--- _id: '849' abstract: - lang: eng text: Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. acknowledgement: |- We thank D. Söll, H. Grosjean, and L. Filonava for comments and suggestions. M.O. and P.D.D. thank the Barcelona Supercomputing Center for CPU/GPU time on MareNostrum/ MinoTauro. P.D.D. is a PEDECIBA (Programa de Desarrollo de las Ciencias Básicas) and an SNI (Sistema Nacional de Investigadores) (ANII, Uruguay) researcher. Funding: This work was supported in part by the Spanish Ministry of Economy and Competitiveness (grants BIO2012-32200, Sev-2012-0208, and BIO2012-32868 to L.R.d.P., F.A.K., and M.O., respectively) and by the Catalan Government (grants 2014-SGR-0771, 2014-SGR-0974, and 2014-SGR-0134 to L.R.d.P., F.A.K., and M.O., respectively). This work was also supported by the Howard Hughes Medical Institute International Early Career Scientist Program (55007424), by a European Research Council (ERC) Starting Grant (335980_EinME to F.K.), and by a grant from the ERC (ERC_SimDNA to M.O). A.G.T. and C.B. are funded by the Spanish Ministry of Economy and Competitiveness (FPDI-2013-17742 and BES-2013-064004, respectively). author: - first_name: Adélaïde full_name: Saint-Léger, Adélaïde last_name: Saint Léger - first_name: Carla full_name: Bello, Carla last_name: Bello - first_name: Pablo full_name: Dans, Pablo D last_name: Dans - first_name: Adrian full_name: Torres, Adrian G last_name: Torres - first_name: Eva full_name: Novoa, Eva M last_name: Novoa - first_name: Noelia full_name: Camacho, Noelia last_name: Camacho - first_name: Modesto full_name: Orozco, Modesto last_name: Orozco - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Lluís full_name: Ribas De Pouplana, Lluís last_name: Ribas De Pouplana citation: ama: Saint Léger A, Bello C, Dans P, et al. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances. 2016;2(4):e1501860-e1501860. doi:10.1126/sciadv.1501860 apa: Saint Léger, A., Bello, C., Dans, P., Torres, A., Novoa, E., Camacho, N., … Ribas De Pouplana, L. (2016). Saturation of recognition elements blocks evolution of new tRNA identities. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.1501860 chicago: Saint Léger, Adélaïde, Carla Bello, Pablo Dans, Adrian Torres, Eva Novoa, Noelia Camacho, Modesto Orozco, Fyodor Kondrashov, and Lluís Ribas De Pouplana. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/sciadv.1501860. ieee: A. Saint Léger et al., “Saturation of recognition elements blocks evolution of new tRNA identities,” Science advances, vol. 2, no. 4. American Association for the Advancement of Science, pp. e1501860–e1501860, 2016. ista: Saint Léger A, Bello C, Dans P, Torres A, Novoa E, Camacho N, Orozco M, Kondrashov F, Ribas De Pouplana L. 2016. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances. 2(4), e1501860–e1501860. mla: Saint Léger, Adélaïde, et al. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances, vol. 2, no. 4, American Association for the Advancement of Science, 2016, pp. e1501860–e1501860, doi:10.1126/sciadv.1501860. short: A. Saint Léger, C. Bello, P. Dans, A. Torres, E. Novoa, N. Camacho, M. Orozco, F. Kondrashov, L. Ribas De Pouplana, Science Advances 2 (2016) e1501860–e1501860. date_created: 2018-12-11T11:48:50Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T08:19:38Z day: '01' doi: 10.1126/sciadv.1501860 extern: 1 intvolume: ' 2' issue: '4' license: https://creativecommons.org/licenses/by-nc/4.0/ month: '04' page: e1501860 - e1501860 publication: Science advances publication_status: published publisher: American Association for the Advancement of Science publist_id: '6798' quality_controlled: 0 status: public title: Saturation of recognition elements blocks evolution of new tRNA identities 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 volume: 2 year: '2016' ... --- _id: '8493' abstract: - lang: eng text: In this paper we study a so-called separatrix map introduced by Zaslavskii–Filonenko (Sov Phys JETP 27:851–857, 1968) and studied by Treschev (Physica D 116(1–2):21–43, 1998; J Nonlinear Sci 12(1):27–58, 2002), Piftankin (Nonlinearity (19):2617–2644, 2006) Piftankin and Treshchëv (Uspekhi Mat Nauk 62(2(374)):3–108, 2007). We derive a second order expansion of this map for trigonometric perturbations. In Castejon et al. (Random iteration of maps of a cylinder and diffusive behavior. Preprint available at arXiv:1501.03319, 2015), Guardia and Kaloshin (Stochastic diffusive behavior through big gaps in a priori unstable systems (in preparation), 2015), and Kaloshin et al. (Normally Hyperbolic Invariant Laminations and diffusive behavior for the generalized Arnold example away from resonances. Preprint available at http://www.terpconnect.umd.edu/vkaloshi/, 2015), applying the results of the present paper, we describe a class of nearly integrable deterministic systems with stochastic diffusive behavior. article_processing_charge: No article_type: original author: - first_name: M. full_name: Guardia, M. last_name: Guardia - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: J. full_name: Zhang, J. last_name: Zhang citation: ama: Guardia M, Kaloshin V, Zhang J. A second order expansion of the separatrix map for trigonometric perturbations of a priori unstable systems. Communications in Mathematical Physics. 2016;348:321-361. doi:10.1007/s00220-016-2705-9 apa: Guardia, M., Kaloshin, V., & Zhang, J. (2016). A second order expansion of the separatrix map for trigonometric perturbations of a priori unstable systems. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-016-2705-9 chicago: Guardia, M., Vadim Kaloshin, and J. Zhang. “A Second Order Expansion of the Separatrix Map for Trigonometric Perturbations of a Priori Unstable Systems.” Communications in Mathematical Physics. Springer Nature, 2016. https://doi.org/10.1007/s00220-016-2705-9. ieee: M. Guardia, V. Kaloshin, and J. Zhang, “A second order expansion of the separatrix map for trigonometric perturbations of a priori unstable systems,” Communications in Mathematical Physics, vol. 348. Springer Nature, pp. 321–361, 2016. ista: Guardia M, Kaloshin V, Zhang J. 2016. A second order expansion of the separatrix map for trigonometric perturbations of a priori unstable systems. Communications in Mathematical Physics. 348, 321–361. mla: Guardia, M., et al. “A Second Order Expansion of the Separatrix Map for Trigonometric Perturbations of a Priori Unstable Systems.” Communications in Mathematical Physics, vol. 348, Springer Nature, 2016, pp. 321–61, doi:10.1007/s00220-016-2705-9. short: M. Guardia, V. Kaloshin, J. Zhang, Communications in Mathematical Physics 348 (2016) 321–361. date_created: 2020-09-18T10:45:50Z date_published: 2016-11-01T00:00:00Z date_updated: 2021-01-12T08:19:39Z day: '01' doi: 10.1007/s00220-016-2705-9 extern: '1' intvolume: ' 348' language: - iso: eng month: '11' oa_version: None page: 321-361 publication: Communications in Mathematical Physics publication_identifier: issn: - 0010-3616 - 1432-0916 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: A second order expansion of the separatrix map for trigonometric perturbations of a priori unstable systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 348 year: '2016' ... --- _id: '8494' abstract: - lang: eng text: "We prove a form of Arnold diffusion in the a-priori stable case. Let\r\nH0(p)+ϵH1(θ,p,t),θ∈Tn,p∈Bn,t∈T=R/T,\r\nbe a nearly integrable system of arbitrary degrees of freedom n⩾2 with a strictly convex H0. We show that for a “generic” ϵH1, there exists an orbit (θ,p) satisfying\r\n∥p(t)−p(0)∥>l(H1)>0,\r\nwhere l(H1) is independent of ϵ. The diffusion orbit travels along a codimension-1 resonance, and the only obstruction to our construction is a finite set of additional resonances.\r\n\r\nFor the proof we use a combination of geometric and variational methods, and manage to adapt tools which have recently been developed in the a-priori unstable case." article_processing_charge: No article_type: original author: - first_name: Patrick full_name: Bernard, Patrick last_name: Bernard - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Ke full_name: Zhang, Ke last_name: Zhang citation: ama: Bernard P, Kaloshin V, Zhang K. Arnold diffusion in arbitrary degrees of freedom and normally hyperbolic invariant cylinders. Acta Mathematica. 2016;217(1):1-79. doi:10.1007/s11511-016-0141-5 apa: Bernard, P., Kaloshin, V., & Zhang, K. (2016). Arnold diffusion in arbitrary degrees of freedom and normally hyperbolic invariant cylinders. Acta Mathematica. Institut Mittag-Leffler. https://doi.org/10.1007/s11511-016-0141-5 chicago: Bernard, Patrick, Vadim Kaloshin, and Ke Zhang. “Arnold Diffusion in Arbitrary Degrees of Freedom and Normally Hyperbolic Invariant Cylinders.” Acta Mathematica. Institut Mittag-Leffler, 2016. https://doi.org/10.1007/s11511-016-0141-5. ieee: P. Bernard, V. Kaloshin, and K. Zhang, “Arnold diffusion in arbitrary degrees of freedom and normally hyperbolic invariant cylinders,” Acta Mathematica, vol. 217, no. 1. Institut Mittag-Leffler, pp. 1–79, 2016. ista: Bernard P, Kaloshin V, Zhang K. 2016. Arnold diffusion in arbitrary degrees of freedom and normally hyperbolic invariant cylinders. Acta Mathematica. 217(1), 1–79. mla: Bernard, Patrick, et al. “Arnold Diffusion in Arbitrary Degrees of Freedom and Normally Hyperbolic Invariant Cylinders.” Acta Mathematica, vol. 217, no. 1, Institut Mittag-Leffler, 2016, pp. 1–79, doi:10.1007/s11511-016-0141-5. short: P. Bernard, V. Kaloshin, K. Zhang, Acta Mathematica 217 (2016) 1–79. date_created: 2020-09-18T10:46:07Z date_published: 2016-09-28T00:00:00Z date_updated: 2021-01-12T08:19:39Z day: '28' doi: 10.1007/s11511-016-0141-5 extern: '1' intvolume: ' 217' issue: '1' language: - iso: eng month: '09' oa_version: None page: 1-79 publication: Acta Mathematica publication_identifier: issn: - 0001-5962 publication_status: published publisher: Institut Mittag-Leffler quality_controlled: '1' status: public title: Arnold diffusion in arbitrary degrees of freedom and normally hyperbolic invariant cylinders type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 217 year: '2016' ... --- _id: '8496' article_processing_charge: No article_type: original author: - first_name: Artur full_name: Avila, Artur last_name: Avila - first_name: Jacopo full_name: De Simoi, Jacopo last_name: De Simoi - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Avila A, De Simoi J, Kaloshin V. An integrable deformation of an ellipse of small eccentricity is an ellipse. Annals of Mathematics. 2016;184(2):527-558. doi:10.4007/annals.2016.184.2.5 apa: Avila, A., De Simoi, J., & Kaloshin, V. (2016). An integrable deformation of an ellipse of small eccentricity is an ellipse. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2016.184.2.5 chicago: Avila, Artur, Jacopo De Simoi, and Vadim Kaloshin. “An Integrable Deformation of an Ellipse of Small Eccentricity Is an Ellipse.” Annals of Mathematics. Princeton University Press, 2016. https://doi.org/10.4007/annals.2016.184.2.5. ieee: A. Avila, J. De Simoi, and V. Kaloshin, “An integrable deformation of an ellipse of small eccentricity is an ellipse,” Annals of Mathematics, vol. 184, no. 2. Princeton University Press, pp. 527–558, 2016. ista: Avila A, De Simoi J, Kaloshin V. 2016. An integrable deformation of an ellipse of small eccentricity is an ellipse. Annals of Mathematics. 184(2), 527–558. mla: Avila, Artur, et al. “An Integrable Deformation of an Ellipse of Small Eccentricity Is an Ellipse.” Annals of Mathematics, vol. 184, no. 2, Princeton University Press, 2016, pp. 527–58, doi:10.4007/annals.2016.184.2.5. short: A. Avila, J. De Simoi, V. Kaloshin, Annals of Mathematics 184 (2016) 527–558. date_created: 2020-09-18T10:46:22Z date_published: 2016-09-01T00:00:00Z date_updated: 2021-01-12T08:19:40Z day: '01' doi: 10.4007/annals.2016.184.2.5 extern: '1' intvolume: ' 184' issue: '2' language: - iso: eng month: '09' oa_version: None page: 527-558 publication: Annals of Mathematics publication_identifier: issn: - 0003-486X publication_status: published publisher: Princeton University Press quality_controlled: '1' status: public title: An integrable deformation of an ellipse of small eccentricity is an ellipse type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 184 year: '2016' ... --- _id: '8497' abstract: - lang: eng text: "We study the dynamics of the restricted planar three-body problem near mean motion resonances, i.e. a resonance involving the Keplerian periods of the two lighter bodies revolving around the most massive one. This problem is often used to model Sun–Jupiter–asteroid systems. For the primaries (Sun and Jupiter), we pick a realistic mass ratio μ=10−3 and a small eccentricity e0>0. The main result is a construction of a variety of non local diffusing orbits which show a drastic change of the osculating (instant) eccentricity of the asteroid, while the osculating semi major axis is kept almost constant. The proof relies on the careful analysis of the circular problem, which has a hyperbolic structure, but for which diffusion is prevented by KAM tori. In the proof we verify certain non-degeneracy conditions numerically.\r\n\r\nBased on the work of Treschev, it is natural to conjecture that the time of diffusion for this problem is ∼−ln(μe0)μ3/2e0. We expect our instability mechanism to apply to realistic values of e0 and we give heuristic arguments in its favor. If so, the applicability of Nekhoroshev theory to the three-body problem as well as the long time stability become questionable.\r\n\r\nIt is well known that, in the Asteroid Belt, located between the orbits of Mars and Jupiter, the distribution of asteroids has the so-called Kirkwood gaps exactly at mean motion resonances of low order. Our mechanism gives a possible explanation of their existence. To relate the existence of Kirkwood gaps with Arnol'd diffusion, we also state a conjecture on its existence for a typical ϵ-perturbation of the product of the pendulum and the rotator. Namely, we predict that a positive conditional measure of initial conditions concentrated in the main resonance exhibits Arnol’d diffusion on time scales −lnϵϵ2." article_processing_charge: No article_type: original author: - first_name: Jacques full_name: Féjoz, Jacques last_name: Féjoz - first_name: Marcel full_name: Guàrdia, Marcel last_name: Guàrdia - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Pablo full_name: Roldán, Pablo last_name: Roldán citation: ama: Féjoz J, Guàrdia M, Kaloshin V, Roldán P. Kirkwood gaps and diffusion along mean motion resonances in the restricted planar three-body problem. Journal of the European Mathematical Society. 2016;18(10):2315-2403. doi:10.4171/jems/642 apa: Féjoz, J., Guàrdia, M., Kaloshin, V., & Roldán, P. (2016). Kirkwood gaps and diffusion along mean motion resonances in the restricted planar three-body problem. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/642 chicago: Féjoz, Jacques, Marcel Guàrdia, Vadim Kaloshin, and Pablo Roldán. “Kirkwood Gaps and Diffusion along Mean Motion Resonances in the Restricted Planar Three-Body Problem.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2016. https://doi.org/10.4171/jems/642. ieee: J. Féjoz, M. Guàrdia, V. Kaloshin, and P. Roldán, “Kirkwood gaps and diffusion along mean motion resonances in the restricted planar three-body problem,” Journal of the European Mathematical Society, vol. 18, no. 10. European Mathematical Society Publishing House, pp. 2315–2403, 2016. ista: Féjoz J, Guàrdia M, Kaloshin V, Roldán P. 2016. Kirkwood gaps and diffusion along mean motion resonances in the restricted planar three-body problem. Journal of the European Mathematical Society. 18(10), 2315–2403. mla: Féjoz, Jacques, et al. “Kirkwood Gaps and Diffusion along Mean Motion Resonances in the Restricted Planar Three-Body Problem.” Journal of the European Mathematical Society, vol. 18, no. 10, European Mathematical Society Publishing House, 2016, pp. 2315–403, doi:10.4171/jems/642. short: J. Féjoz, M. Guàrdia, V. Kaloshin, P. Roldán, Journal of the European Mathematical Society 18 (2016) 2315–2403. date_created: 2020-09-18T10:46:31Z date_published: 2016-09-19T00:00:00Z date_updated: 2021-01-12T08:19:41Z day: '19' doi: 10.4171/jems/642 extern: '1' intvolume: ' 18' issue: '10' language: - iso: eng month: '09' oa_version: None page: 2315-2403 publication: Journal of the European Mathematical Society publication_identifier: issn: - 1435-9855 publication_status: published publisher: European Mathematical Society Publishing House quality_controlled: '1' status: public title: Kirkwood gaps and diffusion along mean motion resonances in the restricted planar three-body problem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2016' ... --- _id: '850' abstract: - lang: eng text: Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea Victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design. acknowledgement: We thank Y. Kulikova and G. Filion for discussion on statistical analysis and I. Osterman, R. Moretti and J. Meiler for technical assistance and M. Friesen for a critical reading of the manuscript. We thank H. Himmelbauer, CRG Genomic Unit and the Russian Science Foundation project (14-50-00150) for sequencing. Experiments were partially carried out using the equipment provided by the IBCH core facility (CKP IBCH). The work was supported by HHMI International Early Career Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329), Spanish Ministry of Economy and Competitiveness Centro de Excelencia Severo Ochoa 2013-2017 grant (SEV-2012-0208), Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat's AGAUR program (2014 SGR 0974), Russian Science Foundation (14-25-00129) and the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013, ERC grant agreement, 335980-EinME). author: - first_name: Karen full_name: Karen Sarkisyan id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Dmitry full_name: Bolotin, Dmitry A last_name: Bolotin - first_name: Margarita full_name: Meer, Margarita V last_name: Meer - first_name: Dinara full_name: Usmanova, Dinara R last_name: Usmanova - first_name: Alexander full_name: Mishin, Alexander S last_name: Mishin - first_name: George full_name: Sharonov, George V last_name: Sharonov - first_name: Dmitry full_name: Ivankov, Dmitry N last_name: Ivankov - first_name: Nina full_name: Bozhanova, Nina G last_name: Bozhanova - first_name: Mikhail full_name: Baranov, Mikhail S last_name: Baranov - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Natalya full_name: Bogatyreva, Natalya S last_name: Bogatyreva - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Evgeny full_name: Egorov, Evgeny S last_name: Egorov - first_name: Maria full_name: Logacheva, Maria D last_name: Logacheva - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Dmitriy full_name: Chudakov, Dmitriy M last_name: Chudakov - first_name: Ekaterina full_name: Putintseva, Ekaterina V last_name: Putintseva - first_name: Ilgar full_name: Mamedov, Ilgar Z last_name: Mamedov - first_name: Dan full_name: Tawfik, Dan S last_name: Tawfik - first_name: Konstantin full_name: Lukyanov, Konstantin A last_name: Lukyanov - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Sarkisyan K, Bolotin D, Meer M, et al. Local fitness landscape of the green fluorescent protein. Nature. 2016;533:397-401. doi:10.1038/nature17995 apa: Sarkisyan, K., Bolotin, D., Meer, M., Usmanova, D., Mishin, A., Sharonov, G., … Kondrashov, F. (2016). Local fitness landscape of the green fluorescent protein. Nature. Nature Publishing Group. https://doi.org/10.1038/nature17995 chicago: Sarkisyan, Karen, Dmitry Bolotin, Margarita Meer, Dinara Usmanova, Alexander Mishin, George Sharonov, Dmitry Ivankov, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature17995. ieee: K. Sarkisyan et al., “Local fitness landscape of the green fluorescent protein,” Nature, vol. 533. Nature Publishing Group, pp. 397–401, 2016. ista: Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533, 397–401. mla: Sarkisyan, Karen, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” Nature, vol. 533, Nature Publishing Group, 2016, pp. 397–401, doi:10.1038/nature17995. short: K. Sarkisyan, D. Bolotin, M. Meer, D. Usmanova, A. Mishin, G. Sharonov, D. Ivankov, N. Bozhanova, M. Baranov, O. Soylemez, N. Bogatyreva, P. Vlasov, E. Egorov, M. Logacheva, A. Kondrashov, D. Chudakov, E. Putintseva, I. Mamedov, D. Tawfik, K. Lukyanov, F. Kondrashov, Nature 533 (2016) 397–401. date_created: 2018-12-11T11:48:50Z date_published: 2016-05-11T00:00:00Z date_updated: 2021-01-12T08:19:42Z day: '11' doi: 10.1038/nature17995 extern: 1 intvolume: ' 533' month: '05' page: 397 - 401 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6799' quality_controlled: 0 status: public title: Local fitness landscape of the green fluorescent protein type: journal_article volume: 533 year: '2016' ... --- _id: '853' abstract: - lang: eng text: A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed a low abundance of methanogenic archaea and enzymes from both the carbon and nitrogen cycles, but a higher abundance of enzymes associated with the sulfur cycle. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the sampled late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments. acknowledgement: This work was supported by grants from the Russian Scientific Fund (14-14-01115) to Elizaveta Rivkina; from the National Science Foundation (DEB-1442262) to Tatiana Vish- nivetskaya; and from the HHMI International Early Career Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329 and Sev-2012-0208), and the AGAUR program (2014 SGR 0974) to Fyodor Kondrashov. Support from the Russian Scientific Fund (14-14-01115) was allocated for sample collection, gDNA isolation, and analysis of metagenomic data. author: - first_name: Elizaveta full_name: Rivkina, Elizaveta last_name: Rivkina - first_name: Lada full_name: Petrovskaya, Lada E last_name: Petrovskaya - first_name: Tatiana full_name: Vishnivetskaya, Tatiana A last_name: Vishnivetskaya - first_name: Kirill full_name: Krivushin, Kirill V last_name: Krivushin - first_name: Lyubov full_name: Shmakova, Lyubov A last_name: Shmakova - first_name: Maria full_name: Tutukina, Maria last_name: Tutukina - first_name: Arthur full_name: Meyers, Arthur J last_name: Meyers - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rivkina E, Petrovskaya L, Vishnivetskaya T, et al. Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. 2016;13(7):2207-2219. doi:10.5194/bg-13-2207-2016 apa: Rivkina, E., Petrovskaya, L., Vishnivetskaya, T., Krivushin, K., Shmakova, L., Tutukina, M., … Kondrashov, F. (2016). Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. European Geosciences Union. https://doi.org/10.5194/bg-13-2207-2016 chicago: Rivkina, Elizaveta, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin, Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences. European Geosciences Union, 2016. https://doi.org/10.5194/bg-13-2207-2016. ieee: E. Rivkina et al., “Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions,” Biogeosciences, vol. 13, no. 7. European Geosciences Union, pp. 2207–2219, 2016. ista: Rivkina E, Petrovskaya L, Vishnivetskaya T, Krivushin K, Shmakova L, Tutukina M, Meyers A, Kondrashov F. 2016. Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. 13(7), 2207–2219. mla: Rivkina, Elizaveta, et al. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences, vol. 13, no. 7, European Geosciences Union, 2016, pp. 2207–19, doi:10.5194/bg-13-2207-2016. short: E. Rivkina, L. Petrovskaya, T. Vishnivetskaya, K. Krivushin, L. Shmakova, M. Tutukina, A. Meyers, F. Kondrashov, Biogeosciences 13 (2016) 2207–2219. date_created: 2018-12-11T11:48:51Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T08:19:54Z day: '01' doi: 10.5194/bg-13-2207-2016 extern: 1 intvolume: ' 13' issue: '7' license: https://creativecommons.org/licenses/by/4.0/ month: '04' page: 2207 - 2219 publication: Biogeosciences publication_status: published publisher: European Geosciences Union publist_id: '6793' quality_controlled: 0 status: public title: Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions 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 volume: 13 year: '2016' ... --- _id: '896' abstract: - lang: eng text: Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins.Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families.We describe a family of nearly 400NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system. acknowledgement: Financial support was provided by EMBO and the DFG SFB 670 'Zellautonome Immunität' to M.L., DFG SFB 680 'Molecular basis of evolutionary innovation' to T.W., DFG SPP1819 to M.L. and T.W., the HHMI International Early Career Scientist Programme (55007424), MINECO (Sev-2012-0208), AGAUR programme (2014 SGR 0974), and an ERC Starting Grant (335980-EinME) to F.K., the European Molecular Biology Laboratory to J.M., the Wellcome Trust to K.H. (zebrafish genome sequencing project) and the National Human Genome Research Institute (NHGRI) grant HG002659 to G.K.L. (gene annotation), and a grant from the Volkswagen Foundation to P.H.S. We thank the CHEOPS support team and the Bundesland Nordrhein Westfalen for making HPC applications freely available at the University of Cologne. author: - first_name: Kerstin full_name: Howe, Kerstin L last_name: Howe - first_name: Philipp full_name: Schiffer, Philipp H last_name: Schiffer - first_name: Julia full_name: Zielinski, Julia G last_name: Zielinski - first_name: Thomas full_name: Wiehe, Thomas H last_name: Wiehe - first_name: Gavin full_name: Laird, Gavin K last_name: Laird - first_name: John full_name: Marioni, John C last_name: Marioni - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Maria full_name: Leptin, Maria last_name: Leptin citation: ama: Howe K, Schiffer P, Zielinski J, et al. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. 2016;6(4). doi:10.1098/rsob.160009 apa: Howe, K., Schiffer, P., Zielinski, J., Wiehe, T., Laird, G., Marioni, J., … Leptin, M. (2016). Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. Royal Society, The. https://doi.org/10.1098/rsob.160009 chicago: Howe, Kerstin, Philipp Schiffer, Julia Zielinski, Thomas Wiehe, Gavin Laird, John Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology. Royal Society, The, 2016. https://doi.org/10.1098/rsob.160009. ieee: K. Howe et al., “Structure and evolutionary history of a large family of NLR proteins in the zebrafish,” Open Biology, vol. 6, no. 4. Royal Society, The, 2016. ista: Howe K, Schiffer P, Zielinski J, Wiehe T, Laird G, Marioni J, Soylemez O, Kondrashov F, Leptin M. 2016. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. 6(4). mla: Howe, Kerstin, et al. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology, vol. 6, no. 4, Royal Society, The, 2016, doi:10.1098/rsob.160009. short: K. Howe, P. Schiffer, J. Zielinski, T. Wiehe, G. Laird, J. Marioni, O. Soylemez, F. Kondrashov, M. Leptin, Open Biology 6 (2016). date_created: 2018-12-11T11:49:04Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T08:21:32Z day: '01' doi: 10.1098/rsob.160009 extern: 1 intvolume: ' 6' issue: '4' month: '01' publication: Open Biology publication_status: published publisher: Royal Society, The publist_id: '6754' quality_controlled: 0 status: public title: Structure and evolutionary history of a large family of NLR proteins in the zebrafish 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 volume: 6 year: '2016' ... --- _id: '1616' abstract: - lang: eng text: The hippocampus plays a key role in learning and memory. Previous studies suggested that the main types of principal neurons, dentate gyrus granule cells (GCs), CA3 pyramidal neurons, and CA1 pyramidal neurons, differ in their activity pattern, with sparse firing in GCs and more frequent firing in CA3 and CA1 pyramidal neurons. It has been assumed but never shown that such different activity may be caused by differential synaptic excitation. To test this hypothesis, we performed high-resolution whole-cell patch-clamp recordings in anesthetized rats in vivo. In contrast to previous in vitro data, both CA3 and CA1 pyramidal neurons fired action potentials spontaneously, with a frequency of ∼3–6 Hz, whereas GCs were silent. Furthermore, both CA3 and CA1 cells primarily fired in bursts. To determine the underlying mechanisms, we quantitatively assessed the frequency of spontaneous excitatory synaptic input, the passive membrane properties, and the active membrane characteristics. Surprisingly, GCs showed comparable synaptic excitation to CA3 and CA1 cells and the highest ratio of excitation versus hyperpolarizing inhibition. Thus, differential synaptic excitation is not responsible for differences in firing. Moreover, the three types of hippocampal neurons markedly differed in their passive properties. While GCs showed the most negative membrane potential, CA3 pyramidal neurons had the highest input resistance and the slowest membrane time constant. The three types of neurons also differed in the active membrane characteristics. GCs showed the highest action potential threshold, but displayed the largest gain of the input-output curves. In conclusion, our results reveal that differential firing of the three main types of hippocampal principal neurons in vivo is not primarily caused by differences in the characteristics of the synaptic input, but by the distinct properties of synaptic integration and input-output transformation. acknowledgement: "The authors thank Jose Guzman for critically reading prior versions of the manuscript. They also thank T. Asenov for\r\nengineering mechanical devices, A. Schlögl for efficient pro-gramming, F. Marr for technical assistance, and E. Kramberger for manuscript editing." article_processing_charge: No author: - first_name: Janina full_name: Kowalski, Janina id: 3F3CA136-F248-11E8-B48F-1D18A9856A87 last_name: Kowalski - 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 - first_name: Alejandro full_name: Pernia-Andrade, Alejandro id: 36963E98-F248-11E8-B48F-1D18A9856A87 last_name: Pernia-Andrade citation: ama: Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 2016;26(5):668-682. doi:10.1002/hipo.22550 apa: Kowalski, J., Gan, J., Jonas, P. M., & Pernia-Andrade, A. (2016). Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22550 chicago: Kowalski, Janina, Jian Gan, Peter M Jonas, and Alejandro Pernia-Andrade. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus. Wiley, 2016. https://doi.org/10.1002/hipo.22550. ieee: J. Kowalski, J. Gan, P. M. Jonas, and A. Pernia-Andrade, “Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats,” Hippocampus, vol. 26, no. 5. Wiley, pp. 668–682, 2016. ista: Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. 2016. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 26(5), 668–682. mla: Kowalski, Janina, et al. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus, vol. 26, no. 5, Wiley, 2016, pp. 668–82, doi:10.1002/hipo.22550. short: J. Kowalski, J. Gan, P.M. Jonas, A. Pernia-Andrade, Hippocampus 26 (2016) 668–682. date_created: 2018-12-11T11:53:03Z date_published: 2016-05-01T00:00:00Z date_updated: 2023-10-17T10:02:02Z day: '01' ddc: - '570' department: - _id: PeJo doi: 10.1002/hipo.22550 file: - access_level: open_access checksum: 284b72b12fbe15474833ed3d4549f86b content_type: application/pdf creator: system date_created: 2018-12-12T10:13:47Z date_updated: 2020-07-14T12:45:07Z file_id: '5033' file_name: IST-2016-469-v1+1_Kowalski_et_al-Hippocampus.pdf file_size: 905348 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 26' issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 668 - 682 publication: Hippocampus publication_identifier: eissn: - 1098-1063 issn: - 1050-9631 publication_status: published publisher: Wiley publist_id: '5550' pubrep_id: '469' quality_controlled: '1' scopus_import: '1' status: public title: Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2016' ... --- _id: '1617' abstract: - lang: eng text: 'We study the discrepancy of jittered sampling sets: such a set P⊂ [0,1]d is generated for fixed m∈ℕ by partitioning [0,1]d into md axis aligned cubes of equal measure and placing a random point inside each of the N=md cubes. We prove that, for N sufficiently large, 1/10 d/N1/2+1/2d ≤EDN∗(P)≤ √d(log N) 1/2/N1/2+1/2d, where the upper bound with an unspecified constant Cd was proven earlier by Beck. Our proof makes crucial use of the sharp Dvoretzky-Kiefer-Wolfowitz inequality and a suitably taylored Bernstein inequality; we have reasons to believe that the upper bound has the sharp scaling in N. Additional heuristics suggest that jittered sampling should be able to improve known bounds on the inverse of the star-discrepancy in the regime N≳dd. We also prove a partition principle showing that every partition of [0,1]d combined with a jittered sampling construction gives rise to a set whose expected squared L2-discrepancy is smaller than that of purely random points.' acknowledgement: We are grateful to the referee whose suggestions greatly improved the quality and clarity of the exposition. author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 - first_name: Stefan full_name: Steinerberger, Stefan last_name: Steinerberger citation: ama: Pausinger F, Steinerberger S. On the discrepancy of jittered sampling. Journal of Complexity. 2016;33:199-216. doi:10.1016/j.jco.2015.11.003 apa: Pausinger, F., & Steinerberger, S. (2016). On the discrepancy of jittered sampling. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.11.003 chicago: Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity. Academic Press, 2016. https://doi.org/10.1016/j.jco.2015.11.003. ieee: F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,” Journal of Complexity, vol. 33. Academic Press, pp. 199–216, 2016. ista: Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling. Journal of Complexity. 33, 199–216. mla: Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity, vol. 33, Academic Press, 2016, pp. 199–216, doi:10.1016/j.jco.2015.11.003. short: F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216. date_created: 2018-12-11T11:53:03Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T06:52:02Z day: '01' department: - _id: HeEd doi: 10.1016/j.jco.2015.11.003 intvolume: ' 33' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.00251 month: '04' oa: 1 oa_version: Submitted Version page: 199 - 216 publication: Journal of Complexity publication_status: published publisher: Academic Press publist_id: '5549' quality_controlled: '1' scopus_import: 1 status: public title: On the discrepancy of jittered sampling type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2016' ... --- _id: '1620' abstract: - lang: eng text: We consider the Bardeen–Cooper–Schrieffer free energy functional for particles interacting via a two-body potential on a microscopic scale and in the presence of weak external fields varying on a macroscopic scale. We study the influence of the external fields on the critical temperature. We show that in the limit where the ratio between the microscopic and macroscopic scale tends to zero, the next to leading order of the critical temperature is determined by the lowest eigenvalue of the linearization of the Ginzburg–Landau equation. acknowledgement: The authors are grateful to I. M. Sigal for useful discussions. Financial support from the US National Science Foundation through Grants PHY-1347399 and DMS-1363432 (R.L.F.), from the Danish council for independent research and from ERC Advanced Grant 321029 (J.P.S.) is acknowledged. author: - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan last_name: Solovej citation: ama: Frank R, Hainzl C, Seiringer R, Solovej J. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 2016;342(1):189-216. doi:10.1007/s00220-015-2526-2 apa: Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2016). The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2526-2 chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-015-2526-2. ieee: R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “The external field dependence of the BCS critical temperature,” Communications in Mathematical Physics, vol. 342, no. 1. Springer, pp. 189–216, 2016. ista: Frank R, Hainzl C, Seiringer R, Solovej J. 2016. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 342(1), 189–216. mla: Frank, Rupert, et al. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics, vol. 342, no. 1, Springer, 2016, pp. 189–216, doi:10.1007/s00220-015-2526-2. short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical Physics 342 (2016) 189–216. date_created: 2018-12-11T11:53:04Z date_published: 2016-02-01T00:00:00Z date_updated: 2021-01-12T06:52:03Z day: '01' department: - _id: RoSe doi: 10.1007/s00220-015-2526-2 intvolume: ' 342' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.2352 month: '02' oa: 1 oa_version: Submitted Version page: 189 - 216 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '5546' quality_controlled: '1' scopus_import: 1 status: public title: The external field dependence of the BCS critical temperature type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 342 year: '2016' ... --- _id: '1622' abstract: - lang: eng text: We prove analogues of the Lieb–Thirring and Hardy–Lieb–Thirring inequalities for many-body quantum systems with fractional kinetic operators and homogeneous interaction potentials, where no anti-symmetry on the wave functions is assumed. These many-body inequalities imply interesting one-body interpolation inequalities, and we show that the corresponding one- and many-body inequalities are actually equivalent in certain cases. acknowledgement: "We thank Jan Philip Solovej, Robert Seiringer and Vladimir Maz’ya for helpful discussions, as well as Rupert Frank\r\nand the anonymous referee for useful comments. Part of this work has been carried out during a visit at the Institut Mittag-Leffler (Stockholm). D.L. acknowledges financial support by the grant KAW 2010.0063 from the Knut and Alice Wallenberg Foundation and the Swedish Research Council grant no. 2013-4734. P.T.N. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. F.P. acknowledges support from the ERC project no. 321029 “The\r\nmathematics of the structure of matter”." author: - first_name: Douglas full_name: Lundholm, Douglas last_name: Lundholm - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Fabian full_name: Portmann, Fabian last_name: Portmann citation: ama: Lundholm D, Nam P, Portmann F. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 2016;219(3):1343-1382. doi:10.1007/s00205-015-0923-5 apa: Lundholm, D., Nam, P., & Portmann, F. (2016). Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-015-0923-5 chicago: Lundholm, Douglas, Phan Nam, and Fabian Portmann. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis. Springer, 2016. https://doi.org/10.1007/s00205-015-0923-5. ieee: D. Lundholm, P. Nam, and F. Portmann, “Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems,” Archive for Rational Mechanics and Analysis, vol. 219, no. 3. Springer, pp. 1343–1382, 2016. ista: Lundholm D, Nam P, Portmann F. 2016. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 219(3), 1343–1382. mla: Lundholm, Douglas, et al. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis, vol. 219, no. 3, Springer, 2016, pp. 1343–82, doi:10.1007/s00205-015-0923-5. short: D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis 219 (2016) 1343–1382. date_created: 2018-12-11T11:53:05Z date_published: 2016-03-01T00:00:00Z date_updated: 2021-01-12T06:52:04Z day: '01' department: - _id: RoSe doi: 10.1007/s00205-015-0923-5 ec_funded: 1 intvolume: ' 219' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1501.04570 month: '03' oa: 1 oa_version: Submitted Version page: 1343 - 1382 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '5542' quality_controlled: '1' scopus_import: 1 status: public title: Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 219 year: '2016' ... --- _id: '1631' abstract: - lang: eng text: 'Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.' author: - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber - 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, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 2016;108:1-12. doi:10.1016/j.tpb.2015.10.008 apa: Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008 chicago: Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008. ieee: J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” Theoretical Population Biology, vol. 108. Academic Press, pp. 1–12, 2016. ista: Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12. mla: Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology, vol. 108, Academic Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008. short: J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12. date_created: 2018-12-11T11:53:08Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T06:52:07Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2015.10.008 ec_funded: 1 file: - access_level: open_access checksum: 6a65ba187994d4ad86c1c509e0ff482a content_type: application/pdf creator: system date_created: 2018-12-12T10:11:12Z date_updated: 2020-07-14T12:45:07Z file_id: '4865' file_name: IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf file_size: 1684043 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 108' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1 - 12 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: '5524' pubrep_id: '465' quality_controlled: '1' scopus_import: 1 status: public title: Spread of pedigree versus genetic ancestry in spatially distributed populations 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: 108 year: '2016' ... --- _id: '1641' abstract: - lang: eng text: The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development. acknowledgement: 'European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ' author: - first_name: Radka full_name: Zemová, Radka last_name: Zemová - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476. doi:10.1007/s00344-015-9553-2 apa: Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. Springer. https://doi.org/10.1007/s00344-015-9553-2 chicago: Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2. ieee: R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35, no. 2. Springer, pp. 465–476, 2016. ista: Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476. mla: Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2. short: R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476. date_created: 2018-12-11T11:53:12Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:52:11Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1007/s00344-015-9553-2 file: - access_level: open_access checksum: 0dc6a300cde6536ceedd2bcdd2060efb content_type: application/pdf creator: system date_created: 2018-12-12T10:08:34Z date_updated: 2020-07-14T12:45:08Z file_id: '4695' file_name: IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf file_size: 5637591 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 35' issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Preprint page: 465 - 476 publication: Journal of Plant Growth Regulation publication_status: published publisher: Springer publist_id: '5512' pubrep_id: '1001' quality_controlled: '1' scopus_import: 1 status: public title: A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1653' abstract: - lang: eng text: "A somewhere statistically binding (SSB) hash, introduced by Hubáček and Wichs (ITCS ’15), can be used to hash a long string x to a short digest y = H hk (x) using a public hashing-key hk. Furthermore, there is a way to set up the hash key hk to make it statistically binding on some arbitrary hidden position i, meaning that: (1) the digest y completely determines the i’th bit (or symbol) of x so that all pre-images of y have the same value in the i’th position, (2) it is computationally infeasible to distinguish the position i on which hk is statistically binding from any other position i’. Lastly, the hash should have a local opening property analogous to Merkle-Tree hashing, meaning that given x and y = H hk (x) it should be possible to create a short proof π that certifies the value of the i’th bit (or symbol) of x without having to provide the entire input x. A similar primitive called a positional accumulator, introduced by Koppula, Lewko and Waters (STOC ’15) further supports dynamic updates of the hashed value. These tools, which are interesting in their own right, also serve as one of the main technical components in several recent works building advanced applications from indistinguishability obfuscation (iO).\r\n\r\nThe prior constructions of SSB hashing and positional accumulators required fully homomorphic encryption (FHE) and iO respectively. In this work, we give new constructions of these tools based on well studied number-theoretic assumptions such as DDH, Phi-Hiding and DCR, as well as a general construction from lossy/injective functions." alternative_title: - LNCS author: - first_name: Tatsuaki full_name: Okamoto, Tatsuaki last_name: Okamoto - 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: Brent full_name: Waters, Brent last_name: Waters - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Okamoto T, Pietrzak KZ, Waters B, Wichs D. New realizations of somewhere statistically binding hashing and positional accumulators. In: Vol 9452. Springer; 2016:121-145. doi:10.1007/978-3-662-48797-6_6' apa: 'Okamoto, T., Pietrzak, K. Z., Waters, B., & Wichs, D. (2016). New realizations of somewhere statistically binding hashing and positional accumulators (Vol. 9452, pp. 121–145). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48797-6_6' chicago: Okamoto, Tatsuaki, Krzysztof Z Pietrzak, Brent Waters, and Daniel Wichs. “New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators,” 9452:121–45. Springer, 2016. https://doi.org/10.1007/978-3-662-48797-6_6. ieee: 'T. Okamoto, K. Z. Pietrzak, B. Waters, and D. Wichs, “New realizations of somewhere statistically binding hashing and positional accumulators,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand, 2016, vol. 9452, pp. 121–145.' ista: 'Okamoto T, Pietrzak KZ, Waters B, Wichs D. 2016. New realizations of somewhere statistically binding hashing and positional accumulators. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 9452, 121–145.' mla: Okamoto, Tatsuaki, et al. New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators. Vol. 9452, Springer, 2016, pp. 121–45, doi:10.1007/978-3-662-48797-6_6. short: T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp. 121–145. conference: end_date: 2015-12-03 location: Auckland, New Zealand name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security' start_date: 2015-11-29 date_created: 2018-12-11T11:53:16Z date_published: 2016-01-08T00:00:00Z date_updated: 2021-01-12T06:52:16Z day: '08' ddc: - '000' department: - _id: KrPi doi: 10.1007/978-3-662-48797-6_6 ec_funded: 1 file: - access_level: open_access checksum: a57711cb660c5b17b42bb47275a00180 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:05Z date_updated: 2020-07-14T12:45:08Z file_id: '4923' file_name: IST-2016-677-v1+1_869.pdf file_size: 580088 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9452' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 121 - 145 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5497' pubrep_id: '677' quality_controlled: '1' scopus_import: 1 status: public title: New realizations of somewhere statistically binding hashing and positional accumulators type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9452 year: '2016' ... --- _id: '1662' abstract: - lang: eng text: We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball. acknowledgement: "This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014." author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 2016;287:674-703. doi:10.1016/j.aim.2015.10.004 apa: Edelsbrunner, H., & Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2015.10.004 chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics. Academic Press, 2016. https://doi.org/10.1016/j.aim.2015.10.004. ieee: H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” Advances in Mathematics, vol. 287. Academic Press, pp. 674–703, 2016. ista: Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703. mla: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics, vol. 287, Academic Press, 2016, pp. 674–703, doi:10.1016/j.aim.2015.10.004. short: H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703. date_created: 2018-12-11T11:53:20Z date_published: 2016-01-10T00:00:00Z date_updated: 2023-09-07T11:41:25Z day: '10' ddc: - '004' department: - _id: HeEd doi: 10.1016/j.aim.2015.10.004 ec_funded: 1 file: - access_level: open_access checksum: f8869ec110c35c852ef6a37425374af7 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:10Z date_updated: 2020-07-14T12:45:10Z file_id: '4928' file_name: IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf file_size: 248985 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' intvolume: ' 287' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 674 - 703 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Advances in Mathematics publication_status: published publisher: Academic Press publist_id: '5488' pubrep_id: '774' quality_controlled: '1' related_material: record: - id: '1399' relation: dissertation_contains status: public scopus_import: 1 status: public title: Approximation and convergence of the intrinsic volume 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: 287 year: '2016' ... --- _id: '1705' abstract: - lang: eng text: Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential. article_processing_charge: Yes (via OA deal) author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Alexandre full_name: Donzé, Alexandre last_name: Donzé - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Radu full_name: Grosu, Radu last_name: Grosu - first_name: Taylor full_name: Johnson, Taylor last_name: Johnson - first_name: Hamed full_name: Ladan, Hamed last_name: Ladan - first_name: Andreas full_name: Podelski, Andreas last_name: Podelski - first_name: Martin full_name: Wehrle, Martin last_name: Wehrle citation: ama: Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 2016;18(4):449-467. doi:10.1007/s10009-015-0393-y apa: Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., … Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-015-0393-y chicago: Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson, Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer. Springer, 2016. https://doi.org/10.1007/s10009-015-0393-y. ieee: S. Bogomolov et al., “Guided search for hybrid systems based on coarse-grained space abstractions,” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4. Springer, pp. 449–467, 2016. ista: Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 18(4), 449–467. mla: Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:10.1007/s10009-015-0393-y. short: S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski, M. Wehrle, International Journal on Software Tools for Technology Transfer 18 (2016) 449–467. date_created: 2018-12-11T11:53:34Z date_published: 2016-08-01T00:00:00Z date_updated: 2021-01-12T06:52:38Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/s10009-015-0393-y ec_funded: 1 file: - access_level: open_access checksum: 31561d7705599a9bd4ea816accc0752e content_type: application/pdf creator: system date_created: 2018-12-12T10:15:26Z date_updated: 2020-07-14T12:45:13Z file_id: '5146' file_name: IST-2016-457-v1+1_s10009-015-0393-y.pdf file_size: 2296522 relation: main_file file_date_updated: 2020-07-14T12:45:13Z has_accepted_license: '1' intvolume: ' 18' issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 449 - 467 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: International Journal on Software Tools for Technology Transfer publication_status: published publisher: Springer publist_id: '5431' pubrep_id: '457' quality_controlled: '1' scopus_import: 1 status: public title: Guided search for hybrid systems based on coarse-grained space abstractions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2016' ... --- _id: '1707' abstract: - lang: eng text: "Volunteer supporters play an important role in modern crisis and disaster management. In the times of mobile Internet devices, help from thousands of volunteers can be requested within a short time span, thus relieving professional helpers from minor chores or geographically spread-out tasks. However, the simultaneous availability of many volunteers also poses new problems. In particular, the volunteer efforts must be well coordinated, or otherwise situations might emerge in which too many idle volunteers at one location become more of a burden than a relief to the professionals.\r\nIn this work, we study the task of optimally assigning volunteers to selected locations, e.g. in order to perform regular measurements, to report on damage, or to distribute information or resources to the population in a crisis situation. We formulate the assignment tasks as an optimization problem and propose an effective and efficient solution procedure. Experiments on real data of the Team Österreich, consisting of over 36,000 Austrian volunteers, show the effectiveness and efficiency of our approach." acknowledgement: The DRIVER FP7 project has received funding from the European Unions Seventh Framework Programme for research, technological development and demonstration under grant agreement no 607798. RE-ACTA was funded within the framework of the Austrian Security Research Programme KIRAS by the Federal Ministry for Transport, Innovation and Technology. article_number: '7402041' author: - first_name: Jasmin full_name: Pielorz, Jasmin id: 49BC895A-F248-11E8-B48F-1D18A9856A87 last_name: Pielorz - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Pielorz J, Lampert C. Optimal geospatial allocation of volunteers for crisis management. In: IEEE; 2016. doi:10.1109/ICT-DM.2015.7402041' apa: 'Pielorz, J., & Lampert, C. (2016). Optimal geospatial allocation of volunteers for crisis management. Presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France: IEEE. https://doi.org/10.1109/ICT-DM.2015.7402041' chicago: Pielorz, Jasmin, and Christoph Lampert. “Optimal Geospatial Allocation of Volunteers for Crisis Management.” IEEE, 2016. https://doi.org/10.1109/ICT-DM.2015.7402041. ieee: 'J. Pielorz and C. Lampert, “Optimal geospatial allocation of volunteers for crisis management,” presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France, 2016.' ista: 'Pielorz J, Lampert C. 2016. Optimal geospatial allocation of volunteers for crisis management. ICT-DM: Information and Communication Technologies for Disaster Management, 7402041.' mla: Pielorz, Jasmin, and Christoph Lampert. Optimal Geospatial Allocation of Volunteers for Crisis Management. 7402041, IEEE, 2016, doi:10.1109/ICT-DM.2015.7402041. short: J. Pielorz, C. Lampert, in:, IEEE, 2016. conference: end_date: 2015-12-02 location: Rennes, France name: 'ICT-DM: Information and Communication Technologies for Disaster Management' start_date: 2015-11-30 date_created: 2018-12-11T11:53:35Z date_published: 2016-02-11T00:00:00Z date_updated: 2021-01-12T06:52:39Z day: '11' department: - _id: ChLa doi: 10.1109/ICT-DM.2015.7402041 language: - iso: eng month: '02' oa_version: None publication_status: published publisher: IEEE publist_id: '5429' quality_controlled: '1' scopus_import: 1 status: public title: Optimal geospatial allocation of volunteers for crisis management type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '173' abstract: - lang: eng text: We calculate admissible values of r such that a square-free polynomial with integer coefficients, no fixed prime divisor and irreducible factors of degree at most 3 takes infinitely many values that are a product of at most r distinct primes. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Andrew full_name: Booker, Andrew last_name: Booker citation: ama: Browning TD, Booker A. Square-free values of reducible polynomials. Discrete Analysis. 2016;8:1-18. doi:10.19086/da.732 apa: Browning, T. D., & Booker, A. (2016). Square-free values of reducible polynomials. Discrete Analysis. https://doi.org/10.19086/da.732 chicago: Browning, Timothy D, and Andrew Booker. “Square-Free Values of Reducible Polynomials.” Discrete Analysis, 2016. https://doi.org/10.19086/da.732. ieee: T. D. Browning and A. Booker, “Square-free values of reducible polynomials,” Discrete Analysis, vol. 8. pp. 1–18, 2016. ista: Browning TD, Booker A. 2016. Square-free values of reducible polynomials. Discrete Analysis. 8, 1–18. mla: Browning, Timothy D., and Andrew Booker. “Square-Free Values of Reducible Polynomials.” Discrete Analysis, vol. 8, 2016, pp. 1–18, doi:10.19086/da.732. short: T.D. Browning, A. Booker, Discrete Analysis 8 (2016) 1–18. date_created: 2018-12-11T11:45:00Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:52:49Z day: '01' doi: 10.19086/da.732 extern: '1' external_id: arxiv: - '1511.00601' intvolume: ' 8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.00601 month: '06' oa: 1 oa_version: Preprint page: 1 - 18 publication: Discrete Analysis publication_status: published publist_id: '7748' quality_controlled: '1' status: public title: Square-free values of reducible polynomials type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2016' ... --- _id: '1794' abstract: - lang: eng text: We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights. acknowledgement: This work has been partially supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 616160. arxiv: 1 author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Rustem full_name: Takhanov, Rustem id: 2CCAC26C-F248-11E8-B48F-1D18A9856A87 last_name: Takhanov citation: ama: Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 2016;76(1):17-46. doi:10.1007/s00453-015-0017-7 apa: Kolmogorov, V., & Takhanov, R. (2016). Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-0017-7 chicago: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-0017-7. ieee: V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs on sequence data,” Algorithmica, vol. 76, no. 1. Springer, pp. 17–46, 2016. ista: Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 76(1), 17–46. mla: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” Algorithmica, vol. 76, no. 1, Springer, 2016, pp. 17–46, doi:10.1007/s00453-015-0017-7. short: V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46. date_created: 2018-12-11T11:54:02Z date_published: 2016-09-01T00:00:00Z date_updated: 2023-10-17T09:51:31Z day: '01' department: - _id: VlKo doi: 10.1007/s00453-015-0017-7 ec_funded: 1 external_id: arxiv: - '1210.0508' intvolume: ' 76' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1210.0508 month: '09' oa: 1 oa_version: Preprint page: 17 - 46 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Algorithmica publication_status: published publisher: Springer publist_id: '5316' quality_controlled: '1' related_material: record: - id: '2272' relation: earlier_version status: public scopus_import: 1 status: public title: Inference algorithms for pattern-based CRFs on sequence data type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 76 year: '2016' ...