht067 chicago: Chai, Xuejun, Gert Münzner, Shanting Zhao, Stefanie Tinnes, Janina Kowalski, Ute Häussler, Christina Young, Carola Haas, and Michael Frotscher. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex. Oxford University Press, 2014. https://doi.org/10.1093/cercor/bht067. ieee: X. Chai et al., “Epilepsy-induced motility of differentiated neurons,” Cerebral Cortex, vol. 24, no. 8. Oxford University Press, pp. 2130–2140, 2014. ista: Chai X, Münzner G, Zhao S, Tinnes S, Kowalski J, Häussler U, Young C, Haas C, Frotscher M. 2014. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 24(8), 2130–2140. mla: Chai, Xuejun, et al. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex, vol. 24, no. 8, Oxford University Press, 2014, pp. 2130–40, doi:10.1093/cercor/bht067. short: X. Chai, G. Münzner, S. Zhao, S. Tinnes, J. Kowalski, U. Häussler, C. Young, C. Haas, M. Frotscher, Cerebral Cortex 24 (2014) 2130–2140. date_created: 2018-12-11T11:56:04Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T06:55:43Z day: '01' department: - _id: PeJo doi: 10.1093/cercor/bht067 intvolume: ' 24' issue: '8' language: - iso: eng month: '08' oa_version: None page: 2130 - 2140 publication: Cerebral Cortex publication_status: published publisher: Oxford University Press publist_id: '4820' quality_controlled: '1' scopus_import: 1 status: public title: Epilepsy-induced motility of differentiated neurons type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '2168' abstract: - lang: eng text: Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail. author: - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - 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: 'Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 2014;95:13-23. doi:10.1016/j.tpb.2014.05.001' apa: 'Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001' chicago: 'Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001.' ieee: 'J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” Theoretical Population Biology, vol. 95. Academic Press, pp. 13–23, 2014.' ista: 'Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.' mla: 'Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95, Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001.' short: J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23. date_created: 2018-12-11T11:56:06Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T06:55:44Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tpb.2014.05.001 ec_funded: 1 file: - access_level: open_access checksum: 979d7a8034e9df198f068f0d251f31bd content_type: application/pdf creator: system date_created: 2018-12-12T10:10:49Z date_updated: 2020-07-14T12:45:31Z file_id: '4839' file_name: IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf file_size: 569005 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' intvolume: ' 95' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 13 - 23 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '4816' pubrep_id: '391' quality_controlled: '1' scopus_import: 1 status: public title: 'Coalescent simulation in continuous space: Algorithms for large neighbourhood size' 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: 95 year: '2014' ... --- _id: '2169' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111 apa: Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1410107111 chicago: Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410107111. ieee: N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014. ista: Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399. mla: Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111. short: N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399. date_created: 2018-12-11T11:56:07Z date_published: 2014-07-22T00:00:00Z date_updated: 2021-01-12T06:55:45Z day: '22' department: - _id: NiBa doi: 10.1073/pnas.1410107111 intvolume: ' 111' issue: '29' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/ month: '07' oa: 1 oa_version: Submitted Version page: 10398 - 10399 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '4815' quality_controlled: '1' scopus_import: 1 status: public title: Diverse forms of selection in evolution and computer science type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '2171' abstract: - lang: eng text: We present LS-CRF, a new method for training cyclic Conditional Random Fields (CRFs) from large datasets that is inspired by classical closed-form expressions for the maximum likelihood parameters of a generative graphical model with tree topology. Training a CRF with LS-CRF requires only solving a set of independent regression problems, each of which can be solved efficiently in closed form or by an iterative solver. This makes LS-CRF orders of magnitude faster than classical CRF training based on probabilistic inference, and at the same time more flexible and easier to implement than other approximate techniques, such as pseudolikelihood or piecewise training. We apply LS-CRF to the task of semantic image segmentation, showing that it achieves on par accuracy to other training techniques at higher speed, thereby allowing efficient CRF training from very large training sets. For example, training a linearly parameterized pairwise CRF on 150,000 images requires less than one hour on a modern workstation. alternative_title: - LNCS author: - first_name: Alexander full_name: Kolesnikov, Alexander id: 2D157DB6-F248-11E8-B48F-1D18A9856A87 last_name: Kolesnikov - first_name: Matthieu full_name: Guillaumin, Matthieu last_name: Guillaumin - first_name: Vittorio full_name: Ferrari, Vittorio last_name: Ferrari - 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, Guillaumin M, Ferrari V, Lampert C. Closed-form approximate CRF training for scalable image segmentation. In: Fleet D, Pajdla T, Schiele B, Tuytelaars T, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8691. Springer; 2014:550-565. doi:10.1007/978-3-319-10578-9_36' apa: 'Kolesnikov, A., Guillaumin, M., Ferrari, V., & Lampert, C. (2014). Closed-form approximate CRF training for scalable image segmentation. In D. Fleet, T. Pajdla, B. Schiele, & T. Tuytelaars (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8691, pp. 550–565). Zurich, Switzerland: Springer. https://doi.org/10.1007/978-3-319-10578-9_36' chicago: Kolesnikov, Alexander, Matthieu Guillaumin, Vittorio Ferrari, and Christoph Lampert. “Closed-Form Approximate CRF Training for Scalable Image Segmentation.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by David Fleet, Tomas Pajdla, Bernt Schiele, and Tinne Tuytelaars, 8691:550–65. Springer, 2014. https://doi.org/10.1007/978-3-319-10578-9_36. ieee: A. Kolesnikov, M. Guillaumin, V. Ferrari, and C. Lampert, “Closed-form approximate CRF training for scalable image segmentation,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Zurich, Switzerland, 2014, vol. 8691, no. PART 3, pp. 550–565. ista: 'Kolesnikov A, Guillaumin M, Ferrari V, Lampert C. 2014. Closed-form approximate CRF training for scalable image segmentation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ECCV: European Conference on Computer Vision, LNCS, vol. 8691, 550–565.' mla: Kolesnikov, Alexander, et al. “Closed-Form Approximate CRF Training for Scalable Image Segmentation.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by David Fleet et al., vol. 8691, no. PART 3, Springer, 2014, pp. 550–65, doi:10.1007/978-3-319-10578-9_36. short: A. Kolesnikov, M. Guillaumin, V. Ferrari, C. Lampert, in:, D. Fleet, T. Pajdla, B. Schiele, T. Tuytelaars (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 550–565. conference: end_date: 2014-09-12 location: Zurich, Switzerland name: 'ECCV: European Conference on Computer Vision' start_date: 2014-09-06 date_created: 2018-12-11T11:56:07Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:55:46Z day: '01' department: - _id: ChLa doi: 10.1007/978-3-319-10578-9_36 ec_funded: 1 editor: - first_name: David full_name: Fleet, David last_name: Fleet - first_name: Tomas full_name: Pajdla, Tomas last_name: Pajdla - first_name: Bernt full_name: Schiele, Bernt last_name: Schiele - first_name: Tinne full_name: Tuytelaars, Tinne last_name: Tuytelaars intvolume: ' 8691' issue: PART 3 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1403.7057 month: '09' oa: 1 oa_version: Submitted Version page: 550 - 565 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_status: published publisher: Springer publist_id: '4813' quality_controlled: '1' scopus_import: 1 status: public title: Closed-form approximate CRF training for scalable image segmentation type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8691 year: '2014' ... --- _id: '2173' abstract: - lang: eng text: "In this work we introduce a new approach to co-classification, i.e. the task of jointly classifying multiple, otherwise independent, data samples. The method we present, named CoConut, is based on the idea of adding a regularizer in the label space to encode certain priors on the resulting labelings. A regularizer that encourages labelings that are smooth across the test set, for instance, can be seen as a test-time variant of the cluster assumption, which has been proven useful at training time in semi-supervised learning. A regularizer that introduces a preference for certain class proportions can be regarded as a prior distribution on the class labels. CoConut can build on existing classifiers without making any assumptions on how they were obtained and without the need to re-train them. The use of a regularizer adds a new level of flexibility. It allows the integration of potentially new information at test time, even in other modalities than what the classifiers were trained on. We evaluate our framework on six datasets, reporting a clear performance gain in classification accuracy compared to the standard classification setup that predicts labels for each test sample separately.\r\n" author: - first_name: Sameh full_name: Khamis, Sameh last_name: Khamis - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Khamis S, Lampert C. CoConut: Co-classification with output space regularization. In: Proceedings of the British Machine Vision Conference 2014. BMVA Press; 2014.' apa: 'Khamis, S., & Lampert, C. (2014). CoConut: Co-classification with output space regularization. In Proceedings of the British Machine Vision Conference 2014. Nottingham, UK: BMVA Press.' chicago: 'Khamis, Sameh, and Christoph Lampert. “CoConut: Co-Classification with Output Space Regularization.” In Proceedings of the British Machine Vision Conference 2014. BMVA Press, 2014.' ieee: 'S. Khamis and C. Lampert, “CoConut: Co-classification with output space regularization,” in Proceedings of the British Machine Vision Conference 2014, Nottingham, UK, 2014.' ista: 'Khamis S, Lampert C. 2014. CoConut: Co-classification with output space regularization. Proceedings of the British Machine Vision Conference 2014. BMVC: British Machine Vision Conference.' mla: 'Khamis, Sameh, and Christoph Lampert. “CoConut: Co-Classification with Output Space Regularization.” Proceedings of the British Machine Vision Conference 2014, BMVA Press, 2014.' short: S. Khamis, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2014, BMVA Press, 2014. conference: end_date: 2014-09-05 location: Nottingham, UK name: 'BMVC: British Machine Vision Conference' start_date: 2014-09-01 date_created: 2018-12-11T11:56:08Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:55:46Z day: '01' ddc: - '000' department: - _id: ChLa ec_funded: 1 file: - access_level: open_access checksum: c4c6d3efdb8ee648faf3e76849839ce2 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:23Z date_updated: 2020-07-14T12:45:31Z file_id: '4683' file_name: IST-2016-490-v1+1_khamis-bmvc2014.pdf file_size: 408172 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: Proceedings of the British Machine Vision Conference 2014 publication_status: published publisher: BMVA Press publist_id: '4811' pubrep_id: '490' quality_controlled: '1' scopus_import: 1 status: public title: 'CoConut: Co-classification with output space regularization' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2172' abstract: - lang: eng text: Fisher Kernels and Deep Learning were two developments with significant impact on large-scale object categorization in the last years. Both approaches were shown to achieve state-of-the-art results on large-scale object categorization datasets, such as ImageNet. Conceptually, however, they are perceived as very different and it is not uncommon for heated debates to spring up when advocates of both paradigms meet at conferences or workshops. In this work, we emphasize the similarities between both architectures rather than their differences and we argue that such a unified view allows us to transfer ideas from one domain to the other. As a concrete example we introduce a method for learning a support vector machine classifier with Fisher kernel at the same time as a task-specific data representation. We reinterpret the setting as a multi-layer feed forward network. Its final layer is the classifier, parameterized by a weight vector, and the two previous layers compute Fisher vectors, parameterized by the coefficients of a Gaussian mixture model. We introduce a gradient descent based learning algorithm that, in contrast to other feature learning techniques, is not just derived from intuition or biological analogy, but has a theoretical justification in the framework of statistical learning theory. Our experiments show that the new training procedure leads to significant improvements in classification accuracy while preserving the modularity and geometric interpretability of a support vector machine setup. author: - first_name: Vladyslav full_name: Sydorov, Vladyslav last_name: Sydorov - first_name: Mayu full_name: Sakurada, Mayu last_name: Sakurada - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Sydorov V, Sakurada M, Lampert C. Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE; 2014:1402-1409. doi:10.1109/CVPR.2014.182' apa: 'Sydorov, V., Sakurada, M., & Lampert, C. (2014). Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (pp. 1402–1409). Columbus, USA: IEEE. https://doi.org/10.1109/CVPR.2014.182' chicago: Sydorov, Vladyslav, Mayu Sakurada, and Christoph Lampert. “Deep Fisher Kernels – End to End Learning of the Fisher Kernel GMM Parameters.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1402–9. IEEE, 2014. https://doi.org/10.1109/CVPR.2014.182. ieee: V. Sydorov, M. Sakurada, and C. Lampert, “Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Columbus, USA, 2014, pp. 1402–1409. ista: 'Sydorov V, Sakurada M, Lampert C. 2014. Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Computer Vision and Pattern Recognition, 1402–1409.' mla: Sydorov, Vladyslav, et al. “Deep Fisher Kernels – End to End Learning of the Fisher Kernel GMM Parameters.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2014, pp. 1402–09, doi:10.1109/CVPR.2014.182. short: V. Sydorov, M. Sakurada, C. Lampert, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2014, pp. 1402–1409. conference: end_date: 2014-06-28 location: Columbus, USA name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2014-06-23 date_created: 2018-12-11T11:56:08Z date_published: 2014-09-24T00:00:00Z date_updated: 2021-01-12T06:55:46Z day: '24' department: - _id: ChLa doi: 10.1109/CVPR.2014.182 ec_funded: 1 language: - iso: eng month: '09' oa_version: None page: 1402 - 1409 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition publication_status: published publisher: IEEE publist_id: '4812' quality_controlled: '1' scopus_import: 1 status: public title: Deep Fisher Kernels – End to end learning of the Fisher Kernel GMM parameters type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2174' abstract: - lang: eng text: 'When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The inpplayfi between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find p the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value.' author: - first_name: Harold full_name: De Vladar, Harold last_name: De Vladar - 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: De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 2014;197(2):749-767. doi:10.1534/genetics.113.159111 apa: De Vladar, H., & Barton, N. H. (2014). Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.159111 chicago: De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.159111. ieee: H. De Vladar and N. H. Barton, “Stability and response of polygenic traits to stabilizing selection and mutation,” Genetics, vol. 197, no. 2. Genetics Society of America, pp. 749–767, 2014. ista: De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 197(2), 749–767. mla: De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics, vol. 197, no. 2, Genetics Society of America, 2014, pp. 749–67, doi:10.1534/genetics.113.159111. short: H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767. date_created: 2018-12-11T11:56:08Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:55:47Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.113.159111 ec_funded: 1 intvolume: ' 197' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.1017 month: '06' oa: 1 oa_version: Submitted Version page: 749 - 767 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '4809' quality_controlled: '1' scopus_import: 1 status: public title: Stability and response of polygenic traits to stabilizing selection and mutation type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 197 year: '2014' ... --- _id: '2179' abstract: - lang: eng text: We extend the proof of the local semicircle law for generalized Wigner matrices given in MR3068390 to the case when the matrix of variances has an eigenvalue -1. In particular, this result provides a short proof of the optimal local Marchenko-Pastur law at the hard edge (i.e. around zero) for sample covariance matrices X*X, where the variances of the entries of X may vary. author: - first_name: Oskari H full_name: Ajanki, Oskari H id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87 last_name: Ajanki - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Ajanki OH, Erdös L, Krüger TH. Local semicircle law with imprimitive variance matrix. Electronic Communications in Probability. 2014;19. doi:10.1214/ECP.v19-3121 apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2014). Local semicircle law with imprimitive variance matrix. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v19-3121 chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Semicircle Law with Imprimitive Variance Matrix.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2014. https://doi.org/10.1214/ECP.v19-3121. ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local semicircle law with imprimitive variance matrix,” Electronic Communications in Probability, vol. 19. Institute of Mathematical Statistics, 2014. ista: Ajanki OH, Erdös L, Krüger TH. 2014. Local semicircle law with imprimitive variance matrix. Electronic Communications in Probability. 19. mla: Ajanki, Oskari H., et al. “Local Semicircle Law with Imprimitive Variance Matrix.” Electronic Communications in Probability, vol. 19, Institute of Mathematical Statistics, 2014, doi:10.1214/ECP.v19-3121. short: O.H. Ajanki, L. Erdös, T.H. Krüger, Electronic Communications in Probability 19 (2014). date_created: 2018-12-11T11:56:10Z date_published: 2014-06-09T00:00:00Z date_updated: 2021-01-12T06:55:48Z day: '09' ddc: - '570' department: - _id: LaEr doi: 10.1214/ECP.v19-3121 file: - access_level: open_access checksum: bd8a041c76d62fe820bf73ff13ce7d1b content_type: application/pdf creator: system date_created: 2018-12-12T10:09:06Z date_updated: 2020-07-14T12:45:31Z file_id: '4729' file_name: IST-2016-426-v1+1_3121-17518-1-PB.pdf file_size: 327322 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' intvolume: ' 19' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Electronic Communications in Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '4803' pubrep_id: '426' quality_controlled: '1' scopus_import: 1 status: public title: Local semicircle law with imprimitive variance matrix tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2014' ... --- _id: '2176' abstract: - lang: eng text: Electron microscopy (EM) allows for the simultaneous visualization of all tissue components at high resolution. However, the extent to which conventional aldehyde fixation and ethanol dehydration of the tissue alter the fine structure of cells and organelles, thereby preventing detection of subtle structural changes induced by an experiment, has remained an issue. Attempts have been made to rapidly freeze tissue to preserve native ultrastructure. Shock-freezing of living tissue under high pressure (high-pressure freezing, HPF) followed by cryosubstitution of the tissue water avoids aldehyde fixation and dehydration in ethanol; the tissue water is immobilized in â ̂1/450 ms, and a close-to-native fine structure of cells, organelles and molecules is preserved. Here we describe a protocol for HPF that is useful to monitor ultrastructural changes associated with functional changes at synapses in the brain but can be applied to many other tissues as well. The procedure requires a high-pressure freezer and takes a minimum of 7 d but can be paused at several points. author: - first_name: Daniel full_name: Studer, Daniel last_name: Studer - first_name: Shanting full_name: Zhao, Shanting last_name: Zhao - first_name: Xuejun full_name: Chai, Xuejun last_name: Chai - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Werner full_name: Graber, Werner last_name: Graber - first_name: Sigrun full_name: Nestel, Sigrun last_name: Nestel - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher citation: ama: Studer D, Zhao S, Chai X, et al. Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue. Nature Protocols. 2014;9(6):1480-1495. doi:10.1038/nprot.2014.099 apa: Studer, D., Zhao, S., Chai, X., Jonas, P. M., Graber, W., Nestel, S., & Frotscher, M. (2014). Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2014.099 chicago: Studer, Daniel, Shanting Zhao, Xuejun Chai, Peter M Jonas, Werner Graber, Sigrun Nestel, and Michael Frotscher. “Capture of Activity-Induced Ultrastructural Changes at Synapses by High-Pressure Freezing of Brain Tissue.” Nature Protocols. Nature Publishing Group, 2014. https://doi.org/10.1038/nprot.2014.099. ieee: D. Studer et al., “Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue,” Nature Protocols, vol. 9, no. 6. Nature Publishing Group, pp. 1480–1495, 2014. ista: Studer D, Zhao S, Chai X, Jonas PM, Graber W, Nestel S, Frotscher M. 2014. Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue. Nature Protocols. 9(6), 1480–1495. mla: Studer, Daniel, et al. “Capture of Activity-Induced Ultrastructural Changes at Synapses by High-Pressure Freezing of Brain Tissue.” Nature Protocols, vol. 9, no. 6, Nature Publishing Group, 2014, pp. 1480–95, doi:10.1038/nprot.2014.099. short: D. Studer, S. Zhao, X. Chai, P.M. Jonas, W. Graber, S. Nestel, M. Frotscher, Nature Protocols 9 (2014) 1480–1495. date_created: 2018-12-11T11:56:09Z date_published: 2014-05-29T00:00:00Z date_updated: 2021-01-12T06:55:47Z day: '29' department: - _id: PeJo doi: 10.1038/nprot.2014.099 intvolume: ' 9' issue: '6' language: - iso: eng month: '05' oa_version: None page: 1480 - 1495 project: - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '4807' quality_controlled: '1' scopus_import: 1 status: public title: Capture of activity-induced ultrastructural changes at synapses by high-pressure freezing of brain tissue type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '2178' abstract: - lang: eng text: We consider the three-state toric homogeneous Markov chain model (THMC) without loops and initial parameters. At time T, the size of the design matrix is 6 × 3 · 2T-1 and the convex hull of its columns is the model polytope. We study the behavior of this polytope for T ≥ 3 and we show that it is defined by 24 facets for all T ≥ 5. Moreover, we give a complete description of these facets. From this, we deduce that the toric ideal associated with the design matrix is generated by binomials of degree at most 6. Our proof is based on a result due to Sturmfels, who gave a bound on the degree of the generators of a toric ideal, provided the normality of the corresponding toric variety. In our setting, we established the normality of the toric variety associated to the THMC model by studying the geometric properties of the model polytope. acknowledgement: Research of Martín del Campo supported in part by NSF Grant DMS-915211. author: - first_name: David full_name: Haws, David last_name: Haws - first_name: Abraham full_name: Martin Del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin Del Campo Sanchez - first_name: Akimichi full_name: Takemura, Akimichi last_name: Takemura - first_name: Ruriko full_name: Yoshida, Ruriko last_name: Yoshida citation: ama: Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. Markov degree of the three-state toric homogeneous Markov chain model. Beitrage zur Algebra und Geometrie. 2014;55(1):161-188. doi:10.1007/s13366-013-0178-y apa: Haws, D., Martin del Campo Sanchez, A., Takemura, A., & Yoshida, R. (2014). Markov degree of the three-state toric homogeneous Markov chain model. Beitrage Zur Algebra Und Geometrie. Springer. https://doi.org/10.1007/s13366-013-0178-y chicago: Haws, David, Abraham Martin del Campo Sanchez, Akimichi Takemura, and Ruriko Yoshida. “Markov Degree of the Three-State Toric Homogeneous Markov Chain Model.” Beitrage Zur Algebra Und Geometrie. Springer, 2014. https://doi.org/10.1007/s13366-013-0178-y. ieee: D. Haws, A. Martin del Campo Sanchez, A. Takemura, and R. Yoshida, “Markov degree of the three-state toric homogeneous Markov chain model,” Beitrage zur Algebra und Geometrie, vol. 55, no. 1. Springer, pp. 161–188, 2014. ista: Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. 2014. Markov degree of the three-state toric homogeneous Markov chain model. Beitrage zur Algebra und Geometrie. 55(1), 161–188. mla: Haws, David, et al. “Markov Degree of the Three-State Toric Homogeneous Markov Chain Model.” Beitrage Zur Algebra Und Geometrie, vol. 55, no. 1, Springer, 2014, pp. 161–88, doi:10.1007/s13366-013-0178-y. short: D. Haws, A. Martin del Campo Sanchez, A. Takemura, R. Yoshida, Beitrage Zur Algebra Und Geometrie 55 (2014) 161–188. date_created: 2018-12-11T11:56:10Z date_published: 2014-03-01T00:00:00Z date_updated: 2021-01-12T06:55:48Z day: '01' department: - _id: CaUh doi: 10.1007/s13366-013-0178-y intvolume: ' 55' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1204.3070 month: '03' oa: 1 oa_version: Submitted Version page: 161 - 188 publication: Beitrage zur Algebra und Geometrie publication_status: published publisher: Springer publist_id: '4804' quality_controlled: '1' scopus_import: 1 status: public title: Markov degree of the three-state toric homogeneous Markov chain model type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '2177' abstract: - lang: eng text: We give evidence for the difficulty of computing Betti numbers of simplicial complexes over a finite field. We do this by reducing the rank computation for sparse matrices with to non-zero entries to computing Betti numbers of simplicial complexes consisting of at most a constant times to simplices. Together with the known reduction in the other direction, this implies that the two problems have the same computational complexity. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Salman full_name: Parsa, Salman id: 4BDBD4F2-F248-11E8-B48F-1D18A9856A87 last_name: Parsa citation: ama: 'Edelsbrunner H, Parsa S. On the computational complexity of betti numbers reductions from matrix rank. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SIAM; 2014:152-160. doi:10.1137/1.9781611973402.11' apa: 'Edelsbrunner, H., & Parsa, S. (2014). On the computational complexity of betti numbers reductions from matrix rank. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 152–160). Portland, USA: SIAM. https://doi.org/10.1137/1.9781611973402.11' chicago: Edelsbrunner, Herbert, and Salman Parsa. “On the Computational Complexity of Betti Numbers Reductions from Matrix Rank.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 152–60. SIAM, 2014. https://doi.org/10.1137/1.9781611973402.11. ieee: H. Edelsbrunner and S. Parsa, “On the computational complexity of betti numbers reductions from matrix rank,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Portland, USA, 2014, pp. 152–160. ista: 'Edelsbrunner H, Parsa S. 2014. On the computational complexity of betti numbers reductions from matrix rank. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 152–160.' mla: Edelsbrunner, Herbert, and Salman Parsa. “On the Computational Complexity of Betti Numbers Reductions from Matrix Rank.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2014, pp. 152–60, doi:10.1137/1.9781611973402.11. short: H. Edelsbrunner, S. Parsa, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2014, pp. 152–160. conference: end_date: 2014-01-07 location: Portland, USA name: 'SODA: Symposium on Discrete Algorithms' start_date: 2014-01-05 date_created: 2018-12-11T11:56:09Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:55:48Z day: '01' department: - _id: HeEd doi: 10.1137/1.9781611973402.11 language: - iso: eng month: '01' oa_version: None page: 152 - 160 publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms publication_status: published publisher: SIAM publist_id: '4805' quality_controlled: '1' scopus_import: 1 status: public title: On the computational complexity of betti numbers reductions from matrix rank type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2185' abstract: - lang: eng text: 'We revisit the classical problem of converting an imperfect source of randomness into a usable cryptographic key. Assume that we have some cryptographic application P that expects a uniformly random m-bit key R and ensures that the best attack (in some complexity class) against P(R) has success probability at most δ. Our goal is to design a key-derivation function (KDF) h that converts any random source X of min-entropy k into a sufficiently "good" key h(X), guaranteeing that P(h(X)) has comparable security δ′ which is ''close'' to δ. Seeded randomness extractors provide a generic way to solve this problem for all applications P, with resulting security δ′ = O(δ), provided that we start with entropy k ≥ m + 2 log (1/δ) - O(1). By a result of Radhakrishnan and Ta-Shma, this bound on k (called the "RT-bound") is also known to be tight in general. Unfortunately, in many situations the loss of 2 log (1/δ) bits of entropy is unacceptable. This motivates the study KDFs with less entropy waste by placing some restrictions on the source X or the application P. In this work we obtain the following new positive and negative results in this regard: - Efficient samplability of the source X does not help beat the RT-bound for general applications. This resolves the SRT (samplable RT) conjecture of Dachman-Soled et al. [DGKM12] in the affirmative, and also shows that the existence of computationally-secure extractors beating the RT-bound implies the existence of one-way functions. - We continue in the line of work initiated by Barak et al. [BDK+11] and construct new information-theoretic KDFs which beat the RT-bound for large but restricted classes of applications. Specifically, we design efficient KDFs that work for all unpredictability applications P (e.g., signatures, MACs, one-way functions, etc.) and can either: (1) extract all of the entropy k = m with a very modest security loss δ′ = O(δ·log (1/δ)), or alternatively, (2) achieve essentially optimal security δ′ = O(δ) with a very modest entropy loss k ≥ m + loglog (1/δ). In comparison, the best prior results from [BDK+11] for this class of applications would only guarantee δ′ = O(√δ) when k = m, and would need k ≥ m + log (1/δ) to get δ′ = O(δ). - The weaker bounds of [BDK+11] hold for a larger class of so-called "square- friendly" applications (which includes all unpredictability, but also some important indistinguishability, applications). Unfortunately, we show that these weaker bounds are tight for the larger class of applications. - We abstract out a clean, information-theoretic notion of (k,δ,δ′)- unpredictability extractors, which guarantee "induced" security δ′ for any δ-secure unpredictability application P, and characterize the parameters achievable for such unpredictability extractors. Of independent interest, we also relate this notion to the previously-known notion of (min-entropy) condensers, and improve the state-of-the-art parameters for such condensers.' alternative_title: - LNCS author: - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Dodis Y, Pietrzak KZ, Wichs D. Key derivation without entropy waste. In: Nguyen P, Oswald E, eds. Vol 8441. Springer; 2014:93-110. doi:10.1007/978-3-642-55220-5_6' apa: 'Dodis, Y., Pietrzak, K. Z., & Wichs, D. (2014). Key derivation without entropy waste. In P. Nguyen & E. Oswald (Eds.) (Vol. 8441, pp. 93–110). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Copenhagen, Denmark: Springer. https://doi.org/10.1007/978-3-642-55220-5_6' chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Daniel Wichs. “Key Derivation without Entropy Waste.” edited by Phong Nguyen and Elisabeth Oswald, 8441:93–110. Springer, 2014. https://doi.org/10.1007/978-3-642-55220-5_6. ieee: 'Y. Dodis, K. Z. Pietrzak, and D. Wichs, “Key derivation without entropy waste,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Copenhagen, Denmark, 2014, vol. 8441, pp. 93–110.' ista: 'Dodis Y, Pietrzak KZ, Wichs D. 2014. Key derivation without entropy waste. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 8441, 93–110.' mla: Dodis, Yevgeniy, et al. Key Derivation without Entropy Waste. Edited by Phong Nguyen and Elisabeth Oswald, vol. 8441, Springer, 2014, pp. 93–110, doi:10.1007/978-3-642-55220-5_6. short: Y. Dodis, K.Z. Pietrzak, D. Wichs, in:, P. Nguyen, E. Oswald (Eds.), Springer, 2014, pp. 93–110. conference: end_date: 2014-05-15 location: Copenhagen, Denmark name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2014-05-11 date_created: 2018-12-11T11:56:12Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:55:51Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-642-55220-5_6 editor: - first_name: Phong full_name: Nguyen, Phong last_name: Nguyen - first_name: Elisabeth full_name: Oswald, Elisabeth last_name: Oswald file: - access_level: open_access checksum: da1aa01221086083b23c92e547b48ff4 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:43Z date_updated: 2020-07-14T12:45:31Z file_id: '4705' file_name: IST-2016-680-v1+1_708.pdf file_size: 505389 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' intvolume: ' 8441' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 93 - 110 publication_status: published publisher: Springer publist_id: '4795' pubrep_id: '680' quality_controlled: '1' scopus_import: 1 status: public title: Key derivation without entropy waste type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8441 year: '2014' ... --- _id: '2180' abstract: - lang: eng text: Weighted majority votes allow one to combine the output of several classifiers or voters. MinCq is a recent algorithm for optimizing the weight of each voter based on the minimization of a theoretical bound over the risk of the vote with elegant PAC-Bayesian generalization guarantees. However, while it has demonstrated good performance when combining weak classifiers, MinCq cannot make use of the useful a priori knowledge that one may have when using a mixture of weak and strong voters. In this paper, we propose P-MinCq, an extension of MinCq that can incorporate such knowledge in the form of a constraint over the distribution of the weights, along with general proofs of convergence that stand in the sample compression setting for data-dependent voters. The approach is applied to a vote of k-NN classifiers with a specific modeling of the voters' performance. P-MinCq significantly outperforms the classic k-NN classifier, a symmetric NN and MinCq using the same voters. We show that it is also competitive with LMNN, a popular metric learning algorithm, and that combining both approaches further reduces the error. acknowledgement: 'This work was funded by the French project SoLSTiCe ANR-13-BS02-01 of the ANR. ' author: - first_name: Aurélien full_name: Bellet, Aurélien last_name: Bellet - first_name: Amaury full_name: Habrard, Amaury last_name: Habrard - first_name: Emilie full_name: Morvant, Emilie id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87 last_name: Morvant orcid: 0000-0002-8301-7240 - first_name: Marc full_name: Sebban, Marc last_name: Sebban citation: ama: Bellet A, Habrard A, Morvant E, Sebban M. Learning a priori constrained weighted majority votes. Machine Learning. 2014;97(1-2):129-154. doi:10.1007/s10994-014-5462-z apa: Bellet, A., Habrard, A., Morvant, E., & Sebban, M. (2014). Learning a priori constrained weighted majority votes. Machine Learning. Springer. https://doi.org/10.1007/s10994-014-5462-z chicago: Bellet, Aurélien, Amaury Habrard, Emilie Morvant, and Marc Sebban. “Learning a Priori Constrained Weighted Majority Votes.” Machine Learning. Springer, 2014. https://doi.org/10.1007/s10994-014-5462-z. ieee: A. Bellet, A. Habrard, E. Morvant, and M. Sebban, “Learning a priori constrained weighted majority votes,” Machine Learning, vol. 97, no. 1–2. Springer, pp. 129–154, 2014. ista: Bellet A, Habrard A, Morvant E, Sebban M. 2014. Learning a priori constrained weighted majority votes. Machine Learning. 97(1–2), 129–154. mla: Bellet, Aurélien, et al. “Learning a Priori Constrained Weighted Majority Votes.” Machine Learning, vol. 97, no. 1–2, Springer, 2014, pp. 129–54, doi:10.1007/s10994-014-5462-z. short: A. Bellet, A. Habrard, E. Morvant, M. Sebban, Machine Learning 97 (2014) 129–154. date_created: 2018-12-11T11:56:10Z date_published: 2014-10-01T00:00:00Z date_updated: 2021-01-12T06:55:49Z day: '01' department: - _id: ChLa doi: 10.1007/s10994-014-5462-z ec_funded: 1 intvolume: ' 97' issue: 1-2 language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01009578/document month: '10' oa: 1 oa_version: Submitted Version page: 129 - 154 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: Machine Learning publication_status: published publisher: Springer publist_id: '4802' quality_controlled: '1' scopus_import: 1 status: public title: Learning a priori constrained weighted majority votes type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2014' ... --- _id: '2184' abstract: - lang: eng text: 'Given topological spaces X,Y, a fundamental problem of algebraic topology is understanding the structure of all continuous maps X→ Y. We consider a computational version, where X,Y are given as finite simplicial complexes, and the goal is to compute [X,Y], that is, all homotopy classes of suchmaps.We solve this problem in the stable range, where for some d ≥ 2, we have dim X ≤ 2d-2 and Y is (d-1)-connected; in particular, Y can be the d-dimensional sphere Sd. The algorithm combines classical tools and ideas from homotopy theory (obstruction theory, Postnikov systems, and simplicial sets) with algorithmic tools from effective algebraic topology (locally effective simplicial sets and objects with effective homology). In contrast, [X,Y] is known to be uncomputable for general X,Y, since for X = S1 it includes a well known undecidable problem: testing triviality of the fundamental group of Y. In follow-up papers, the algorithm is shown to run in polynomial time for d fixed, and extended to other problems, such as the extension problem, where we are given a subspace A ⊂ X and a map A→ Y and ask whether it extends to a map X → Y, or computing the Z2-index-everything in the stable range. Outside the stable range, the extension problem is undecidable.' acknowledgement: The research by M. K. was supported by project GAUK 49209. The research by M. K. was also supported by project 1M0545 by the Ministry of Education of the Czech Republic and by Center of Excellence { Inst. for Theor. Comput. Sci., Prague (project P202/12/G061 of GACR). The research by U. W. was supported by the Swiss National Science Foundation (SNF Projects 200021-125309, 200020-138230, and PP00P2-138948). article_number: '17 ' author: - first_name: Martin full_name: Čadek, Martin last_name: Čadek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Francis full_name: Sergeraert, Francis last_name: Sergeraert - first_name: Lukáš full_name: Vokřínek, Lukáš last_name: Vokřínek - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. Computing all maps into a sphere. Journal of the ACM. 2014;61(3). doi:10.1145/2597629 apa: Čadek, M., Krcál, M., Matoušek, J., Sergeraert, F., Vokřínek, L., & Wagner, U. (2014). Computing all maps into a sphere. Journal of the ACM. ACM. https://doi.org/10.1145/2597629 chicago: Čadek, Martin, Marek Krcál, Jiří Matoušek, Francis Sergeraert, Lukáš Vokřínek, and Uli Wagner. “Computing All Maps into a Sphere.” Journal of the ACM. ACM, 2014. https://doi.org/10.1145/2597629. ieee: M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, and U. Wagner, “Computing all maps into a sphere,” Journal of the ACM, vol. 61, no. 3. ACM, 2014. ista: Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. 2014. Computing all maps into a sphere. Journal of the ACM. 61(3), 17. mla: Čadek, Martin, et al. “Computing All Maps into a Sphere.” Journal of the ACM, vol. 61, no. 3, 17, ACM, 2014, doi:10.1145/2597629. short: M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, U. Wagner, Journal of the ACM 61 (2014). date_created: 2018-12-11T11:56:12Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T06:55:50Z day: '01' department: - _id: UlWa - _id: HeEd doi: 10.1145/2597629 intvolume: ' 61' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1105.6257 month: '05' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '4797' quality_controlled: '1' scopus_import: 1 status: public title: Computing all maps into a sphere type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2014' ... --- _id: '2183' abstract: - lang: eng text: 'We describe a simple adaptive network of coupled chaotic maps. The network reaches a stationary state (frozen topology) for all values of the coupling parameter, although the dynamics of the maps at the nodes of the network can be nontrivial. The structure of the network shows interesting hierarchical properties and in certain parameter regions the dynamics is polysynchronous: Nodes can be divided in differently synchronized classes but, contrary to cluster synchronization, nodes in the same class need not be connected to each other. These complicated synchrony patterns have been conjectured to play roles in systems biology and circuits. The adaptive system we study describes ways whereby this behavior can evolve from undifferentiated nodes.' acknowledgement: "V.B.S. is partially supported by contract MEC (Grant No. AYA2010-22111-C03-02).\r\n" article_number: '062809' article_processing_charge: No author: - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: Paul full_name: Glendinning, Paul last_name: Glendinning citation: ama: Botella Soler V, Glendinning P. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(6). doi:10.1103/PhysRevE.89.062809 apa: Botella Soler, V., & Glendinning, P. (2014). Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.062809 chicago: Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.062809. ieee: V. Botella Soler and P. Glendinning, “Hierarchy and polysynchrony in an adaptive network ,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6. American Institute of Physics, 2014. ista: Botella Soler V, Glendinning P. 2014. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(6), 062809. mla: Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6, 062809, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.062809. short: V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014). date_created: 2018-12-11T11:56:11Z date_published: 2014-06-16T00:00:00Z date_updated: 2022-08-25T14:04:45Z day: '16' department: - _id: GaTk doi: 10.1103/PhysRevE.89.062809 ec_funded: 1 intvolume: ' 89' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1403.3209 month: '06' 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 E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '4798' quality_controlled: '1' scopus_import: '1' status: public title: 'Hierarchy and polysynchrony in an adaptive network ' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '2186' abstract: - lang: eng text: We prove the existence of scattering states for the defocusing cubic Gross-Pitaevskii (GP) hierarchy in ℝ3. Moreover, we show that an exponential energy growth condition commonly used in the well-posedness theory of the GP hierarchy is, in a specific sense, necessary. In fact, we prove that without the latter, there exist initial data for the focusing cubic GP hierarchy for which instantaneous blowup occurs. author: - first_name: Thomas full_name: Chen, Thomas last_name: Chen - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Nataša full_name: Pavlović, Nataša last_name: Pavlović - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Chen T, Hainzl C, Pavlović N, Seiringer R. On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters in Mathematical Physics. 2014;104(7):871-891. doi:10.1007/s11005-014-0693-2 apa: Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2014). On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-014-0693-2 chicago: Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “On the Well-Posedness and Scattering for the Gross-Pitaevskii Hierarchy via Quantum de Finetti.” Letters in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s11005-014-0693-2. ieee: T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti,” Letters in Mathematical Physics, vol. 104, no. 7. Springer, pp. 871–891, 2014. ista: Chen T, Hainzl C, Pavlović N, Seiringer R. 2014. On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti. Letters in Mathematical Physics. 104(7), 871–891. mla: Chen, Thomas, et al. “On the Well-Posedness and Scattering for the Gross-Pitaevskii Hierarchy via Quantum de Finetti.” Letters in Mathematical Physics, vol. 104, no. 7, Springer, 2014, pp. 871–91, doi:10.1007/s11005-014-0693-2. short: T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Letters in Mathematical Physics 104 (2014) 871–891. date_created: 2018-12-11T11:56:12Z date_published: 2014-05-07T00:00:00Z date_updated: 2021-01-12T06:55:51Z day: '07' department: - _id: RoSe doi: 10.1007/s11005-014-0693-2 intvolume: ' 104' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1311.2136 month: '05' oa: 1 oa_version: Submitted Version page: 871 - 891 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '4793' quality_controlled: '1' scopus_import: 1 status: public title: On the well-posedness and scattering for the Gross-Pitaevskii hierarchy via quantum de Finetti type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 104 year: '2014' ... --- _id: '2187' abstract: - lang: eng text: 'Systems should not only be correct but also robust in the sense that they behave reasonably in unexpected situations. This article addresses synthesis of robust reactive systems from temporal specifications. Existing methods allow arbitrary behavior if assumptions in the specification are violated. To overcome this, we define two robustness notions, combine them, and show how to enforce them in synthesis. The first notion applies to safety properties: If safety assumptions are violated temporarily, we require that the system recovers to normal operation with as few errors as possible. The second notion requires that, if liveness assumptions are violated, as many guarantees as possible should be fulfilled nevertheless. We present a synthesis procedure achieving this for the important class of GR(1) specifications, and establish complexity bounds. We also present an implementation of a special case of robustness, and show experimental results.' article_processing_charge: No article_type: original author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Karin full_name: Greimel, Karin last_name: Greimel - 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: Georg full_name: Hofferek, Georg last_name: Hofferek - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Bettina full_name: Könighofer, Bettina last_name: Könighofer - first_name: Robert full_name: Könighofer, Robert last_name: Könighofer citation: ama: Bloem R, Chatterjee K, Greimel K, et al. Synthesizing robust systems. Acta Informatica. 2014;51(3-4):193-220. doi:10.1007/s00236-013-0191-5 apa: Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., Hofferek, G., Jobstmann, B., … Könighofer, R. (2014). Synthesizing robust systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-013-0191-5 chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, Georg Hofferek, Barbara Jobstmann, Bettina Könighofer, and Robert Könighofer. “Synthesizing Robust Systems.” Acta Informatica. Springer, 2014. https://doi.org/10.1007/s00236-013-0191-5. ieee: R. Bloem et al., “Synthesizing robust systems,” Acta Informatica, vol. 51, no. 3–4. Springer, pp. 193–220, 2014. ista: Bloem R, Chatterjee K, Greimel K, Henzinger TA, Hofferek G, Jobstmann B, Könighofer B, Könighofer R. 2014. Synthesizing robust systems. Acta Informatica. 51(3–4), 193–220. mla: Bloem, Roderick, et al. “Synthesizing Robust Systems.” Acta Informatica, vol. 51, no. 3–4, Springer, 2014, pp. 193–220, doi:10.1007/s00236-013-0191-5. short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, G. Hofferek, B. Jobstmann, B. Könighofer, R. Könighofer, Acta Informatica 51 (2014) 193–220. date_created: 2018-12-11T11:56:13Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:55:51Z day: '01' ddc: - '621' department: - _id: KrCh - _id: ToHe doi: 10.1007/s00236-013-0191-5 ec_funded: 1 file: - access_level: open_access checksum: d7f560f3d923f0f00aa10a0652f83273 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:44Z date_updated: 2020-07-14T12:45:31Z file_id: '5234' file_name: IST-2012-71-v1+1_Synthesizing_robust_systems.pdf file_size: 169523 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' intvolume: ' 51' issue: 3-4 language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 193 - 220 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Acta Informatica publication_status: published publisher: Springer publist_id: '4787' pubrep_id: '71' quality_controlled: '1' scopus_import: 1 status: public title: Synthesizing robust systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2014' ... --- _id: '2188' abstract: - lang: eng text: Although plant and animal cells use a similar core mechanism to deliver proteins to the plasma membrane, their different lifestyle, body organization and specific cell structures resulted in the acquisition of regulatory mechanisms that vary in the two kingdoms. In particular, cell polarity regulators do not seem to be conserved, because genes encoding key components are absent in plant genomes. In plants, the broad knowledge on polarity derives from the study of auxin transporters, the PIN-FORMED proteins, in the model plant Arabidopsis thaliana. In animals, much information is provided from the study of polarity in epithelial cells that exhibit basolateral and luminal apical polarities, separated by tight junctions. In this review, we summarize the similarities and differences of the polarization mechanisms between plants and animals and survey the main genetic approaches that have been used to characterize new genes involved in polarity establishment in plants, including the frequently used forward and reverse genetics screens as well as a novel chemical genetics approach that is expected to overcome the limitation of classical genetics methods. acknowledgement: "This work was supported by a grant from the Research Foundation-Flanders (Odysseus).\r\n\r\n" article_number: '140017' author: - first_name: Urszula full_name: Kania, Urszula id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Matyas full_name: Fendrych, Matyas last_name: Fendrych - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kania U, Fendrych M, Friml J. Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biology. 2014;4(APRIL). doi:10.1098/rsob.140017 apa: Kania, U., Fendrych, M., & Friml, J. (2014). Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biology. Royal Society. https://doi.org/10.1098/rsob.140017 chicago: Kania, Urszula, Matyas Fendrych, and Jiří Friml. “Polar Delivery in Plants; Commonalities and Differences to Animal Epithelial Cells.” Open Biology. Royal Society, 2014. https://doi.org/10.1098/rsob.140017. ieee: U. Kania, M. Fendrych, and J. Friml, “Polar delivery in plants; commonalities and differences to animal epithelial cells,” Open Biology, vol. 4, no. APRIL. Royal Society, 2014. ista: Kania U, Fendrych M, Friml J. 2014. Polar delivery in plants; commonalities and differences to animal epithelial cells. Open Biology. 4(APRIL), 140017. mla: Kania, Urszula, et al. “Polar Delivery in Plants; Commonalities and Differences to Animal Epithelial Cells.” Open Biology, vol. 4, no. APRIL, 140017, Royal Society, 2014, doi:10.1098/rsob.140017. short: U. Kania, M. Fendrych, J. Friml, Open Biology 4 (2014). date_created: 2018-12-11T11:56:13Z date_published: 2014-04-16T00:00:00Z date_updated: 2021-01-12T06:55:52Z day: '16' ddc: - '570' department: - _id: JiFr doi: 10.1098/rsob.140017 file: - access_level: open_access checksum: 2020627feff36cf0799167c84149fa75 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:40Z date_updated: 2020-07-14T12:45:31Z file_id: '5025' file_name: IST-2016-441-v1+1_140017.full.pdf file_size: 682570 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' intvolume: ' 4' issue: APRIL language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Open Biology publication_status: published publisher: Royal Society publist_id: '4786' pubrep_id: '441' quality_controlled: '1' scopus_import: 1 status: public title: Polar delivery in plants; commonalities and differences to animal epithelial cells 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: 4 year: '2014' ... --- _id: '2189' abstract: - lang: fre text: En apprentissage automatique, nous parlons d'adaptation de domaine lorsque les données de test (cibles) et d'apprentissage (sources) sont générées selon différentes distributions. Nous devons donc développer des algorithmes de classification capables de s'adapter à une nouvelle distribution, pour laquelle aucune information sur les étiquettes n'est disponible. Nous attaquons cette problématique sous l'angle de l'approche PAC-Bayésienne qui se focalise sur l'apprentissage de modèles définis comme des votes de majorité sur un ensemble de fonctions. Dans ce contexte, nous introduisons PV-MinCq une version adaptative de l'algorithme (non adaptatif) MinCq. PV-MinCq suit le principe suivant. Nous transférons les étiquettes sources aux points cibles proches pour ensuite appliquer MinCq sur l'échantillon cible ``auto-étiqueté'' (justifié par une borne théorique). Plus précisément, nous définissons un auto-étiquetage non itératif qui se focalise dans les régions où les distributions marginales source et cible sont les plus similaires. Dans un second temps, nous étudions l'influence de notre auto-étiquetage pour en déduire une procédure de validation des hyperparamètres. Finalement, notre approche montre des résultats empiriques prometteurs. article_processing_charge: No author: - first_name: Emilie full_name: Morvant, Emilie id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87 last_name: Morvant orcid: 0000-0002-8301-7240 citation: ama: 'Morvant E. Adaptation de domaine de vote de majorité par auto-étiquetage non itératif. In: Vol 1. Elsevier; 2014:49-58.' apa: 'Morvant, E. (2014). Adaptation de domaine de vote de majorité par auto-étiquetage non itératif (Vol. 1, pp. 49–58). Presented at the CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference), Saint-Etienne, France: Elsevier.' chicago: Morvant, Emilie. “Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage Non Itératif,” 1:49–58. Elsevier, 2014. ieee: 'E. Morvant, “Adaptation de domaine de vote de majorité par auto-étiquetage non itératif,” presented at the CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference), Saint-Etienne, France, 2014, vol. 1, pp. 49–58.' ista: 'Morvant E. 2014. Adaptation de domaine de vote de majorité par auto-étiquetage non itératif. CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference) vol. 1, 49–58.' mla: Morvant, Emilie. Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage Non Itératif. Vol. 1, Elsevier, 2014, pp. 49–58. short: E. Morvant, in:, Elsevier, 2014, pp. 49–58. conference: location: Saint-Etienne, France name: 'CAP: Conférence Francophone sur l''Apprentissage Automatique (Machine Learning French Conference)' date_created: 2018-12-11T11:56:13Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:55:52Z day: '01' department: - _id: ChLa intvolume: ' 1' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01005776/ month: '07' oa: 1 oa_version: Preprint page: 49-58 publication_status: published publisher: Elsevier publist_id: '4785' quality_controlled: '1' status: public title: Adaptation de domaine de vote de majorité par auto-étiquetage non itératif type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2014' ... --- _id: '2190' abstract: - lang: eng text: We present a new algorithm to construct a (generalized) deterministic Rabin automaton for an LTL formula φ. The automaton is the product of a master automaton and an array of slave automata, one for each G-subformula of φ. The slave automaton for G ψ is in charge of recognizing whether FG ψ holds. As opposed to standard determinization procedures, the states of all our automata have a clear logical structure, which allows for various optimizations. Our construction subsumes former algorithms for fragments of LTL. Experimental results show improvement in the sizes of the resulting automata compared to existing methods. acknowledgement: The author is on leave from Faculty of Informatics, Masaryk University, Czech Republic, and partially supported by the Czech Science Foundation, grant No. P202/12/G061. alternative_title: - LNCS author: - first_name: Javier full_name: Esparza, Javier last_name: Esparza - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: 'Esparza J, Kretinsky J. From LTL to deterministic automata: A safraless compositional approach. In: Vol 8559. Springer; 2014:192-208. doi:10.1007/978-3-319-08867-9_13' apa: 'Esparza, J., & Kretinsky, J. (2014). From LTL to deterministic automata: A safraless compositional approach (Vol. 8559, pp. 192–208). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/978-3-319-08867-9_13' chicago: 'Esparza, Javier, and Jan Kretinsky. “From LTL to Deterministic Automata: A Safraless Compositional Approach,” 8559:192–208. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_13.' ieee: 'J. Esparza and J. Kretinsky, “From LTL to deterministic automata: A safraless compositional approach,” presented at the CAV: Computer Aided Verification, 2014, vol. 8559, pp. 192–208.' ista: 'Esparza J, Kretinsky J. 2014. From LTL to deterministic automata: A safraless compositional approach. CAV: Computer Aided Verification, LNCS, vol. 8559, 192–208.' mla: 'Esparza, Javier, and Jan Kretinsky. From LTL to Deterministic Automata: A Safraless Compositional Approach. Vol. 8559, Springer, 2014, pp. 192–208, doi:10.1007/978-3-319-08867-9_13.' short: J. Esparza, J. Kretinsky, in:, Springer, 2014, pp. 192–208. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T11:56:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:55:53Z day: '01' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-319-08867-9_13 ec_funded: 1 intvolume: ' 8559' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.3388 month: '01' oa: 1 oa_version: Submitted Version page: 192 - 208 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication_status: published publisher: Springer publist_id: '4784' quality_controlled: '1' status: public title: 'From LTL to deterministic automata: A safraless compositional approach' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8559 year: '2014' ... --- _id: '2208' abstract: - lang: eng text: 'We propose to detect quadrupole interactions of neutral ultracold atoms via their induced mean-field shift. We consider a Mott insulator state of spin-polarized atoms in a two-dimensional optical square lattice. The quadrupole moments of the atoms are aligned by an external magnetic field. As the alignment angle is varied, the mean-field shift shows a characteristic angular dependence, which constitutes the defining signature of the quadrupole interaction. For the 3P2 states of Yb and Sr atoms, we find a frequency shift of the order of tens of Hertz, which can be realistically detected in experiment with current technology. We compare our results to the mean-field shift of a spin-polarized quasi-two-dimensional Fermi gas in continuum. ' article_number: '043616' author: - first_name: Martin full_name: Lahrz, Martin last_name: Lahrz - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Klaus full_name: Sengstock, Klaus last_name: Sengstock - first_name: Christoph full_name: Becker, Christoph last_name: Becker - first_name: Ludwig full_name: Mathey, Ludwig last_name: Mathey citation: ama: Lahrz M, Lemeshko M, Sengstock K, Becker C, Mathey L. Detecting quadrupole interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular, and Optical Physics. 2014;89(4). doi:10.1103/PhysRevA.89.043616 apa: Lahrz, M., Lemeshko, M., Sengstock, K., Becker, C., & Mathey, L. (2014). Detecting quadrupole interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.89.043616 chicago: Lahrz, Martin, Mikhail Lemeshko, Klaus Sengstock, Christoph Becker, and Ludwig Mathey. “Detecting Quadrupole Interactions in Ultracold Fermi Gases.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevA.89.043616. ieee: M. Lahrz, M. Lemeshko, K. Sengstock, C. Becker, and L. Mathey, “Detecting quadrupole interactions in ultracold Fermi gases,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 89, no. 4. American Physical Society, 2014. ista: Lahrz M, Lemeshko M, Sengstock K, Becker C, Mathey L. 2014. Detecting quadrupole interactions in ultracold Fermi gases. Physical Review A - Atomic, Molecular, and Optical Physics. 89(4), 043616. mla: Lahrz, Martin, et al. “Detecting Quadrupole Interactions in Ultracold Fermi Gases.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 89, no. 4, 043616, American Physical Society, 2014, doi:10.1103/PhysRevA.89.043616. short: M. Lahrz, M. Lemeshko, K. Sengstock, C. Becker, L. Mathey, Physical Review A - Atomic, Molecular, and Optical Physics 89 (2014). date_created: 2018-12-11T11:56:20Z date_published: 2014-04-23T00:00:00Z date_updated: 2021-01-12T06:55:59Z day: '23' doi: 10.1103/PhysRevA.89.043616 extern: '1' intvolume: ' 89' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0873 month: '04' oa: 1 oa_version: Submitted Version publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4764' quality_controlled: '1' status: public title: Detecting quadrupole interactions in ultracold Fermi gases type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '2214' abstract: - lang: eng text: A hallmark of immune cell trafficking is directional guidance via gradients of soluble or surface bound chemokines. Vascular endothelial cells produce, transport and deposit either their own chemokines or chemokines produced by the underlying stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold for these chemokine pools, but it is unclear how steep chemokine gradients are sustained between the lumenal and ablumenal aspects of blood vessels. Addressing this question by semi-quantitative immunostaining of HS moieties around blood vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal lamina of resting and inflamed post capillary skin venules, as well as in high endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx probe further suggested that their lumenal glycocalyx contains much lower HS density than their basolateral extracellular matrix (ECM). This polarized HS pattern was observed also in isolated resting and inflamed microvascular dermal cells. Notably, progressive skin inflammation resulted in massive ECM deposition and in further HS enrichment around skin post capillary venules and their associated pericytes. Inflammation-dependent HS enrichment was not compromised in mice deficient in the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature patterns steep gradients of HS scaffolds between their lumenal and basolateral endothelial aspects, and that inflammatory processes can further enrich the HS content nearby inflamed vessels. We propose that chemokine gradients between the lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold gradients. acknowledgement: Michael Sixt's research is supported by the European Research Council (ERC Starting grant). article_number: e85699 author: - first_name: Liat full_name: Stoler Barak, Liat last_name: Stoler Barak - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - first_name: Elias full_name: Shezen, Elias last_name: Shezen - first_name: Miki full_name: Hatzav, Miki last_name: Hatzav - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Ronen full_name: Alon, Ronen last_name: Alon citation: ama: Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085699 apa: Stoler Barak, L., Moussion, C., Shezen, E., Hatzav, M., Sixt, M. K., & Alon, R. (2014). Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0085699 chicago: Stoler Barak, Liat, Christine Moussion, Elias Shezen, Miki Hatzav, Michael K Sixt, and Ronen Alon. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0085699. ieee: L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M. K. Sixt, and R. Alon, “Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects,” PLoS One, vol. 9, no. 1. Public Library of Science, 2014. ista: Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. 2014. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. 9(1), e85699. mla: Stoler Barak, Liat, et al. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” PLoS One, vol. 9, no. 1, e85699, Public Library of Science, 2014, doi:10.1371/journal.pone.0085699. short: L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M.K. Sixt, R. Alon, PLoS One 9 (2014). date_created: 2018-12-11T11:56:22Z date_published: 2014-01-22T00:00:00Z date_updated: 2021-01-12T06:56:03Z day: '22' ddc: - '570' department: - _id: MiSi doi: 10.1371/journal.pone.0085699 ec_funded: 1 file: - access_level: open_access checksum: 84a8033bda2e07e39405f5acc85f4eca content_type: application/pdf creator: system date_created: 2018-12-12T10:07:48Z date_updated: 2020-07-14T12:45:33Z file_id: '4646' file_name: IST-2016-433-v1+1_journal.pone.0085699.pdf file_size: 12634775 relation: main_file file_date_updated: 2020-07-14T12:45:33Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 25A76F58-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '289720' name: Stromal Cell-immune Cell Interactions in Health and Disease publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4756' pubrep_id: '433' quality_controlled: '1' scopus_import: 1 status: public title: Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '2215' abstract: - lang: eng text: Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events. acknowledgement: J.R. was supported by a Boehringer Ingelheim Fonds PhD stipend. author: - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Claudio full_name: Lademann, Claudio last_name: Lademann - first_name: Stefan full_name: Jentsch, Stefan last_name: Jentsch citation: ama: Renkawitz J, Lademann C, Jentsch S. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 2014;15(6):369-383. doi:10.1038/nrm3805 apa: Renkawitz, J., Lademann, C., & Jentsch, S. (2014). Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3805 chicago: Renkawitz, Jörg, Claudio Lademann, and Stefan Jentsch. “Mechanisms and Principles of Homology Search during Recombination.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/nrm3805. ieee: J. Renkawitz, C. Lademann, and S. Jentsch, “Mechanisms and principles of homology search during recombination,” Nature Reviews Molecular Cell Biology, vol. 15, no. 6. Nature Publishing Group, pp. 369–383, 2014. ista: Renkawitz J, Lademann C, Jentsch S. 2014. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 15(6), 369–383. mla: Renkawitz, Jörg, et al. “Mechanisms and Principles of Homology Search during Recombination.” Nature Reviews Molecular Cell Biology, vol. 15, no. 6, Nature Publishing Group, 2014, pp. 369–83, doi:10.1038/nrm3805. short: J. Renkawitz, C. Lademann, S. Jentsch, Nature Reviews Molecular Cell Biology 15 (2014) 369–383. date_created: 2018-12-11T11:56:22Z date_published: 2014-05-14T00:00:00Z date_updated: 2021-01-12T06:56:03Z day: '14' department: - _id: MiSi doi: 10.1038/nrm3805 intvolume: ' 15' issue: '6' language: - iso: eng month: '05' oa_version: None page: 369 - 383 publication: Nature Reviews Molecular Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '4755' quality_controlled: '1' scopus_import: 1 status: public title: Mechanisms and principles of homology search during recombination type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '2223' abstract: - lang: eng text: Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes. author: - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Mugurel full_name: Feraru, Mugurel last_name: Feraru - first_name: Michiko full_name: Sasabe, Michiko last_name: Sasabe - first_name: Tomomi full_name: Ishikawa, Tomomi last_name: Ishikawa - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Tatsuo full_name: Kakimoto, Tatsuo last_name: Kakimoto - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 2014;55(4):737-749. doi:10.1093/pcp/pct196 apa: Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa, T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pct196 chicago: Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pct196. ieee: H. Tanaka et al., “BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis,” Plant and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 737–749, 2014. ista: Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 55(4), 737–749. mla: Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49, doi:10.1093/pcp/pct196. short: H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa, J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749. date_created: 2018-12-11T11:56:25Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:56:07Z day: '01' ddc: - '570' department: - _id: JiFr doi: 10.1093/pcp/pct196 ec_funded: 1 file: - access_level: open_access checksum: b781a76b32ac35a520256453c3ba9433 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:25Z date_updated: 2020-07-14T12:45:34Z file_id: '5076' file_name: IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf file_size: 2028111 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 55' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://repository.ist.ac.at/id/eprint/431 month: '04' oa: 1 oa_version: Published Version page: 737 - 749 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants - _id: 256BDAB0-B435-11E9-9278-68D0E5697425 name: Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur publication: Plant and Cell Physiology publication_identifier: issn: - '00320781' publication_status: published publisher: Oxford University Press publist_id: '4741' pubrep_id: '431' quality_controlled: '1' scopus_import: 1 status: public title: BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '2225' abstract: - lang: eng text: "We consider sample covariance matrices of the form X∗X, where X is an M×N matrix with independent random entries. We prove the isotropic local Marchenko-Pastur law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the identity in the sense of quadratic forms. More precisely, we establish sharp high-probability bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout the entire spectrum away from 0. We also prove analogous results for generalized Wigner matrices.\r\n" article_number: '33' author: - first_name: Alex full_name: Bloemendal, Alex last_name: Bloemendal - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles - first_name: Horng full_name: Yau, Horng last_name: Yau - first_name: Jun full_name: Yin, Jun last_name: Yin citation: ama: Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. 2014;19. doi:10.1214/EJP.v19-3054 apa: Bloemendal, A., Erdös, L., Knowles, A., Yau, H., & Yin, J. (2014). Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v19-3054 chicago: Bloemendal, Alex, László Erdös, Antti Knowles, Horng Yau, and Jun Yin. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2014. https://doi.org/10.1214/EJP.v19-3054. ieee: A. Bloemendal, L. Erdös, A. Knowles, H. Yau, and J. Yin, “Isotropic local laws for sample covariance and generalized Wigner matrices,” Electronic Journal of Probability, vol. 19. Institute of Mathematical Statistics, 2014. ista: Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. 2014. Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. 19, 33. mla: Bloemendal, Alex, et al. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” Electronic Journal of Probability, vol. 19, 33, Institute of Mathematical Statistics, 2014, doi:10.1214/EJP.v19-3054. short: A. Bloemendal, L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 19 (2014). date_created: 2018-12-11T11:56:25Z date_published: 2014-03-15T00:00:00Z date_updated: 2021-01-12T06:56:07Z day: '15' ddc: - '510' department: - _id: LaEr doi: 10.1214/EJP.v19-3054 ec_funded: 1 file: - access_level: open_access checksum: 7eb297ff367a2ee73b21b6dd1e1948e4 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:06Z date_updated: 2020-07-14T12:45:34Z file_id: '5055' file_name: IST-2016-427-v1+1_3054-16624-4-PB.pdf file_size: 810150 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 19' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Journal of Probability publication_identifier: issn: - '10836489' publication_status: published publisher: Institute of Mathematical Statistics publist_id: '4739' pubrep_id: '427' quality_controlled: '1' status: public title: Isotropic local laws for sample covariance and generalized Wigner matrices 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: 19 year: '2014' ... --- _id: '2222' abstract: - lang: eng text: Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation. author: - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Tomoko full_name: Dainobu, Tomoko last_name: Dainobu - first_name: Hirotomo full_name: Takatsuka, Hirotomo last_name: Takatsuka - first_name: Teruyo full_name: Okada, Teruyo last_name: Okada - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Hiroo full_name: Fukuda, Hiroo last_name: Fukuda citation: ama: Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 2014;55(4):750-763. doi:10.1093/pcp/pcu012 apa: Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml, J., & Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcu012 chicago: Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka, Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pcu012. ieee: S. Naramoto et al., “VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis,” Plant and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014. ista: Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763. mla: Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:10.1093/pcp/pcu012. short: S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml, H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763. date_created: 2018-12-11T11:56:24Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:56:06Z day: '01' department: - _id: JiFr doi: 10.1093/pcp/pcu012 ec_funded: 1 intvolume: ' 55' issue: '4' language: - iso: eng month: '04' oa_version: None page: 750 - 763 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant and Cell Physiology publication_identifier: issn: - '00320781' publication_status: published publisher: Oxford University Press publist_id: '4742' quality_controlled: '1' scopus_import: 1 status: public title: VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '2224' abstract: - lang: eng text: This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet. article_number: '025503' author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 citation: ama: Altmeyer S. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 2014;46(2). doi:10.1088/0169-5983/46/2/025503 apa: Altmeyer, S. (2014). On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. IOP Publishing Ltd. https://doi.org/10.1088/0169-5983/46/2/025503 chicago: Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” Fluid Dynamics Research. IOP Publishing Ltd., 2014. https://doi.org/10.1088/0169-5983/46/2/025503. ieee: S. Altmeyer, “On secondary instabilities generating footbridges between spiral vortex flow,” Fluid Dynamics Research, vol. 46, no. 2. IOP Publishing Ltd., 2014. ista: Altmeyer S. 2014. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 46(2), 025503. mla: Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” Fluid Dynamics Research, vol. 46, no. 2, 025503, IOP Publishing Ltd., 2014, doi:10.1088/0169-5983/46/2/025503. short: S. Altmeyer, Fluid Dynamics Research 46 (2014). date_created: 2018-12-11T11:56:25Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:56:07Z day: '01' department: - _id: BjHo doi: 10.1088/0169-5983/46/2/025503 intvolume: ' 46' issue: '2' language: - iso: eng month: '04' oa_version: None publication: Fluid Dynamics Research publication_identifier: issn: - '01695983' publication_status: published publisher: IOP Publishing Ltd. publist_id: '4740' quality_controlled: '1' scopus_import: 1 status: public title: On secondary instabilities generating footbridges between spiral vortex flow type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2014' ... --- _id: '2219' abstract: - lang: eng text: Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext (IND-CCA) secure public-key encryption scheme from the learning parity with noise (LPN) assumption. In this work we give an alternative scheme which is conceptually simpler and more efficient. At the core of our construction is a trapdoor technique originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which we adapt to the LPN setting. The main technical tool is a new double-trapdoor mechanism, together with a trapdoor switching lemma based on a computational variant of the leftover hash lemma. alternative_title: - LNCS author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Daniel full_name: Masny, Daniel last_name: Masny - 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: 'Kiltz E, Masny D, Pietrzak KZ. Simple chosen-ciphertext security from low noise LPN. In: Vol 8383. Springer; 2014:1-18. doi:10.1007/978-3-642-54631-0_1' apa: 'Kiltz, E., Masny, D., & Pietrzak, K. Z. (2014). Simple chosen-ciphertext security from low noise LPN (Vol. 8383, pp. 1–18). Presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, Springer. https://doi.org/10.1007/978-3-642-54631-0_1' chicago: Kiltz, Eike, Daniel Masny, and Krzysztof Z Pietrzak. “Simple Chosen-Ciphertext Security from Low Noise LPN,” 8383:1–18. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_1. ieee: 'E. Kiltz, D. Masny, and K. Z. Pietrzak, “Simple chosen-ciphertext security from low noise LPN,” presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, 2014, vol. 8383, pp. 1–18.' ista: 'Kiltz E, Masny D, Pietrzak KZ. 2014. Simple chosen-ciphertext security from low noise LPN. IACR: International Conference on Practice and Theory in Public-Key Cryptography, LNCS, vol. 8383, 1–18.' mla: Kiltz, Eike, et al. Simple Chosen-Ciphertext Security from Low Noise LPN. Vol. 8383, Springer, 2014, pp. 1–18, doi:10.1007/978-3-642-54631-0_1. short: E. Kiltz, D. Masny, K.Z. Pietrzak, in:, Springer, 2014, pp. 1–18. conference: name: 'IACR: International Conference on Practice and Theory in Public-Key Cryptography' date_created: 2018-12-11T11:56:24Z date_published: 2014-03-01T00:00:00Z date_updated: 2021-01-12T06:56:05Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-54631-0_1 intvolume: ' 8383' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2015/401 month: '03' oa: 1 oa_version: Submitted Version page: 1 - 18 publication_identifier: isbn: - 978-364254630-3 publication_status: published publisher: Springer publist_id: '4748' quality_controlled: '1' scopus_import: 1 status: public title: Simple chosen-ciphertext security from low noise LPN type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8383 year: '2014' ... --- _id: '2220' abstract: - lang: eng text: In this issue of Chemistry & Biology, Cokol and colleagues report a systematic study of drug interactions between antifungal compounds. Suppressive drug interactions occur more frequently than previously realized and come in different flavors with interesting implications. author: - first_name: Marjon full_name: De Vos, Marjon id: 3111FFAC-F248-11E8-B48F-1D18A9856A87 last_name: De Vos - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals. Chemistry and Biology. 2014;21(4):439-440. doi:10.1016/j.chembiol.2014.04.004 apa: de Vos, M., & Bollenbach, M. T. (2014). Suppressive drug interactions between antifungals. Chemistry and Biology. Cell Press. https://doi.org/10.1016/j.chembiol.2014.04.004 chicago: Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology. Cell Press, 2014. https://doi.org/10.1016/j.chembiol.2014.04.004. ieee: M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,” Chemistry and Biology, vol. 21, no. 4. Cell Press, pp. 439–440, 2014. ista: de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals. Chemistry and Biology. 21(4), 439–440. mla: de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology, vol. 21, no. 4, Cell Press, 2014, pp. 439–40, doi:10.1016/j.chembiol.2014.04.004. short: M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440. date_created: 2018-12-11T11:56:24Z date_published: 2014-04-24T00:00:00Z date_updated: 2021-01-12T06:56:06Z day: '24' department: - _id: ToBo doi: 10.1016/j.chembiol.2014.04.004 external_id: pmid: - '24766845' intvolume: ' 21' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/24766845 month: '04' oa: 1 oa_version: Published Version page: 439 - 440 pmid: 1 publication: Chemistry and Biology publication_identifier: issn: - '10745521' publication_status: published publisher: Cell Press publist_id: '4747' quality_controlled: '1' scopus_import: 1 status: public title: Suppressive drug interactions between antifungals type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2014' ... --- _id: '2233' abstract: - lang: eng text: ' A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, valuing a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by λi, where the discount factor λ is a fixed rational number greater than 1. The value of a word is the minimal value of the automaton runs on it. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, reflecting the assumption that earlier weights are more important than later weights. Unfortunately, determinization of NDAs, which is often essential in formal verification, is, in general, not possible. We provide positive news, showing that every NDA with an integral discount factor is determinizable. We complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: for every nonintegral rational discount factor λ, there is a nondeterminizable λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. For general NDAs, we look into approximate determinization, which is always possible as the influence of a word''s suffix decays. We show that the naive approach, of unfolding the automaton computations up to a sufficient level, is doubly exponential in the discount factor. We provide an alternative construction for approximate determinization, which is singly exponential in the discount factor, in the precision, and in the number of states. We also prove matching lower bounds, showing that the exponential dependency on each of these three parameters cannot be avoided. All our results hold equally for automata over finite words and for automata over infinite words. ' author: - first_name: Udi full_name: Boker, Udi last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Boker U, Henzinger TA. Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. 2014;10(1). doi:10.2168/LMCS-10(1:10)2014 apa: Boker, U., & Henzinger, T. A. (2014). Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-10(1:10)2014 chicago: Boker, Udi, and Thomas A Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2014. https://doi.org/10.2168/LMCS-10(1:10)2014. ieee: U. Boker and T. A. Henzinger, “Exact and approximate determinization of discounted-sum automata,” Logical Methods in Computer Science, vol. 10, no. 1. International Federation of Computational Logic, 2014. ista: Boker U, Henzinger TA. 2014. Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. 10(1). mla: Boker, Udi, and Thomas A. Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” Logical Methods in Computer Science, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:10)2014. short: U. Boker, T.A. Henzinger, Logical Methods in Computer Science 10 (2014). date_created: 2018-12-11T11:56:28Z date_published: 2014-02-13T00:00:00Z date_updated: 2021-01-12T06:56:11Z day: '13' ddc: - '000' department: - _id: ToHe doi: 10.2168/LMCS-10(1:10)2014 ec_funded: 1 file: - access_level: open_access checksum: 9f6ea2e2d8d4a32ff0becc29d835bbf8 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:45Z date_updated: 2020-07-14T12:45:34Z file_id: '4643' file_name: IST-2015-389-v1+1_1401.3957.pdf file_size: 550936 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 10' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _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: Logical Methods in Computer Science publication_identifier: issn: - '18605974' publication_status: published publisher: International Federation of Computational Logic publist_id: '4728' pubrep_id: '389' quality_controlled: '1' scopus_import: 1 status: public title: Exact and approximate determinization of discounted-sum automata 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: 10 year: '2014' ... --- _id: '2230' abstract: - lang: eng text: Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals. article_number: '16' 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: Christoph full_name: Schmidt Hieber, Christoph last_name: Schmidt Hieber citation: ama: 'Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 2014;8(FEB). doi:10.3389/fninf.2014.00016' apa: 'Guzmán, J., Schlögl, A., & Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. Frontiers Research Foundation. https://doi.org/10.3389/fninf.2014.00016' chicago: 'Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” Frontiers in Neuroinformatics. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fninf.2014.00016.' ieee: 'J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” Frontiers in Neuroinformatics, vol. 8, no. FEB. Frontiers Research Foundation, 2014.' ista: 'Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.' mla: 'Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” Frontiers in Neuroinformatics, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:10.3389/fninf.2014.00016.' short: J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014). date_created: 2018-12-11T11:56:27Z date_published: 2014-02-21T00:00:00Z date_updated: 2021-01-12T06:56:09Z day: '21' ddc: - '570' department: - _id: ScienComp - _id: PeJo doi: 10.3389/fninf.2014.00016 file: - access_level: open_access checksum: eeca00bba7232ff7d27db83321f6ea30 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:17Z date_updated: 2020-07-14T12:45:34Z file_id: '4935' file_name: IST-2016-425-v1+1_fninf-08-00016.pdf file_size: 2883372 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 8' issue: FEB language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Frontiers in Neuroinformatics publication_identifier: issn: - '16625196' publication_status: published publisher: Frontiers Research Foundation publist_id: '4731' pubrep_id: '425' quality_controlled: '1' scopus_import: 1 status: public title: 'Stimfit: Quantifying electrophysiological data with Python' 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: 8 year: '2014' ... --- _id: '2228' abstract: - lang: eng text: Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing. author: - first_name: Hua full_name: Hu, Hua id: 4AC0145C-F248-11E8-B48F-1D18A9856A87 last_name: Hu - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 2014;17(5):686-693. doi:10.1038/nn.3678 apa: Hu, H., & Jonas, P. M. (2014). A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3678 chicago: Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience. Nature Publishing Group, 2014. https://doi.org/10.1038/nn.3678. ieee: H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons,” Nature Neuroscience, vol. 17, no. 5. Nature Publishing Group, pp. 686–693, 2014. ista: Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693. mla: Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:10.1038/nn.3678. short: H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693. date_created: 2018-12-11T11:56:26Z date_published: 2014-03-23T00:00:00Z date_updated: 2021-01-12T06:56:08Z day: '23' department: - _id: PeJo doi: 10.1038/nn.3678 ec_funded: 1 intvolume: ' 17' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/ month: '03' oa: 1 oa_version: Submitted Version page: 686-693 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: Nature Neuroscience publication_identifier: issn: - '10976256' publication_status: published publisher: Nature Publishing Group publist_id: '4733' quality_controlled: '1' scopus_import: 1 status: public title: A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2014' ... --- _id: '2229' abstract: - lang: eng text: The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose "microdomain" coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity. author: - first_name: Nicholas full_name: Vyleta, Nicholas id: 36C4978E-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - 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, Jonas PM. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 2014;343(6171):665-670. doi:10.1126/science.1244811 apa: Vyleta, N., & Jonas, P. M. (2014). Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1244811 chicago: Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1244811. ieee: N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse,” Science, vol. 343, no. 6171. American Association for the Advancement of Science, pp. 665–670, 2014. ista: Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670. mla: Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” Science, vol. 343, no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70, doi:10.1126/science.1244811. short: N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670. date_created: 2018-12-11T11:56:27Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:56:09Z day: '01' department: - _id: PeJo doi: 10.1126/science.1244811 ec_funded: 1 intvolume: ' 343' issue: '6171' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/ month: '02' oa: 1 oa_version: Submitted Version page: 665 - 670 project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: Science publication_identifier: issn: - '00368075' publication_status: published publisher: American Association for the Advancement of Science publist_id: '4732' quality_controlled: '1' scopus_import: 1 status: public title: Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 343 year: '2014' ... --- _id: '2232' abstract: - lang: eng text: The purpose of this contribution is to summarize and discuss recent advances regarding the onset of turbulence in shear flows. The absence of a clear-cut instability mechanism, the spatio-temporal intermittent character and extremely long lived transients are some of the major difficulties encountered in these flows and have hindered progress towards understanding the transition process. We will show for the case of pipe flow that concepts from nonlinear dynamics and statistical physics can help to explain the onset of turbulence. In particular, the turbulent structures (puffs) observed close to onset are spatially localized chaotic transients and their lifetimes increase super-exponentially with Reynolds number. At the same time fluctuations of individual turbulent puffs can (although very rarely) lead to the nucleation of new puffs. The competition between these two stochastic processes gives rise to a non-equilibrium phase transition where turbulence changes from a super-transient to a sustained state. article_number: P02001 article_processing_charge: No article_type: original author: - first_name: Baofang full_name: Song, Baofang id: a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72 last_name: Song - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014;2014(2). doi:10.1088/1742-5468/2014/02/P02001 apa: Song, B., & Hof, B. (2014). Deterministic and stochastic aspects of the transition to turbulence. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/2014/02/P02001 chicago: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing, 2014. https://doi.org/10.1088/1742-5468/2014/02/P02001. ieee: B. Song and B. Hof, “Deterministic and stochastic aspects of the transition to turbulence,” Journal of Statistical Mechanics Theory and Experiment, vol. 2014, no. 2. IOP Publishing, 2014. ista: Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2), P02001. mla: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” Journal of Statistical Mechanics Theory and Experiment, vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:10.1088/1742-5468/2014/02/P02001. short: B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014 (2014). date_created: 2018-12-11T11:56:28Z date_published: 2014-02-01T00:00:00Z date_updated: 2022-06-10T10:13:15Z day: '01' department: - _id: BjHo doi: 10.1088/1742-5468/2014/02/P02001 external_id: arxiv: - '1403.4516' intvolume: ' 2014' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1403.4516 month: '02' oa: 1 oa_version: Submitted Version publication: Journal of Statistical Mechanics Theory and Experiment publication_identifier: issn: - '17425468' publication_status: published publisher: IOP Publishing publist_id: '4729' quality_controlled: '1' status: public title: Deterministic and stochastic aspects of the transition to turbulence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2014 year: '2014' ... --- _id: '2231' abstract: - lang: eng text: Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail. author: - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014 apa: Rieckh, G., & Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2014.01.014 chicago: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal. Biophysical Society, 2014. https://doi.org/10.1016/j.bpj.2014.01.014. ieee: G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014. ista: Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204. mla: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014. short: G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204. date_created: 2018-12-11T11:56:28Z date_published: 2014-03-04T00:00:00Z date_updated: 2021-01-12T06:56:10Z day: '04' department: - _id: GaTk doi: 10.1016/j.bpj.2014.01.014 external_id: pmid: - '24606943' intvolume: ' 106' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/ month: '03' oa: 1 oa_version: Submitted Version page: 1194 - 1204 pmid: 1 publication: Biophysical Journal publication_identifier: issn: - '00063495' publication_status: published publisher: Biophysical Society publist_id: '4730' quality_controlled: '1' scopus_import: 1 status: public title: Noise and information transmission in promoters with multiple internal states type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 106 year: '2014' ... --- _id: '2226' abstract: - lang: eng text: Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability. article_number: '013001' author: - first_name: Liang full_name: Shi, Liang last_name: Shi - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Andreas full_name: Tilgner, Andreas last_name: Tilgner citation: ama: Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(1). doi:10.1103/PhysRevE.89.013001 apa: Shi, L., Hof, B., & Tilgner, A. (2014). Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.013001 chicago: Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette Flow.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.013001. ieee: L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 1. American Institute of Physics, 2014. ista: Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001. mla: Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 1, 013001, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.013001. short: L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014). date_created: 2018-12-11T11:56:26Z date_published: 2014-01-06T00:00:00Z date_updated: 2021-01-12T06:56:08Z day: '06' department: - _id: BjHo doi: 10.1103/PhysRevE.89.013001 intvolume: ' 89' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1312.5095 month: '01' oa: 1 oa_version: Submitted Version project: - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_identifier: issn: - '15393755' publication_status: published publisher: American Institute of Physics publist_id: '4737' quality_controlled: '1' scopus_import: 1 status: public title: Transient growth of Ekman-Couette flow type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '2227' abstract: - lang: eng text: The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent. article_processing_charge: No author: - first_name: Eduardo full_name: Cires Rodriguez, Eduardo id: 2AD56A7A-F248-11E8-B48F-1D18A9856A87 last_name: Cires Rodriguez - first_name: Matthias full_name: Baltisberger, Matthias last_name: Baltisberger - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Pablo full_name: Vargas, Pablo last_name: Vargas - first_name: José full_name: Prieto, José last_name: Prieto citation: ama: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 2014;14(1):1-10. doi:10.1007/s13127-013-0150-6 apa: Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., & Prieto, J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. Springer. https://doi.org/10.1007/s13127-013-0150-6 chicago: Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” Organisms Diversity and Evolution. Springer, 2014. https://doi.org/10.1007/s13127-013-0150-6. ieee: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto, “Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences,” Organisms Diversity and Evolution, vol. 14, no. 1. Springer, pp. 1–10, 2014. ista: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10. mla: Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” Organisms Diversity and Evolution, vol. 14, no. 1, Springer, 2014, pp. 1–10, doi:10.1007/s13127-013-0150-6. short: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms Diversity and Evolution 14 (2014) 1–10. date_created: 2018-12-11T11:56:26Z date_published: 2014-03-01T00:00:00Z date_updated: 2022-08-25T14:42:46Z day: '01' department: - _id: JiFr - _id: EvBe doi: 10.1007/s13127-013-0150-6 intvolume: ' 14' issue: '1' language: - iso: eng month: '03' oa_version: None page: 1 - 10 publication: Organisms Diversity and Evolution publication_identifier: issn: - '14396092' publication_status: published publisher: Springer publist_id: '4734' quality_controlled: '1' scopus_import: '1' status: public title: Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '2234' abstract: - lang: eng text: We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with κ limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for ε-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for ε-approximation, for all ε > 0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be ε-approximated in time polynomial in the size of the MDP and 1/ε, and exponential in the number of limit-average functions, for all ε > 0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results. author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Václav full_name: Brožek, Václav last_name: Brožek - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera citation: ama: Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. 2014;10(1). doi:10.2168/LMCS-10(1:13)2014 apa: Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., & Kučera, A. (2014). Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-10(1:13)2014 chicago: Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Markov Decision Processes with Multiple Long-Run Average Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2014. https://doi.org/10.2168/LMCS-10(1:13)2014. ieee: T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Markov decision processes with multiple long-run average objectives,” Logical Methods in Computer Science, vol. 10, no. 1. International Federation of Computational Logic, 2014. ista: Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2014. Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. 10(1). mla: Brázdil, Tomáš, et al. “Markov Decision Processes with Multiple Long-Run Average Objectives.” Logical Methods in Computer Science, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:13)2014. short: T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, Logical Methods in Computer Science 10 (2014). date_created: 2018-12-11T11:56:29Z date_published: 2014-02-14T00:00:00Z date_updated: 2021-01-12T06:56:11Z day: '14' ddc: - '000' department: - _id: KrCh doi: 10.2168/LMCS-10(1:13)2014 ec_funded: 1 file: - access_level: open_access checksum: 803edcc2d8c1acfba44a9ec43a5eb9f0 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:57Z date_updated: 2020-07-14T12:45:34Z file_id: '4656' file_name: IST-2016-428-v1+1_1104.3489.pdf file_size: 375388 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 10' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://repository.ist.ac.at/id/eprint/428 month: '02' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Logical Methods in Computer Science publication_identifier: issn: - '18605974' publication_status: published publisher: International Federation of Computational Logic publist_id: '4727' pubrep_id: '428' quality_controlled: '1' scopus_import: 1 status: public title: Markov decision processes with multiple long-run average objectives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2014' ... --- _id: '2236' abstract: - lang: eng text: Consider a joint distribution (X,A) on a set. We show that for any family of distinguishers, there exists a simulator such that 1 no function in can distinguish (X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient than the functions in. For the most interesting settings of the parameters (in particular, the cryptographic case where X has superlogarithmic min-entropy, ε > 0 is negligible and consists of circuits of polynomial size), we can make the simulator h deterministic. As an illustrative application of our theorem, we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09. Our proof is simpler and quantitatively much better than the original proof using the dense model theorem, giving meaningful security guarantees if instantiated with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and Pass gave an interactive variant of our main theorem, and used it to investigate weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version of our theorem using their new uniform min-max theorem. alternative_title: - LNCS author: - first_name: Dimitar full_name: Jetchev, Dimitar last_name: Jetchev - 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: 'Jetchev D, Pietrzak KZ. How to fake auxiliary input. In: Lindell Y, ed. Vol 8349. Springer; 2014:566-590. doi:10.1007/978-3-642-54242-8_24' apa: 'Jetchev, D., & Pietrzak, K. Z. (2014). How to fake auxiliary input. In Y. Lindell (Ed.) (Vol. 8349, pp. 566–590). Presented at the TCC: Theory of Cryptography Conference, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54242-8_24' chicago: Jetchev, Dimitar, and Krzysztof Z Pietrzak. “How to Fake Auxiliary Input.” edited by Yehuda Lindell, 8349:566–90. Springer, 2014. https://doi.org/10.1007/978-3-642-54242-8_24. ieee: 'D. Jetchev and K. Z. Pietrzak, “How to fake auxiliary input,” presented at the TCC: Theory of Cryptography Conference, San Diego, USA, 2014, vol. 8349, pp. 566–590.' ista: 'Jetchev D, Pietrzak KZ. 2014. How to fake auxiliary input. TCC: Theory of Cryptography Conference, LNCS, vol. 8349, 566–590.' mla: Jetchev, Dimitar, and Krzysztof Z. Pietrzak. How to Fake Auxiliary Input. Edited by Yehuda Lindell, vol. 8349, Springer, 2014, pp. 566–90, doi:10.1007/978-3-642-54242-8_24. short: D. Jetchev, K.Z. Pietrzak, in:, Y. Lindell (Ed.), Springer, 2014, pp. 566–590. conference: end_date: 2014-02-26 location: San Diego, USA name: 'TCC: Theory of Cryptography Conference' start_date: 2014-02-24 date_created: 2018-12-11T11:56:29Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:56:12Z day: '01' ddc: - '004' department: - _id: KrPi doi: 10.1007/978-3-642-54242-8_24 ec_funded: 1 editor: - first_name: Yehuda full_name: Lindell, Yehuda last_name: Lindell file: - access_level: open_access checksum: 42960325c29dcd8d832edadcc3ce0045 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:21Z date_updated: 2020-07-14T12:45:34Z file_id: '5275' file_name: IST-2016-681-v1+1_869_1_.pdf file_size: 313528 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 8349' language: - iso: eng main_file_link: - open_access: '1' url: https://repository.ist.ac.at/id/eprint/681 month: '02' oa: 1 oa_version: Submitted Version page: 566 - 590 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_identifier: isbn: - 978-364254241-1 publication_status: published publisher: Springer publist_id: '4725' pubrep_id: '681' quality_controlled: '1' status: public title: How to fake auxiliary input type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8349 year: '2014' ... --- _id: '2240' abstract: - lang: eng text: Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis. author: - first_name: Astrid full_name: Gadeyne, Astrid last_name: Gadeyne - first_name: Clara full_name: Sánchez Rodríguez, Clara last_name: Sánchez Rodríguez - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Simone full_name: Di Rubbo, Simone last_name: Di Rubbo - first_name: Henrik full_name: Zauber, Henrik last_name: Zauber - first_name: Kevin full_name: Vanneste, Kevin last_name: Vanneste - first_name: Jelle full_name: Van Leene, Jelle last_name: Van Leene - first_name: Nancy full_name: De Winne, Nancy last_name: De Winne - first_name: Dominique full_name: Eeckhout, Dominique last_name: Eeckhout - first_name: Geert full_name: Persiau, Geert last_name: Persiau - first_name: Eveline full_name: Van De Slijke, Eveline last_name: Van De Slijke - first_name: Bernard full_name: Cannoot, Bernard last_name: Cannoot - first_name: Leen full_name: Vercruysse, Leen last_name: Vercruysse - first_name: Jonathan full_name: Mayers, Jonathan last_name: Mayers - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Urszula full_name: Kania, Urszula id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Matthias full_name: Ehrlich, Matthias last_name: Ehrlich - first_name: Alois full_name: Schweighofer, Alois last_name: Schweighofer - first_name: Tijs full_name: Ketelaar, Tijs last_name: Ketelaar - first_name: Steven full_name: Maere, Steven last_name: Maere - first_name: Sebastian full_name: Bednarek, Sebastian last_name: Bednarek - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Kris full_name: Gevaert, Kris last_name: Gevaert - first_name: Erwin full_name: Witters, Erwin last_name: Witters - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova - first_name: Staffan full_name: Persson, Staffan last_name: Persson - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Daniël full_name: Van Damme, Daniël last_name: Van Damme citation: ama: Gadeyne A, Sánchez Rodríguez C, Vanneste S, et al. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. 2014;156(4):691-704. doi:10.1016/j.cell.2014.01.039 apa: Gadeyne, A., Sánchez Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H., Vanneste, K., … Van Damme, D. (2014). The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.01.039 chicago: Gadeyne, Astrid, Clara Sánchez Rodríguez, Steffen Vanneste, Simone Di Rubbo, Henrik Zauber, Kevin Vanneste, Jelle Van Leene, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” Cell. Cell Press, 2014. https://doi.org/10.1016/j.cell.2014.01.039. ieee: A. Gadeyne et al., “The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants,” Cell, vol. 156, no. 4. Cell Press, pp. 691–704, 2014. ista: Gadeyne A, Sánchez Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Mayers J, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar T, Maere S, Bednarek S, Friml J, Gevaert K, Witters E, Russinova E, Persson S, De Jaeger G, Van Damme D. 2014. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. 156(4), 691–704. mla: Gadeyne, Astrid, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” Cell, vol. 156, no. 4, Cell Press, 2014, pp. 691–704, doi:10.1016/j.cell.2014.01.039. short: A. Gadeyne, C. Sánchez Rodríguez, S. Vanneste, S. Di Rubbo, H. Zauber, K. Vanneste, J. Van Leene, N. De Winne, D. Eeckhout, G. Persiau, E. Van De Slijke, B. Cannoot, L. Vercruysse, J. Mayers, M. Adamowski, U. Kania, M. Ehrlich, A. Schweighofer, T. Ketelaar, S. Maere, S. Bednarek, J. Friml, K. Gevaert, E. Witters, E. Russinova, S. Persson, G. De Jaeger, D. Van Damme, Cell 156 (2014) 691–704. date_created: 2018-12-11T11:56:31Z date_published: 2014-02-13T00:00:00Z date_updated: 2021-01-12T06:56:13Z day: '13' department: - _id: JiFr doi: 10.1016/j.cell.2014.01.039 intvolume: ' 156' issue: '4' language: - iso: eng month: '02' oa_version: None page: 691 - 704 publication: Cell publication_identifier: issn: - '00928674' publication_status: published publisher: Cell Press publist_id: '4721' quality_controlled: '1' scopus_import: 1 status: public title: The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 156 year: '2014' ... --- _id: '2239' abstract: - lang: eng text: The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce battery transition systems. In this model, a battery is viewed as consisting of two parts-the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank. Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the !-regular modelchecking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots. author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - 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: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna citation: ama: 'Boker U, Henzinger TA, Radhakrishna A. Battery transition systems. In: Vol 49. ACM; 2014:595-606. doi:10.1145/2535838.2535875' apa: 'Boker, U., Henzinger, T. A., & Radhakrishna, A. (2014). Battery transition systems (Vol. 49, pp. 595–606). Presented at the POPL: Principles of Programming Languages, San Diego, USA: ACM. https://doi.org/10.1145/2535838.2535875' chicago: Boker, Udi, Thomas A Henzinger, and Arjun Radhakrishna. “Battery Transition Systems,” 49:595–606. ACM, 2014. https://doi.org/10.1145/2535838.2535875. ieee: 'U. Boker, T. A. Henzinger, and A. Radhakrishna, “Battery transition systems,” presented at the POPL: Principles of Programming Languages, San Diego, USA, 2014, vol. 49, no. 1, pp. 595–606.' ista: 'Boker U, Henzinger TA, Radhakrishna A. 2014. Battery transition systems. POPL: Principles of Programming Languages vol. 49, 595–606.' mla: Boker, Udi, et al. Battery Transition Systems. Vol. 49, no. 1, ACM, 2014, pp. 595–606, doi:10.1145/2535838.2535875. short: U. Boker, T.A. Henzinger, A. Radhakrishna, in:, ACM, 2014, pp. 595–606. conference: end_date: 2014-01-24 location: San Diego, USA name: 'POPL: Principles of Programming Languages' start_date: 2014-01-22 date_created: 2018-12-11T11:56:30Z date_published: 2014-01-13T00:00:00Z date_updated: 2021-01-12T06:56:13Z day: '13' department: - _id: ToHe doi: 10.1145/2535838.2535875 ec_funded: 1 intvolume: ' 49' issue: '1' language: - iso: eng month: '01' oa_version: None page: 595 - 606 project: - _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_identifier: isbn: - 978-145032544-8 publication_status: published publisher: ACM publist_id: '4722' quality_controlled: '1' scopus_import: 1 status: public title: Battery transition systems type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2014' ... --- _id: '2235' abstract: - lang: eng text: Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators. author: - first_name: Matthias full_name: Fürst, Matthias id: 393B1196-F248-11E8-B48F-1D18A9856A87 last_name: Fürst orcid: 0000-0002-3712-925X - first_name: Dino full_name: Mcmahon, Dino last_name: Mcmahon - first_name: Juliet full_name: Osborne, Juliet last_name: Osborne - first_name: Robert full_name: Paxton, Robert last_name: Paxton - first_name: Mark full_name: Brown, Mark last_name: Brown citation: ama: Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 2014;506(7488):364-366. doi:10.1038/nature12977 apa: Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., & Brown, M. (2014). Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12977 chicago: Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature12977. ieee: M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations between honeybees and bumblebees as a threat to wild pollinators,” Nature, vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014. ista: Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488), 364–366. mla: Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” Nature, vol. 506, no. 7488, Nature Publishing Group, 2014, pp. 364–66, doi:10.1038/nature12977. short: M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014) 364–366. date_created: 2018-12-11T11:56:29Z date_published: 2014-02-20T00:00:00Z date_updated: 2021-01-12T06:56:11Z day: '20' department: - _id: SyCr doi: 10.1038/nature12977 intvolume: ' 506' issue: '7488' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/ month: '02' oa: 1 oa_version: Submitted Version page: 364 - 366 publication: Nature publication_identifier: issn: - '00280836' publication_status: published publisher: Nature Publishing Group publist_id: '4726' quality_controlled: '1' scopus_import: 1 status: public title: Disease associations between honeybees and bumblebees as a threat to wild pollinators type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 506 year: '2014' ... --- _id: '2241' abstract: - lang: eng text: 'The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage.' author: - first_name: Kaoru full_name: Beppu, Kaoru last_name: Beppu - first_name: Takuya full_name: Sasaki, Takuya last_name: Sasaki - first_name: Kenji full_name: Tanaka, Kenji last_name: Tanaka - first_name: Akihiro full_name: Yamanaka, Akihiro last_name: Yamanaka - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Ko full_name: Matsui, Ko last_name: Matsui citation: ama: Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 2014;81(2):314-320. doi:10.1016/j.neuron.2013.11.011 apa: Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R., & Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.11.011 chicago: Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2013.11.011. ieee: K. Beppu et al., “Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage,” Neuron, vol. 81, no. 2. Elsevier, pp. 314–320, 2014. ista: Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K. 2014. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 81(2), 314–320. mla: Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” Neuron, vol. 81, no. 2, Elsevier, 2014, pp. 314–20, doi:10.1016/j.neuron.2013.11.011. short: K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K. Matsui, Neuron 81 (2014) 314–320. date_created: 2018-12-11T11:56:31Z date_published: 2014-01-22T00:00:00Z date_updated: 2021-01-12T06:56:14Z day: '22' department: - _id: RySh doi: 10.1016/j.neuron.2013.11.011 intvolume: ' 81' issue: '2' language: - iso: eng month: '01' oa_version: None page: 314 - 320 publication: Neuron publication_identifier: issn: - '08966273' publication_status: published publisher: Elsevier publist_id: '4715' quality_controlled: '1' scopus_import: 1 status: public title: Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2014' ... --- _id: '2245' abstract: - lang: eng text: 'Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. ' alternative_title: - Methods in Molecular Biology author: - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Petr full_name: Skůpa, Petr last_name: Skůpa - first_name: Petre full_name: Dobrev, Petre last_name: Dobrev - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds. Plant Chemical Genomics. Vol 1056. Methods in Molecular Biology. Springer; 2014:255-264. doi:10.1007/978-1-62703-592-7_23' apa: 'Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., & Friml, J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In G. Hicks & S. Robert (Eds.), Plant Chemical Genomics (Vol. 1056, pp. 255–264). Springer. https://doi.org/10.1007/978-1-62703-592-7_23' chicago: 'Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” In Plant Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64. Methods in Molecular Biology. Springer, 2014. https://doi.org/10.1007/978-1-62703-592-7_23.' ieee: 'S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml, “Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters,” in Plant Chemical Genomics, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014, pp. 255–264.' ista: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Plant Chemical Genomics. Methods in Molecular Biology, vol. 1056, 255–264.' mla: 'Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” Plant Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, vol. 1056, Springer, 2014, pp. 255–64, doi:10.1007/978-1-62703-592-7_23.' short: S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:, G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264. date_created: 2018-12-11T11:56:32Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:56:15Z day: '01' department: - _id: JiFr doi: 10.1007/978-1-62703-592-7_23 editor: - first_name: Glenn full_name: Hicks, Glenn last_name: Hicks - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert intvolume: ' 1056' language: - iso: eng month: '01' oa_version: None page: 255 - 264 publication: Plant Chemical Genomics publication_identifier: issn: - '10643745' publication_status: published publisher: Springer publist_id: '4704' quality_controlled: '1' scopus_import: 1 series_title: Methods in Molecular Biology status: public title: 'Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters' type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1056 year: '2014' ... --- _id: '2246' abstract: - lang: eng text: 'Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. ' author: - first_name: Andrey full_name: Grinshpun, Andrey last_name: Grinshpun - first_name: Pakawat full_name: Phalitnonkiat, Pakawat last_name: Phalitnonkiat - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin - first_name: Andrei full_name: Tarfulea, Andrei last_name: Tarfulea citation: ama: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller and parity games. Theoretical Computer Science. 2014;521:73-91. doi:10.1016/j.tcs.2013.11.032 apa: Grinshpun, A., Phalitnonkiat, P., Rubin, S., & Tarfulea, A. (2014). Alternating traps in Muller and parity games. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2013.11.032 chicago: Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea. “Alternating Traps in Muller and Parity Games.” Theoretical Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2013.11.032. ieee: A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps in Muller and parity games,” Theoretical Computer Science, vol. 521. Elsevier, pp. 73–91, 2014. ista: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps in Muller and parity games. Theoretical Computer Science. 521, 73–91. mla: Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” Theoretical Computer Science, vol. 521, Elsevier, 2014, pp. 73–91, doi:10.1016/j.tcs.2013.11.032. short: A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer Science 521 (2014) 73–91. date_created: 2018-12-11T11:56:33Z date_published: 2014-02-13T00:00:00Z date_updated: 2021-01-12T06:56:16Z day: '13' department: - _id: KrCh doi: 10.1016/j.tcs.2013.11.032 intvolume: ' 521' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.3777 month: '02' oa: 1 oa_version: Submitted Version page: 73 - 91 publication: Theoretical Computer Science publication_identifier: issn: - '03043975' publication_status: published publisher: Elsevier publist_id: '4703' quality_controlled: '1' scopus_import: 1 status: public title: Alternating traps in Muller and parity games type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 521 year: '2014' ... --- _id: '2242' abstract: - lang: eng text: MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages. author: - first_name: Anne full_name: Dueck, Anne last_name: Dueck - first_name: Alexander full_name: Eichner, Alexander id: 4DFA52AE-F248-11E8-B48F-1D18A9856A87 last_name: Eichner - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Gunter full_name: Meister, Gunter last_name: Meister citation: ama: Dueck A, Eichner A, Sixt MK, Meister G. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. 2014;588(4):632-640. doi:10.1016/j.febslet.2014.01.009 apa: Dueck, A., Eichner, A., Sixt, M. K., & Meister, G. (2014). A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. Elsevier. https://doi.org/10.1016/j.febslet.2014.01.009 chicago: Dueck, Anne, Alexander Eichner, Michael K Sixt, and Gunter Meister. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” FEBS Letters. Elsevier, 2014. https://doi.org/10.1016/j.febslet.2014.01.009. ieee: A. Dueck, A. Eichner, M. K. Sixt, and G. Meister, “A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation,” FEBS Letters, vol. 588, no. 4. Elsevier, pp. 632–640, 2014. ista: Dueck A, Eichner A, Sixt MK, Meister G. 2014. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. 588(4), 632–640. mla: Dueck, Anne, et al. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” FEBS Letters, vol. 588, no. 4, Elsevier, 2014, pp. 632–40, doi:10.1016/j.febslet.2014.01.009. short: A. Dueck, A. Eichner, M.K. Sixt, G. Meister, FEBS Letters 588 (2014) 632–640. date_created: 2018-12-11T11:56:31Z date_published: 2014-02-14T00:00:00Z date_updated: 2021-01-12T06:56:14Z day: '14' department: - _id: MiSi doi: 10.1016/j.febslet.2014.01.009 intvolume: ' 588' issue: '4' language: - iso: eng month: '02' oa_version: None page: 632 - 640 publication: FEBS Letters publication_identifier: issn: - '00145793' publication_status: published publisher: Elsevier publist_id: '4714' quality_controlled: '1' scopus_import: 1 status: public title: A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 588 year: '2014' ... --- _id: '2250' abstract: - lang: eng text: The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as "genus specific" by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virionsd. author: - first_name: Durga full_name: Kuchibhatla, Durga last_name: Kuchibhatla - first_name: Westley full_name: Sherman, Westley last_name: Sherman - first_name: Betty full_name: Chung, Betty last_name: Chung - first_name: Shelley full_name: Cook, Shelley last_name: Cook - first_name: Georg full_name: Schneider, Georg id: 329095A0-F248-11E8-B48F-1D18A9856A87 last_name: Schneider - first_name: Birgit full_name: Eisenhaber, Birgit last_name: Eisenhaber - first_name: David full_name: Karlin, David last_name: Karlin citation: ama: Kuchibhatla D, Sherman W, Chung B, et al. Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently “orphan” viral proteins. Journal of Virology. 2014;88(1):10-20. doi:10.1128/JVI.02595-13 apa: Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber, B., & Karlin, D. (2014). Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently “orphan” viral proteins. Journal of Virology. ASM. https://doi.org/10.1128/JVI.02595-13 chicago: Kuchibhatla, Durga, Westley Sherman, Betty Chung, Shelley Cook, Georg Schneider, Birgit Eisenhaber, and David Karlin. “Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’ Viral Proteins.” Journal of Virology. ASM, 2014. https://doi.org/10.1128/JVI.02595-13. ieee: D. Kuchibhatla et al., “Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’ viral proteins,” Journal of Virology, vol. 88, no. 1. ASM, pp. 10–20, 2014. ista: Kuchibhatla D, Sherman W, Chung B, Cook S, Schneider G, Eisenhaber B, Karlin D. 2014. Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’ viral proteins. Journal of Virology. 88(1), 10–20. mla: Kuchibhatla, Durga, et al. “Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’ Viral Proteins.” Journal of Virology, vol. 88, no. 1, ASM, 2014, pp. 10–20, doi:10.1128/JVI.02595-13. short: D. Kuchibhatla, W. Sherman, B. Chung, S. Cook, G. Schneider, B. Eisenhaber, D. Karlin, Journal of Virology 88 (2014) 10–20. date_created: 2018-12-11T11:56:34Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:56:17Z day: '01' ddc: - '570' department: - _id: MD doi: 10.1128/JVI.02595-13 file: - access_level: open_access checksum: 2c121b5e884992dfec5605bdf4e659da content_type: application/pdf creator: system date_created: 2018-12-12T10:13:43Z date_updated: 2020-07-14T12:45:34Z file_id: '5029' file_name: IST-2016-417-v1+1_J._Virol.-2014-Kuchibhatla-10-20.pdf file_size: 825756 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 88' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 10 - 20 publication: Journal of Virology publication_identifier: issn: - 0022538X publication_status: published publisher: ASM publist_id: '4698' pubrep_id: '417' quality_controlled: '1' scopus_import: 1 status: public title: Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins 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: 88 year: '2014' ... --- _id: '2254' abstract: - lang: eng text: Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus. author: - first_name: Alejandro full_name: Pernia-Andrade, Alejandro id: 36963E98-F248-11E8-B48F-1D18A9856A87 last_name: Pernia-Andrade - 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: Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 2014;81(1):140-152. doi:10.1016/j.neuron.2013.09.046 apa: Pernia-Andrade, A., & Jonas, P. M. (2014). Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.046 chicago: Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2013.09.046. ieee: A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations,” Neuron, vol. 81, no. 1. Elsevier, pp. 140–152, 2014. ista: Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 81(1), 140–152. mla: Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” Neuron, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:10.1016/j.neuron.2013.09.046. short: A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152. date_created: 2018-12-11T11:56:35Z date_published: 2014-01-08T00:00:00Z date_updated: 2021-01-12T06:56:19Z day: '08' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2013.09.046 ec_funded: 1 file: - access_level: open_access checksum: 438547cfcd9045a22f065f2019f07849 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:48Z date_updated: 2020-07-14T12:45:35Z file_id: '4773' file_name: IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf file_size: 4373072 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' intvolume: ' 81' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 140 - 152 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: Neuron publication_identifier: issn: - '08966273' publication_status: published publisher: Elsevier publist_id: '4692' pubrep_id: '422' quality_controlled: '1' scopus_import: 1 status: public title: Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2014' ... --- _id: '2251' abstract: - lang: eng text: 'Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps.' acknowledgement: CC BY 3.0 article_number: '20120528' article_processing_charge: No author: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: David full_name: Dupret, David last_name: Dupret citation: ama: Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2014;369(1635). doi:10.1098/rstb.2012.0528 apa: Csicsvari, J. L., & Dupret, D. (2014). Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2012.0528 chicago: Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2014. https://doi.org/10.1098/rstb.2012.0528. ieee: J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and learning-associated hippocampal maps,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635. Royal Society, The, 2014. ista: Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 369(1635), 20120528. mla: Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635, 20120528, Royal Society, The, 2014, doi:10.1098/rstb.2012.0528. short: J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 369 (2014). date_created: 2018-12-11T11:56:34Z date_published: 2014-02-05T00:00:00Z date_updated: 2021-01-12T06:56:18Z day: '05' ddc: - '570' department: - _id: JoCs doi: 10.1098/rstb.2012.0528 external_id: pmid: - '24366138' file: - access_level: open_access checksum: 51beb33de71c9c19e0c205a20d206f9a content_type: application/pdf creator: system date_created: 2018-12-12T10:13:24Z date_updated: 2020-07-14T12:45:34Z file_id: '5006' file_name: IST-2016-527-v1+1_20120528.full.pdf file_size: 771896 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 369' issue: '1635' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_identifier: issn: - '09628436' publication_status: published publisher: Royal Society, The publist_id: '4697' pubrep_id: '527' quality_controlled: '1' scopus_import: 1 status: public title: Sharp wave/ripple network oscillations and learning-associated hippocampal 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 369 year: '2014' ... --- _id: '2253' abstract: - lang: eng text: Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation. article_processing_charge: No article_type: original author: - first_name: Aurélien full_name: Bailly, Aurélien last_name: Bailly - first_name: Bangjun full_name: Wang, Bangjun last_name: Wang - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Stephan full_name: Pollmann, Stephan last_name: Pollmann - first_name: Daniel full_name: Schenck, Daniel last_name: Schenck - first_name: Hartwig full_name: Lüthen, Hartwig last_name: Lüthen - first_name: Alexander full_name: Schulz, Alexander last_name: Schulz - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Markus full_name: Geisler, Markus last_name: Geisler citation: ama: Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 2014;77(1):108-118. doi:10.1111/tpj.12369 apa: Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., … Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/tpj.12369 chicago: Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” Plant Journal. Wiley-Blackwell, 2014. https://doi.org/10.1111/tpj.12369. ieee: A. Bailly et al., “Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth,” Plant Journal, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014. ista: Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 77(1), 108–118. mla: Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” Plant Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:10.1111/tpj.12369. short: A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz, J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118. date_created: 2018-12-11T11:56:35Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:56:18Z day: '01' department: - _id: JiFr doi: 10.1111/tpj.12369 intvolume: ' 77' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/tpj.12369 month: '01' oa: 1 oa_version: Published Version page: 108 - 118 project: - _id: 256BDAB0-B435-11E9-9278-68D0E5697425 name: Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur publication: Plant Journal publication_identifier: issn: - '09607412' publication_status: published publisher: Wiley-Blackwell publist_id: '4694' quality_controlled: '1' scopus_import: 1 status: public title: Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2014' ... --- _id: '2248' abstract: - lang: eng text: 'Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.' author: - first_name: Daniel full_name: Capek, Daniel id: 31C42484-F248-11E8-B48F-1D18A9856A87 last_name: Capek orcid: 0000-0001-5199-9940 - first_name: Brian full_name: Metscher, Brian last_name: Metscher - first_name: Gerd full_name: Müller, Gerd last_name: Müller citation: ama: 'Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2014;322(1):1-12. doi:10.1002/jez.b.22545' apa: 'Capek, D., Metscher, B., & Müller, G. (2014). Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley-Blackwell. https://doi.org/10.1002/jez.b.22545' chicago: 'Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/jez.b.22545.' ieee: 'D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic approach to avian digit homology,” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 322, no. 1. Wiley-Blackwell, pp. 1–12, 2014.' ista: 'Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 322(1), 1–12.' mla: 'Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12, doi:10.1002/jez.b.22545.' short: 'D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322 (2014) 1–12.' date_created: 2018-12-11T11:56:33Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:56:16Z day: '01' department: - _id: CaHe doi: 10.1002/jez.b.22545 intvolume: ' 322' issue: '1' language: - iso: eng month: '01' oa_version: None page: 1 - 12 publication: 'Journal of Experimental Zoology Part B: Molecular and Developmental Evolution' publication_identifier: issn: - '15525007' publication_status: published publisher: Wiley-Blackwell publist_id: '4701' quality_controlled: '1' scopus_import: 1 status: public title: 'Thumbs down: A molecular-morphogenetic approach to avian digit homology' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 322 year: '2014' ... --- _id: '2249' abstract: - lang: eng text: The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes. author: - first_name: Yani full_name: Chen, Yani last_name: Chen - first_name: Kyaw full_name: Aung, Kyaw last_name: Aung - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Kathryn full_name: Walicki, Kathryn last_name: Walicki - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Federica full_name: Brandizzí, Federica last_name: Brandizzí citation: ama: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 2014;77(1):97-107. doi:10.1111/tpj.12373 apa: Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., & Brandizzí, F. (2014). Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/tpj.12373 chicago: Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” Plant Journal. Wiley-Blackwell, 2014. https://doi.org/10.1111/tpj.12373. ieee: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation of the unfolded protein response and auxin signaling,” Plant Journal, vol. 77, no. 1. Wiley-Blackwell, pp. 97–107, 2014. ista: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107. mla: Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” Plant Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107, doi:10.1111/tpj.12373. short: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal 77 (2014) 97–107. date_created: 2018-12-11T11:56:34Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:56:17Z day: '01' department: - _id: JiFr doi: 10.1111/tpj.12373 intvolume: ' 77' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/ month: '01' oa: 1 oa_version: Submitted Version page: 97 - 107 publication: Plant Journal publication_identifier: issn: - '09607412' publication_status: published publisher: Wiley-Blackwell publist_id: '4699' quality_controlled: '1' scopus_import: 1 status: public title: Inter-regulation of the unfolded protein response and auxin signaling type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2014' ... --- _id: '2252' abstract: - lang: eng text: The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila. article_processing_charge: No author: - first_name: Sujal full_name: Phadke, Sujal last_name: Phadke - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Tuan full_name: Pham, Tuan last_name: Pham - first_name: Stephanie full_name: Pham, Stephanie last_name: Pham - first_name: Rebecca full_name: Zufall, Rebecca last_name: Zufall citation: ama: Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063 apa: Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063 chicago: Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University Press, 2014. https://doi.org/10.1093/jhered/est063. ieee: S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014. ista: Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135. mla: Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063. short: S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135. date_created: 2018-12-11T11:56:35Z date_published: 2014-01-01T00:00:00Z date_updated: 2022-08-25T14:45:42Z day: '01' department: - _id: NiBa doi: 10.1093/jhered/est063 intvolume: ' 105' issue: '1' language: - iso: eng month: '01' oa_version: None page: 130 - 135 publication: Journal of Heredity publication_identifier: issn: - '00221503' publication_status: published publisher: Oxford University Press publist_id: '4695' quality_controlled: '1' scopus_import: '1' status: public title: Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 105 year: '2014' ...