--- _id: '2090' author: - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Craig full_name: Donner, Craig last_name: Donner - first_name: Chien full_name: Tu, Chien last_name: Tu - first_name: Janet full_name: McAndless, Janet M last_name: Mcandless - first_name: Jinho full_name: Lee, Jinho last_name: Lee - first_name: Addy full_name: Ngan, Addy last_name: Ngan - first_name: Henrik full_name: Jensen, Henrik W last_name: Jensen - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: 'Bickel B, Weyrich T, Matusik W, et al. Processing and editing of faces using a measurement-based skin reflectance model. In: ACM; 2006. doi:10.1145/1179849.1180059' apa: 'Bickel, B., Weyrich, T., Matusik, W., Pfister, H., Donner, C., Tu, C., … Groß, M. (2006). Processing and editing of faces using a measurement-based skin reflectance model. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/1179849.1180059' chicago: Bickel, Bernd, Tim Weyrich, Wojciech Matusik, Hanspeter Pfister, Craig Donner, Chien Tu, Janet Mcandless, et al. “Processing and Editing of Faces Using a Measurement-Based Skin Reflectance Model.” ACM, 2006. https://doi.org/10.1145/1179849.1180059. ieee: 'B. Bickel et al., “Processing and editing of faces using a measurement-based skin reflectance model,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2006.' ista: 'Bickel B, Weyrich T, Matusik W, Pfister H, Donner C, Tu C, Mcandless J, Lee J, Ngan A, Jensen H, Groß M. 2006. Processing and editing of faces using a measurement-based skin reflectance model. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques.' mla: Bickel, Bernd, et al. Processing and Editing of Faces Using a Measurement-Based Skin Reflectance Model. ACM, 2006, doi:10.1145/1179849.1180059. short: B. Bickel, T. Weyrich, W. Matusik, H. Pfister, C. Donner, C. Tu, J. Mcandless, J. Lee, A. Ngan, H. Jensen, M. Groß, in:, ACM, 2006. conference: name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' date_created: 2018-12-11T11:55:39Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T06:55:15Z day: '01' doi: 10.1145/1179849.1180059 extern: 1 month: '07' publication_status: published publisher: ACM publist_id: '4945' quality_controlled: 0 status: public title: Processing and editing of faces using a measurement-based skin reflectance model type: conference year: '2006' ... --- _id: '2134' abstract: - lang: eng text: Predissociation of the N+2 C 2Σ+u(v') vibrational levels with v' ≥ 3 was observed via dispersed C 2Σ+u → X 2Σ+g fluorescence in the spectral range of 165–208 nm after resonant 1s−1π*(vr) excitation of N2 and its subsequent autoionization into the N+2 C state. This range is dominated by lines in atomic nitrogen, by overlapped C 2Σ+u(v') → X 2Σ+g(v'') vibrational band sequences with Δv = const and broad unresolved band systems (D, (2))2Πg(v') → A2Πu(v'') in the N+2 molecular ion. With very high fluorescence resolution of about 0.1 nm FWHM individual C 2Σ+u(v') → X 2Σ+g(v'') vibrational bands have been resolved. Calculation of the observed fluorescence spectra by taking into account predissociation and molecular rotation describes well the shape of both individual vibrational bands C 2Σ+u(v') → X 2Σ+g(v'') and the whole band system. acknowledgement: This work has been supported by the Deutsche Forschungsgemeinschaft (DFG) and by the Bundesministerium für Bildung und Forschung (BMBF) (Förderkennzeichen 05 ES3XBA/5 and IB/DLR RUS 02/037). The cooperation between the groups at the universities of Kaiserslautern and Rostov-on-Don was supported by the Alexander-von-Humboldt Foundation within the framework of an institute partnership with funds from BMBF author: - first_name: Arno full_name: Ehresmann, Arno last_name: Ehresmann - first_name: Lutz full_name: Werner, Lutz last_name: Werner - first_name: Stefan full_name: Klumpp, Stefan last_name: Klumpp - first_name: Ph full_name: Demekhin, Ph V last_name: Demekhin - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: V. full_name: Sukhorukov, V. L last_name: Sukhorukov - first_name: Karl full_name: Schartner, Karl H last_name: Schartner - first_name: Hans full_name: Schmoranzer, Hans P last_name: Schmoranzer citation: ama: 'Ehresmann A, Werner L, Klumpp S, et al. Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule. Journal of Physics B: Atomic, Molecular and Optical Physics. 2006;39(6):L119-L126. doi:10.1088/0953-4075/39/6/L03' apa: 'Ehresmann, A., Werner, L., Klumpp, S., Demekhin, P., Lemeshko, M., Sukhorukov, V., … Schmoranzer, H. (2006). Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd. https://doi.org/10.1088/0953-4075/39/6/L03' chicago: 'Ehresmann, Arno, Lutz Werner, Stefan Klumpp, Ph Demekhin, Mikhail Lemeshko, V. Sukhorukov, Karl Schartner, and Hans Schmoranzer. “Predissociation of the N+2(C 2Σ+u) State Observed via C 2Σ+u → X 2Σ+g Fluorescence after Resonant 1s−1π* Excitation of N2 Molecule.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd., 2006. https://doi.org/10.1088/0953-4075/39/6/L03.' ieee: 'A. Ehresmann et al., “Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 39, no. 6. IOP Publishing Ltd., pp. L119–L126, 2006.' ista: 'Ehresmann A, Werner L, Klumpp S, Demekhin P, Lemeshko M, Sukhorukov V, Schartner K, Schmoranzer H. 2006. Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule. Journal of Physics B: Atomic, Molecular and Optical Physics. 39(6), L119–L126.' mla: 'Ehresmann, Arno, et al. “Predissociation of the N+2(C 2Σ+u) State Observed via C 2Σ+u → X 2Σ+g Fluorescence after Resonant 1s−1π* Excitation of N2 Molecule.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 39, no. 6, IOP Publishing Ltd., 2006, pp. L119–26, doi:10.1088/0953-4075/39/6/L03.' short: 'A. Ehresmann, L. Werner, S. Klumpp, P. Demekhin, M. Lemeshko, V. Sukhorukov, K. Schartner, H. Schmoranzer, Journal of Physics B: Atomic, Molecular and Optical Physics 39 (2006) L119–L126.' date_created: 2018-12-11T11:55:54Z date_published: 2006-03-28T00:00:00Z date_updated: 2021-01-12T06:55:31Z day: '28' doi: 10.1088/0953-4075/39/6/L03 extern: 1 intvolume: ' 39' issue: '6' month: '03' page: L119 - L126 publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics' publication_status: published publisher: IOP Publishing Ltd. publist_id: '4900' quality_controlled: 0 status: public title: Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule type: journal_article volume: 39 year: '2006' ... --- _id: '213' abstract: - lang: eng text: For any integers d,n ≥2, let X ⊂ Pn be a non‐singular hypersurface of degree d that is defined over the rational numbers. The main result in this paper is a proof that the number of rational points on X which have height at most B is O(Bn − 1 + ɛ), for any ɛ > 0. The implied constant in this estimate depends at most upon d, ɛ and n. 2000 Mathematics Subject Classification 11D45 (primary), 11G35, 14G05 (secondary). acknowledgement: EPSRC grant number GR/R93155/01 author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath-Brown, Roger last_name: Heath Brown - first_name: Jason full_name: Starr, Jason M last_name: Starr citation: ama: Browning TD, Heath Brown R, Starr J. The density of rational points on non-singular hypersurfaces, II. Proceedings of the London Mathematical Society. 2006;93(2):273-303. doi:https://doi.org/10.1112/S0024611506015784 apa: Browning, T. D., Heath Brown, R., & Starr, J. (2006). The density of rational points on non-singular hypersurfaces, II. Proceedings of the London Mathematical Society. John Wiley and Sons Ltd. https://doi.org/10.1112/S0024611506015784 chicago: Browning, Timothy D, Roger Heath Brown, and Jason Starr. “The Density of Rational Points on Non-Singular Hypersurfaces, II.” Proceedings of the London Mathematical Society. John Wiley and Sons Ltd, 2006. https://doi.org/10.1112/S0024611506015784. ieee: T. D. Browning, R. Heath Brown, and J. Starr, “The density of rational points on non-singular hypersurfaces, II,” Proceedings of the London Mathematical Society, vol. 93, no. 2. John Wiley and Sons Ltd, pp. 273–303, 2006. ista: Browning TD, Heath Brown R, Starr J. 2006. The density of rational points on non-singular hypersurfaces, II. Proceedings of the London Mathematical Society. 93(2), 273–303. mla: Browning, Timothy D., et al. “The Density of Rational Points on Non-Singular Hypersurfaces, II.” Proceedings of the London Mathematical Society, vol. 93, no. 2, John Wiley and Sons Ltd, 2006, pp. 273–303, doi:https://doi.org/10.1112/S0024611506015784. short: T.D. Browning, R. Heath Brown, J. Starr, Proceedings of the London Mathematical Society 93 (2006) 273–303. date_created: 2018-12-11T11:45:14Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T06:55:29Z day: '01' doi: https://doi.org/10.1112/S0024611506015784 extern: 1 intvolume: ' 93' issue: '2' month: '09' page: 273 - 303 publication: Proceedings of the London Mathematical Society publication_status: published publisher: John Wiley and Sons Ltd publist_id: '7698' quality_controlled: 0 status: public title: The density of rational points on non-singular hypersurfaces, II type: journal_article volume: 93 year: '2006' ... --- _id: '2144' abstract: - lang: eng text: 'Temperature dependent preedge and extended x-ray absorption fine structure measurements at the Zr K edge for the perovskite-type zirconates Pb Zr0.515 Ti0.485 O3 (PZT), PbZr O3 (PZ), and BaZr O3 are performed. To carry out a more accurate study of the weak reconstruction of the local atomic structure we employed a combination of two techniques: (i) analysis of the preedge fine structure, and (ii) analysis of the Fourier transform of the difference between χ (k) functions obtained at different temperatures. A detailed investigation of local atomic structure in the cubic phase for all the crystals is also performed. It is shown that neither the displacive nor the order-disorder model can describe correctly the changes of local atomic structure during phase transitions in PZ and PZT. A spherical model describing the local atomic structure of perovskite-type crystals suffering structural phase transitions is proposed.' acknowledgement: The studies were supported by the Russian Ministry of Science and Education Grant No. R662. E.N. acknowledges partial support from the French Government *CNOUS. author: - first_name: Rostislav full_name: Vedrinskiǐ, Rostislav V last_name: Vedrinskiǐ - first_name: Elena full_name: Nazarenko, Elena S last_name: Nazarenko - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Vivian full_name: Nassif, Vivian M last_name: Nassif - first_name: Olivier full_name: Proux, Olivier last_name: Proux - first_name: Alexander full_name: Novakovich, Alexander A last_name: Novakovich - first_name: Yves full_name: Joly, Yves last_name: Joly citation: ama: Vedrinskiǐ R, Nazarenko E, Lemeshko M, et al. Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates. Physical Review B - Condensed Matter and Materials Physics. 2006;73(13). doi:10.1103/PhysRevB.73.134109 apa: Vedrinskiǐ, R., Nazarenko, E., Lemeshko, M., Nassif, V., Proux, O., Novakovich, A., & Joly, Y. (2006). Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.73.134109 chicago: Vedrinskiǐ, Rostislav, Elena Nazarenko, Mikhail Lemeshko, Vivian Nassif, Olivier Proux, Alexander Novakovich, and Yves Joly. “Temperature Dependent XAFS Studies of Local Atomic Structure of the Perovskite-Type Zirconates.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2006. https://doi.org/10.1103/PhysRevB.73.134109. ieee: R. Vedrinskiǐ et al., “Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates,” Physical Review B - Condensed Matter and Materials Physics, vol. 73, no. 13. American Physical Society, 2006. ista: Vedrinskiǐ R, Nazarenko E, Lemeshko M, Nassif V, Proux O, Novakovich A, Joly Y. 2006. Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates. Physical Review B - Condensed Matter and Materials Physics. 73(13). mla: Vedrinskiǐ, Rostislav, et al. “Temperature Dependent XAFS Studies of Local Atomic Structure of the Perovskite-Type Zirconates.” Physical Review B - Condensed Matter and Materials Physics, vol. 73, no. 13, American Physical Society, 2006, doi:10.1103/PhysRevB.73.134109. short: R. Vedrinskiǐ, E. Nazarenko, M. Lemeshko, V. Nassif, O. Proux, A. Novakovich, Y. Joly, Physical Review B - Condensed Matter and Materials Physics 73 (2006). date_created: 2018-12-11T11:55:58Z date_published: 2006-04-17T00:00:00Z date_updated: 2021-01-12T06:55:34Z day: '17' doi: 10.1103/PhysRevB.73.134109 extern: 1 intvolume: ' 73' issue: '13' month: '04' publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '4881' quality_controlled: 0 status: public title: Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates type: journal_article volume: 73 year: '2006' ... --- _id: '2142' abstract: - lang: eng text: Fluorescence from fragments formed after the de-excitation of the N*2(1s−1π*) resonance has been measured in the spectral range of 135–190 nm. This range is dominated by lines in atomic nitrogen and lines formed by overlapping C2Σ+u(v') → X2Σ+g(v'') bands with Δv = const in the N+2 molecular ion which result from the spectator Auger decays of the N*2(1s−1π*(vr)) resonances. Ab initio calculations of the corresponding potential curves and transition probabilities showed that the observed irregular intensity dependence of the C2Σ+u(v') → X2Σ+g(v'')(Δv = const) fluorescence lines on the vibrational quantum number vr is due to transitions between vibrational levels during the reaction N2(v0 = 0)→ N*2(1s−1π*(vr)) Longrightarrow C2Σ+u(v') → X2Σ+g(v''). author: - first_name: Arno full_name: Ehresmann, Arno last_name: Ehresmann - first_name: Lutz full_name: Werner, Lutz last_name: Werner - first_name: Stefan full_name: Klumpp, Stefan last_name: Klumpp - first_name: S full_name: Lucht, S last_name: Lucht - first_name: Hans full_name: Schmoranzer, Hans P last_name: Schmoranzer - first_name: Sascha full_name: Mickat, Sascha last_name: Mickat - first_name: Rüdiger full_name: Schill, Rüdiger H last_name: Schill - first_name: Karl full_name: Schartner, Karl H last_name: Schartner - first_name: Philipp full_name: Demekhin, Philipp last_name: Demekhin - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Victor full_name: Sukhorukov, Victor L last_name: Sukhorukov citation: ama: 'Ehresmann A, Werner L, Klumpp S, et al. Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance. Journal of Physics B: Atomic, Molecular and Optical Physics. 2006;39(2):283-304. doi:10.1088/0953-4075/39/2/006' apa: 'Ehresmann, A., Werner, L., Klumpp, S., Lucht, S., Schmoranzer, H., Mickat, S., … Sukhorukov, V. (2006). Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd. https://doi.org/10.1088/0953-4075/39/2/006' chicago: 'Ehresmann, Arno, Lutz Werner, Stefan Klumpp, S Lucht, Hans Schmoranzer, Sascha Mickat, Rüdiger Schill, et al. “Studying the N+2(C2Σ+u → X2Σ+g) Fluorescence Excited via the 1s−1π* Resonance.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd., 2006. https://doi.org/10.1088/0953-4075/39/2/006.' ieee: 'A. Ehresmann et al., “Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 39, no. 2. IOP Publishing Ltd., pp. 283–304, 2006.' ista: 'Ehresmann A, Werner L, Klumpp S, Lucht S, Schmoranzer H, Mickat S, Schill R, Schartner K, Demekhin P, Lemeshko M, Sukhorukov V. 2006. Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance. Journal of Physics B: Atomic, Molecular and Optical Physics. 39(2), 283–304.' mla: 'Ehresmann, Arno, et al. “Studying the N+2(C2Σ+u → X2Σ+g) Fluorescence Excited via the 1s−1π* Resonance.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 39, no. 2, IOP Publishing Ltd., 2006, pp. 283–304, doi:10.1088/0953-4075/39/2/006.' short: 'A. Ehresmann, L. Werner, S. Klumpp, S. Lucht, H. Schmoranzer, S. Mickat, R. Schill, K. Schartner, P. Demekhin, M. Lemeshko, V. Sukhorukov, Journal of Physics B: Atomic, Molecular and Optical Physics 39 (2006) 283–304.' date_created: 2018-12-11T11:55:57Z date_published: 2006-01-28T00:00:00Z date_updated: 2021-01-12T06:55:34Z day: '28' doi: 10.1088/0953-4075/39/2/006 extern: 1 intvolume: ' 39' issue: '2' month: '01' page: 283 - 304 publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics' publication_status: published publisher: IOP Publishing Ltd. publist_id: '4882' quality_controlled: 0 status: public title: Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance type: journal_article volume: 39 year: '2006' ... --- _id: '215' abstract: - lang: eng text: For any n≥3, let F ∈ Z[X0,...,Xn ] be a form of degree d *≥5 that defines a non-singular hypersurface X ⊂ Pn . The main result in this paper is a proof of the fact that the number N (F ; B) of Q-rational points on X which have height at most B satisfiesN (F ; B) = Od,ε,n (Bn −1+ε ), for any ε > 0. The implied constant in this estimate depends at most upon d, ε and n. New estimates are also obtained for the number of representations of a positive integer as the sum of three dth powers, and for the paucity of integer solutions to equal sums of like polynomials.* author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath-Brown, Roger last_name: Heath Brown citation: ama: Browning TD, Heath Brown R. The density of rational points on non-singular hypersurfaces, I. Bulletin of the London Mathematical Society. 2006;38(3):401-410. doi:10.1112/S0024609305018412 apa: Browning, T. D., & Heath Brown, R. (2006). The density of rational points on non-singular hypersurfaces, I. Bulletin of the London Mathematical Society. Wiley-Blackwell. https://doi.org/10.1112/S0024609305018412 chicago: Browning, Timothy D, and Roger Heath Brown. “The Density of Rational Points on Non-Singular Hypersurfaces, I.” Bulletin of the London Mathematical Society. Wiley-Blackwell, 2006. https://doi.org/10.1112/S0024609305018412. ieee: T. D. Browning and R. Heath Brown, “The density of rational points on non-singular hypersurfaces, I,” Bulletin of the London Mathematical Society, vol. 38, no. 3. Wiley-Blackwell, pp. 401–410, 2006. ista: Browning TD, Heath Brown R. 2006. The density of rational points on non-singular hypersurfaces, I. Bulletin of the London Mathematical Society. 38(3), 401–410. mla: Browning, Timothy D., and Roger Heath Brown. “The Density of Rational Points on Non-Singular Hypersurfaces, I.” Bulletin of the London Mathematical Society, vol. 38, no. 3, Wiley-Blackwell, 2006, pp. 401–10, doi:10.1112/S0024609305018412. short: T.D. Browning, R. Heath Brown, Bulletin of the London Mathematical Society 38 (2006) 401–410. date_created: 2018-12-11T11:45:15Z date_published: 2006-12-23T00:00:00Z date_updated: 2021-01-12T06:55:36Z day: '23' doi: 10.1112/S0024609305018412 extern: 1 intvolume: ' 38' issue: '3' month: '12' page: 401 - 410 publication: Bulletin of the London Mathematical Society publication_status: published publisher: Wiley-Blackwell publist_id: '7697' quality_controlled: 0 status: public title: The density of rational points on non-singular hypersurfaces, I type: journal_article volume: 38 year: '2006' ... --- _id: '216' abstract: - lang: eng text: For any N ≥ 2, let Z ⊂ ℙN be a geometrically integral algebraic variety of degree d. This article is concerned with the number Nz(B) of ℚ-rational points on Z which have height at most B. For any ε > 0, we establish the estimate NZ(B) = O d,ε,N(Bdim Z+ε), provided that d ≥ 6. As indicated, the implied constant depends at most on d, ε, and N. author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath-Brown, Roger last_name: Heath Brown - first_name: Per full_name: Salberger, Per last_name: Salberger citation: ama: Browning TD, Heath Brown R, Salberger P. Counting rational points on algebraic varieties. Duke Mathematical Journal. 2006;132(3):545-578. doi:10.1215/S0012-7094-06-13236-2 apa: Browning, T. D., Heath Brown, R., & Salberger, P. (2006). Counting rational points on algebraic varieties. Duke Mathematical Journal. Unknown. https://doi.org/10.1215/S0012-7094-06-13236-2 chicago: Browning, Timothy D, Roger Heath Brown, and Per Salberger. “Counting Rational Points on Algebraic Varieties.” Duke Mathematical Journal. Unknown, 2006. https://doi.org/10.1215/S0012-7094-06-13236-2. ieee: T. D. Browning, R. Heath Brown, and P. Salberger, “Counting rational points on algebraic varieties,” Duke Mathematical Journal, vol. 132, no. 3. Unknown, pp. 545–578, 2006. ista: Browning TD, Heath Brown R, Salberger P. 2006. Counting rational points on algebraic varieties. Duke Mathematical Journal. 132(3), 545–578. mla: Browning, Timothy D., et al. “Counting Rational Points on Algebraic Varieties.” Duke Mathematical Journal, vol. 132, no. 3, Unknown, 2006, pp. 545–78, doi:10.1215/S0012-7094-06-13236-2. short: T.D. Browning, R. Heath Brown, P. Salberger, Duke Mathematical Journal 132 (2006) 545–578. date_created: 2018-12-11T11:45:15Z date_published: 2006-04-15T00:00:00Z date_updated: 2021-01-12T06:55:41Z day: '15' doi: 10.1215/S0012-7094-06-13236-2 extern: 1 intvolume: ' 132' issue: '3' month: '04' page: 545 - 578 publication: Duke Mathematical Journal publication_status: published publisher: Unknown publist_id: '7696' quality_controlled: 0 status: public title: Counting rational points on algebraic varieties type: journal_article volume: 132 year: '2006' ... --- _id: '218' abstract: - lang: eng text: This paper is concerned with the average order of certain arithmetic functions, as they range over the values taken by binary forms. author: - first_name: Régis full_name: de la Bretèche, Régis last_name: De La Bretèche - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: De La Bretèche R, Browning TD. Sums of arithmetic functions over values of binary forms. Acta Arithmetica. 2006;125(3):291-304. doi:10.4064/aa125-3-6 apa: De La Bretèche, R., & Browning, T. D. (2006). Sums of arithmetic functions over values of binary forms. Acta Arithmetica. Instytut Matematyczny. https://doi.org/10.4064/aa125-3-6 chicago: De La Bretèche, Régis, and Timothy D Browning. “Sums of Arithmetic Functions over Values of Binary Forms.” Acta Arithmetica. Instytut Matematyczny, 2006. https://doi.org/10.4064/aa125-3-6. ieee: R. De La Bretèche and T. D. Browning, “Sums of arithmetic functions over values of binary forms,” Acta Arithmetica, vol. 125, no. 3. Instytut Matematyczny, pp. 291–304, 2006. ista: De La Bretèche R, Browning TD. 2006. Sums of arithmetic functions over values of binary forms. Acta Arithmetica. 125(3), 291–304. mla: De La Bretèche, Régis, and Timothy D. Browning. “Sums of Arithmetic Functions over Values of Binary Forms.” Acta Arithmetica, vol. 125, no. 3, Instytut Matematyczny, 2006, pp. 291–304, doi:10.4064/aa125-3-6. short: R. De La Bretèche, T.D. Browning, Acta Arithmetica 125 (2006) 291–304. date_created: 2018-12-11T11:45:16Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T06:55:49Z day: '01' doi: 10.4064/aa125-3-6 extern: 1 intvolume: ' 125' issue: '3' month: '01' page: 291 - 304 publication: Acta Arithmetica publication_status: published publisher: Instytut Matematyczny publist_id: '7694' quality_controlled: 0 status: public title: Sums of arithmetic functions over values of binary forms type: journal_article volume: 125 year: '2006' ... --- _id: '2333' alternative_title: - Contemporary Mathematics author: - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan P last_name: Solovej citation: ama: 'Lieb É, Seiringer R, Solovej J. Ground-state energy of a dilute Fermi gas. In: Vol 412. American Mathematical Society; 2006:239-248. doi:10.1090/conm/412' apa: Lieb, É., Seiringer, R., & Solovej, J. (2006). Ground-state energy of a dilute Fermi gas (Vol. 412, pp. 239–248). Presented at the Differential Equations and Mathematical Physics, American Mathematical Society. https://doi.org/10.1090/conm/412 chicago: Lieb, Élliott, Robert Seiringer, and Jan Solovej. “Ground-State Energy of a Dilute Fermi Gas,” 412:239–48. American Mathematical Society, 2006. https://doi.org/10.1090/conm/412. ieee: É. Lieb, R. Seiringer, and J. Solovej, “Ground-state energy of a dilute Fermi gas,” presented at the Differential Equations and Mathematical Physics, 2006, vol. 412, pp. 239–248. ista: Lieb É, Seiringer R, Solovej J. 2006. Ground-state energy of a dilute Fermi gas. Differential Equations and Mathematical Physics, Contemporary Mathematics, vol. 412, 239–248. mla: Lieb, Élliott, et al. Ground-State Energy of a Dilute Fermi Gas. Vol. 412, American Mathematical Society, 2006, pp. 239–48, doi:10.1090/conm/412. short: É. Lieb, R. Seiringer, J. Solovej, in:, American Mathematical Society, 2006, pp. 239–248. conference: name: Differential Equations and Mathematical Physics date_created: 2018-12-11T11:57:03Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T06:56:51Z day: '01' doi: 10.1090/conm/412 extern: 1 intvolume: ' 412' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0507049 month: '01' oa: 1 page: 239 - 248 publication_status: published publisher: American Mathematical Society publist_id: '4593' quality_controlled: 0 status: public title: Ground-state energy of a dilute Fermi gas type: conference volume: 412 year: '2006' ... --- _id: '2334' author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: 'Seiringer R, Lieb É, Yngvason J. One-dimensional behavior of dilute, trapped Bose gases in traps. In: Zambrini J, ed. World Scientific Publishing; 2006. doi:10.1007/s00220-003-0993-3' apa: 'Seiringer, R., Lieb, É., & Yngvason, J. (2006). One-dimensional behavior of dilute, trapped Bose gases in traps. In J. Zambrini (Ed.). Presented at the ICMP: International Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1007/s00220-003-0993-3' chicago: Seiringer, Robert, Élliott Lieb, and Jakob Yngvason. “One-Dimensional Behavior of Dilute, Trapped Bose Gases in Traps.” edited by Jean Zambrini. World Scientific Publishing, 2006. https://doi.org/10.1007/s00220-003-0993-3. ieee: 'R. Seiringer, É. Lieb, and J. Yngvason, “One-dimensional behavior of dilute, trapped Bose gases in traps,” presented at the ICMP: International Congress on Mathematical Physics, 2006.' ista: 'Seiringer R, Lieb É, Yngvason J. 2006. One-dimensional behavior of dilute, trapped Bose gases in traps. ICMP: International Congress on Mathematical Physics.' mla: Seiringer, Robert, et al. One-Dimensional Behavior of Dilute, Trapped Bose Gases in Traps. Edited by Jean Zambrini, World Scientific Publishing, 2006, doi:10.1007/s00220-003-0993-3. short: R. Seiringer, É. Lieb, J. Yngvason, in:, J. Zambrini (Ed.), World Scientific Publishing, 2006. conference: name: 'ICMP: International Congress on Mathematical Physics' date_created: 2018-12-11T11:57:03Z date_published: 2006-03-07T00:00:00Z date_updated: 2021-01-12T06:56:51Z day: '07' doi: 10.1007/s00220-003-0993-3 editor: - first_name: Jean full_name: Zambrini, Jean-Claude last_name: Zambrini extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0305025 month: '03' oa: 1 publication_status: published publisher: World Scientific Publishing publist_id: '4592' quality_controlled: 0 status: public title: One-dimensional behavior of dilute, trapped Bose gases in traps type: conference year: '2006' ... --- _id: '2363' abstract: - lang: eng text: ' We prove that the Gross-Pitaevskii equation correctly describes the ground state energy and corresponding one-particle density matrix of rotating, dilute, trapped Bose gases with repulsive two-body interactions. We also show that there is 100% Bose-Einstein condensation. While a proof that the GP equation correctly describes non-rotating or slowly rotating gases was known for some time, the rapidly rotating case was unclear because the Bose (i.e., symmetric) ground state is not the lowest eigenstate of the Hamiltonian in this case. We have been able to overcome this difficulty with the aid of coherent states. Our proof also conceptually simplifies the previous proof for the slowly rotating case. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state. ' author: - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Lieb É, Seiringer R. Derivation of the Gross-Pitaevskii equation for rotating Bose gases. Communications in Mathematical Physics. 2006;264(2):505-537. doi:10.1007/s00220-006-1524-9 apa: Lieb, É., & Seiringer, R. (2006). Derivation of the Gross-Pitaevskii equation for rotating Bose gases. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-006-1524-9 chicago: Lieb, Élliott, and Robert Seiringer. “Derivation of the Gross-Pitaevskii Equation for Rotating Bose Gases.” Communications in Mathematical Physics. Springer, 2006. https://doi.org/10.1007/s00220-006-1524-9. ieee: É. Lieb and R. Seiringer, “Derivation of the Gross-Pitaevskii equation for rotating Bose gases,” Communications in Mathematical Physics, vol. 264, no. 2. Springer, pp. 505–537, 2006. ista: Lieb É, Seiringer R. 2006. Derivation of the Gross-Pitaevskii equation for rotating Bose gases. Communications in Mathematical Physics. 264(2), 505–537. mla: Lieb, Élliott, and Robert Seiringer. “Derivation of the Gross-Pitaevskii Equation for Rotating Bose Gases.” Communications in Mathematical Physics, vol. 264, no. 2, Springer, 2006, pp. 505–37, doi:10.1007/s00220-006-1524-9. short: É. Lieb, R. Seiringer, Communications in Mathematical Physics 264 (2006) 505–537. date_created: 2018-12-11T11:57:13Z date_published: 2006-01-01T00:00:00Z date_updated: 2020-07-14T12:45:40Z day: '01' doi: 10.1007/s00220-006-1524-9 extern: 1 intvolume: ' 264' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0504042 month: '01' oa: 1 page: 505 - 537 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4561' quality_controlled: 0 status: public title: Derivation of the Gross-Pitaevskii equation for rotating Bose gases type: review volume: 264 year: '2006' ... --- _id: '2364' abstract: - lang: eng text: We present an inequality that gives a lower bound on the expectation value of certain two-body interaction potentials in a general state on Fock space in terms of the corresponding expectation value for thermal equilibrium states of non-interacting systems and the difference in the free energy. This bound can be viewed as a rigorous version of first-order perturbation theory for many-body systems at positive temperature. As an application, we give a proof of the first two terms in a high density (and high temperature) expansion of the free energy of jellium with Coulomb interactions, both in the fermionic and bosonic case. For bosons, our method works above the transition temperature (for the non-interacting gas) for Bose-Einstein condensation. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. A correlation estimate for quantum many-body systems at positive temperature. Reviews in Mathematical Physics. 2006;18(3):233-253. doi:10.1142/S0129055X06002632 apa: Seiringer, R. (2006). A correlation estimate for quantum many-body systems at positive temperature. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X06002632 chicago: Seiringer, Robert. “A Correlation Estimate for Quantum Many-Body Systems at Positive Temperature.” Reviews in Mathematical Physics. World Scientific Publishing, 2006. https://doi.org/10.1142/S0129055X06002632. ieee: R. Seiringer, “A correlation estimate for quantum many-body systems at positive temperature,” Reviews in Mathematical Physics, vol. 18, no. 3. World Scientific Publishing, pp. 233–253, 2006. ista: Seiringer R. 2006. A correlation estimate for quantum many-body systems at positive temperature. Reviews in Mathematical Physics. 18(3), 233–253. mla: Seiringer, Robert. “A Correlation Estimate for Quantum Many-Body Systems at Positive Temperature.” Reviews in Mathematical Physics, vol. 18, no. 3, World Scientific Publishing, 2006, pp. 233–53, doi:10.1142/S0129055X06002632. short: R. Seiringer, Reviews in Mathematical Physics 18 (2006) 233–253. date_created: 2018-12-11T11:57:14Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T06:57:02Z day: '01' doi: 10.1142/S0129055X06002632 extern: 1 intvolume: ' 18' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0601051 month: '04' oa: 1 page: 233 - 253 publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '4562' quality_controlled: 0 status: public title: A correlation estimate for quantum many-body systems at positive temperature type: journal_article volume: 18 year: '2006' ... --- _id: '2365' abstract: - lang: eng text: We consider a gas of fermions with non-zero spin at temperature T and chemical potential μ. We show that if the range of the interparticle interaction is small compared to the mean particle distance, the thermodynamic pressure differs to leading order from the corresponding expression for non-interacting particles by a term proportional to the scattering length of the interparticle interaction. This is true for any repulsive interaction, including hard cores. The result is uniform in the temperature as long as T is of the same order as the Fermi temperature, or smaller. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. The thermodynamic pressure of a dilute fermi gas. Communications in Mathematical Physics. 2006;261(3):729-757. doi:10.1007/s00220-005-1433-3 apa: Seiringer, R. (2006). The thermodynamic pressure of a dilute fermi gas. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-005-1433-3 chicago: Seiringer, Robert. “The Thermodynamic Pressure of a Dilute Fermi Gas.” Communications in Mathematical Physics. Springer, 2006. https://doi.org/10.1007/s00220-005-1433-3. ieee: R. Seiringer, “The thermodynamic pressure of a dilute fermi gas,” Communications in Mathematical Physics, vol. 261, no. 3. Springer, pp. 729–757, 2006. ista: Seiringer R. 2006. The thermodynamic pressure of a dilute fermi gas. Communications in Mathematical Physics. 261(3), 729–757. mla: Seiringer, Robert. “The Thermodynamic Pressure of a Dilute Fermi Gas.” Communications in Mathematical Physics, vol. 261, no. 3, Springer, 2006, pp. 729–57, doi:10.1007/s00220-005-1433-3. short: R. Seiringer, Communications in Mathematical Physics 261 (2006) 729–757. date_created: 2018-12-11T11:57:14Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T06:57:02Z day: '01' doi: 10.1007/s00220-005-1433-3 extern: 1 intvolume: ' 261' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0412086 month: '02' oa: 1 page: 729 - 757 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4563' quality_controlled: 0 status: public title: The thermodynamic pressure of a dilute fermi gas type: journal_article volume: 261 year: '2006' ... --- _id: '2366' abstract: - lang: eng text: Inequalities are derived for power sums of the real part and the modulus of the eigenvalues of a Schrödinger operator with a complex-valued potential. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Ari full_name: Laptev, Ari last_name: Laptev - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Laptev A, Lieb É, Seiringer R. Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials. Letters in Mathematical Physics. 2006;77(3):309-316. doi:10.1007/s11005-006-0095-1 apa: Frank, R., Laptev, A., Lieb, É., & Seiringer, R. (2006). Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-006-0095-1 chicago: Frank, Rupert, Ari Laptev, Élliott Lieb, and Robert Seiringer. “Lieb-Thirring Inequalities for Schrödinger Operators with Complex-Valued Potentials.” Letters in Mathematical Physics. Springer, 2006. https://doi.org/10.1007/s11005-006-0095-1. ieee: R. Frank, A. Laptev, É. Lieb, and R. Seiringer, “Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials,” Letters in Mathematical Physics, vol. 77, no. 3. Springer, pp. 309–316, 2006. ista: Frank R, Laptev A, Lieb É, Seiringer R. 2006. Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials. Letters in Mathematical Physics. 77(3), 309–316. mla: Frank, Rupert, et al. “Lieb-Thirring Inequalities for Schrödinger Operators with Complex-Valued Potentials.” Letters in Mathematical Physics, vol. 77, no. 3, Springer, 2006, pp. 309–16, doi:10.1007/s11005-006-0095-1. short: R. Frank, A. Laptev, É. Lieb, R. Seiringer, Letters in Mathematical Physics 77 (2006) 309–316. date_created: 2018-12-11T11:57:15Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T06:57:03Z day: '01' doi: 10.1007/s11005-006-0095-1 extern: 1 intvolume: ' 77' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0605017 month: '09' oa: 1 page: 309 - 316 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '4560' quality_controlled: 0 status: public title: Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials type: journal_article volume: 77 year: '2006' ... --- _id: '2368' abstract: - lang: eng text: The recent experimental success in creating Bose-Einstein condensates of alkali atoms, honored by the Nobel prize awards in 2001 [1,5], led to renewed interest in the mathematical description of interacting Bose gases. alternative_title: - LNP author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Seiringer R. Dilute, trapped Bose gases and Bose-Einstein condensation. In: Dereziński J, Siedentop H, eds. Large Coulomb Systems. Vol 695. Springer; 2006:249-274. doi:10.1007/3-540-32579-4_6' apa: Seiringer, R. (2006). Dilute, trapped Bose gases and Bose-Einstein condensation. In J. Dereziński & H. Siedentop (Eds.), Large Coulomb Systems (Vol. 695, pp. 249–274). Springer. https://doi.org/10.1007/3-540-32579-4_6 chicago: Seiringer, Robert. “Dilute, Trapped Bose Gases and Bose-Einstein Condensation.” In Large Coulomb Systems, edited by Jan Dereziński and Heinz Siedentop, 695:249–74. Springer, 2006. https://doi.org/10.1007/3-540-32579-4_6. ieee: R. Seiringer, “Dilute, trapped Bose gases and Bose-Einstein condensation,” in Large Coulomb Systems, vol. 695, J. Dereziński and H. Siedentop, Eds. Springer, 2006, pp. 249–274. ista: 'Seiringer R. 2006.Dilute, trapped Bose gases and Bose-Einstein condensation. In: Large Coulomb Systems. LNP, vol. 695, 249–274.' mla: Seiringer, Robert. “Dilute, Trapped Bose Gases and Bose-Einstein Condensation.” Large Coulomb Systems, edited by Jan Dereziński and Heinz Siedentop, vol. 695, Springer, 2006, pp. 249–74, doi:10.1007/3-540-32579-4_6. short: R. Seiringer, in:, J. Dereziński, H. Siedentop (Eds.), Large Coulomb Systems, Springer, 2006, pp. 249–274. date_created: 2018-12-11T11:57:15Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T06:57:03Z day: '01' doi: 10.1007/3-540-32579-4_6 editor: - first_name: Jan full_name: Dereziński, Jan last_name: Dereziński - first_name: Heinz full_name: Siedentop, Heinz last_name: Siedentop extern: 1 intvolume: ' 695' month: '01' page: 249 - 274 publication: Large Coulomb Systems publication_status: published publisher: Springer publist_id: '4558' quality_controlled: 0 status: public title: Dilute, trapped Bose gases and Bose-Einstein condensation type: book_chapter volume: 695 year: '2006' ... --- _id: '2369' abstract: - lang: eng text: One of the most remarkable recent developments in the study of ultracold Bose gases is the observation of a reversible transition from a Bose Einstein condensate to a state composed of localized atoms as the strength of a periodic, optical trapping potential is varied. In [1] a model of this phenomenon has been analyzed rigorously. The gas is a hard core lattice gas and the optical lattice is modeled by a periodic potential of strength λ. For small λ and temperature Bose- Einstein condensation (BEC) is proved to occur, while at large λ BEC disappears, even in the ground state, which is a Mott-insulator state with a characteristic gap. The inter-particle interaction is essential for this effect. This contribution gives a pedagogical survey of these results. alternative_title: - LNP author: - first_name: Michael full_name: Aizenman, Michael last_name: Aizenman - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan P last_name: Solovej - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: 'Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. Bose-Einstein condensation as a quantum phase transition in an optical lattice. In: Asch J, Joye A, eds. Mathematical Physics of Quantum Mechanics. Vol 690. Springer; 2006:199-215. doi:10.1007/b11573432' apa: Aizenman, M., Lieb, É., Seiringer, R., Solovej, J., & Yngvason, J. (2006). Bose-Einstein condensation as a quantum phase transition in an optical lattice. In J. Asch & A. Joye (Eds.), Mathematical Physics of Quantum Mechanics (Vol. 690, pp. 199–215). Springer. https://doi.org/10.1007/b11573432 chicago: Aizenman, Michael, Élliott Lieb, Robert Seiringer, Jan Solovej, and Jakob Yngvason. “Bose-Einstein Condensation as a Quantum Phase Transition in an Optical Lattice.” In Mathematical Physics of Quantum Mechanics, edited by Joachim Asch and Alain Joye, 690:199–215. Springer, 2006. https://doi.org/10.1007/b11573432. ieee: M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, and J. Yngvason, “Bose-Einstein condensation as a quantum phase transition in an optical lattice,” in Mathematical Physics of Quantum Mechanics, vol. 690, J. Asch and A. Joye, Eds. Springer, 2006, pp. 199–215. ista: 'Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. 2006.Bose-Einstein condensation as a quantum phase transition in an optical lattice. In: Mathematical Physics of Quantum Mechanics. LNP, vol. 690, 199–215.' mla: Aizenman, Michael, et al. “Bose-Einstein Condensation as a Quantum Phase Transition in an Optical Lattice.” Mathematical Physics of Quantum Mechanics, edited by Joachim Asch and Alain Joye, vol. 690, Springer, 2006, pp. 199–215, doi:10.1007/b11573432. short: M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, J. Yngvason, in:, J. Asch, A. Joye (Eds.), Mathematical Physics of Quantum Mechanics, Springer, 2006, pp. 199–215. date_created: 2018-12-11T11:57:16Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T06:57:04Z day: '01' doi: 10.1007/b11573432 editor: - first_name: Joachim full_name: Asch, Joachim last_name: Asch - first_name: Alain full_name: Joye, Alain last_name: Joye extern: 1 intvolume: ' 690' main_file_link: - open_access: '1' url: http://arxiv.org/abs/cond-mat/0412034 month: '01' oa: 1 page: 199 - 215 publication: Mathematical Physics of Quantum Mechanics publication_status: published publisher: Springer publist_id: '4559' quality_controlled: 0 status: public title: Bose-Einstein condensation as a quantum phase transition in an optical lattice type: book_chapter volume: 690 year: '2006' ... --- _id: '2416' alternative_title: - Algorithms and Combinatorics author: - first_name: Jørgen full_name: Bang-Jensen, Jørgen last_name: Bang Jensen - first_name: Bruce full_name: Reed, Bruce last_name: Reed - first_name: Bruce full_name: Schacht, Bruce last_name: Schacht - first_name: Robert full_name: Šámal, Robert last_name: Šámal - first_name: Bjarne full_name: Toft, Bjarne last_name: Toft - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Bang Jensen J, Reed B, Schacht B, Šámal R, Toft B, Wagner U. On six problems posed by Jarik Nešetřil. In: Topics in Discrete Mathematics. Vol 26. Springer; 2006:613-627. doi:10.1007/3-540-33700-8_30' apa: Bang Jensen, J., Reed, B., Schacht, B., Šámal, R., Toft, B., & Wagner, U. (2006). On six problems posed by Jarik Nešetřil. In Topics in Discrete Mathematics (Vol. 26, pp. 613–627). Springer. https://doi.org/10.1007/3-540-33700-8_30 chicago: Bang Jensen, Jørgen, Bruce Reed, Bruce Schacht, Robert Šámal, Bjarne Toft, and Uli Wagner. “On Six Problems Posed by Jarik Nešetřil.” In Topics in Discrete Mathematics, 26:613–27. Springer, 2006. https://doi.org/10.1007/3-540-33700-8_30. ieee: J. Bang Jensen, B. Reed, B. Schacht, R. Šámal, B. Toft, and U. Wagner, “On six problems posed by Jarik Nešetřil,” in Topics in Discrete Mathematics, vol. 26, Springer, 2006, pp. 613–627. ista: 'Bang Jensen J, Reed B, Schacht B, Šámal R, Toft B, Wagner U. 2006.On six problems posed by Jarik Nešetřil. In: Topics in Discrete Mathematics. Algorithms and Combinatorics, vol. 26, 613–627.' mla: Bang Jensen, Jørgen, et al. “On Six Problems Posed by Jarik Nešetřil.” Topics in Discrete Mathematics, vol. 26, Springer, 2006, pp. 613–27, doi:10.1007/3-540-33700-8_30. short: J. Bang Jensen, B. Reed, B. Schacht, R. Šámal, B. Toft, U. Wagner, in:, Topics in Discrete Mathematics, Springer, 2006, pp. 613–627. date_created: 2018-12-11T11:57:32Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T06:57:21Z day: '01' doi: 10.1007/3-540-33700-8_30 extern: 1 intvolume: ' 26' month: '01' page: 613 - 627 publication: Topics in Discrete Mathematics publication_status: published publisher: Springer publist_id: '4509' quality_controlled: 0 status: public title: On six problems posed by Jarik Nešetřil type: book_chapter volume: 26 year: '2006' ... --- _id: '2430' abstract: - lang: eng text: We consider an online version of the conflict-free coloring of a set of points on the line, where each newly inserted point must be assigned a color upon insertion, and at all times the coloring has to be conflict-free, in the sense that in every interval I there is a color that appears exactly once in I. We present deterministic and randomized algorithms for achieving this goal, and analyze their performance, that is, the maximum number of colors that they need to use, as a function of the number n of inserted points. We first show that a natural and simple (deterministic) approach may perform rather poorly, requiring Ω(√̃) colors in the worst case. We then derive two efficient variants of this simple algorithm. The first is deterministic and uses O(log 2 n) colors, and the second is randomized and uses O(log n) colors with high probability. We also show that the O(log 2 n) bound on the number of colors used by our deterministic algorithm is tight on the worst case. We also analyze the performance of the simplest proposed algorithm when the points are inserted in a random order and present an incomplete analysis that indicates that, with high probability, it uses only O(log n) colors. Finally, we show that in the extension of this problem to two dimensions, where the relevant ranges are disks, n colors may be required in the worst case. author: - first_name: Ke full_name: Chent, Ke last_name: Chent - first_name: Amos full_name: Fiat, Amos last_name: Fiat - first_name: Haim full_name: Kaplan, Haim last_name: Kaplan - first_name: Meital full_name: Levy, Meital B last_name: Levy - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Elchanan full_name: Mossel, Elchanan last_name: Mossel - first_name: János full_name: Pach, János last_name: Pach - first_name: Micha full_name: Sharir, Micha last_name: Sharir - first_name: Shakhar full_name: Smorodinsky, Shakhar last_name: Smorodinsky - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Emo full_name: Welzl, Emo last_name: Welzl citation: ama: Chent K, Fiat A, Kaplan H, et al. Online conflict-free coloring for intervals. SIAM Journal on Computing. 2006;36(5):1342-1359. doi:10.1137/S0097539704446682 apa: Chent, K., Fiat, A., Kaplan, H., Levy, M., Matoušek, J., Mossel, E., … Welzl, E. (2006). Online conflict-free coloring for intervals. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/S0097539704446682 chicago: Chent, Ke, Amos Fiat, Haim Kaplan, Meital Levy, Jiří Matoušek, Elchanan Mossel, János Pach, et al. “Online Conflict-Free Coloring for Intervals.” SIAM Journal on Computing. SIAM, 2006. https://doi.org/10.1137/S0097539704446682. ieee: K. Chent et al., “Online conflict-free coloring for intervals,” SIAM Journal on Computing, vol. 36, no. 5. SIAM, pp. 1342–1359, 2006. ista: Chent K, Fiat A, Kaplan H, Levy M, Matoušek J, Mossel E, Pach J, Sharir M, Smorodinsky S, Wagner U, Welzl E. 2006. Online conflict-free coloring for intervals. SIAM Journal on Computing. 36(5), 1342–1359. mla: Chent, Ke, et al. “Online Conflict-Free Coloring for Intervals.” SIAM Journal on Computing, vol. 36, no. 5, SIAM, 2006, pp. 1342–59, doi:10.1137/S0097539704446682. short: K. Chent, A. Fiat, H. Kaplan, M. Levy, J. Matoušek, E. Mossel, J. Pach, M. Sharir, S. Smorodinsky, U. Wagner, E. Welzl, SIAM Journal on Computing 36 (2006) 1342–1359. date_created: 2018-12-11T11:57:37Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T06:57:26Z day: '01' doi: 10.1137/S0097539704446682 extern: 1 intvolume: ' 36' issue: '5' month: '01' page: 1342 - 1359 publication: SIAM Journal on Computing publication_status: published publisher: SIAM publist_id: '4490' quality_controlled: 0 status: public title: Online conflict-free coloring for intervals type: journal_article volume: 36 year: '2006' ... --- _id: '2431' abstract: - lang: eng text: We prove an upper bound, tight up to a factor of 2, for the number of vertices of level at most t in an arrangement of n halfspaces in R , for arbitrary n and d (in particular, the dimension d is not considered constant). This partially settles a conjecture of Eckhoff, Linhart, and Welzl. Up to the factor of 2, the result generalizes McMullen's Upper Bound Theorem for convex polytopes (the case ℓ = O) and extends a theorem of Linhart for the case d ≤ 4. Moreover, the bound sharpens asymptotic estimates obtained by Clarkson and Shor. The proof is based on the h-matrix of the arrangement (a generalization, introduced by Mulmuley, of the h-vector of a convex polytope). We show that bounding appropriate sums of entries of this matrix reduces to a lemma about quadrupels of sets with certain intersection properties, and we prove this lemma, up to a factor of 2, using tools from multilinear algebra. This extends an approach of Alon and Kalai, who used linear algebra methods for an alternative proof of the classical Upper Bound Theorem. The bounds for the entries of the h-matrix also imply bounds for the number of i-dimensional faces, i > 0, at level at most ℓ. Furthermore, we discuss a connection with crossing numbers of graphs that was one of the main motivations for investigating exact bounds that are valid for arbitrary dimensions. alternative_title: - IEEE Conference Proceedings author: - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Wagner U. On a geometric generalization of the Upper Bound Theorem. In: IEEE; 2006:635-645. doi:10.1109/FOCS.2006.53' apa: 'Wagner, U. (2006). On a geometric generalization of the Upper Bound Theorem (pp. 635–645). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2006.53' chicago: Wagner, Uli. “On a Geometric Generalization of the Upper Bound Theorem,” 635–45. IEEE, 2006. https://doi.org/10.1109/FOCS.2006.53. ieee: 'U. Wagner, “On a geometric generalization of the Upper Bound Theorem,” presented at the FOCS: Foundations of Computer Science, 2006, pp. 635–645.' ista: 'Wagner U. 2006. On a geometric generalization of the Upper Bound Theorem. FOCS: Foundations of Computer Science, IEEE Conference Proceedings, , 635–645.' mla: Wagner, Uli. On a Geometric Generalization of the Upper Bound Theorem. IEEE, 2006, pp. 635–45, doi:10.1109/FOCS.2006.53. short: U. Wagner, in:, IEEE, 2006, pp. 635–645. conference: name: 'FOCS: Foundations of Computer Science' date_created: 2018-12-11T11:57:37Z date_published: 2006-06-08T00:00:00Z date_updated: 2021-01-12T06:57:27Z day: '08' doi: 10.1109/FOCS.2006.53 extern: 1 month: '06' page: 635 - 645 publication_status: published publisher: IEEE publist_id: '4489' quality_controlled: 0 status: public title: On a geometric generalization of the Upper Bound Theorem type: conference year: '2006' ... --- _id: '2429' abstract: - lang: eng text: 'We show, with an elementary proof, that the number of halving simplices in a set of n points in 4 in general position is O(n4-2/45). This improves the previous bound of O(n4-1/134). Our main new ingredient is a bound on the maximum number of halving simplices intersecting a fixed 2-plane. ' author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Micha full_name: Sharir, Micha last_name: Sharir - first_name: Shakhar full_name: Smorodinsky, Shakhar last_name: Smorodinsky - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Matoušek J, Sharir M, Smorodinsky S, Wagner U. K-sets in four dimensions. Discrete & Computational Geometry. 2006;35(2):177-191. doi:10.1007/s00454-005-1200-4 apa: Matoušek, J., Sharir, M., Smorodinsky, S., & Wagner, U. (2006). K-sets in four dimensions. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-005-1200-4 chicago: Matoušek, Jiří, Micha Sharir, Shakhar Smorodinsky, and Uli Wagner. “K-Sets in Four Dimensions.” Discrete & Computational Geometry. Springer, 2006. https://doi.org/10.1007/s00454-005-1200-4. ieee: J. Matoušek, M. Sharir, S. Smorodinsky, and U. Wagner, “K-sets in four dimensions,” Discrete & Computational Geometry, vol. 35, no. 2. Springer, pp. 177–191, 2006. ista: Matoušek J, Sharir M, Smorodinsky S, Wagner U. 2006. K-sets in four dimensions. Discrete & Computational Geometry. 35(2), 177–191. mla: Matoušek, Jiří, et al. “K-Sets in Four Dimensions.” Discrete & Computational Geometry, vol. 35, no. 2, Springer, 2006, pp. 177–91, doi:10.1007/s00454-005-1200-4. short: J. Matoušek, M. Sharir, S. Smorodinsky, U. Wagner, Discrete & Computational Geometry 35 (2006) 177–191. date_created: 2018-12-11T11:57:37Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T06:57:26Z day: '01' doi: 10.1007/s00454-005-1200-4 extern: 1 intvolume: ' 35' issue: '2' month: '02' page: 177 - 191 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '4495' quality_controlled: 0 status: public title: K-sets in four dimensions type: journal_article volume: 35 year: '2006' ... --- _id: '2659' abstract: - lang: eng text: Transmembrane AMPA receptor regulatory proteins (TARPs), including stargazin/γ-2, are associated with AMPA receptors and participate in their surface delivery and anchoring at the postsynaptic membrane. TARPs may also act as a positive modulator of the AMPA receptor ion channel function; however, little is known about other TARP members except for stargazin/γ-2. We examined the synaptic localization of stargazin/γ-2 and γ-8 by immunoelectron microscopy and biochemical analysis. The analysis of sodium dodecyl sulfate-digested freeze-fracture replica labeling revealed that stargazin/γ-2 was concentrated in the postsynaptic area, whereas γ-8 was distributed both in synaptic and extra-synaptic plasma membranes of the hippocampal neuron. When a synaptic plasma membrane-enriched brain fraction was treated with Triton X-100 and separated by sucrose density gradient ultracentrifugation, a large proportion of NMDA receptor and stargazin/γ-2 was accumulated in raft-enriched fractions, whereas AMPA receptor and γ-8 were distributed in both the raft-enriched fractions and other Triton-insoluble fractions. Phosphorylation of stargazin/γ-2 and γ-8 was regulated by different sets of kinases and phosphatases in cultured cortical neurons. These results suggested that stargazin/γ-2 and γ-8 have distinct roles in postsynaptic membranes under the regulation of different intracellular signaling pathways. author: - first_name: Mihoko full_name: Inamura, Mihoko last_name: Inamura - first_name: Makoto full_name: Itakura, Makoto last_name: Itakura - first_name: Hirotsugu full_name: Okamoto, Hirotsugu last_name: Okamoto - first_name: Sumio full_name: Hoka, Sumio last_name: Hoka - first_name: Akira full_name: Mizoguchi, Akira last_name: Mizoguchi - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Saori full_name: Yamamori, Saori last_name: Yamamori - first_name: Masami full_name: Takahashi, Masami last_name: Takahashi citation: ama: Inamura M, Itakura M, Okamoto H, et al. Differential localization and regulation of stargazin-like protein, γ-8 and stargazin in the plasma membrane of hippocampal and cortical neurons. Neuroscience Research. 2006;55(1):45-53. doi:10.1016/j.neures.2006.01.004 apa: Inamura, M., Itakura, M., Okamoto, H., Hoka, S., Mizoguchi, A., Fukazawa, Y., … Takahashi, M. (2006). Differential localization and regulation of stargazin-like protein, γ-8 and stargazin in the plasma membrane of hippocampal and cortical neurons. Neuroscience Research. Elsevier. https://doi.org/10.1016/j.neures.2006.01.004 chicago: Inamura, Mihoko, Makoto Itakura, Hirotsugu Okamoto, Sumio Hoka, Akira Mizoguchi, Yugo Fukazawa, Ryuichi Shigemoto, Saori Yamamori, and Masami Takahashi. “ Differential Localization and Regulation of Stargazin-like Protein, γ-8 and Stargazin in the Plasma Membrane of Hippocampal and Cortical Neurons.” Neuroscience Research. Elsevier, 2006. https://doi.org/10.1016/j.neures.2006.01.004. ieee: M. Inamura et al., “ Differential localization and regulation of stargazin-like protein, γ-8 and stargazin in the plasma membrane of hippocampal and cortical neurons,” Neuroscience Research, vol. 55, no. 1. Elsevier, pp. 45–53, 2006. ista: Inamura M, Itakura M, Okamoto H, Hoka S, Mizoguchi A, Fukazawa Y, Shigemoto R, Yamamori S, Takahashi M. 2006. Differential localization and regulation of stargazin-like protein, γ-8 and stargazin in the plasma membrane of hippocampal and cortical neurons. Neuroscience Research. 55(1), 45–53. mla: Inamura, Mihoko, et al. “ Differential Localization and Regulation of Stargazin-like Protein, γ-8 and Stargazin in the Plasma Membrane of Hippocampal and Cortical Neurons.” Neuroscience Research, vol. 55, no. 1, Elsevier, 2006, pp. 45–53, doi:10.1016/j.neures.2006.01.004. short: M. Inamura, M. Itakura, H. Okamoto, S. Hoka, A. Mizoguchi, Y. Fukazawa, R. Shigemoto, S. Yamamori, M. Takahashi, Neuroscience Research 55 (2006) 45–53. date_created: 2018-12-11T11:58:55Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T06:58:52Z day: '01' doi: 10.1016/j.neures.2006.01.004 extern: 1 intvolume: ' 55' issue: '1' month: '05' page: 45 - 53 publication: Neuroscience Research publication_status: published publisher: Elsevier publist_id: '4238' quality_controlled: 0 status: public title: ' Differential localization and regulation of stargazin-like protein, γ-8 and stargazin in the plasma membrane of hippocampal and cortical neurons' type: journal_article volume: 55 year: '2006' ... --- _id: '2657' abstract: - lang: eng text: The highest densities of the two metabotropic GABA subunits, GABA B1 and GABAB2, have been reported as occurring around the glutamatergic synapses between Purkinje cell spines and parallel fibre varicosities. In order to determine how this distribution is achieved during development, we investigated the expression pattern and the cellular and subcellular localization of the GABAB1 and GABAB2 subunits in the rat cerebellum during postnatal development. At the light microscopic level, immunoreactivity for the GABAB1 and GABAB2 subunits was very prominent in the developing molecular layer, especially in Purkinje cells. Using double immunofluorescence, we demonstrated that GABAB1 was transiently expressed in glial cells. At the electron microscopic level, immunoreactivity for GABAB receptors was always detected both pre- and postsynaptically. Presynaptically, GABAB1 and GABAB2 were localized in the extrasynaptic membrane of parallel fibres at all ages, and only rarely in GABAergic axons. Postsynaptically, GABAB receptors were localized to the extrasynaptic and perisynaptic plasma membrane of Purkinje cell dendrites and spines throughout development. Quantitative analysis and three-dimensional reconstructions further revealed a progressive developmental movement of the GABAB1 subunit on the surface of Purkinje cells from dendritic shafts to its final destination, the dendritic spines. Together, these results indicate that GABAB receptors undergo dynamic regulation during cerebellar development in association with the establishment and maturation of glutamatergic synapses to Purkinje cells. author: - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Luján R, Shigemoto R. Localization of metabotropic GABA receptor subunits GABAB1 and GABAB2 relative to synaptic sites in the rat developing cerebellum. European Journal of Neuroscience. 2006;23(6):1479-1490. doi:10.1111/j.1460-9568.2006.04669.x apa: Luján, R., & Shigemoto, R. (2006). Localization of metabotropic GABA receptor subunits GABAB1 and GABAB2 relative to synaptic sites in the rat developing cerebellum. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2006.04669.x chicago: Luján, Rafael, and Ryuichi Shigemoto. “Localization of Metabotropic GABA Receptor Subunits GABAB1 and GABAB2 Relative to Synaptic Sites in the Rat Developing Cerebellum.” European Journal of Neuroscience. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1460-9568.2006.04669.x. ieee: R. Luján and R. Shigemoto, “Localization of metabotropic GABA receptor subunits GABAB1 and GABAB2 relative to synaptic sites in the rat developing cerebellum,” European Journal of Neuroscience, vol. 23, no. 6. Wiley-Blackwell, pp. 1479–1490, 2006. ista: Luján R, Shigemoto R. 2006. Localization of metabotropic GABA receptor subunits GABAB1 and GABAB2 relative to synaptic sites in the rat developing cerebellum. European Journal of Neuroscience. 23(6), 1479–1490. mla: Luján, Rafael, and Ryuichi Shigemoto. “Localization of Metabotropic GABA Receptor Subunits GABAB1 and GABAB2 Relative to Synaptic Sites in the Rat Developing Cerebellum.” European Journal of Neuroscience, vol. 23, no. 6, Wiley-Blackwell, 2006, pp. 1479–90, doi:10.1111/j.1460-9568.2006.04669.x. short: R. Luján, R. Shigemoto, European Journal of Neuroscience 23 (2006) 1479–1490. date_created: 2018-12-11T11:58:54Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T06:58:52Z day: '01' doi: 10.1111/j.1460-9568.2006.04669.x extern: 1 intvolume: ' 23' issue: '6' month: '03' page: 1479 - 1490 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '4239' quality_controlled: 0 status: public title: Localization of metabotropic GABA receptor subunits GABAB1 and GABAB2 relative to synaptic sites in the rat developing cerebellum type: journal_article volume: 23 year: '2006' ... --- _id: '2663' abstract: - lang: eng text: The rocker mice are hereditary ataxic mutants that carry a point mutation in the gene encoding the CaV2.1 (P/Q-type) Ca2+ channel α1 subunit, and show the mildest symptoms among the reported CaV2.1 mutant mice. We studied the basic characteristics of the rocker mutant Ca2+ channel and their impacts on excitatory synaptic transmission in cerebellar Purkinje cells (PCs). In acutely dissociated PC somas, the rocker mutant channel showed a moderate reduction in Ca2+ channel current density, whereas its kinetics and voltage dependency of gating remained nearly normal. Despite the small changes in channel function, synaptic transmission in the parallel fiber (PF)-PC synapses was severely impaired. The climbing fiber inputs onto PCs showed a moderate impairment but could elicit normal complex spikes. Presynaptic function of the PF-PC synapses, however, was unexpectedly almost normal in terms of paired-pulse facilitation, sensitivity to extracellular Ca2+ concentration and glutamate concentration in synaptic clefts. Electron microscopic analyses including freeze-fracture replica labeling revealed that both the number and density of postsynaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors substantially decreased without gross structural changes of the PF-PC synapses. We also observed an abnormal arborization of PC dendrites in young adult rocker mice (∼ 1 month old). These lines of evidence suggest that even a moderate dysfunction of CaV2.1 Ca2+ channel can cause substantial changes in postsynaptic molecular composition of the PF-PC synapses and dendritic structure of PCs. author: - first_name: Takashi full_name: Kodama, Takashi last_name: Kodama - first_name: Yuko full_name: Itsukaichi-Nishida, Yuko last_name: Itsukaichi Nishida - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Minoru full_name: Wakamori, Minoru last_name: Wakamori - first_name: Mariko full_name: Miyata, Mariko last_name: Miyata - first_name: Elek full_name: Molnár, Elek last_name: Molnár - first_name: Yasuo full_name: Mori, Yasuo last_name: Mori - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Keiji full_name: Imoto, Keiji last_name: Imoto citation: ama: Kodama T, Itsukaichi Nishida Y, Fukazawa Y, et al. A CaV2.1 calcium channel mutation rocker reduces the number of postsynaptic AMPA receptors in parallel fiber-Purkinje cell synapses. European Journal of Neuroscience. 2006;24(11):2993-3007. doi:10.1111/j.1460-9568.2006.05191.x apa: Kodama, T., Itsukaichi Nishida, Y., Fukazawa, Y., Wakamori, M., Miyata, M., Molnár, E., … Imoto, K. (2006). A CaV2.1 calcium channel mutation rocker reduces the number of postsynaptic AMPA receptors in parallel fiber-Purkinje cell synapses. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2006.05191.x chicago: Kodama, Takashi, Yuko Itsukaichi Nishida, Yugo Fukazawa, Minoru Wakamori, Mariko Miyata, Elek Molnár, Yasuo Mori, Ryuichi Shigemoto, and Keiji Imoto. “A CaV2.1 Calcium Channel Mutation Rocker Reduces the Number of Postsynaptic AMPA Receptors in Parallel Fiber-Purkinje Cell Synapses.” European Journal of Neuroscience. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1460-9568.2006.05191.x. ieee: T. Kodama et al., “A CaV2.1 calcium channel mutation rocker reduces the number of postsynaptic AMPA receptors in parallel fiber-Purkinje cell synapses,” European Journal of Neuroscience, vol. 24, no. 11. Wiley-Blackwell, pp. 2993–3007, 2006. ista: Kodama T, Itsukaichi Nishida Y, Fukazawa Y, Wakamori M, Miyata M, Molnár E, Mori Y, Shigemoto R, Imoto K. 2006. A CaV2.1 calcium channel mutation rocker reduces the number of postsynaptic AMPA receptors in parallel fiber-Purkinje cell synapses. European Journal of Neuroscience. 24(11), 2993–3007. mla: Kodama, Takashi, et al. “A CaV2.1 Calcium Channel Mutation Rocker Reduces the Number of Postsynaptic AMPA Receptors in Parallel Fiber-Purkinje Cell Synapses.” European Journal of Neuroscience, vol. 24, no. 11, Wiley-Blackwell, 2006, pp. 2993–3007, doi:10.1111/j.1460-9568.2006.05191.x. short: T. Kodama, Y. Itsukaichi Nishida, Y. Fukazawa, M. Wakamori, M. Miyata, E. Molnár, Y. Mori, R. Shigemoto, K. Imoto, European Journal of Neuroscience 24 (2006) 2993–3007. date_created: 2018-12-11T11:58:56Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T06:58:54Z day: '01' doi: 10.1111/j.1460-9568.2006.05191.x extern: 1 intvolume: ' 24' issue: '11' month: '12' page: 2993 - 3007 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '4233' quality_controlled: 0 status: public title: A CaV2.1 calcium channel mutation rocker reduces the number of postsynaptic AMPA receptors in parallel fiber-Purkinje cell synapses type: journal_article volume: 24 year: '2006' ... --- _id: '2661' abstract: - lang: eng text: GABAB receptors are the G protein-coupled receptors for the main inhibitory neurotransmitter in the brain, γ-aminobutyric acid (GABA). Molecular diversity in the GABAB system arises from the GABAB1a and GABAB1b subunit isoforms that solely differ in their ectodomains by a pair of sushi repeats that is unique to GABAB1a. Using a combined genetic, physiological, and morphological approach, we now demonstrate that GABAB1 isoforms localize to distinct synaptic sites and convey separate functions in vivo. At hippocampal CA3-to-CA1 synapses, GABAB1a assembles heteroreceptors inhibiting glutamate release, while predominantly GABAB1b mediates postsynaptic inhibition. Electron microscopy reveals a synaptic distribution of GABAB1 isoforms that agrees with the observed functional differences. Transfected CA3 neurons selectively express GABAB1a in distal axons, suggesting that the sushi repeats, a conserved protein interaction motif, specify heteroreceptor localization. The constitutive absence of GABAB1a but not GABAB1b results in impaired synaptic plasticity and hippocampus-dependent memory, emphasizing molecular differences in synaptic GABAB functions. author: - first_name: Réjan full_name: Vigot, Réjan last_name: Vigot - first_name: Samuel full_name: Barbieri, Samuel last_name: Barbieri - first_name: Hans full_name: Bräuner-Osborne, Hans last_name: Bräuner Osborne - first_name: Rostislav full_name: Tureček, Rostislav last_name: Tureček - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Yan full_name: Zhang, Yan Ping last_name: Zhang - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Laura full_name: Jacobson, Laura H last_name: Jacobson - first_name: Barbara full_name: Biermann, Barbara last_name: Biermann - first_name: Jean full_name: Fritschy, Jean-Marc last_name: Fritschy - first_name: Claire full_name: Vacher, Claire-Marie last_name: Vacher - first_name: Matthias full_name: Müller, Matthias P last_name: Müller - first_name: Gilles full_name: Sansig, Gilles last_name: Sansig - first_name: Nicole full_name: Guetg, Nicole last_name: Guetg - first_name: John full_name: Cryan, John F last_name: Cryan - first_name: Klemens full_name: Kaupmann, Klemens last_name: Kaupmann - first_name: Martin full_name: Gassmann, Martin last_name: Gassmann - first_name: Thomas full_name: Oertner, Thomas G last_name: Oertner - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler citation: ama: Vigot R, Barbieri S, Bräuner Osborne H, et al. Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants. Neuron. 2006;50(4):589-601. doi:10.1016/j.neuron.2006.04.014 apa: Vigot, R., Barbieri, S., Bräuner Osborne, H., Tureček, R., Shigemoto, R., Zhang, Y., … Bettler, B. (2006). Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2006.04.014 chicago: Vigot, Réjan, Samuel Barbieri, Hans Bräuner Osborne, Rostislav Tureček, Ryuichi Shigemoto, Yan Zhang, Rafael Luján, et al. “Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2006.04.014. ieee: R. Vigot et al., “Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants,” Neuron, vol. 50, no. 4. Elsevier, pp. 589–601, 2006. ista: Vigot R, Barbieri S, Bräuner Osborne H, Tureček R, Shigemoto R, Zhang Y, Luján R, Jacobson L, Biermann B, Fritschy J, Vacher C, Müller M, Sansig G, Guetg N, Cryan J, Kaupmann K, Gassmann M, Oertner T, Bettler B. 2006. Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants. Neuron. 50(4), 589–601. mla: Vigot, Réjan, et al. “Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants.” Neuron, vol. 50, no. 4, Elsevier, 2006, pp. 589–601, doi:10.1016/j.neuron.2006.04.014. short: R. Vigot, S. Barbieri, H. Bräuner Osborne, R. Tureček, R. Shigemoto, Y. Zhang, R. Luján, L. Jacobson, B. Biermann, J. Fritschy, C. Vacher, M. Müller, G. Sansig, N. Guetg, J. Cryan, K. Kaupmann, M. Gassmann, T. Oertner, B. Bettler, Neuron 50 (2006) 589–601. date_created: 2018-12-11T11:58:56Z date_published: 2006-05-18T00:00:00Z date_updated: 2021-01-12T06:58:54Z day: '18' doi: 10.1016/j.neuron.2006.04.014 extern: 1 intvolume: ' 50' issue: '4' month: '05' page: 589 - 601 publication: Neuron publication_status: published publisher: Elsevier publist_id: '4237' quality_controlled: 0 status: public title: Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants type: journal_article volume: 50 year: '2006' ... --- _id: '2662' abstract: - lang: eng text: G-protein-coupled inwardly rectifying K+ channels (Kir3 channels) coupled to metabotropic GABAB receptors are essential for the control of neuronal excitation. To determine the distribution of Kir3 channels and their spatial relationship to GABAB receptors on hippocampal pyramidal cells, we used a high-resolution immunocytochemical approach. Immunoreactivity for the Kir3.2 subunit was most abundant postsynaptically and localized to the extrasynaptic plasma membrane of dendritic shafts and spines of principal cells. Quantitative analysis of immunogold particles for Kir3.2 revealed an enrichment of the protein around putative glutamatergic synapses on dendritic spines, similar to that of GABA B1. Consistent with this observation, a high degree of coclustering of Kir3.2 and GABAB1 was revealed around excitatory synapses by the highly sensitive SDS-digested freeze-fracture replica immunolabeling. In contrast, in dendritic shafts receptors and channels were found to be mainly segregated. These results suggest that Kir3.2-containing K+ channels on dendritic spines preferentially mediate the effect of GABA, whereas channels on dendritic shafts are likely to be activated by other neurotransmitters as well. Thus, Kir3 channels, localized to different subcellular compartments of hippocampal principal cells, appear to be differentially involved in synaptic integration in pyramidal cell dendrites. author: - first_name: Ákos full_name: Kulik, Ákos last_name: Kulik - first_name: Imre full_name: Vida, Imre last_name: Vida - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Nicole full_name: Guetg, Nicole last_name: Guetg - first_name: Yu full_name: Kasugai, Yu last_name: Kasugai - first_name: Cheryl full_name: Marker, Cheryl L last_name: Marker - first_name: Franck full_name: Rigato, Franck last_name: Rigato - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Kevin full_name: Wickman, Kevin D last_name: Wickman - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Kulik Á, Vida I, Fukazawa Y, et al. Compartment-dependent colocalization of Kir3.2-containing K+ channels and GABAB receptors in hippocampal pyramidal cells. Journal of Neuroscience. 2006;26(16):4289-4297. doi:10.1523/JNEUROSCI.4178-05.2006 apa: Kulik, Á., Vida, I., Fukazawa, Y., Guetg, N., Kasugai, Y., Marker, C., … Shigemoto, R. (2006). Compartment-dependent colocalization of Kir3.2-containing K+ channels and GABAB receptors in hippocampal pyramidal cells. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.4178-05.2006 chicago: Kulik, Ákos, Imre Vida, Yugo Fukazawa, Nicole Guetg, Yu Kasugai, Cheryl Marker, Franck Rigato, et al. “Compartment-Dependent Colocalization of Kir3.2-Containing K+ Channels and GABAB Receptors in Hippocampal Pyramidal Cells.” Journal of Neuroscience. Society for Neuroscience, 2006. https://doi.org/10.1523/JNEUROSCI.4178-05.2006. ieee: Á. Kulik et al., “Compartment-dependent colocalization of Kir3.2-containing K+ channels and GABAB receptors in hippocampal pyramidal cells,” Journal of Neuroscience, vol. 26, no. 16. Society for Neuroscience, pp. 4289–4297, 2006. ista: Kulik Á, Vida I, Fukazawa Y, Guetg N, Kasugai Y, Marker C, Rigato F, Bettler B, Wickman K, Frotscher M, Shigemoto R. 2006. Compartment-dependent colocalization of Kir3.2-containing K+ channels and GABAB receptors in hippocampal pyramidal cells. Journal of Neuroscience. 26(16), 4289–4297. mla: Kulik, Ákos, et al. “Compartment-Dependent Colocalization of Kir3.2-Containing K+ Channels and GABAB Receptors in Hippocampal Pyramidal Cells.” Journal of Neuroscience, vol. 26, no. 16, Society for Neuroscience, 2006, pp. 4289–97, doi:10.1523/JNEUROSCI.4178-05.2006. short: Á. Kulik, I. Vida, Y. Fukazawa, N. Guetg, Y. Kasugai, C. Marker, F. Rigato, B. Bettler, K. Wickman, M. Frotscher, R. Shigemoto, Journal of Neuroscience 26 (2006) 4289–4297. date_created: 2018-12-11T11:58:56Z date_published: 2006-04-19T00:00:00Z date_updated: 2021-01-12T06:58:54Z day: '19' doi: 10.1523/JNEUROSCI.4178-05.2006 extern: 1 intvolume: ' 26' issue: '16' month: '04' page: 4289 - 4297 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4235' quality_controlled: 0 status: public title: Compartment-dependent colocalization of Kir3.2-containing K+ channels and GABAB receptors in hippocampal pyramidal cells type: journal_article volume: 26 year: '2006' ... --- _id: '2660' abstract: - lang: eng text: Pavlovian fear conditioning, a simple form of associative learning, is thought to involve the induction of associative, NMDA receptor-dependent long-term potentiation (LTP) in the lateral amygdala. Using a combined genetic and electrophysiological approach, we show here that lack of a specific GABAB receptor subtype, GABAB(1a,2), unmasks a nonassociative, NMDA receptor-independent form of presynaptic LTP at cortico-amygdala afferents. Moreover, the level of presynaptic GABA B(1a,2) receptor activation, and hence the balance between associative and nonassociative forms of LTP, can be dynamically modulated by local inhibitory activity. At the behavioral level, genetic loss of GABA B(1a) results in a generalization of conditioned fear to nonconditioned stimuli. Our findings indicate that presynaptic inhibition through GABAB(1a,2) receptors serves as an activity-dependent constraint on the induction of homosynaptic plasticity, which may be important to prevent the generalization of conditioned fear. author: - first_name: Hamdy full_name: Shaban, Hamdy last_name: Shaban - first_name: Yann full_name: Humeau, Yann last_name: Humeau - first_name: Cyril full_name: Herry, Cyril last_name: Herry - first_name: Guillaume full_name: Cassasus, Guillaume last_name: Cassasus - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Stéphane full_name: Ciocchi, Stéphane last_name: Ciocchi - first_name: Samuel full_name: Barbieri, Samuel last_name: Barbieri - first_name: Herman full_name: Van Der Putten, Herman V last_name: Van Der Putten - first_name: Klemens full_name: Kaupmann, Klemens last_name: Kaupmann - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Andreas full_name: Lüthi, Andreas last_name: Lüthi citation: ama: Shaban H, Humeau Y, Herry C, et al. Generalization of amygdala LTP and conditioned fear in the absence of presynaptic inhibition. Nature Neuroscience. 2006;9(8):1028-1035. doi:10.1038/nn1732 apa: Shaban, H., Humeau, Y., Herry, C., Cassasus, G., Shigemoto, R., Ciocchi, S., … Lüthi, A. (2006). Generalization of amygdala LTP and conditioned fear in the absence of presynaptic inhibition. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn1732 chicago: Shaban, Hamdy, Yann Humeau, Cyril Herry, Guillaume Cassasus, Ryuichi Shigemoto, Stéphane Ciocchi, Samuel Barbieri, et al. “Generalization of Amygdala LTP and Conditioned Fear in the Absence of Presynaptic Inhibition.” Nature Neuroscience. Nature Publishing Group, 2006. https://doi.org/10.1038/nn1732. ieee: H. Shaban et al., “Generalization of amygdala LTP and conditioned fear in the absence of presynaptic inhibition,” Nature Neuroscience, vol. 9, no. 8. Nature Publishing Group, pp. 1028–1035, 2006. ista: Shaban H, Humeau Y, Herry C, Cassasus G, Shigemoto R, Ciocchi S, Barbieri S, Van Der Putten H, Kaupmann K, Bettler B, Lüthi A. 2006. Generalization of amygdala LTP and conditioned fear in the absence of presynaptic inhibition. Nature Neuroscience. 9(8), 1028–1035. mla: Shaban, Hamdy, et al. “Generalization of Amygdala LTP and Conditioned Fear in the Absence of Presynaptic Inhibition.” Nature Neuroscience, vol. 9, no. 8, Nature Publishing Group, 2006, pp. 1028–35, doi:10.1038/nn1732. short: H. Shaban, Y. Humeau, C. Herry, G. Cassasus, R. Shigemoto, S. Ciocchi, S. Barbieri, H. Van Der Putten, K. Kaupmann, B. Bettler, A. Lüthi, Nature Neuroscience 9 (2006) 1028–1035. date_created: 2018-12-11T11:58:55Z date_published: 2006-08-01T00:00:00Z date_updated: 2021-01-12T06:58:53Z day: '01' doi: 10.1038/nn1732 extern: 1 intvolume: ' 9' issue: '8' month: '08' page: 1028 - 1035 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '4236' quality_controlled: 0 status: public title: Generalization of amygdala LTP and conditioned fear in the absence of presynaptic inhibition type: journal_article volume: 9 year: '2006' ... --- _id: '2664' abstract: - lang: eng text: Metabotropic glutamate receptors (mGlus) are a family of G-protein-coupled receptors activated by the neurotransmitter glutamate. Molecular cloning has revealed eight different subtypes (mGlu1-8) with distinct molecular and pharmacological properties. Multiplicity in this receptor family is further generated through alternative splicing. mGlus activate a multitude of signalling pathways important for modulating neuronal excitability, synaptic plasticity and feedback regulation of neurotransmitter release. In this review, we summarize anatomical findings (from our work and that of other laboratories) describing their distribution in the central nervous system. Recent evidence regarding the localization of these receptors in peripheral tissues will also be examined. The distinct regional, cellular and subcellular distribution of mGlus in the brain will be discussed in view of their relationship to neurotransmitter release sites and of possible functional implications. author: - first_name: Francesco full_name: Ferraguti, Francesco last_name: Ferraguti - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Ferraguti F, Shigemoto R. Metabotropic glutamate receptors. Cell and Tissue Research. 2006;326(2):483-504. doi:10.1007/s00441-006-0266-5 apa: Ferraguti, F., & Shigemoto, R. (2006). Metabotropic glutamate receptors. Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0266-5 chicago: Ferraguti, Francesco, and Ryuichi Shigemoto. “Metabotropic Glutamate Receptors.” Cell and Tissue Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0266-5. ieee: F. Ferraguti and R. Shigemoto, “Metabotropic glutamate receptors,” Cell and Tissue Research, vol. 326, no. 2. Springer, pp. 483–504, 2006. ista: Ferraguti F, Shigemoto R. 2006. Metabotropic glutamate receptors. Cell and Tissue Research. 326(2), 483–504. mla: Ferraguti, Francesco, and Ryuichi Shigemoto. “Metabotropic Glutamate Receptors.” Cell and Tissue Research, vol. 326, no. 2, Springer, 2006, pp. 483–504, doi:10.1007/s00441-006-0266-5. short: F. Ferraguti, R. Shigemoto, Cell and Tissue Research 326 (2006) 483–504. date_created: 2018-12-11T11:58:57Z date_published: 2006-11-01T00:00:00Z date_updated: 2020-07-14T12:45:44Z day: '01' doi: 10.1007/s00441-006-0266-5 extern: 1 intvolume: ' 326' issue: '2' month: '11' page: 483 - 504 publication: Cell and Tissue Research publication_status: published publisher: Springer publist_id: '4234' quality_controlled: 0 status: public title: Metabotropic glutamate receptors type: review volume: 326 year: '2006' ... --- _id: '2747' abstract: - lang: eng text: Consider a system of N bosons on the three-dimensional unit torus interacting via a pair potential N 2V(N(x i - x j)) where x = (x i, . . ., x N) denotes the positions of the particles. Suppose that the initial data ψ N,0 satisfies the condition 〈ψ N,0, H 2 Nψ N,0) ≤ C N 2 where H N is the Hamiltonian of the Bose system. This condition is satisfied if ψ N,0 = W Nφ N,t where W N is an approximate ground state to H N and φ N,0 is regular. Let ψ N,t denote the solution to the Schrödinger equation with Hamiltonian H N. Gross and Pitaevskii proposed to model the dynamics of such a system by a nonlinear Schrödinger equation, the Gross-Pitaevskii (GP) equation. The GP hierarchy is an infinite BBGKY hierarchy of equations so that if u t solves the GP equation, then the family of k-particle density matrices ⊗ k |u t?〉 〈 t | solves the GP hierarchy. We prove that as N → ∞ the limit points of the k-particle density matrices of ψ N,t are solutions of the GP hierarchy. Our analysis requires that the N-boson dynamics be described by a modified Hamiltonian that cuts off the pair interactions whenever at least three particles come into a region with diameter much smaller than the typical interparticle distance. Our proof can be extended to a modified Hamiltonian that only forbids at least n particles from coming close together for any fixed n. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Schlein B, Yau H. Derivation of the Gross-Pitaevskii hierarchy for the dynamics of Bose-Einstein condensate. Communications on Pure and Applied Mathematics. 2006;59(12):1659-1741. doi:10.1002/cpa.20123 apa: Erdös, L., Schlein, B., & Yau, H. (2006). Derivation of the Gross-Pitaevskii hierarchy for the dynamics of Bose-Einstein condensate. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.20123 chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Derivation of the Gross-Pitaevskii Hierarchy for the Dynamics of Bose-Einstein Condensate.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2006. https://doi.org/10.1002/cpa.20123. ieee: L. Erdös, B. Schlein, and H. Yau, “Derivation of the Gross-Pitaevskii hierarchy for the dynamics of Bose-Einstein condensate,” Communications on Pure and Applied Mathematics, vol. 59, no. 12. Wiley-Blackwell, pp. 1659–1741, 2006. ista: Erdös L, Schlein B, Yau H. 2006. Derivation of the Gross-Pitaevskii hierarchy for the dynamics of Bose-Einstein condensate. Communications on Pure and Applied Mathematics. 59(12), 1659–1741. mla: Erdös, László, et al. “Derivation of the Gross-Pitaevskii Hierarchy for the Dynamics of Bose-Einstein Condensate.” Communications on Pure and Applied Mathematics, vol. 59, no. 12, Wiley-Blackwell, 2006, pp. 1659–741, doi:10.1002/cpa.20123. short: L. Erdös, B. Schlein, H. Yau, Communications on Pure and Applied Mathematics 59 (2006) 1659–1741. date_created: 2018-12-11T11:59:23Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T06:59:26Z day: '01' doi: 10.1002/cpa.20123 extern: 1 intvolume: ' 59' issue: '12' month: '12' page: 1659 - 1741 publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley-Blackwell publist_id: '4145' quality_controlled: 0 status: public title: Derivation of the Gross-Pitaevskii hierarchy for the dynamics of Bose-Einstein condensate type: journal_article volume: 59 year: '2006' ... --- _id: '2745' abstract: - lang: eng text: 'We consider the dynamics of N boson systems interacting through a pair potential N -1 V a (x i -x j ) where V a (x)=a -3 V(x/a). We denote the solution to the N-particle Schrödinger equation by Ψ N, t . Recall that the Gross-Pitaevskii (GP) equation is a nonlinear Schrödinger equation and the GP hierarchy is an infinite BBGKY hierarchy of equations so that if u t solves the GP equation, then the family of k-particle density matrices [InlineMediaObject not available: see fulltext.] solves the GP hierarchy. Under the assumption that a = Nε for 0 < ε < 3/5, we prove that as N→∞ the limit points of the k-particle density matrices of Ψ N, t are solutions of the GP hierarchy with the coupling constant in the nonlinear term of the GP equation given by ∫ V (x)dx. The uniqueness of the solutions of this hierarchy remains an open question.' author: - first_name: Alexander full_name: Elgart, Alexander last_name: Elgart - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Elgart A, Erdös L, Schlein B, Yau H. Gross-Pitaevskii equation as the mean field limit of weakly coupled bosons. Archive for Rational Mechanics and Analysis. 2006;179(2):265-283. doi:10.1007/s00205-005-0388-z apa: Elgart, A., Erdös, L., Schlein, B., & Yau, H. (2006). Gross-Pitaevskii equation as the mean field limit of weakly coupled bosons. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-005-0388-z chicago: Elgart, Alexander, László Erdös, Benjamin Schlein, and Horng Yau. “Gross-Pitaevskii Equation as the Mean Field Limit of Weakly Coupled Bosons.” Archive for Rational Mechanics and Analysis. Springer, 2006. https://doi.org/10.1007/s00205-005-0388-z. ieee: A. Elgart, L. Erdös, B. Schlein, and H. Yau, “Gross-Pitaevskii equation as the mean field limit of weakly coupled bosons,” Archive for Rational Mechanics and Analysis, vol. 179, no. 2. Springer, pp. 265–283, 2006. ista: Elgart A, Erdös L, Schlein B, Yau H. 2006. Gross-Pitaevskii equation as the mean field limit of weakly coupled bosons. Archive for Rational Mechanics and Analysis. 179(2), 265–283. mla: Elgart, Alexander, et al. “Gross-Pitaevskii Equation as the Mean Field Limit of Weakly Coupled Bosons.” Archive for Rational Mechanics and Analysis, vol. 179, no. 2, Springer, 2006, pp. 265–83, doi:10.1007/s00205-005-0388-z. short: A. Elgart, L. Erdös, B. Schlein, H. Yau, Archive for Rational Mechanics and Analysis 179 (2006) 265–283. date_created: 2018-12-11T11:59:22Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T06:59:25Z day: '01' doi: 10.1007/s00205-005-0388-z extern: 1 intvolume: ' 179' issue: '2' month: '02' page: 265 - 283 publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '4147' quality_controlled: 0 status: public title: Gross-Pitaevskii equation as the mean field limit of weakly coupled bosons type: journal_article volume: 179 year: '2006' ... --- _id: '2746' abstract: - lang: eng text: We consider random Schrödinger equations on Rd or Zd for d ≥ 3 with uncorrelated, identically distributed random potential. Denote by λ the coupling constant and ψt the solution with initial data ψ0. alternative_title: - LNP author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Manfred full_name: Salmhofer, Manfred last_name: Salmhofer - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: 'Erdös L, Salmhofer M, Yau H. Towards the quantum Brownian motion. In: Vol 690. World Scientific Publishing; 2006:233-257. doi:10.1007/3-540-34273-7_18' apa: 'Erdös, L., Salmhofer, M., & Yau, H. (2006). Towards the quantum Brownian motion (Vol. 690, pp. 233–257). Presented at the QMath: Mathematical Results in Quantum Physics, World Scientific Publishing. https://doi.org/10.1007/3-540-34273-7_18' chicago: Erdös, László, Manfred Salmhofer, and Horng Yau. “Towards the Quantum Brownian Motion,” 690:233–57. World Scientific Publishing, 2006. https://doi.org/10.1007/3-540-34273-7_18. ieee: 'L. Erdös, M. Salmhofer, and H. Yau, “Towards the quantum Brownian motion,” presented at the QMath: Mathematical Results in Quantum Physics, 2006, vol. 690, pp. 233–257.' ista: 'Erdös L, Salmhofer M, Yau H. 2006. Towards the quantum Brownian motion. QMath: Mathematical Results in Quantum Physics, LNP, vol. 690, 233–257.' mla: Erdös, László, et al. Towards the Quantum Brownian Motion. Vol. 690, World Scientific Publishing, 2006, pp. 233–57, doi:10.1007/3-540-34273-7_18. short: L. Erdös, M. Salmhofer, H. Yau, in:, World Scientific Publishing, 2006, pp. 233–257. conference: name: 'QMath: Mathematical Results in Quantum Physics' date_created: 2018-12-11T11:59:23Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T06:59:25Z day: '01' doi: 10.1007/3-540-34273-7_18 extern: 1 intvolume: ' 690' month: '01' page: 233 - 257 publication_status: published publisher: World Scientific Publishing publist_id: '4146' quality_controlled: 0 status: public title: Towards the quantum Brownian motion type: conference volume: 690 year: '2006' ... --- _id: '2791' abstract: - lang: eng text: Generally, the motion of fluids is smooth and laminar at low speeds but becomes highly disordered and turbulent as the velocity increases. The transition from laminar to turbulent flow can involve a sequence of instabilities in which the system realizes progressively more complicated states, or it can occur suddenly. Once the transition has taken place, it is generally assumed that, under steady conditions, the turbulent state will persist indefinitely. The flow of a fluid down a straight pipe provides a ubiquitous example of a shear flow undergoing a sudden transition from laminar to turbulent motion. Extensive calculations and experimental studies have shown that, at relatively low flow rates, turbulence in pipes is transient, and is characterized by an exponential distribution of lifetimes. They also suggest that for Reynolds numbers exceeding a critical value the lifetime diverges (that is, becomes infinitely large), marking a change from transient to persistent turbulence. Here we present experimental data and numerical calculations covering more than two decades of lifetimes, showing that the lifetime does not in fact diverge but rather increases exponentially with the Reynolds number. This implies that turbulence in pipes is only a transient event (contrary to the commonly accepted view), and that the turbulent and laminar states remain dynamically connected, suggesting avenues for turbulence control. author: - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Jerry full_name: Westerweel, Jerry last_name: Westerweel - first_name: Tobias full_name: Schneider, Tobias M last_name: Schneider - first_name: Bruno full_name: Eckhardt, Bruno last_name: Eckhardt citation: ama: Hof B, Westerweel J, Schneider T, Eckhardt B. Finite lifetime of turbulence in shear flows. Nature. 2006;443(7107):59-62. doi:10.1038/nature05089 apa: Hof, B., Westerweel, J., Schneider, T., & Eckhardt, B. (2006). Finite lifetime of turbulence in shear flows. Nature. Nature Publishing Group. https://doi.org/10.1038/nature05089 chicago: Hof, Björn, Jerry Westerweel, Tobias Schneider, and Bruno Eckhardt. “Finite Lifetime of Turbulence in Shear Flows.” Nature. Nature Publishing Group, 2006. https://doi.org/10.1038/nature05089. ieee: B. Hof, J. Westerweel, T. Schneider, and B. Eckhardt, “Finite lifetime of turbulence in shear flows,” Nature, vol. 443, no. 7107. Nature Publishing Group, pp. 59–62, 2006. ista: Hof B, Westerweel J, Schneider T, Eckhardt B. 2006. Finite lifetime of turbulence in shear flows. Nature. 443(7107), 59–62. mla: Hof, Björn, et al. “Finite Lifetime of Turbulence in Shear Flows.” Nature, vol. 443, no. 7107, Nature Publishing Group, 2006, pp. 59–62, doi:10.1038/nature05089. short: B. Hof, J. Westerweel, T. Schneider, B. Eckhardt, Nature 443 (2006) 59–62. date_created: 2018-12-11T11:59:37Z date_published: 2006-09-07T00:00:00Z date_updated: 2021-01-12T06:59:44Z day: '07' doi: 10.1038/nature05089 extern: 1 intvolume: ' 443' issue: '7107' month: '09' page: 59 - 62 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '4098' quality_controlled: 0 status: public title: Finite lifetime of turbulence in shear flows type: journal_article volume: 443 year: '2006' ... --- _id: '2792' abstract: - lang: eng text: Transition to turbulence in pipe flow has posed a riddle in fluid dynamics since the pioneering experiments of Reynolds[1]. Although the laminar flow is linearly stable for all flow rates, practical pipe flows become turbulent at large enough flow speeds. Turbulence arises suddenly and fully without distinct steps and without a clear critical point. The complexity of this problem has puzzled mathematicians, physicists and engineers for more than a century and no satisfactory explanation of this problem has been given. In a very recent theoretical approach it has been suggested that unstable solutions of the Navier Stokes equations may hold the key to understanding this problem. In numerical studies such unstable states have been identified as exact solutions for the idealized case of a pipe with periodic boundary conditions[2, 3]. These solutions have the form of waves extending through the entire pipe and travelling in the streamwise direction at a phase speed close to the bulk velocity of the fluid. With the aid of a recently developed high-speed stereoscopic Particle Image Velocimetry (PIV) system, we were able to observe transients of such unstable solutions in turbulent pipe flow[4]. author: - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Casimir full_name: van Doorne, Casimir W last_name: Van Doorne - first_name: Jerry full_name: Westerweel, Jerry last_name: Westerweel - first_name: Frans full_name: Nieuwstadt, Frans T last_name: Nieuwstadt citation: ama: Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. Observation of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and its Applications. 2006;78:109-114. doi:10.1007/1-4020-4159-4_11 apa: Hof, B., Van Doorne, C., Westerweel, J., & Nieuwstadt, F. (2006). Observation of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and Its Applications. Springer. https://doi.org/10.1007/1-4020-4159-4_11 chicago: Hof, Björn, Casimir Van Doorne, Jerry Westerweel, and Frans Nieuwstadt. “Observation of Nonlinear Travelling Waves in Turbulent Pipe Flow.” Fluid Mechanics and Its Applications. Springer, 2006. https://doi.org/10.1007/1-4020-4159-4_11. ieee: B. Hof, C. Van Doorne, J. Westerweel, and F. Nieuwstadt, “Observation of nonlinear travelling waves in turbulent pipe flow,” Fluid Mechanics and its Applications, vol. 78. Springer, pp. 109–114, 2006. ista: Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. 2006. Observation of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and its Applications. 78, 109–114. mla: Hof, Björn, et al. “Observation of Nonlinear Travelling Waves in Turbulent Pipe Flow.” Fluid Mechanics and Its Applications, vol. 78, Springer, 2006, pp. 109–14, doi:10.1007/1-4020-4159-4_11. short: B. Hof, C. Van Doorne, J. Westerweel, F. Nieuwstadt, Fluid Mechanics and Its Applications 78 (2006) 109–114. date_created: 2018-12-11T11:59:37Z date_published: 2006-01-18T00:00:00Z date_updated: 2021-01-12T06:59:45Z day: '18' doi: 10.1007/1-4020-4159-4_11 extern: 1 intvolume: ' 78' month: '01' page: 109 - 114 publication: Fluid Mechanics and its Applications publication_status: published publisher: Springer publist_id: '4097' quality_controlled: 0 status: public title: Observation of nonlinear travelling waves in turbulent pipe flow type: journal_article volume: 78 year: '2006' ... --- _id: '2894' abstract: - lang: eng text: IL-10 is a potent anti-inflammatory and immunomodulatory cytokine, exerting major effects in the degree and quality of the immune response. Using a newly generated IL-10 reporter mouse model, which easily allows the study of IL-10 expression from each allele in a single cell, we report here for the first time that IL-10 is predominantly monoallelic expressed in CD4+ T cells. Furthermore, we have compelling evidence that this expression pattern is not due to parental imprinting, allelic exclusion, or strong allelic bias. Instead, our results support a stochastic regulation mechanism, in which the probability to initiate allelic transcription depends on the strength of TCR signaling and subsequent capacity to overcome restrictions imposed by chromatin hypoacetylation. In vivo Ag-experienced T cells show a higher basal probability to transcribe IL-10 when compared with naive cells, yet still show mostly monoallelic IL-10 expression. Finally, statistical analysis on allelic expression data shows transcriptional independence between both alleles. We conclude that CD4+ T cells have a low probability for IL-10 allelic activation resulting in a predominantly monoallelic expression pattern, and that IL-10 expression appears to be stochastically regulated by controlling the frequency of expressing cells, rather than absolute protein levels per cell. author: - first_name: Dinis full_name: Calado, Dinis P last_name: Calado - first_name: Tiago full_name: Tiago Paixao id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Dan full_name: Holmberg, Dan last_name: Holmberg - first_name: Matthias full_name: Haury, Matthias last_name: Haury citation: ama: Calado D, Paixao T, Holmberg D, Haury M. Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. 2006;177(8):5358-5364. doi:10.4049/jimmunol.177.8.5358 apa: Calado, D., Paixao, T., Holmberg, D., & Haury, M. (2006). Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. American Association of Immunologists. https://doi.org/10.4049/jimmunol.177.8.5358 chicago: Calado, Dinis, Tiago Paixao, Dan Holmberg, and Matthias Haury. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology. American Association of Immunologists, 2006. https://doi.org/10.4049/jimmunol.177.8.5358 . ieee: D. Calado, T. Paixao, D. Holmberg, and M. Haury, “Stochastic Monoallelic Expression of IL 10 in T Cells,” Journal of Immunology, vol. 177, no. 8. American Association of Immunologists, pp. 5358–5364, 2006. ista: Calado D, Paixao T, Holmberg D, Haury M. 2006. Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. 177(8), 5358–5364. mla: Calado, Dinis, et al. “Stochastic Monoallelic Expression of IL 10 in T Cells.” Journal of Immunology, vol. 177, no. 8, American Association of Immunologists, 2006, pp. 5358–64, doi:10.4049/jimmunol.177.8.5358 . short: D. Calado, T. Paixao, D. Holmberg, M. Haury, Journal of Immunology 177 (2006) 5358–5364. date_created: 2018-12-11T12:00:11Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:00:32Z day: '01' doi: '10.4049/jimmunol.177.8.5358 ' extern: 1 intvolume: ' 177' issue: '8' month: '01' page: 5358 - 5364 publication: Journal of Immunology publication_status: published publisher: American Association of Immunologists publist_id: '3864' quality_controlled: 0 status: public title: Stochastic Monoallelic Expression of IL 10 in T Cells type: journal_article volume: 177 year: '2006' ... --- _id: '2921' abstract: - lang: eng text: Most binocular stereo algorithms assume that all scene elements are visible from both cameras. Scene elements that are visible from only one camera, known as occlusions, pose an important challenge for stereo. Occlusions are important for segmentation, because they appear near discontinuities. However, stereo algorithms tend to ignore occlusions because of their difficulty. One reason is that occlusions require the input images to be treated symmetrically, which complicates the problem formulation. Worse, certain depth maps imply physically impossible scene configurations, and must be excluded from the output. In this chapter we approach the problem of binocular stereo with occlusions from an energy minimization viewpoint. We begin by reviewing traditional stereo methods that do not handle occlusions. If occlusions are ignored, it is easy to formulate the stereo problem as a pixel labeling problem, which leads to an energy function that is common in early vision. This kind of energy function can he minimized using graph cuts, which is a combinatorial optimization technique that has proven to be very effective for low-level vision problems. Motivated by this, we have designed two graph cut stereo algorithms that are designed to handle occlusions. These algorithms produce promising experimental results on real data with ground truth. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Ramin full_name: Zabih, Ramin last_name: Zabih citation: ama: 'Kolmogorov V, Zabih R. Graph cut algorithms for binocular stereo with occlusions. In: Handbook of Mathematical Models in Computer Vision. Springer; 2006:423-427. doi:10.1007/0-387-28831-7_26' apa: Kolmogorov, V., & Zabih, R. (2006). Graph cut algorithms for binocular stereo with occlusions. In Handbook of Mathematical Models in Computer Vision (pp. 423–427). Springer. https://doi.org/10.1007/0-387-28831-7_26 chicago: Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular Stereo with Occlusions.” In Handbook of Mathematical Models in Computer Vision, 423–27. Springer, 2006. https://doi.org/10.1007/0-387-28831-7_26. ieee: V. Kolmogorov and R. Zabih, “Graph cut algorithms for binocular stereo with occlusions,” in Handbook of Mathematical Models in Computer Vision, Springer, 2006, pp. 423–427. ista: 'Kolmogorov V, Zabih R. 2006.Graph cut algorithms for binocular stereo with occlusions. In: Handbook of Mathematical Models in Computer Vision. , 423–427.' mla: Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular Stereo with Occlusions.” Handbook of Mathematical Models in Computer Vision, Springer, 2006, pp. 423–27, doi:10.1007/0-387-28831-7_26. short: V. Kolmogorov, R. Zabih, in:, Handbook of Mathematical Models in Computer Vision, Springer, 2006, pp. 423–427. date_created: 2018-12-11T12:00:21Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:00:42Z day: '01' doi: 10.1007/0-387-28831-7_26 extern: 1 month: '01' page: 423 - 427 publication: Handbook of Mathematical Models in Computer Vision publication_status: published publisher: Springer publist_id: '3816' quality_controlled: 0 status: public title: Graph cut algorithms for binocular stereo with occlusions type: book_chapter year: '2006' ... --- _id: '3002' abstract: - lang: eng text: Arabidopsis thaliana is currently the most important model organism for basic molecular plant research. It is also a favourable model for developmental biology, as its embryogenesis follows a nearly invariant pattern of cell divisions and cell type specifications. Study of embryogenesis can involve genetic, physiological or biochemical approaches, but is always limited by the inaccessibility of the embryos which develop deep inside maternal tissue. Thus, for developmental studies, there is an increasing demand for methods which allow embryogenesis under artificial conditions, providing better accessibility to experimental manipulation. In this chapter, we address theoretical aspects of embryo culture, give some thoughts on which embryo culture system is suited best for which application and finally discuss three current methods which have been successfully used in Arabidopsis embryo culture. © 2006 Springer-Verlag Berlin Heidelberg. alternative_title: - Plant Cell Monographs author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Sauer M, Friml J. In vitro culture of Arabidopsis embryos. In: Mujib A, Šamaj J, eds. Somatic Embryogenesis. Vol 2. Springer; 2006:343-354. doi:10.1007/7089_020' apa: Sauer, M., & Friml, J. (2006). In vitro culture of Arabidopsis embryos. In A. Mujib & J. Šamaj (Eds.), Somatic Embryogenesis (Vol. 2, pp. 343–354). Springer. https://doi.org/10.1007/7089_020 chicago: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.” In Somatic Embryogenesis, edited by Abdul Mujib and Jozef Šamaj, 2:343–54. Springer, 2006. https://doi.org/10.1007/7089_020. ieee: M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos,” in Somatic Embryogenesis, vol. 2, A. Mujib and J. Šamaj, Eds. Springer, 2006, pp. 343–354. ista: 'Sauer M, Friml J. 2006.In vitro culture of Arabidopsis embryos. In: Somatic Embryogenesis. Plant Cell Monographs, vol. 2, 343–354.' mla: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.” Somatic Embryogenesis, edited by Abdul Mujib and Jozef Šamaj, vol. 2, Springer, 2006, pp. 343–54, doi:10.1007/7089_020. short: M. Sauer, J. Friml, in:, A. Mujib, J. Šamaj (Eds.), Somatic Embryogenesis, Springer, 2006, pp. 343–354. date_created: 2018-12-11T12:00:48Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:40:23Z day: '01' doi: 10.1007/7089_020 editor: - first_name: Abdul full_name: Mujib, Abdul last_name: Mujib - first_name: Jozef full_name: Šamaj, Jozef last_name: Šamaj extern: 1 intvolume: ' 2' month: '01' page: 343 - 354 publication: Somatic Embryogenesis publication_status: published publisher: Springer publist_id: '3699' quality_controlled: 0 status: public title: In vitro culture of Arabidopsis embryos type: book_chapter volume: 2 year: '2006' ... --- _id: '3012' abstract: - lang: eng text: Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux. author: - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Rodolphe full_name: Bouchard, Rodolphe last_name: Bouchard - first_name: Joshua full_name: Blakeslee, Joshua last_name: Blakeslee - first_name: Melinda F full_name: Melinda Abas id: 3CFB3B1C-F248-11E8-B48F-1D18A9856A87 last_name: Abas - first_name: Daniela full_name: Seifertová, Daniela last_name: Seifertová - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Zerihun full_name: Tadele, Zerihun last_name: Tadele - first_name: Martin full_name: Kubeš, Martin last_name: Kubeš - first_name: Milada full_name: Čovanová, Milada last_name: Čovanová - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Petr full_name: Skůpa, Petr last_name: Skůpa - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Lucie full_name: Perry, Lucie last_name: Perry - first_name: Pavel full_name: Křeček, Pavel last_name: Křeček - first_name: Ok full_name: Lee, Ok Ran last_name: Lee - first_name: Gerald full_name: Fink, Gerald R last_name: Fink - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Angus full_name: Murphy, Angus S last_name: Murphy - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Petrášek J, Mravec J, Bouchard R, et al. PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. 2006;312(5775):914-918. doi:10.1126/science.1123542 apa: Petrášek, J., Mravec, J., Bouchard, R., Blakeslee, J., Abas, M. F., Seifertová, D., … Friml, J. (2006). PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1123542 chicago: Petrášek, Jan, Jozef Mravec, Rodolphe Bouchard, Joshua Blakeslee, Melinda F Abas, Daniela Seifertová, Justyna Wiśniewska, et al. “PIN Proteins Perform a Rate-Limiting Function in Cellular Auxin Efflux.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1123542. ieee: J. Petrášek et al., “PIN proteins perform a rate-limiting function in cellular auxin efflux,” Science, vol. 312, no. 5775. American Association for the Advancement of Science, pp. 914–918, 2006. ista: Petrášek J, Mravec J, Bouchard R, Blakeslee J, Abas MF, Seifertová D, Wiśniewska J, Tadele Z, Kubeš M, Čovanová M, Dhonukshe P, Skůpa P, Benková E, Perry L, Křeček P, Lee O, Fink G, Geisler M, Murphy A, Luschnig C, Zažímalová E, Friml J. 2006. PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. 312(5775), 914–918. mla: Petrášek, Jan, et al. “PIN Proteins Perform a Rate-Limiting Function in Cellular Auxin Efflux.” Science, vol. 312, no. 5775, American Association for the Advancement of Science, 2006, pp. 914–18, doi:10.1126/science.1123542. short: J. Petrášek, J. Mravec, R. Bouchard, J. Blakeslee, M.F. Abas, D. Seifertová, J. Wiśniewska, Z. Tadele, M. Kubeš, M. Čovanová, P. Dhonukshe, P. Skůpa, E. Benková, L. Perry, P. Křeček, O. Lee, G. Fink, M. Geisler, A. Murphy, C. Luschnig, E. Zažímalová, J. Friml, Science 312 (2006) 914–918. date_created: 2018-12-11T12:00:51Z date_published: 2006-05-12T00:00:00Z date_updated: 2021-01-12T07:40:27Z day: '12' doi: 10.1126/science.1123542 extern: 1 intvolume: ' 312' issue: '5775' month: '05' page: 914 - 918 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3690' quality_controlled: 0 status: public title: PIN proteins perform a rate-limiting function in cellular auxin efflux type: journal_article volume: 312 year: '2006' ... --- _id: '3010' abstract: - lang: eng text: The formation of the leaf vascular pattern has fascinated biologists for centuries. In the early leaf primordium, complex networks of procambial cells emerge from homogeneous subepidermal tissue. The molecular nature of the underlying positional information is unknown, but various lines of evidence implicate gradually restricted transport routes of the plant hormone auxin in defining sites of procambium formation. Here we show that a crucial member of the AtPIN family of auxin-efflux-associated proteins, AtPIN1, is expressed prior to pre-procambial and procambial cell fate markers in domains that become restricted toward sites of procambium formation. Subcellular AtPIN1 polarity indicates that auxin is directed to distinct "convergence points" in the epidermis, from where it defines the positions of major veins. Integrated polarities in all emerging veins indicate auxin drainage toward pre-existing veins, but veins display divergent polarities as they become connected at both ends. Auxin application and transport inhibition reveal that convergence point positioning and AtPIN1 expression domain dynamics are self-organizing, auxin-transport-dependent processes. We derive a model for self-regulated, reiterative patterning of all vein orders and postulate at its onset a common epidermal auxin-focusing mechanism for major-vein positioning and phyllotactic patterning. author: - first_name: Enrico full_name: Scarpella, Enrico last_name: Scarpella - first_name: Danielle full_name: Marcos, Danielle last_name: Marcos - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Thomas full_name: Berleth, Thomas last_name: Berleth citation: ama: Scarpella E, Marcos D, Friml J, Berleth T. Control of leaf vascular patterning by polar auxin transport. Genes and Development. 2006;20(8):1015-1027. doi:10.1101/gad.1402406 apa: Scarpella, E., Marcos, D., Friml, J., & Berleth, T. (2006). Control of leaf vascular patterning by polar auxin transport. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.1402406 chicago: Scarpella, Enrico, Danielle Marcos, Jiří Friml, and Thomas Berleth. “Control of Leaf Vascular Patterning by Polar Auxin Transport.” Genes and Development. Cold Spring Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.1402406. ieee: E. Scarpella, D. Marcos, J. Friml, and T. Berleth, “Control of leaf vascular patterning by polar auxin transport,” Genes and Development, vol. 20, no. 8. Cold Spring Harbor Laboratory Press, pp. 1015–1027, 2006. ista: Scarpella E, Marcos D, Friml J, Berleth T. 2006. Control of leaf vascular patterning by polar auxin transport. Genes and Development. 20(8), 1015–1027. mla: Scarpella, Enrico, et al. “Control of Leaf Vascular Patterning by Polar Auxin Transport.” Genes and Development, vol. 20, no. 8, Cold Spring Harbor Laboratory Press, 2006, pp. 1015–27, doi:10.1101/gad.1402406. short: E. Scarpella, D. Marcos, J. Friml, T. Berleth, Genes and Development 20 (2006) 1015–1027. date_created: 2018-12-11T12:00:51Z date_published: 2006-04-15T00:00:00Z date_updated: 2021-01-12T07:40:26Z day: '15' doi: 10.1101/gad.1402406 extern: 1 intvolume: ' 20' issue: '8' month: '04' page: 1015 - 1027 publication: Genes and Development publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '3692' quality_controlled: 0 status: public title: Control of leaf vascular patterning by polar auxin transport type: journal_article volume: 20 year: '2006' ... --- _id: '3007' abstract: - lang: eng text: Root gravitropism describes the orientation of root growth along the gravity vector and is mediated by differential cell elongation in the root meristem. This response requires the coordinated, asymmetric distribution of the phytohormone auxin within the root meristem, and depends on the concerted activities of PIN proteins and AUX1 - members of the auxin transport pathway. Here, we show that intracellular trafficking and proteasome activity combine to control PIN2 degradation during root gravitropism. Following gravi-stimulation, proteasome-dependent variations in PIN2 localization and degradation at the upper and lower sides of the root result in asymmetric distribution of PIN2. Ubiquitination of PIN2 occurs in a proteasome-dependent manner, indicating that the proteasome is involved in the control of PIN2 turnover. Stabilization of PIN2 affects its abundance and distribution, and leads to defects in auxin distribution and gravitropic responses. We describe the effects of auxin on PIN2 localization and protein levels, indicating that redistribution of auxin during the gravitropic response may be involved in the regulation of PIN2 protein. author: - first_name: Lindy full_name: Abas, Lindy last_name: Abas - first_name: René full_name: Benjamins, René last_name: Benjamins - first_name: Nenad full_name: Malenica, Nenad last_name: Malenica - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Jeanette full_name: Moulinier-Anzola, Jeanette C last_name: Moulinier Anzola - first_name: Tobias full_name: Sieberer, Tobias last_name: Sieberer - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig citation: ama: Abas L, Benjamins R, Malenica N, et al. Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. Nature Cell Biology. 2006;8(3):249-256. doi:10.1038/ncb1369 apa: Abas, L., Benjamins, R., Malenica, N., Paciorek, T., Wiśniewska, J., Moulinier Anzola, J., … Luschnig, C. (2006). Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1369 chicago: Abas, Lindy, René Benjamins, Nenad Malenica, Tomasz Paciorek, Justyna Wiśniewska, Jeanette Moulinier Anzola, Tobias Sieberer, Jiří Friml, and Christian Luschnig. “Intracellular Trafficking and Proteolysis of the Arabidopsis Auxin-Efflux Facilitator PIN2 Are Involved in Root Gravitropism.” Nature Cell Biology. Nature Publishing Group, 2006. https://doi.org/10.1038/ncb1369. ieee: L. Abas et al., “Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism,” Nature Cell Biology, vol. 8, no. 3. Nature Publishing Group, pp. 249–256, 2006. ista: Abas L, Benjamins R, Malenica N, Paciorek T, Wiśniewska J, Moulinier Anzola J, Sieberer T, Friml J, Luschnig C. 2006. Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. Nature Cell Biology. 8(3), 249–256. mla: Abas, Lindy, et al. “Intracellular Trafficking and Proteolysis of the Arabidopsis Auxin-Efflux Facilitator PIN2 Are Involved in Root Gravitropism.” Nature Cell Biology, vol. 8, no. 3, Nature Publishing Group, 2006, pp. 249–56, doi:10.1038/ncb1369. short: L. Abas, R. Benjamins, N. Malenica, T. Paciorek, J. Wiśniewska, J. Moulinier Anzola, T. Sieberer, J. Friml, C. Luschnig, Nature Cell Biology 8 (2006) 249–256. date_created: 2018-12-11T12:00:50Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:40:25Z day: '01' doi: 10.1038/ncb1369 extern: 1 intvolume: ' 8' issue: '3' month: '03' page: 249 - 256 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '3694' quality_controlled: 0 status: public title: Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism type: journal_article volume: 8 year: '2006' ... --- _id: '3006' abstract: - lang: eng text: 'Dividing plant cells perform a remarkable task of building a new cell wall within the cytoplasm in a few minutes. A long-standing paradigm claims that this primordial cell wall, known as the cell plate, is generated by delivery of newly synthesized material from Golgi apparatus-originated secretory vesicles. Here, we show that, in diverse plant species, cell surface material, including plasma membrane proteins, cell wall components, and exogenously applied endocytic tracers, is rapidly delivered to the forming cell plate. Importantly, this occurs even when de novo protein synthesis is blocked. In addition, cytokinesis-specific syntaxin KNOLLE as well as plasma membrane (PM) resident proteins localize to endosomes that fuse to initiate the cell plate. The rate of endocytosis is strongly enhanced during cell plate formation, and its genetic or pharmacological inhibition leads to cytokinesis defects. Our results reveal that endocytic delivery of cell surface material significantly contributes to cell plate formation during plant cytokinesis. ' author: - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: František full_name: Baluška, František last_name: Baluška - first_name: Markus full_name: Schlicht, Markus last_name: Schlicht - first_name: Andrej full_name: Hlavacka, Andrej last_name: Hlavacka - first_name: Jozef full_name: Šamaj, Jozef last_name: Šamaj - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Theodorus full_name: Gadella, Theodorus W last_name: Gadella citation: ama: Dhonukshe P, Baluška F, Schlicht M, et al. Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Developmental Cell. 2006;10(1):137-150. doi:10.1016/j.devcel.2005.11.015 apa: Dhonukshe, P., Baluška, F., Schlicht, M., Hlavacka, A., Šamaj, J., Friml, J., & Gadella, T. (2006). Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2005.11.015 chicago: Dhonukshe, Pankaj, František Baluška, Markus Schlicht, Andrej Hlavacka, Jozef Šamaj, Jiří Friml, and Theodorus Gadella. “Endocytosis of Cell Surface Material Mediates Cell Plate Formation during Plant Cytokinesis.” Developmental Cell. Cell Press, 2006. https://doi.org/10.1016/j.devcel.2005.11.015. ieee: P. Dhonukshe et al., “Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis,” Developmental Cell, vol. 10, no. 1. Cell Press, pp. 137–150, 2006. ista: Dhonukshe P, Baluška F, Schlicht M, Hlavacka A, Šamaj J, Friml J, Gadella T. 2006. Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Developmental Cell. 10(1), 137–150. mla: Dhonukshe, Pankaj, et al. “Endocytosis of Cell Surface Material Mediates Cell Plate Formation during Plant Cytokinesis.” Developmental Cell, vol. 10, no. 1, Cell Press, 2006, pp. 137–50, doi:10.1016/j.devcel.2005.11.015. short: P. Dhonukshe, F. Baluška, M. Schlicht, A. Hlavacka, J. Šamaj, J. Friml, T. Gadella, Developmental Cell 10 (2006) 137–150. date_created: 2018-12-11T12:00:49Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:40:24Z day: '01' doi: 10.1016/j.devcel.2005.11.015 extern: 1 intvolume: ' 10' issue: '1' month: '01' page: 137 - 150 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3696' quality_controlled: 0 status: public title: Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis type: journal_article volume: 10 year: '2006' ... --- _id: '3011' abstract: - lang: eng text: Polar flow of the phytohormone auxin requires plasma membrane‐associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed the importance of PIN polar positions for directional auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity signals directly demonstrates that PIN polarity is a primary factor in determining the direction of auxin flow in meristematic tissues. This finding provides a crucial piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN polarity. author: - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Jian full_name: Xu, Jian last_name: Xu - first_name: Daniela full_name: Seifertová, Daniela last_name: Seifertová - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Kamil full_name: Růžička, Kamil last_name: Růžička - first_name: Ikram full_name: Blilou, Ikram last_name: Blilou - first_name: David full_name: Rouquié, David last_name: Rouquié - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Wiśniewska J, Xu J, Seifertová D, et al. Polar PIN localization directs auxin flow in plants. Science. 2006;312(5775). doi:10.1126/science.1121356 apa: Wiśniewska, J., Xu, J., Seifertová, D., Brewer, P., Růžička, K., Blilou, I., … Friml, J. (2006). Polar PIN localization directs auxin flow in plants. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1121356 chicago: Wiśniewska, Justyna, Jian Xu, Daniela Seifertová, Philip Brewer, Kamil Růžička, Ikram Blilou, David Rouquié, Eva Benková, Ben Scheres, and Jiří Friml. “Polar PIN Localization Directs Auxin Flow in Plants.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121356. ieee: J. Wiśniewska et al., “Polar PIN localization directs auxin flow in plants,” Science, vol. 312, no. 5775. American Association for the Advancement of Science, 2006. ista: Wiśniewska J, Xu J, Seifertová D, Brewer P, Růžička K, Blilou I, Rouquié D, Benková E, Scheres B, Friml J. 2006. Polar PIN localization directs auxin flow in plants. Science. 312(5775). mla: Wiśniewska, Justyna, et al. “Polar PIN Localization Directs Auxin Flow in Plants.” Science, vol. 312, no. 5775, American Association for the Advancement of Science, 2006, doi:10.1126/science.1121356. short: J. Wiśniewska, J. Xu, D. Seifertová, P. Brewer, K. Růžička, I. Blilou, D. Rouquié, E. Benková, B. Scheres, J. Friml, Science 312 (2006). date_created: 2018-12-11T12:00:51Z date_published: 2006-05-12T00:00:00Z date_updated: 2021-01-12T07:40:27Z day: '12' doi: 10.1126/science.1121356 extern: 1 intvolume: ' 312' issue: '5775' month: '05' publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3691' quality_controlled: 0 status: public title: Polar PIN localization directs auxin flow in plants type: journal_article volume: 312 year: '2006' ... --- _id: '3005' author: - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Philip full_name: Benfey, Philip last_name: Benfey - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Thomas full_name: Berleth, Thomas last_name: Berleth - first_name: Niko full_name: Geldner, Niko last_name: Geldner - first_name: Markus full_name: Grebe, Markus last_name: Grebe - first_name: Marcus full_name: Heisler, Marcus last_name: Heisler - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Gerd full_name: Jürgens, Gerd last_name: Jürgens - first_name: Thomas full_name: Laux, Thomas last_name: Laux - first_name: Keith full_name: Lindsey, Keith last_name: Lindsey - first_name: Wolfgang full_name: Lukowitz, Wolfgang last_name: Lukowitz - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Ramón full_name: Torres Ruiz, Ramón last_name: Torres Ruiz - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová citation: ama: 'Friml J, Benfey P, Benková E, et al. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 2006;11(1):12-14. doi:10.1016/j.tplants.2005.11.010' apa: 'Friml, J., Benfey, P., Benková, E., Bennett, M., Berleth, T., Geldner, N., … Zažímalová, E. (2006). Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2005.11.010' chicago: 'Friml, Jiří, Philip Benfey, Eva Benková, Malcolm Bennett, Thomas Berleth, Niko Geldner, Markus Grebe, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science. Cell Press, 2006. https://doi.org/10.1016/j.tplants.2005.11.010.' ieee: 'J. Friml et al., “Apical-basal polarity: Why plant cells don’t stand on their heads,” Trends in Plant Science, vol. 11, no. 1. Cell Press, pp. 12–14, 2006.' ista: 'Friml J, Benfey P, Benková E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejátko J, Jürgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, Scheres B, Swarup R, Torres Ruiz R, Weijers D, Zažímalová E. 2006. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 11(1), 12–14.' mla: 'Friml, Jiří, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science, vol. 11, no. 1, Cell Press, 2006, pp. 12–14, doi:10.1016/j.tplants.2005.11.010.' short: J. Friml, P. Benfey, E. Benková, M. Bennett, T. Berleth, N. Geldner, M. Grebe, M. Heisler, J. Hejátko, G. Jürgens, T. Laux, K. Lindsey, W. Lukowitz, C. Luschnig, R. Offringa, B. Scheres, R. Swarup, R. Torres Ruiz, D. Weijers, E. Zažímalová, Trends in Plant Science 11 (2006) 12–14. date_created: 2018-12-11T12:00:49Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:40:24Z day: '01' doi: 10.1016/j.tplants.2005.11.010 extern: '1' intvolume: ' 11' issue: '1' language: - iso: eng month: '01' oa_version: None page: 12 - 14 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '3697' status: public title: 'Apical-basal polarity: Why plant cells don''t stand on their heads' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2006' ... --- _id: '3008' abstract: - lang: eng text: Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution. author: - first_name: Jian full_name: Xu, Jian last_name: Xu - first_name: Hugo full_name: Hofhuis, Hugo last_name: Hofhuis - first_name: Renze full_name: Heidstra, Renze last_name: Heidstra - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ben full_name: Scheres, Ben last_name: Scheres citation: ama: Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. A molecular framework for plant regeneration. Science. 2006;311(5759):385-388. doi:10.1126/science.1121790 apa: Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J., & Scheres, B. (2006). A molecular framework for plant regeneration. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1121790 chicago: Xu, Jian, Hugo Hofhuis, Renze Heidstra, Michael Sauer, Jiří Friml, and Ben Scheres. “A Molecular Framework for Plant Regeneration.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121790. ieee: J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, and B. Scheres, “A molecular framework for plant regeneration,” Science, vol. 311, no. 5759. American Association for the Advancement of Science, pp. 385–388, 2006. ista: Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. 2006. A molecular framework for plant regeneration. Science. 311(5759), 385–388. mla: Xu, Jian, et al. “A Molecular Framework for Plant Regeneration.” Science, vol. 311, no. 5759, American Association for the Advancement of Science, 2006, pp. 385–88, doi:10.1126/science.1121790. short: J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, B. Scheres, Science 311 (2006) 385–388. date_created: 2018-12-11T12:00:50Z date_published: 2006-01-20T00:00:00Z date_updated: 2021-01-12T07:40:25Z day: '20' doi: 10.1126/science.1121790 extern: 1 intvolume: ' 311' issue: '5759' month: '01' page: 385 - 388 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3695' quality_controlled: 0 status: public title: A molecular framework for plant regeneration type: journal_article volume: 311 year: '2006' ... --- _id: '3009' author: - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Paciorek T, Friml J. Auxin signaling. Journal of Cell Science. 2006;119(7):1199-1202. doi:10.1242/jcs.02910 apa: Paciorek, T., & Friml, J. (2006). Auxin signaling. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02910 chicago: Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02910. ieee: T. Paciorek and J. Friml, “Auxin signaling,” Journal of Cell Science, vol. 119, no. 7. Company of Biologists, pp. 1199–1202, 2006. ista: Paciorek T, Friml J. 2006. Auxin signaling. Journal of Cell Science. 119(7), 1199–1202. mla: Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science, vol. 119, no. 7, Company of Biologists, 2006, pp. 1199–202, doi:10.1242/jcs.02910. short: T. Paciorek, J. Friml, Journal of Cell Science 119 (2006) 1199–1202. date_created: 2018-12-11T12:00:50Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:40:25Z day: '01' doi: 10.1242/jcs.02910 extern: '1' external_id: pmid: - ' 16554435' intvolume: ' 119' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/16554435 month: '01' oa: 1 oa_version: Published Version page: 1199 - 1202 pmid: 1 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '3693' quality_controlled: '1' status: public title: Auxin signaling type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2006' ... --- _id: '3016' abstract: - lang: eng text: Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants. article_processing_charge: No author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jozef full_name: Balla, Jozef last_name: Balla - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Vilém full_name: Reinöhl, Vilém last_name: Reinöhl - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Sauer M, Balla J, Luschnig C, et al. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 2006;20(20):2902-2911. doi:10.1101/gad.390806 apa: Sauer, M., Balla, J., Luschnig, C., Wiśniewska, J., Reinöhl, V., Friml, J., & Benková, E. (2006). Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.390806 chicago: Sauer, Michael, Jozef Balla, Christian Luschnig, Justyna Wiśniewska, Vilém Reinöhl, Jiří Friml, and Eva Benková. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development. Cold Spring Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.390806. ieee: M. Sauer et al., “Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity,” Genes and Development, vol. 20, no. 20. Cold Spring Harbor Laboratory Press, pp. 2902–2911, 2006. ista: Sauer M, Balla J, Luschnig C, Wiśniewska J, Reinöhl V, Friml J, Benková E. 2006. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 20(20), 2902–2911. mla: Sauer, Michael, et al. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development, vol. 20, no. 20, Cold Spring Harbor Laboratory Press, 2006, pp. 2902–11, doi:10.1101/gad.390806. short: M. Sauer, J. Balla, C. Luschnig, J. Wiśniewska, V. Reinöhl, J. Friml, E. Benková, Genes and Development 20 (2006) 2902–2911. date_created: 2018-12-11T12:00:53Z date_published: 2006-10-15T00:00:00Z date_updated: 2021-11-16T07:53:09Z day: '15' doi: 10.1101/gad.390806 extern: '1' intvolume: ' 20' issue: '20' language: - iso: eng month: '10' oa_version: None page: 2902 - 2911 publication: Genes and Development publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '3686' related_material: link: - relation: erratum url: http://genesdev.cshlp.org/content/21/11/1431.short status: public title: Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 20 year: '2006' ... --- _id: '3017' abstract: - lang: eng text: The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events. author: - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Philip full_name: Brewer, Philip last_name: Brewer - 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, Dhonukshe P, Brewer P, Friml J. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 2006;63(23):2738-2754. doi:10.1007/s00018-006-6116-5' apa: 'Tanaka, H., Dhonukshe, P., Brewer, P., & Friml, J. (2006). Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. Birkhäuser. https://doi.org/10.1007/s00018-006-6116-5' chicago: 'Tanaka, Hirokazu, Pankaj Dhonukshe, Philip Brewer, and Jiří Friml. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences. Birkhäuser, 2006. https://doi.org/10.1007/s00018-006-6116-5.' ieee: 'H. Tanaka, P. Dhonukshe, P. Brewer, and J. Friml, “Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development,” Cellular and Molecular Life Sciences, vol. 63, no. 23. Birkhäuser, pp. 2738–2754, 2006.' ista: 'Tanaka H, Dhonukshe P, Brewer P, Friml J. 2006. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 63(23), 2738–2754.' mla: 'Tanaka, Hirokazu, et al. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences, vol. 63, no. 23, Birkhäuser, 2006, pp. 2738–54, doi:10.1007/s00018-006-6116-5.' short: H. Tanaka, P. Dhonukshe, P. Brewer, J. Friml, Cellular and Molecular Life Sciences 63 (2006) 2738–2754. date_created: 2018-12-11T12:00:53Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:40:29Z day: '01' doi: 10.1007/s00018-006-6116-5 extern: '1' intvolume: ' 63' issue: '23' language: - iso: eng month: '12' oa_version: None page: 2738 - 2754 publication: Cellular and Molecular Life Sciences publication_status: published publisher: Birkhäuser publist_id: '3685' quality_controlled: '1' status: public title: 'Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2006' ... --- _id: '3018' abstract: - lang: eng text: The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport. author: - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 2006;18(11):3171-3181. doi:10.1105/tpc.106.042770 apa: Kleine Vehn, J., Dhonukshe, P., Swarup, R., Bennett, M., & Friml, J. (2006). Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.106.042770 chicago: Kleine Vehn, Jürgen, Pankaj Dhonukshe, Ranjan Swarup, Malcolm Bennett, and Jiří Friml. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell. American Society of Plant Biologists, 2006. https://doi.org/10.1105/tpc.106.042770. ieee: J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, and J. Friml, “Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1,” Plant Cell, vol. 18, no. 11. American Society of Plant Biologists, pp. 3171–3181, 2006. ista: Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. 2006. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 18(11), 3171–3181. mla: Kleine Vehn, Jürgen, et al. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell, vol. 18, no. 11, American Society of Plant Biologists, 2006, pp. 3171–81, doi:10.1105/tpc.106.042770. short: J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, J. Friml, Plant Cell 18 (2006) 3171–3181. date_created: 2018-12-11T12:00:53Z date_published: 2006-11-01T00:00:00Z date_updated: 2021-01-12T07:40:29Z day: '01' doi: 10.1105/tpc.106.042770 extern: 1 intvolume: ' 18' issue: '11' month: '11' page: 3171 - 3181 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3684' quality_controlled: 0 status: public title: Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1 type: journal_article volume: 18 year: '2006' ... --- _id: '3020' abstract: - lang: eng text: High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used. author: - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Ikram full_name: Blilou, Ikram last_name: Blilou - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 2006;1(4):1939-1946. doi:10.1038/nprot.2006.333 apa: Hejátko, J., Blilou, I., Brewer, P., Friml, J., Scheres, B., & Benková, E. (2006). In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.333 chicago: Hejátko, Jan, Ikram Blilou, Philip Brewer, Jiří Friml, Ben Scheres, and Eva Benková. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.333. ieee: J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, and E. Benková, “In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 1939–1946, 2006. ista: Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. 2006. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 1(4), 1939–1946. mla: Hejátko, Jan, et al. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 1939–46, doi:10.1038/nprot.2006.333. short: J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, E. Benková, Nature Protocols 1 (2006) 1939–1946. date_created: 2018-12-11T12:00:54Z date_published: 2006-11-01T00:00:00Z date_updated: 2021-01-12T07:40:30Z day: '01' doi: 10.1038/nprot.2006.333 extern: 1 intvolume: ' 1' issue: '4' month: '11' page: 1939 - 1946 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3683' quality_controlled: 0 status: public title: In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples type: journal_article volume: 1 year: '2006' ... --- _id: '3015' abstract: - lang: eng text: 'As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount ''immunolocalization'' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days.' author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Sauer M, Paciorek T, Benková E, Friml J. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 2006;1(1):98-103. doi:10.1038/nprot.2006.15 apa: Sauer, M., Paciorek, T., Benková, E., & Friml, J. (2006). Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.15 chicago: Sauer, Michael, Tomasz Paciorek, Eva Benková, and Jiří Friml. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.15. ieee: M. Sauer, T. Paciorek, E. Benková, and J. Friml, “Immunocytochemical techniques for whole mount in situ protein localization in plants,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 98–103, 2006. ista: Sauer M, Paciorek T, Benková E, Friml J. 2006. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 1(1), 98–103. mla: Sauer, Michael, et al. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 98–103, doi:10.1038/nprot.2006.15. short: M. Sauer, T. Paciorek, E. Benková, J. Friml, Nature Protocols 1 (2006) 98–103. date_created: 2018-12-11T12:00:52Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:40:28Z day: '01' doi: 10.1038/nprot.2006.15 extern: 1 intvolume: ' 1' issue: '1' month: '06' page: 98 - 103 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3688' quality_controlled: 0 status: public title: Immunocytochemical techniques for whole mount in situ protein localization in plants type: journal_article volume: 1 year: '2006' ... --- _id: '3013' abstract: - lang: eng text: 'There is a growing demand for methods that allow rapid and reliable in situ localization of proteins in plant cells. The immunocytochemistry protocol presented here can be used routinely to observe protein localization patterns in tissue sections of various plant species. This protocol is especially suitable for plant species with more-complex tissue architecture (such as maize, Zea mays), which makes it difficult to use an easier whole-mount procedure for protein localization. To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding and tissue-sectioning step. The protocol consists of the following procedures: chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing, rehydration, blocking and antibody incubation. The detailed protocol, recommended controls and troubleshooting are presented here, along with examples of applications.' author: - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jozef full_name: Balla, Jozef last_name: Balla - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 2006;1(1):104-107. doi:10.1038/nprot.2006.16 apa: Paciorek, T., Sauer, M., Balla, J., Wiśniewska, J., & Friml, J. (2006). Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.16 chicago: Paciorek, Tomasz, Michael Sauer, Jozef Balla, Justyna Wiśniewska, and Jiří Friml. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.16. ieee: T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, and J. Friml, “Immunocytochemical technique for protein localization in sections of plant tissues,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 104–107, 2006. ista: Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. 2006. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 1(1), 104–107. mla: Paciorek, Tomasz, et al. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 104–07, doi:10.1038/nprot.2006.16. short: T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, J. Friml, Nature Protocols 1 (2006) 104–107. date_created: 2018-12-11T12:00:52Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:40:27Z day: '01' doi: 10.1038/nprot.2006.16 extern: 1 intvolume: ' 1' issue: '1' month: '06' page: 104 - 107 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3689' quality_controlled: 0 status: public title: Immunocytochemical technique for protein localization in sections of plant tissues type: journal_article volume: 1 year: '2006' ... --- _id: '3014' abstract: - lang: eng text: Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days. author: - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Marcus full_name: Heisler, Marcus G last_name: Heisler - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Brewer P, Heisler M, Hejátko J, Friml J, Benková E. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 2006;1(3):1462-1467. doi:10.1038/nprot.2006.226 apa: Brewer, P., Heisler, M., Hejátko, J., Friml, J., & Benková, E. (2006). In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.226 chicago: Brewer, Philip, Marcus Heisler, Jan Hejátko, Jiří Friml, and Eva Benková. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.226. ieee: P. Brewer, M. Heisler, J. Hejátko, J. Friml, and E. Benková, “In situ hybridization for mRNA detection in Arabidopsis tissue sections,” Nature Protocols, vol. 1, no. 3. Nature Publishing Group, pp. 1462–1467, 2006. ista: Brewer P, Heisler M, Hejátko J, Friml J, Benková E. 2006. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 1(3), 1462–1467. mla: Brewer, Philip, et al. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols, vol. 1, no. 3, Nature Publishing Group, 2006, pp. 1462–67, doi:10.1038/nprot.2006.226. short: P. Brewer, M. Heisler, J. Hejátko, J. Friml, E. Benková, Nature Protocols 1 (2006) 1462–1467. date_created: 2018-12-11T12:00:52Z date_published: 2006-08-01T00:00:00Z date_updated: 2021-01-12T07:40:28Z day: '01' doi: 10.1038/nprot.2006.226 extern: 1 intvolume: ' 1' issue: '3' month: '08' page: 1462 - 1467 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3687' quality_controlled: 0 status: public title: In situ hybridization for mRNA detection in Arabidopsis tissue sections type: journal_article volume: 1 year: '2006' ... --- _id: '3152' abstract: - lang: eng text: The basic concepts of the molecular machinery that mediates cell migration have been gleaned from cell culture systems. However, the three-dimensional environment within an organism presents migrating cells with a much greater challenge. They must move between and among other cells while interpreting multiple attractive and repulsive cues to choose their proper path. They must coordinate their cell adhesion with their surroundings and know when to start and stop moving. New insights into the control of these remaining mysteries have emerged from genetic dissection and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos. In this review, we first describe germ cell migration in cellular and mechanistic detail in these different model systems. We then compare these systems to highlight the emerging principles. Finally, we contrast the migration of germ cells with that of immune and cancer cells to outline the conserved and different mechanisms. author: - first_name: Prabhat full_name: Kunwar, Prabhat S last_name: Kunwar - first_name: Daria E full_name: Daria Siekhaus id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Ruth full_name: Lehmann, Ruth last_name: Lehmann citation: ama: Kunwar P, Siekhaus DE, Lehmann R. In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. 2006;22:237-265. doi:10.1146/annurev.cellbio.22.010305.103337 apa: Kunwar, P., Siekhaus, D. E., & Lehmann, R. (2006). In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev.cellbio.22.010305.103337 chicago: Kunwar, Prabhat, Daria E Siekhaus, and Ruth Lehmann. “In Vivo Migration A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2006. https://doi.org/10.1146/annurev.cellbio.22.010305.103337. ieee: P. Kunwar, D. E. Siekhaus, and R. Lehmann, “In vivo migration A germ cell perspective,” Annual Review of Cell and Developmental Biology, vol. 22. Annual Reviews, pp. 237–265, 2006. ista: Kunwar P, Siekhaus DE, Lehmann R. 2006. In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. 22, 237–265. mla: Kunwar, Prabhat, et al. “In Vivo Migration A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology, vol. 22, Annual Reviews, 2006, pp. 237–65, doi:10.1146/annurev.cellbio.22.010305.103337. short: P. Kunwar, D.E. Siekhaus, R. Lehmann, Annual Review of Cell and Developmental Biology 22 (2006) 237–265. date_created: 2018-12-11T12:01:42Z date_published: 2006-06-14T00:00:00Z date_updated: 2021-01-12T07:41:25Z day: '14' doi: 10.1146/annurev.cellbio.22.010305.103337 extern: 1 intvolume: ' 22' month: '06' page: 237 - 265 publication: Annual Review of Cell and Developmental Biology publication_status: published publisher: Annual Reviews publist_id: '3543' quality_controlled: 0 status: public title: In vivo migration A germ cell perspective type: journal_article volume: 22 year: '2006' ... --- _id: '3189' abstract: - lang: eng text: This paper presents an algorithm capable of real-time separation of foreground from background in monocular video sequences. Automatic segmentation of layers from colour/contrast or from motion alone is known to be error-prone. Here motion, colour and contrast cues are probabilistically fused together with spatial and temporal priors to infer layers accurately and efficiently. Central to our algorithm is the fact that pixel velocities are not needed, thus removing the need for optical flow estimation, with its tendency to error and computational expense. Instead, an efficient motion vs non-motion classifier is trained to operate directly and jointly on intensity-change and contrast. Its output is then fused with colour information. The prior on segmentation is represented by a second order, temporal, Hidden Markov Model, together with a spatial MRF favouring coherence except where contrast is high. Finally, accurate layer segmentation and explicit occlusion detection are efficiently achieved by binary graph cut. The segmentation accuracy of the proposed algorithm is quantitatively evaluated with respect to existing ground-truth data and found to be comparable to the accuracy of a state of the art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated in the application of live background substitution and shown to generate convincingly good quality composite video. author: - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer segmentation of live video. In: Vol 1. IEEE; 2006:53-60. doi:10.1109/CVPR.2006.69' apa: 'Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2006). Bilayer segmentation of live video (Vol. 1, pp. 53–60). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.69' chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov. “Bilayer Segmentation of Live Video,” 1:53–60. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.69. ieee: 'A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer segmentation of live video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2006, vol. 1, pp. 53–60.' ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2006. Bilayer segmentation of live video. CVPR: Computer Vision and Pattern Recognition vol. 1, 53–60.' mla: Criminisi, Antonio, et al. Bilayer Segmentation of Live Video. Vol. 1, IEEE, 2006, pp. 53–60, doi:10.1109/CVPR.2006.69. short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, IEEE, 2006, pp. 53–60. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:54Z date_published: 2006-07-05T00:00:00Z date_updated: 2021-01-12T07:41:40Z day: '05' doi: 10.1109/CVPR.2006.69 extern: 1 intvolume: ' 1' main_file_link: - open_access: '0' url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/criminisi_cvpr06.pdf month: '07' page: 53 - 60 publication_status: published publisher: IEEE publist_id: '3494' quality_controlled: 0 status: public title: Bilayer segmentation of live video type: conference volume: 1 year: '2006' ... --- _id: '3190' abstract: - lang: eng text: Algorithms for discrete energy minimization are of fundamental importance in computer vision. In this paper, we focus on the recent technique proposed by Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW). It was inspired by the problem of maximizing a lower bound on the energy. However, the algorithm is not guaranteed to increase this bound - it may actually go down. In addition, TRW does not always converge. We develop a modification of this algorithm which we call sequential tree-reweighted message passing. Its main property is that the bound is guaranteed not to decrease. We also give a weak tree agreement condition which characterizes local maxima of the bound with respect to TRW algorithms. We prove that our algorithm has a limit point that achieves weak tree agreement. Finally, we show that, our algorithm requires half as much memory as traditional message passing approaches. Experimental results demonstrate that on certain synthetic and real problems, our algorithm outperforms both the ordinary belief propagation and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition, on stereo problems with Potts interactions, we obtain a lower energy than graph cuts. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(10):1568-1583. doi:10.1109/TPAMI.2006.200 apa: Kolmogorov, V. (2006). Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.200 chicago: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.200. ieee: V. Kolmogorov, “Convergent tree reweighted message passing for energy minimization,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 10. IEEE, pp. 1568–1583, 2006. ista: Kolmogorov V. 2006. Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(10), 1568–1583. mla: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 10, IEEE, 2006, pp. 1568–83, doi:10.1109/TPAMI.2006.200. short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 1568–1583. date_created: 2018-12-11T12:01:55Z date_published: 2006-08-21T00:00:00Z date_updated: 2021-01-12T07:41:41Z day: '21' doi: 10.1109/TPAMI.2006.200 extern: 1 intvolume: ' 28' issue: '10' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67371/trw_maxproduct_aistats05.pdf month: '08' page: 1568 - 1583 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '3495' quality_controlled: 0 status: public title: Convergent tree reweighted message passing for energy minimization type: journal_article volume: 28 year: '2006' ... --- _id: '3188' abstract: - lang: eng text: 'We introduce the term cosegmentation which denotes the task of segmenting simultaneously the common parts of an image pair. A generative model for cosegmentation is presented. Inference in the model leads to minimizing an energy with an MRF term encoding spatial coherency and a global constraint which attempts to match the appearance histograms of the common parts. This energy has not been proposed previously and its optimization is challenging and NP-hard. For this problem a novel optimization scheme which we call trust region graph cuts is presented. We demonstrate that this framework has the potential to improve a wide range of research: Object driven image retrieval, video tracking and segmentation, and interactive image editing. The power of the framework lies in its generality, the common part can be a rigid/non-rigid object (or scene), observed from different viewpoints or even similar objects of the same class.' author: - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Thomas full_name: Minka, Thomas P last_name: Minka - first_name: Andrew full_name: Blake, Andrew last_name: Blake citation: ama: 'Rother C, Kolmogorov V, Minka T, Blake A. Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs. In: IEEE; 2006:993-1000. doi:10.1109/CVPR.2006.91' apa: 'Rother, C., Kolmogorov, V., Minka, T., & Blake, A. (2006). Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs (pp. 993–1000). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.91' chicago: Rother, Carsten, Vladimir Kolmogorov, Thomas Minka, and Andrew Blake. “Cosegmentation of Image Pairs by Histogram Matching - Incorporating a Global Constraint into MRFs,” 993–1000. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.91. ieee: 'C. Rother, V. Kolmogorov, T. Minka, and A. Blake, “Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs,” presented at the CVPR: Computer Vision and Pattern Recognition, 2006, pp. 993–1000.' ista: 'Rother C, Kolmogorov V, Minka T, Blake A. 2006. Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs. CVPR: Computer Vision and Pattern Recognition, 993–1000.' mla: Rother, Carsten, et al. Cosegmentation of Image Pairs by Histogram Matching - Incorporating a Global Constraint into MRFs. IEEE, 2006, pp. 993–1000, doi:10.1109/CVPR.2006.91. short: C. Rother, V. Kolmogorov, T. Minka, A. Blake, in:, IEEE, 2006, pp. 993–1000. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:54Z date_published: 2006-07-05T00:00:00Z date_updated: 2021-01-12T07:41:40Z day: '05' doi: 10.1109/CVPR.2006.91 extern: 1 month: '07' page: 993 - 1000 publication_status: published publisher: IEEE publist_id: '3493' quality_controlled: 0 status: public title: Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs type: conference year: '2006' ... --- _id: '3214' abstract: - lang: eng text: |- The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key. Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers. But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation. acknowledgement: Most of this work was done while the K. Pietrzak was a PhD student at ETH where he was supported by the Swiss National Science Foundation, project No. 200020- 103847/1. Currently he is partially supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 ECRYPT. alternative_title: - LNCS author: - first_name: Ueli full_name: Maurer, Ueli M last_name: Maurer - first_name: Yvonne full_name: Oswald, Yvonne A last_name: Oswald - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Johan full_name: Sjödin, Johan last_name: Sjödin citation: ama: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. Luby Rackoff ciphers from weak round functions . In: Vol 4004. Springer; 2006:391-408. doi:10.1007/11761679_24' apa: 'Maurer, U., Oswald, Y., Pietrzak, K. Z., & Sjödin, J. (2006). Luby Rackoff ciphers from weak round functions (Vol. 4004, pp. 391–408). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_24' chicago: Maurer, Ueli, Yvonne Oswald, Krzysztof Z Pietrzak, and Johan Sjödin. “Luby Rackoff Ciphers from Weak Round Functions ,” 4004:391–408. Springer, 2006. https://doi.org/10.1007/11761679_24. ieee: 'U. Maurer, Y. Oswald, K. Z. Pietrzak, and J. Sjödin, “Luby Rackoff ciphers from weak round functions ,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol. 4004, pp. 391–408.' ista: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. 2006. Luby Rackoff ciphers from weak round functions . EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 391–408.' mla: Maurer, Ueli, et al. Luby Rackoff Ciphers from Weak Round Functions . Vol. 4004, Springer, 2006, pp. 391–408, doi:10.1007/11761679_24. short: U. Maurer, Y. Oswald, K.Z. Pietrzak, J. Sjödin, in:, Springer, 2006, pp. 391–408. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:03Z date_published: 2006-07-11T00:00:00Z date_updated: 2021-01-12T07:41:51Z day: '11' doi: 10.1007/11761679_24 extern: 1 intvolume: ' 4004' month: '07' page: 391 - 408 publication_status: published publisher: Springer publist_id: '3465' quality_controlled: 0 status: public title: 'Luby Rackoff ciphers from weak round functions ' type: conference volume: 4004 year: '2006' ... --- _id: '3215' abstract: - lang: eng text: 'Most cryptographic primitives such as encryption, authentication or secret sharing require randomness. Usually one assumes that perfect randomness is available, but those primitives might also be realized under weaker assumptions. In this work we continue the study of building secure cryptographic primitives from imperfect random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows that there exists a (high-entropy) source of randomness allowing for perfect encryption of a bit, and yet from which one cannot extract even a single weakly random bit, separating encryption from extraction. Our main result separates encryption from 2-out-2 secret sharing (both in the information-theoretic and in the computational settings): any source which can be used to achieve one-bit encryption also can be used for 2-out-2 secret sharing of one bit, but the converse is false, even for high-entropy sources. Therefore, possibility of extraction strictly implies encryption, which in turn strictly implies 2-out-2 secret sharing.' acknowledgement: Supported in part by NSF career award CCR-0133806 and NSF grant CCR-0311095. Supported by the Swiss National Science Foundation, project No. 200020-103847/1. alternative_title: - LNCS author: - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Bartosz full_name: Przydatek, Bartosz last_name: Przydatek citation: ama: 'Dodis Y, Pietrzak KZ, Przydatek B. Separating sources for encryption and secret sharing. In: Vol 3876. Springer; 2006:601-616. doi:10.1007/11681878_31' apa: 'Dodis, Y., Pietrzak, K. Z., & Przydatek, B. (2006). Separating sources for encryption and secret sharing (Vol. 3876, pp. 601–616). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/11681878_31' chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Bartosz Przydatek. “Separating Sources for Encryption and Secret Sharing,” 3876:601–16. Springer, 2006. https://doi.org/10.1007/11681878_31. ieee: 'Y. Dodis, K. Z. Pietrzak, and B. Przydatek, “Separating sources for encryption and secret sharing,” presented at the TCC: Theory of Cryptography Conference, 2006, vol. 3876, pp. 601–616.' ista: 'Dodis Y, Pietrzak KZ, Przydatek B. 2006. Separating sources for encryption and secret sharing. TCC: Theory of Cryptography Conference, LNCS, vol. 3876, 601–616.' mla: Dodis, Yevgeniy, et al. Separating Sources for Encryption and Secret Sharing. Vol. 3876, Springer, 2006, pp. 601–16, doi:10.1007/11681878_31. short: Y. Dodis, K.Z. Pietrzak, B. Przydatek, in:, Springer, 2006, pp. 601–616. conference: name: 'TCC: Theory of Cryptography Conference' date_created: 2018-12-11T12:02:04Z date_published: 2006-04-11T00:00:00Z date_updated: 2021-01-12T07:41:51Z day: '11' doi: 10.1007/11681878_31 extern: 1 intvolume: ' 3876' month: '04' page: 601 - 616 publication_status: published publisher: Springer publist_id: '3466' quality_controlled: 0 status: public title: Separating sources for encryption and secret sharing type: conference volume: 3876 year: '2006' ... --- _id: '3217' abstract: - lang: eng text: |- To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true. To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not. acknowledgement: Author was supported during the writing of this work by the Swiss National Science Foundation, project No. 200020-103847/1. Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Composition implies adaptive security in minicrypt. In: Vol 4004. Springer; 2006:328-338. doi:10.1007/11761679_20' apa: 'Pietrzak, K. Z. (2006). Composition implies adaptive security in minicrypt (Vol. 4004, pp. 328–338). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_20' chicago: Pietrzak, Krzysztof Z. “Composition Implies Adaptive Security in Minicrypt,” 4004:328–38. Springer, 2006. https://doi.org/10.1007/11761679_20. ieee: 'K. Z. Pietrzak, “Composition implies adaptive security in minicrypt,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol. 4004, pp. 328–338.' ista: 'Pietrzak KZ. 2006. Composition implies adaptive security in minicrypt. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 328–338.' mla: Pietrzak, Krzysztof Z. Composition Implies Adaptive Security in Minicrypt. Vol. 4004, Springer, 2006, pp. 328–38, doi:10.1007/11761679_20. short: K.Z. Pietrzak, in:, Springer, 2006, pp. 328–338. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:04Z date_published: 2006-07-11T00:00:00Z date_updated: 2021-01-12T07:41:52Z day: '11' doi: 10.1007/11761679_20 extern: 1 intvolume: ' 4004' month: '07' page: 328 - 338 publication_status: published publisher: Springer publist_id: '3464' quality_controlled: 0 status: public title: Composition implies adaptive security in minicrypt type: conference volume: 4004 year: '2006' ... --- _id: '3216' abstract: - lang: eng text: |- We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04]. The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found. acknowledgement: Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 ECRYPT. alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. A tight bound for EMAC. In: Vol 4052. Springer; 2006:168-179. doi:10.1007/11787006_15' apa: 'Pietrzak, K. Z. (2006). A tight bound for EMAC (Vol. 4052, pp. 168–179). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11787006_15' chicago: Pietrzak, Krzysztof Z. “A Tight Bound for EMAC,” 4052:168–79. Springer, 2006. https://doi.org/10.1007/11787006_15. ieee: 'K. Z. Pietrzak, “A tight bound for EMAC,” presented at the ICALP: Automata, Languages and Programming, 2006, vol. 4052, pp. 168–179.' ista: 'Pietrzak KZ. 2006. A tight bound for EMAC. ICALP: Automata, Languages and Programming, LNCS, vol. 4052, 168–179.' mla: Pietrzak, Krzysztof Z. A Tight Bound for EMAC. Vol. 4052, Springer, 2006, pp. 168–79, doi:10.1007/11787006_15. short: K.Z. Pietrzak, in:, Springer, 2006, pp. 168–179. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:02:04Z date_published: 2006-07-28T00:00:00Z date_updated: 2021-01-12T07:41:52Z day: '28' doi: 10.1007/11787006_15 extern: 1 intvolume: ' 4052' month: '07' page: 168 - 179 publication_status: published publisher: Springer publist_id: '3463' quality_controlled: 0 status: public title: A tight bound for EMAC type: conference volume: 4052 year: '2006' ... --- _id: '3522' abstract: - lang: eng text: We observed sharp wave/ripples (SWR) during exploration within brief (< 2.4 s) interruptions of or during theta oscillations. CA1 network responses of SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility or sleep were similar. However, neuronal activity during eSWR was location dependent, and eSWR-related firing was stronger inside the place field than outside. The eSPW-related firing increase was stronger than the baseline increase inside compared to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs. Pairs of cells with similar place fields and/or correlated firing during exploration showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential activation of place cells was not required for the reactivation of waking co-firing patterns; cell pairs with symmetrical cross-correlations still showed reactivated waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing during eSWRs facilitates initial associations between cells with similar place fields that enable place-related ensemble patterns to recur during subsequent sleep-SWRs. author: - first_name: Joseph full_name: Joseph O'Neill id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Timothy full_name: Senior,Timothy last_name: Senior - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: O’Neill J, Senior T, Csicsvari JL. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 2006;49(1):143-155. doi:10.1016/j.neuron.2005.10.037 apa: O’Neill, J., Senior, T., & Csicsvari, J. L. (2006). Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.10.037 chicago: O’Neill, Joseph, Timothy Senior, and Jozsef L Csicsvari. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.10.037. ieee: J. O’Neill, T. Senior, and J. L. Csicsvari, “Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior,” Neuron, vol. 49, no. 1. Elsevier, pp. 143–155, 2006. ista: O’Neill J, Senior T, Csicsvari JL. 2006. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 49(1), 143–155. mla: O’Neill, Joseph, et al. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron, vol. 49, no. 1, Elsevier, 2006, pp. 143–55, doi:10.1016/j.neuron.2005.10.037. short: J. O’Neill, T. Senior, J.L. Csicsvari, Neuron 49 (2006) 143–155. date_created: 2018-12-11T12:03:46Z date_published: 2006-01-05T00:00:00Z date_updated: 2021-01-12T07:44:03Z day: '05' doi: 10.1016/j.neuron.2005.10.037 extern: 1 intvolume: ' 49' issue: '1' month: '01' page: 143 - 155 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2863' quality_controlled: 0 status: public title: Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior type: journal_article volume: 49 year: '2006' ... --- _id: '3607' abstract: - lang: eng text: We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance–attributable to epistasis rather than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences. author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Turelli M, Barton NH. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 2006;60(9):1763-1776. doi:10.1111/j.0014-3820.2006.tb00521.x apa: Turelli, M., & Barton, N. H. (2006). Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x chicago: Turelli, Michael, and Nicholas H Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x. ieee: M. Turelli and N. H. Barton, “Will population bottlenecks and multilocus epistasis increase additive genetic variance?,” Evolution; International Journal of Organic Evolution, vol. 60, no. 9. Wiley-Blackwell, pp. 1763–1776, 2006. ista: Turelli M, Barton NH. 2006. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 60(9), 1763–1776. mla: Turelli, Michael, and Nicholas H. Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution, vol. 60, no. 9, Wiley-Blackwell, 2006, pp. 1763–76, doi:10.1111/j.0014-3820.2006.tb00521.x. short: M. Turelli, N.H. Barton, Evolution; International Journal of Organic Evolution 60 (2006) 1763–1776. date_created: 2018-12-11T12:04:13Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:44:37Z day: '01' doi: 10.1111/j.0014-3820.2006.tb00521.x extern: 1 intvolume: ' 60' issue: '9' month: '09' page: 1763 - 1776 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2776' quality_controlled: 0 status: public title: Will population bottlenecks and multilocus epistasis increase additive genetic variance? type: journal_article volume: 60 year: '2006' ... --- _id: '3683' abstract: - lang: eng text: Many algorithms to remove distortion from document images have be proposed in recent years, but so far there is no reliable method for comparing their performance. In this paper we propose a collection of methods to measure the quality of such restoration algorithms for document image which show a non-linear distortion due to perspective or page curl. For the result from these measurement to be meaningful, a common data set of ground truth is required. We therefore started with the buildup of a document image database that is meant to serve as a common data basis for all kinds of restoration from images of 3D-shaped document. The long term goal would be to establish this database and following extensions in the area of document image dewarping as an as fruitful and indispensable tool as e.g. the NIST database is for OCR, or the Caltech database is for object and face recognition. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Lampert C, Breuel T. Objective quality measurement for geometric document image restoration. In: Springer; 2006.' apa: 'Lampert, C., & Breuel, T. (2006). Objective quality measurement for geometric document image restoration. Presented at the DAS: Document Analysis Systems, Springer.' chicago: Lampert, Christoph, and Thomas Breuel. “Objective Quality Measurement for Geometric Document Image Restoration.” Springer, 2006. ieee: 'C. Lampert and T. Breuel, “Objective quality measurement for geometric document image restoration,” presented at the DAS: Document Analysis Systems, 2006.' ista: 'Lampert C, Breuel T. 2006. Objective quality measurement for geometric document image restoration. DAS: Document Analysis Systems.' mla: Lampert, Christoph, and Thomas Breuel. Objective Quality Measurement for Geometric Document Image Restoration. Springer, 2006. short: C. Lampert, T. Breuel, in:, Springer, 2006. conference: name: 'DAS: Document Analysis Systems' date_created: 2018-12-11T12:04:36Z date_published: 2006-03-16T00:00:00Z date_updated: 2021-01-12T07:45:07Z day: '16' extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/lampert-das2006.pdf month: '03' publication_status: published publisher: Springer publist_id: '2692' quality_controlled: 0 status: public title: Objective quality measurement for geometric document image restoration type: conference year: '2006' ... --- _id: '3685' abstract: - lang: eng text: 'Video compression currently is dominated by engineering and fine-tuned heuristic methods. In this paper, we propose to instead apply the well-developed machinery of machine learning in order to support the optimization of existing video encoders and the creation of new ones. Exemplarily, we show how by machine learning we can improve one encoding step that is crucial for the performance of all current video standards: macroblock mode decision. By formulating the problem in a Bayesian setup, we show that macroblock mode decision can be reduced to a classification problem with a cost function for misclassification that is sample dependent. We demonstrate how to apply different machine learning techniques to obtain suitable classifiers and we show in detailed experiments that all of these perform better than the state-of-the-art heuristic method' author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Lampert C. Machine learning for video compression: Macroblock mode decision. In: IEEE; 2006:936-940. doi:10.1109/ICPR.2006.778' apa: 'Lampert, C. (2006). Machine learning for video compression: Macroblock mode decision (pp. 936–940). Presented at the ICPR: International Conference on Pattern Recognition, IEEE. https://doi.org/10.1109/ICPR.2006.778' chicago: 'Lampert, Christoph. “Machine Learning for Video Compression: Macroblock Mode Decision,” 936–40. IEEE, 2006. https://doi.org/10.1109/ICPR.2006.778.' ieee: 'C. Lampert, “Machine learning for video compression: Macroblock mode decision,” presented at the ICPR: International Conference on Pattern Recognition, 2006, pp. 936–940.' ista: 'Lampert C. 2006. Machine learning for video compression: Macroblock mode decision. ICPR: International Conference on Pattern Recognition, 936–940.' mla: 'Lampert, Christoph. Machine Learning for Video Compression: Macroblock Mode Decision. IEEE, 2006, pp. 936–40, doi:10.1109/ICPR.2006.778.' short: C. Lampert, in:, IEEE, 2006, pp. 936–940. conference: name: 'ICPR: International Conference on Pattern Recognition' date_created: 2018-12-11T12:04:37Z date_published: 2006-09-18T00:00:00Z date_updated: 2021-01-12T07:45:08Z day: '18' doi: 10.1109/ICPR.2006.778 extern: 1 month: '09' page: 936 - 940 publication_status: published publisher: IEEE publist_id: '2689' quality_controlled: 0 status: public title: 'Machine learning for video compression: Macroblock mode decision' type: conference year: '2006' ... --- _id: '3750' abstract: - lang: eng text: We applied a single-cell assay to characterize how transcription dynamics affects protein expression levels of a tetracycline-inducible gene expression system. Transcriptional activity of the tetracycline promoter in response to a steady level of inducer is steady in ΔacrAB efflux mutant but pulsating in wildtype Escherichia coli cells. We found that the expression level of the green fluorescent protein is several folds higher in ΔacrAB efflux mutant than in wildtype cells. author: - first_name: Thuc full_name: Le,Thuc T. last_name: Le - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Philippe full_name: Cluzel,Philippe last_name: Cluzel citation: ama: Le T, Guet CC, Cluzel P. Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. 2006;48(1):28-31. apa: Le, T., Guet, C. C., & Cluzel, P. (2006). Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. Elsevier. chicago: Le, Thuc, Calin C Guet, and Philippe Cluzel. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification. Elsevier, 2006. ieee: T. Le, C. C. Guet, and P. Cluzel, “Protein expression enhancement in efflux-deleted mutant bacteria,” Protein Expression and Purification, vol. 48, no. 1. Elsevier, pp. 28–31, 2006. ista: Le T, Guet CC, Cluzel P. 2006. Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. 48(1), 28–31. mla: Le, Thuc, et al. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification, vol. 48, no. 1, Elsevier, 2006, pp. 28–31. short: T. Le, C.C. Guet, P. Cluzel, Protein Expression and Purification 48 (2006) 28–31. date_created: 2018-12-11T12:04:58Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T07:51:56Z day: '01' extern: 1 intvolume: ' 48' issue: '1' month: '07' page: 28 - 31 publication: Protein Expression and Purification publication_status: published publisher: Elsevier publist_id: '2478' quality_controlled: 0 status: public title: Protein expression enhancement in efflux-deleted mutant bacteria type: journal_article volume: 48 year: '2006' ... --- _id: '3767' abstract: - lang: eng text: Models of RNA secondary structure folding are widely used to study evolution in theory and simulation. However, systematic studies of the parameters involved are rare. In this paper, we study by simulation how RNA evolution is influenced by three different factors, namely the mutation rate, scaling of the fitness function, and distance measure. We found that for low mutation rates the qualitative evolutionary behavior is robust with respect to the scaling of the fitness function. For efficient mutation rates, which are close to the error threshold, scaling and distance measure have a strong influence on the evolutionary behavior. A global distance measure that takes sequence information additively into account lowers the error threshold. When using a local sequence-structure alignment for the distance, we observed a smoother evolution of the fitness over time. Finally, in addition to the well known error threshold, we identify another threshold of the mutation rate, called divergence threshold, where the qualitative transient behavior changes from a localized to an exploratory search. author: - first_name: Anne full_name: Anne Kupczok id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Peter full_name: Dittrich,Peter last_name: Dittrich citation: ama: Kupczok A, Dittrich P. Determinants of simulated RNA evolution. Journal of Theoretical Biology. 2006;238(3):726-735. doi:10.1016/j.jtbi.2005.06.019 apa: Kupczok, A., & Dittrich, P. (2006). Determinants of simulated RNA evolution. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.06.019 chicago: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.06.019. ieee: A. Kupczok and P. Dittrich, “Determinants of simulated RNA evolution.,” Journal of Theoretical Biology, vol. 238, no. 3. Elsevier, pp. 726–35, 2006. ista: Kupczok A, Dittrich P. 2006. Determinants of simulated RNA evolution. Journal of Theoretical Biology. 238(3), 726–35. mla: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.” Journal of Theoretical Biology, vol. 238, no. 3, Elsevier, 2006, pp. 726–35, doi:10.1016/j.jtbi.2005.06.019. short: A. Kupczok, P. Dittrich, Journal of Theoretical Biology 238 (2006) 726–35. date_created: 2018-12-11T12:05:03Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:03Z day: '01' doi: 10.1016/j.jtbi.2005.06.019 extern: 1 intvolume: ' 238' issue: '3' month: '01' page: 726 - 35 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '2461' quality_controlled: 0 status: public title: Determinants of simulated RNA evolution. type: journal_article volume: 238 year: '2006' ... --- _id: '3813' abstract: - lang: eng text: Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed in principal neurons in the central nervous system. However, Ih in inhibitory GABAergic interneurons is less well characterized. We examined the functional properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of 5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent membrane time constant. ZD 7288 blocked a hyperpolarization-activated current in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288 were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of the activation curve of Ih was -83.9 mV, and the activation time constant at -120 mV was 190 ms. Single-cell expression analysis using reverse transcription followed by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD 7288 increased the current threshold for evoking antidromic action potentials by extracellular stimulation, consistent with the expression of Ih in BC axons. Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs, to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged, consistent with the presence of Ih in inhibitory terminals. In conclusion, our results suggest that Ih channels are expressed in the somatodendritic region, axon and presynaptic elements of fast-spiking BCs in the hippocampus. author: - first_name: Yexica full_name: Aponte, Yexica last_name: Aponte - first_name: Cheng full_name: Lien, Cheng-Chang last_name: Lien - first_name: Ellen full_name: Reisinger, Ellen last_name: Reisinger - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Aponte Y, Lien C, Reisinger E, Jonas PM. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 2006;574(Pt 1):229-243. doi:10.1113/jphysiol.2005.104042 apa: Aponte, Y., Lien, C., Reisinger, E., & Jonas, P. M. (2006). Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2005.104042 chicago: Aponte, Yexica, Cheng Lien, Ellen Reisinger, and Peter M Jonas. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology. Wiley-Blackwell, 2006. https://doi.org/10.1113/jphysiol.2005.104042. ieee: Y. Aponte, C. Lien, E. Reisinger, and P. M. Jonas, “Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus,” Journal of Physiology, vol. 574, no. Pt 1. Wiley-Blackwell, pp. 229–43, 2006. ista: Aponte Y, Lien C, Reisinger E, Jonas PM. 2006. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 574(Pt 1), 229–43. mla: Aponte, Yexica, et al. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology, vol. 574, no. Pt 1, Wiley-Blackwell, 2006, pp. 229–43, doi:10.1113/jphysiol.2005.104042. short: Y. Aponte, C. Lien, E. Reisinger, P.M. Jonas, Journal of Physiology 574 (2006) 229–43. date_created: 2018-12-11T12:05:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:23Z day: '01' doi: 10.1113/jphysiol.2005.104042 extern: 1 intvolume: ' 574' issue: Pt 1 main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817792/ month: '01' oa: 1 page: 229 - 43 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '2397' quality_controlled: 0 status: public title: Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus type: journal_article volume: 574 year: '2006' ... --- _id: '3814' abstract: - lang: eng text: The axon terminals (mossy fibers) of hippocampal dentate granule cells form characteristic synaptic connections with large spines or excrescences of both hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled mossy fibers and immunolabeling of target cells with interneuron markers has revealed that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic inhibitory interneurons rather than to excitatory principal cells, although the functional implications of these quantitative differences are unclear. Following a brief description of the "classical" mossy fiber synapse on excrescences of CA3 pyramidal cells, the present review focuses on the contacts formed between granule cells and GABAergic interneurons, both normally and after synaptic reorganization. In response to deafferentation of mossy cell target cells, which include both granule cells and interneurons, mossy fibers "sprout" new axon collaterals that form a band of supragranular mossy fibers in the inner molecular layer of the dentate gyrus. Although most newly formed recurrent mossy fibers establish synapses with granule cells, there is an apparently convergent input of new mossy fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are observed in chronically epileptic rats and may be the structural correlate of the granule cell hyperinhibition observed in these animals in vivo. Together, the findings reviewed here establish mossy fiber synapses as an important component of inhibitory circuits in the hippocampus. author: - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Robert full_name: Sloviter, Robert S last_name: Sloviter citation: ama: Frotscher M, Jonas PM, Sloviter R. Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. 2006;326(2):361-367. doi:10.1007/s00441-006-0269-2 apa: Frotscher, M., Jonas, P. M., & Sloviter, R. (2006). Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0269-2 chicago: Frotscher, Michael, Peter M Jonas, and Robert Sloviter. “Synapses Formed by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0269-2. ieee: M. Frotscher, P. M. Jonas, and R. Sloviter, “Synapses formed by normal and abnormal hippocampal mossy fibers (Review),” Cell and Tissue Research, vol. 326, no. 2. Springer, pp. 361–7, 2006. ista: Frotscher M, Jonas PM, Sloviter R. 2006. Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. 326(2), 361–7. mla: Frotscher, Michael, et al. “Synapses Formed by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue Research, vol. 326, no. 2, Springer, 2006, pp. 361–67, doi:10.1007/s00441-006-0269-2. short: M. Frotscher, P.M. Jonas, R. Sloviter, Cell and Tissue Research 326 (2006) 361–7. date_created: 2018-12-11T12:05:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:35Z day: '01' doi: 10.1007/s00441-006-0269-2 extern: 1 intvolume: ' 326' issue: '2' month: '01' page: 361 - 7 publication: Cell and Tissue Research publication_status: published publisher: Springer publist_id: '2395' quality_controlled: 0 status: public title: Synapses formed by normal and abnormal hippocampal mossy fibers (Review) type: review volume: 326 year: '2006' ... --- _id: '3815' abstract: - lang: eng text: It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network. author: - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2' apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2' chicago: 'Bischofberger, Josef, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology. Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.' ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network,” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–72, 2006.' ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. 453(3), 361–72.' mla: 'Bischofberger, Josef, et al. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.' short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 361–72.' date_created: 2018-12-11T12:05:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:24Z day: '01' doi: 10.1007/s00424-006-0093-2 extern: 1 intvolume: ' 453' issue: '3' month: '01' page: 361 - 72 publication: 'Pflugers Archiv : European Journal of Physiology' publication_status: published publisher: Springer publist_id: '2396' quality_controlled: 0 status: public title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network type: journal_article volume: 453 year: '2006' ... --- _id: '3811' abstract: - lang: eng text: Networks of GABAergic neurons are key elements in the generation of gamma oscillations in the brain. Computational studies suggested that the emergence of coherent oscillations requires hyperpolarizing inhibition. Here, we show that GABA(A) receptor-mediated inhibition in mature interneurons of the hippocampal dentate gyrus is shunting rather than hyperpolarizing. Unexpectedly, when shunting inhibition is incorporated into a structured interneuron network model with fast and strong synapses, coherent oscillations emerge. In comparison to hyperpolarizing inhibition, networks with shunting inhibition show several advantages. First, oscillations are generated with smaller tonic excitatory drive. Second, network frequencies are tuned to the gamma band. Finally, robustness against heterogeneity in the excitatory drive is markedly improved. In single interneurons, shunting inhibition shortens the interspike interval for low levels of drive but prolongs it for high levels, leading to homogenization of neuronal firing rates. Thus, shunting inhibition may confer increased robustness to gamma oscillations in the brain. author: - first_name: Imre full_name: Vida, Imre last_name: Vida - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vida I, Bartos M, Jonas PM. Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. 2006;49(1):107-117. doi:10.1016/j.neuron.2005.11.036 apa: Vida, I., Bartos, M., & Jonas, P. M. (2006). Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.11.036 chicago: Vida, Imre, Marlene Bartos, and Peter M Jonas. “Shunting Inhibition Improves Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.11.036. ieee: I. Vida, M. Bartos, and P. M. Jonas, “Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates,” Neuron, vol. 49, no. 1. Elsevier, pp. 107–17, 2006. ista: Vida I, Bartos M, Jonas PM. 2006. Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. 49(1), 107–17. mla: Vida, Imre, et al. “Shunting Inhibition Improves Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron, vol. 49, no. 1, Elsevier, 2006, pp. 107–17, doi:10.1016/j.neuron.2005.11.036. short: I. Vida, M. Bartos, P.M. Jonas, Neuron 49 (2006) 107–17. date_created: 2018-12-11T12:05:18Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:22Z day: '01' doi: 10.1016/j.neuron.2005.11.036 extern: 1 intvolume: ' 49' issue: '1' month: '01' page: 107 - 17 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2398' quality_controlled: 0 status: public title: Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates type: journal_article volume: 49 year: '2006' ... --- _id: '3817' author: - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Eckart full_name: Gundelfinger, Eckart last_name: Gundelfinger - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Erwin full_name: Neher, Erwin last_name: Neher - first_name: Peter full_name: Seeburg, Peter last_name: Seeburg citation: ama: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. 2006;326(2):203-204. doi:10.1007/s00441-006-0325-y apa: Frotscher, M., Gundelfinger, E., Jonas, P. M., Neher, E., & Seeburg, P. (2006). The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0325-y chicago: Frotscher, Michael, Eckart Gundelfinger, Peter M Jonas, Erwin Neher, and Peter Seeburg. “The Most Important Recent Advances in Synapse Research from My Point of View--and What Remains to Be Done.” Cell and Tissue Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0325-y. ieee: M. Frotscher, E. Gundelfinger, P. M. Jonas, E. Neher, and P. Seeburg, “The most important recent advances in synapse research from my point of view--and what remains to be done,” Cell and Tissue Research, vol. 326, no. 2. Springer, pp. 203–4, 2006. ista: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. 2006. The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. 326(2), 203–4. mla: Frotscher, Michael, et al. “The Most Important Recent Advances in Synapse Research from My Point of View--and What Remains to Be Done.” Cell and Tissue Research, vol. 326, no. 2, Springer, 2006, pp. 203–04, doi:10.1007/s00441-006-0325-y. short: M. Frotscher, E. Gundelfinger, P.M. Jonas, E. Neher, P. Seeburg, Cell and Tissue Research 326 (2006) 203–4. date_created: 2018-12-11T12:05:20Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:24Z day: '01' doi: 10.1007/s00441-006-0325-y extern: 1 intvolume: ' 326' issue: '2' month: '01' page: 203 - 4 publication: Cell and Tissue Research publication_status: published publisher: Springer publist_id: '2394' quality_controlled: 0 status: public title: The most important recent advances in synapse research from my point of view--and what remains to be done type: journal_article volume: 326 year: '2006' ... --- _id: '3912' abstract: - lang: eng text: Invasive species often dramatically change native species communities by directly and indirectly out-competing native species. We studied the direct interference abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA & ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers towards three native Lasius ant species that occur at the edge of a L. neglectus supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus (OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack rate of L. neglectus and behavioural dominance throughout the aggressive encounters. Attacks of L. neglectus were performed fastest and most frequent against L. grandis, and also the highest antennation frequencies were observed in encounters between these two species. This could be due to the largest difference in body size, or due to a greater overlap in ecological niche between L. neglectus and L. grandis compared to the other two native species. There was only weak support for L. neglectus workers from the periphery of the supercolony to be more aggressive relative to workers from the centre, even though the former encounter native ant species on a daily basis at the edge of the supercolony. author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Suzanne full_name: Lommen, Suzanne last_name: Lommen - first_name: Klaus full_name: Petersen, Klaus last_name: Petersen - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen citation: ama: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 2006;9:13-19.' apa: 'Cremer, S., Ugelvig, L. V., Lommen, S., Petersen, K., & Pedersen, J. (2006). Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. Österreichische Gesellschaft für Entomofaunistik.' chicago: 'Cremer, Sylvia, Line V Ugelvig, Suzanne Lommen, Klaus Petersen, and Jes Pedersen. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News. Österreichische Gesellschaft für Entomofaunistik, 2006.' ieee: 'S. Cremer, L. V. Ugelvig, S. Lommen, K. Petersen, and J. Pedersen, “Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain,” Myrmecological News, vol. 9. Österreichische Gesellschaft für Entomofaunistik, pp. 13–19, 2006.' ista: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. 2006. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 9, 13–19.' mla: 'Cremer, Sylvia, et al. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News, vol. 9, Österreichische Gesellschaft für Entomofaunistik, 2006, pp. 13–19.' short: S. Cremer, L.V. Ugelvig, S. Lommen, K. Petersen, J. Pedersen, Myrmecological News 9 (2006) 13–19. date_created: 2018-12-11T12:05:51Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:53:09Z day: '01' extern: '1' intvolume: ' 9' language: - iso: eng month: '12' oa_version: None page: 13 - 19 publication: Myrmecological News publication_status: published publisher: Österreichische Gesellschaft für Entomofaunistik publist_id: '2239' status: public title: 'Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2006' ... --- _id: '3914' abstract: - lang: eng text: We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable. author: - first_name: Karl full_name: Moder, Karl last_name: Moder - first_name: Birgit full_name: Schlick Steiner, Birgit last_name: Schlick Steiner - first_name: Florian full_name: Steiner, Florian last_name: Steiner - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Erhard full_name: Christian, Erhard last_name: Christian - first_name: Bernhard full_name: Seifert, Bernhard last_name: Seifert citation: ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x' apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., & Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x' chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.' ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B. Seifert, “Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study,” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.' ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. 2006. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 45(1), 82–87.' mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87, doi:10.1111/j.1439-0469.2006.00372.x.' short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert, Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87. date_created: 2018-12-11T12:05:52Z date_published: 2006-08-29T00:00:00Z date_updated: 2021-01-12T07:53:10Z day: '29' doi: 10.1111/j.1439-0469.2006.00372.x extern: '1' intvolume: ' 45' issue: '1' language: - iso: eng month: '08' oa_version: None page: 82 - 87 publication: Journal of Zoological Systematics and Evolutionary Research publication_status: published publisher: Wiley-Blackwell publist_id: '2241' status: public title: 'Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2006' ... --- _id: '3913' abstract: - lang: eng text: Many invasive ant species, such as the Argentine ant or the red imported fire ant, have huge colonies with thousands of mass-foraging workers, which quickly monopolise resources and therefore represent a considerable threat to the native ant fauna. Cardiocondyla obscurior and several other species of this myrmicine genus have similarly been transferred throughout the tropics by human activities. However, because their colonies are tiny and workers forage solitarily, Cardiocondyla are often not recognized as successful invaders. Here, we document that the life history of Cardiocondyla closely resembles that of the more conspicuous tramp species, with polygyny, intranidal mating, budding, worker sterility, low genetic variability, and possibly also unicoloniality. Given that introduced Cardiocondyla may locally reach a very high population density, the effects of these stealthy invaders on the native arthropod fauna should receive more attention. author: - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Norbert full_name: Eckl, Norbert last_name: Eckl - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf citation: ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4' apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4' chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer, 2006. https://doi.org/10.1007/s00040-005-0847-4.' ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer, pp. 1–7, 2006.' ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.' mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.' short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7. date_created: 2018-12-11T12:05:51Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:53:09Z day: '01' doi: 10.1007/s00040-005-0847-4 extern: '1' intvolume: ' 53' issue: '1' language: - iso: eng month: '02' oa_version: None page: 1 - 7 publication: Insectes Sociaux publication_status: published publisher: Springer publist_id: '2240' status: public title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2006' ... --- _id: '3932' abstract: - lang: eng text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and tissue content of EGFR has been directly associated with poor prognosis in patients with ovarian cancer. The uPA system plays a role in pericellular proteolysis, cell migration, invasion, and is over-expressed in ovarian cancer. This study explored the effects of EGF on uPAR expression in the ovarian cancer cell line OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration assay, time-lapse video microscopy, real-time PCR, assays for cellular binding of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well as EGF-stimulated cells, is present only in the intact, not the cleaved, form. Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas non-occupied receptor sites were not increased. In addition, EGF treatment resulted in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased internalization of uPAR, since the complex is internalized together with uPAR. Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression of uPAR. In addition, we found an immediate increase of uPAR after exposing the cells to EGF and this was accompanied by a transient increase of cell migration. The increase of cell surface uPAR in response to EGF is accompanied by increased release of the soluble form of uPAR (suPAR) to the medium as well as by increased cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis inhibitor colchicine even though cell migration was inhibited, suggesting that the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased cell surface uPAR in response to EGF stimulation results from mobilization of uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and decreased internalization and degradation of uPAR. Both the anti-uPAR antibody R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa inhibited cell migration in response to uPA as well as to EGF, suggesting that EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.' author: - first_name: Emir full_name: Henic, Emir last_name: Henic - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Stefan full_name: Hansson, Stefan last_name: Hansson - first_name: Gunilla full_name: Høyer-Hansen, Gunilla last_name: Høyer Hansen - first_name: Bertil full_name: Casslén, Bertil last_name: Casslén citation: ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038 apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006). EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038 chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology. Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038. ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp. 28–39, 2006. ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 101(1), 28–39. mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology, vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038. short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic Oncology 101 (2006) 28–39. date_created: 2018-12-11T12:05:57Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:53:17Z day: '01' doi: 10.1016/j.ygyno.2005.09.038 extern: 1 intvolume: ' 101' issue: '1' month: '04' page: 28 - 39 publication: Gynecologic Oncology publication_status: published publisher: Elsevier publist_id: '2194' quality_controlled: 0 status: public title: EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor type: journal_article volume: 101 year: '2006' ... --- _id: '3978' abstract: - lang: eng text: Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. author: - first_name: Yih full_name: Ban, Yih-En Andrew last_name: Ban - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph - first_name: Pei full_name: Zhou, Pei last_name: Zhou - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 2006;62(4):852-864. doi:10.1002/prot.20811' apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811' chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.' ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality of NMR structures by local density of protons,” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.' ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 62(4), 852–864.' mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.' short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function and Bioinformatics 62 (2006) 852–864.' date_created: 2018-12-11T12:06:14Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:53:36Z day: '01' doi: 10.1002/prot.20811 extern: 1 intvolume: ' 62' issue: '4' month: '03' page: 852 - 864 publication: 'Proteins: Structure, Function and Bioinformatics' publication_status: published publisher: Wiley-Blackwell publist_id: '2146' quality_controlled: 0 status: public title: Evaluating the quality of NMR structures by local density of protons type: journal_article volume: 62 year: '2006' ... --- _id: '3979' abstract: - lang: eng text: Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion. author: - first_name: Yih full_name: Ban, Yih-En Andrew last_name: Ban - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes. Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957 apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957 chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957. ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006. ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein complexes. Journal of the ACM. 53(3), 361–378. mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957. short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378. date_created: 2018-12-11T12:06:14Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T07:53:37Z day: '01' doi: 10.1145/1147954.1147957 extern: 1 intvolume: ' 53' issue: '3' month: '05' page: 361 - 378 publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '2147' quality_controlled: 0 status: public title: Interface surfaces for protein-protein complexes type: journal_article volume: 53 year: '2006' ... --- _id: '3980' abstract: - lang: eng text: Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking. author: - first_name: Pankaj full_name: Agarwal, Pankaj K last_name: Agarwal - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Yusu full_name: Wang, Yusu last_name: Wang citation: ama: Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8 apa: Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8 chicago: Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer, 2006. https://doi.org/10.1007/s00454-006-1265-8. ieee: P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer, pp. 553–572, 2006. ista: Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 36(4), 553–572. mla: Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8. short: P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational Geometry 36 (2006) 553–572. date_created: 2018-12-11T12:06:15Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:53:38Z day: '01' doi: 10.1007/s00454-006-1265-8 extern: 1 intvolume: ' 36' issue: '4' month: '12' page: 553 - 572 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2148' quality_controlled: 0 status: public title: Extreme elevation on a 2-manifold type: journal_article volume: 36 year: '2006' ... --- _id: '4345' abstract: - lang: eng text: Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert. author: - first_name: Patrick full_name: Patrick Danowski id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Lambert full_name: Heller,Lambert last_name: Heller citation: ama: Danowski P, Heller L. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 2006;40(11):1250-1271. doi:424 apa: Danowski, P., & Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. Zentral- und Landesbibliothek Berlin. https://doi.org/424 chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst. Zentral- und Landesbibliothek Berlin, 2006. https://doi.org/424. ieee: P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,” Bibliotheksdienst, vol. 40, no. 11. Zentral- und Landesbibliothek Berlin, pp. 1250–1271, 2006. ista: Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 40(11), 1250–1271. mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst, vol. 40, no. 11, Zentral- und Landesbibliothek Berlin, 2006, pp. 1250–71, doi:424. short: P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271. date_created: 2018-12-11T12:08:23Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:17Z day: '01' doi: '424' extern: 1 intvolume: ' 40' issue: '11' main_file_link: - open_access: '0' url: http://www.zlb.de/aktivitaeten/bd_neu/heftinhalte2006/DigitaleBib011106.pdf month: '01' page: 1250 - 1271 publication: Bibliotheksdienst publication_status: published publisher: Zentral- und Landesbibliothek Berlin publist_id: '1229' quality_controlled: 0 status: public title: Bibliothek 2.0 - Die Bibliothek der Zukunft? type: journal_article volume: 40 year: '2006' ... --- _id: '4352' abstract: - lang: eng text: 'Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance.' author: - first_name: Jan full_name: Conn, Jan E last_name: Conn - first_name: Joseph full_name: Vineis, Joseph H last_name: Vineis - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: David full_name: Onyabe, David Y last_name: Onyabe - first_name: Richard full_name: Wilkerson, Richard C last_name: Wilkerson - first_name: Marinete full_name: Povoa, Marinete M last_name: Povoa citation: ama: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 2006;74(5):798-806. apa: Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa, M. (2006). Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene. chicago: Conn, Jan, Joseph Vineis, Jonathan P Bollback, David Onyabe, Richard Wilkerson, and Marinete Povoa. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene, 2006. ieee: J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa, “Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil,” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene, pp. 798–806, 2006. ista: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 2006. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 74(5), 798–806. mla: Conn, Jan, et al. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5, American Society of Tropical Medicine and Hygiene, 2006, pp. 798–806. short: J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806. date_created: 2018-12-11T12:08:25Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T07:56:20Z day: '01' extern: 1 intvolume: ' 74' issue: '5' main_file_link: - open_access: '0' url: http://www.ajtmh.org/content/74/5/798.full month: '05' page: 798 - 806 publication: The American Journal of Tropical Medicine and Hygiene publication_status: published publisher: American Society of Tropical Medicine and Hygiene publist_id: '1108' quality_controlled: 0 status: public title: Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil type: journal_article volume: 74 year: '2006' ... --- _id: '4351' abstract: - lang: eng text: 'BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.' author: - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88' apa: 'Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88' chicago: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics. BioMed Central, 2006. https://doi.org/10.1186/1471-2105-7-88.' ieee: 'J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.' ista: 'Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 7.' mla: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.' short: J.P. Bollback, BMC Bioinformatics 7 (2006). date_created: 2018-12-11T12:08:25Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:20Z day: '01' doi: 10.1186/1471-2105-7-88 extern: 1 intvolume: ' 7' month: '01' publication: BMC Bioinformatics publication_status: published publisher: BioMed Central publist_id: '1109' quality_controlled: 0 status: public title: 'SIMMAP: stochastic character mapping of discrete traits on phylogenies' 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: 7 year: '2006' ... --- _id: '3180' abstract: - lang: eng text: 'One of the most exciting advances in early vision has been the development of efficient energy minimization algorithms. Many early vision tasks require labeling each pixel with some quantity such as depth or texture. While many such problems can be elegantly expressed in the language of Markov Random Fields (MRF''s), the resulting energy minimization problems were widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. Unfortunately, most papers define their own energy function, which is minimized with a specific algorithm of their choice. As a result, the tradeoffs among different energy minimization algorithms are not well understood. In this paper we describe a set of energy minimization benchmarks, which we use to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods - graph cuts, LBP, and tree-reweighted message passing - as well as the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching and interactive segmentation. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods with minimal overhead. We expect that the availability of our benchmarks and interface will make it significantly easier for vision researchers to adopt the best method for their specific problems. Benchmarks, code, results and images are available at http://vision.middlebury.edu/MRF.' author: - first_name: Richard full_name: Szeliski, Richard S last_name: Szeliski - first_name: Ramin full_name: Zabih, Ramin last_name: Zabih - first_name: Daniel full_name: Scharstein, Daniel last_name: Scharstein - first_name: Olga full_name: Veksler, Olga last_name: Veksler - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Aseem full_name: Agarwala, Aseem last_name: Agarwala - first_name: Marshall full_name: Tappen, Marshall F last_name: Tappen - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization methods for Markov random fields. In: Vol 3952. Springer; 2006:16-29. doi:10.1007/11744047_2' apa: 'Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala, A., … Rother, C. (2006). A comparative study of energy minimization methods for Markov random fields (Vol. 3952, pp. 16–29). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_2' chicago: Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative Study of Energy Minimization Methods for Markov Random Fields,” 3952:16–29. Springer, 2006. https://doi.org/10.1007/11744047_2. ieee: 'R. Szeliski et al., “A comparative study of energy minimization methods for Markov random fields,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952, pp. 16–29.' ista: 'Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C. 2006. A comparative study of energy minimization methods for Markov random fields. ECCV: European Conference on Computer Vision vol. 3952, 16–29.' mla: Szeliski, Richard, et al. A Comparative Study of Energy Minimization Methods for Markov Random Fields. Vol. 3952, Springer, 2006, pp. 16–29, doi:10.1007/11744047_2. short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala, M. Tappen, C. Rother, in:, Springer, 2006, pp. 16–29. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:51Z date_published: 2006-05-03T00:00:00Z date_updated: 2021-01-12T07:41:37Z day: '03' doi: 10.1007/11744047_2 extern: 1 intvolume: ' 3952' main_file_link: - open_access: '0' url: http://research-srv.microsoft.com/pubs/67896/szsvkatr-eccv06.pdf month: '05' page: 16 - 29 publication_status: published publisher: Springer publist_id: '3499' quality_controlled: 0 status: public title: A comparative study of energy minimization methods for Markov random fields type: conference volume: 3952 year: '2006' ... --- _id: '3184' abstract: - lang: eng text: 'Algorithms for discrete energy minimization play a fundamental role for low-level vision. Known techniques include graph cuts, belief propagation (BP) and recently introduced tree-reweighted message passing (TRW). So far, the standard benchmark for their comparison has been a 4-connected grid-graph arising in pixel-labelling stereo. This minimization problem, however, has been largely solved: recent work shows that for many scenes TRW finds the global optimum. Furthermore, it is known that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions into account. We propose the problem of stereo with occlusions as a new test bed for minimization algorithms. This is a more challenging graph since it has much larger connectivity, and it also serves as a better stereo model. An attractive feature of this problem is that increased connectivity does not result in increased complexity of message passing algorithms. Indeed, one contribution of this paper is to show that sophisticated implementations of BP and TRW have the same time and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion of our experimental study is that for our problem graph cut outperforms both TRW and BP considerably. TRW achieves consistently a lower energy than BP. However, as connectivity increases the speed of convergence of TRW becomes slower. Unlike 4-connected grids, the difference between the energy of the best optimization method and the lower bound of TRW appears significant. This shows the hardness of the problem and motivates future research.' alternative_title: - LNCS author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1' apa: 'Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1' chicago: Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1. ieee: 'V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms for highly connected graphs,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952 LNCS, pp. 1–15.' ista: 'Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS, vol. 3952 LNCS, 1–15.' mla: Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp. 1–15, doi:10.1007/11744047_1. short: V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:52Z date_published: 2006-05-03T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '03' doi: 10.1007/11744047_1 extern: 1 main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf month: '05' page: 1 - 15 publication_status: published publisher: Springer publist_id: '3498' quality_controlled: 0 status: public title: Comparison of energy minimization algorithms for highly connected graphs type: conference volume: 3952 LNCS year: '2006' ... --- _id: '3185' abstract: - lang: eng text: This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193 apa: Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006). Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193 chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193. ieee: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492, 2006. ista: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492. mla: Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193. short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492. date_created: 2018-12-11T12:01:53Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '01' doi: 10.1109/TPAMI.2006.193 extern: 1 intvolume: ' 28' issue: '9' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf month: '09' page: 1480 - 1492 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '3496' quality_controlled: 0 status: public title: Probabilistic fusion of stereo with color and contrast for bilayer segmentation type: journal_article volume: 28 year: '2006' ... --- _id: '3186' abstract: - lang: eng text: We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion. alternative_title: - LNCS author: - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Daniel full_name: Cremers, Daniel last_name: Cremers - first_name: Andrew full_name: Delong, Andrew last_name: Delong citation: ama: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32' apa: 'Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32' chicago: Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer, 2006. https://doi.org/10.1007/11744078_32. ieee: 'Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3953, pp. 409–422.' ista: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision, LNCS, vol. 3953, 409–422.' mla: Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32. short: Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp. 409–422. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:53Z date_published: 2006-04-28T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '28' doi: 10.1007/11744078_32 extern: 1 intvolume: ' 3953' month: '04' page: 409 - 422 publication_status: published publisher: Springer publist_id: '3497' quality_controlled: 0 status: public title: An integral solution to surface evolution PDEs via geo cuts type: conference volume: 3953 year: '2006' ... --- _id: '3404' alternative_title: - Manuals in Biomedical Research author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Ravi full_name: Sawhney, Ravi K last_name: Sawhney - first_name: Martin full_name: Stark, Martin last_name: Stark - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing; 2006:213-284.' apa: Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force microscopy. In Techniques in Microscopy for Biomedical Applications (Vol. 2, pp. 213–284). World Scientific Publishing. chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic Force Microscopy.” In Techniques in Microscopy for Biomedical Applications, 2:213–84. World Scientific Publishing, 2006. ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,” in Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–284. ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical Research, vol. 2, 213–284.' mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–84. short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284. date_created: 2018-12-11T12:03:09Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:43:15Z day: '28' extern: 1 intvolume: ' 2' month: '09' page: 213 - 284 publication: Techniques in Microscopy for Biomedical Applications publication_status: published publisher: World Scientific Publishing publist_id: '2998' quality_controlled: 0 status: public title: Atomic force microscopy type: book_chapter volume: 2 year: '2006' ... --- _id: '3413' abstract: - lang: eng text: |- Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids. Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded. We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state. author: - first_name: Max full_name: Kessler, Max last_name: Kessler - first_name: Kay full_name: Gottschalk, Kay E last_name: Gottschalk - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Hermann full_name: Gaub, Hermann last_name: Gaub citation: ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065 apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006). Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065 chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065. ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin folds into the membrane against an external force,” Journal of Molecular Biology, vol. 357, no. 2. Elsevier, pp. 644–654, 2006. ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 357(2), 644–654. mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier, 2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065. short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of Molecular Biology 357 (2006) 644–654. date_created: 2018-12-11T12:03:12Z date_published: 2006-03-24T00:00:00Z date_updated: 2021-01-12T07:43:18Z day: '24' doi: 10.1016/j.jmb.2005.12.065 extern: 1 intvolume: ' 357' issue: '2' month: '03' page: 644 - 654 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '2988' quality_controlled: 0 status: public title: Bacteriorhodopsin folds into the membrane against an external force type: journal_article volume: 357 year: '2006' ... --- _id: '3414' abstract: - lang: eng text: Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter. author: - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Christine full_name: Ziegler, Christine last_name: Ziegler - first_name: Werner full_name: Kühlbrandt, Werner last_name: Kühlbrandt - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028 apa: Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., & Mueller, D. (2006). Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.10.028 chicago: Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt, and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.10.028. ieee: A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli,” Journal of Molecular Biology, vol. 355, no. 1. Elsevier, pp. 2–8, 2006. ista: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 355(1), 2–8. mla: Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology, vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:10.1016/j.jmb.2005.10.028. short: A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 355 (2006) 2–8. date_created: 2018-12-11T12:03:12Z date_published: 2006-01-06T00:00:00Z date_updated: 2021-01-12T07:43:19Z day: '06' doi: 10.1016/j.jmb.2005.10.028 extern: 1 intvolume: ' 355' issue: '1' month: '01' page: 2 - 8 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '2987' quality_controlled: 0 status: public title: Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli type: journal_article volume: 355 year: '2006' ... --- _id: '3415' author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: David full_name: Cisneros, David last_name: Cisneros - first_name: Tanuj full_name: Sapra, Tanuj K last_name: Sapra - first_name: Jens full_name: Struckmeier, Jens last_name: Struckmeier - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031 apa: Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., & Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031 chicago: Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier, and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031. ieee: H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller, “Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology of Aging, vol. 27. Elsevier, pp. 546–561, 2006. ista: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 27, 546–561. mla: Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging, vol. 27, Elsevier, 2006, pp. 546–61, doi:10.1016/j.neurobiolaging.2005.03.031. short: H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller, Neurobiology of Aging 27 (2006) 546–561. date_created: 2018-12-11T12:03:12Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:27Z day: '01' doi: 10.1016/j.neurobiolaging.2005.03.031 extern: 1 intvolume: ' 27' month: '01' page: 546 - 561 publication: Neurobiology of Aging publication_status: published publisher: Elsevier publist_id: '2986' quality_controlled: 0 status: public title: Imaging and detecting molecular interactions of single membrane proteins type: review volume: 27 year: '2006' ... --- _id: '3437' abstract: - lang: eng text: The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models. author: - first_name: Andrea full_name: Betancourt, Andrea J last_name: Betancourt - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006' apa: 'Betancourt, A., & Bollback, J. P. (2006). Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006' chicago: 'Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development. Elsevier, 2006. https://doi.org/10.1016/j.gde.2006.10.006.' ieee: 'A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution,” Current Opinion in Genetics & Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.' ista: 'Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 16(6), 618–623.' mla: 'Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp. 618–23, doi:10.1016/j.gde.2006.10.006.' short: A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development 16 (2006) 618–623. date_created: 2018-12-11T12:03:19Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:43:27Z day: '01' doi: 10.1016/j.gde.2006.10.006 extern: 1 intvolume: ' 16' issue: '6' month: '12' page: 618 - 623 publication: Current Opinion in Genetics & Development publication_status: published publisher: Elsevier publist_id: '2963' quality_controlled: 0 status: public title: 'Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution' type: journal_article volume: 16 year: '2006' ... --- _id: '3431' abstract: - lang: eng text: Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses. author: - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: E. full_name: Schneidman, E. last_name: Schneidman - first_name: M. full_name: Berry, M. J. last_name: Berry - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4. apa: Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models for networks of real neurons. ArXiv. ArXiv. chicago: Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006. ieee: G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006. ista: Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks of real neurons. ArXiv, 1–4, . mla: Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4. short: G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4. date_created: 2018-12-11T12:03:18Z date_published: 2006-11-22T00:00:00Z date_updated: 2021-01-12T07:43:25Z day: '22' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/q-bio/0611072 month: '11' oa: 1 page: 1 - 4 publication: ArXiv publication_status: published publisher: ArXiv publist_id: '2969' quality_controlled: 0 status: public title: Ising models for networks of real neurons type: preprint year: '2006' ... --- _id: '3449' abstract: - lang: eng text: We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rhada full_name: Jagadeesan, Rhada last_name: Jagadeesan - first_name: Corin full_name: Pitcher, Corin last_name: Pitcher citation: ama: 'Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82. doi:10.1109/CSFW.2006.14' apa: 'Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls (pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14' chicago: Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14. ieee: 'K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented at the CSF: Computer Security Foundations, 2006, pp. 70–82.' ista: 'Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer Security Foundations, 70–82.' mla: Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82, doi:10.1109/CSFW.2006.14. short: K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82. conference: name: 'CSF: Computer Security Foundations' date_created: 2018-12-11T12:03:23Z date_published: 2006-07-31T00:00:00Z date_updated: 2021-01-12T07:43:32Z day: '31' doi: 10.1109/CSFW.2006.14 extern: 1 month: '07' page: 70 - 82 publication_status: published publisher: IEEE publist_id: '2938' quality_controlled: 0 status: public title: Games for controls type: conference year: '2006' ... --- _id: '3463' abstract: - lang: eng text: It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network. author: - first_name: Joseph full_name: Bischofberger, Joseph last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2' apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2' chicago: 'Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology. Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.' ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review),” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–372, 2006.' ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 453(3), 361–372.' mla: 'Bischofberger, Joseph, et al. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.' short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 361–372.' date_created: 2018-12-11T12:03:28Z date_published: 2006-12-01T00:00:00Z date_updated: 2019-04-26T07:22:28Z day: '01' doi: 10.1007/s00424-006-0093-2 extern: 1 intvolume: ' 453' issue: '3' month: '12' page: 361 - 372 publication: 'Pflugers Archiv : European Journal of Physiology' publication_status: published publisher: Springer publist_id: '2924' quality_controlled: 0 status: public title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review) type: review volume: 453 year: '2006' ... --- _id: '3499' abstract: - lang: eng text: 'We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. ' acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR- 0234690, and by the SNSF under the Indo-Swiss Joint Research Programme. alternative_title: - 'LNCS ' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207. Springer; 2006:271-286. doi:10.1007/11874683_18' apa: 'Chatterjee, K. (2006). Nash equilibrium for upward-closed objectives (Vol. 4207, pp. 271–286). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_18' chicago: Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,” 4207:271–86. Springer, 2006. https://doi.org/10.1007/11874683_18. ieee: 'K. Chatterjee, “Nash equilibrium for upward-closed objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 271–286.' ista: 'Chatterjee K. 2006. Nash equilibrium for upward-closed objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 271–286.' mla: Chatterjee, Krishnendu. Nash Equilibrium for Upward-Closed Objectives. Vol. 4207, Springer, 2006, pp. 271–86, doi:10.1007/11874683_18. short: K. Chatterjee, in:, Springer, 2006, pp. 271–286. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:03:39Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:43:52Z day: '28' doi: 10.1007/11874683_18 extern: 1 intvolume: ' 4207' month: '09' page: 271 - 286 publication_status: published publisher: Springer publist_id: '2888' quality_controlled: 0 status: public title: Nash equilibrium for upward-closed objectives type: conference volume: 4207 year: '2006' ... --- _id: '3500' abstract: - lang: eng text: The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n). acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610 and the SNSF under the Indo-Swiss Joint Research Programme. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Chatterjee K, Henzinger TA, Piterman N. Algorithms for Büchi Games. In: ACM; 2006.' apa: 'Chatterjee, K., Henzinger, T. A., & Piterman, N. (2006). Algorithms for Büchi Games. Presented at the GDV: Games in Design and Verification, ACM.' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms for Büchi Games.” ACM, 2006. ieee: 'K. Chatterjee, T. A. Henzinger, and N. Piterman, “Algorithms for Büchi Games,” presented at the GDV: Games in Design and Verification, 2006.' ista: 'Chatterjee K, Henzinger TA, Piterman N. 2006. Algorithms for Büchi Games. GDV: Games in Design and Verification.' mla: Chatterjee, Krishnendu, et al. Algorithms for Büchi Games. ACM, 2006. short: K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006. conference: name: 'GDV: Games in Design and Verification' date_created: 2018-12-11T12:03:39Z date_published: 2006-08-21T00:00:00Z date_updated: 2021-01-12T07:43:53Z day: '21' extern: 1 main_file_link: - open_access: '0' url: http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf month: '08' publication_status: published publisher: ACM publist_id: '2887' quality_controlled: 0 status: public title: Algorithms for Büchi Games type: conference year: '2006' ... --- _id: '3510' abstract: - lang: eng text: Embodiments automatically generate an accurate network of watertight NURBS patches from polygonal models of objects while automatically detecting and preserving character lines thereon. These embodiments generate from an initial triangulation of the surface, a hierarchy of progressively coarser triangulations of the surface by performing a sequence of edge contractions using a greedy algorithm that selects edge contractions by their numerical properties. Operations are also performed to connect the triangulations in the hierarchy using homeomorphisms that preserve the topology of the initial triangulation in the coarsest triangulation. A desired quadrangulation of the surface can then be generated by homeomorphically mapping edges of a coarsest triangulation in the hierarchy back to the initial triangulation. This quadrangulation is topologically consistent with the initial triangulation and is defined by a plurality of quadrangular patches. These quadrangular patches are linked together by a (U, V) mesh that is guaranteed to be continuous at patch boundaries. A grid is then preferably fit to each of the quadrangles in the resulting quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles. A watertight NURBS model may be generated from the resulting quadrangulation. applicant: - Raindrop Geomagic, Inc. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu - first_name: Dmitry full_name: Nekhayev, Dmitry last_name: Nekhayev - first_name: Michael full_name: Facello, Michael last_name: Facello - first_name: Steven full_name: Williams, Steven last_name: Williams citation: ama: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. 2006. apa: Edelsbrunner, H., Fu, P., Nekhayev, D., Facello, M., & Williams, S. (2006). Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. chicago: Edelsbrunner, Herbert, Ping Fu, Dmitry Nekhayev, Michael Facello, and Steven Williams. “Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism,” 2006. ieee: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, and S. Williams, “Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.” 2006. ista: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. 2006. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. mla: Edelsbrunner, Herbert, et al. Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism. 2006. short: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006). date_created: 2018-12-11T12:03:42Z date_published: 2006-02-07T00:00:00Z date_updated: 2022-01-05T12:58:26Z day: '07' extern: '1' ipc: G06F 7/60 ; G06F 17/10 ; G06F 101/00 ipn: US6996505B1 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US6996505 month: '02' oa: 1 oa_version: Published Version publication_date: 2006-02-07 publist_id: '2877' status: public title: Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3511' abstract: - lang: eng text: 'Methods, apparatus and computer program products provide efficient techniques for designing and printing shells of hearing-aid devices with a high degree of quality assurance and reliability and with a reduced number of manual and time consuming production steps and operations. These techniques also preferably provide hearing-aid shells having internal volumes that can approach a maximum allowable ratio of internal volume relative to external volume. These high internal volumes facilitate the inclusion of hearing-aid electrical components having higher degrees of functionality and/or the use of smaller and less conspicuous hearing-aid shells. A preferred method includes operations to generate a watertight digital model of a hearing-aid shell by thickening a three-dimensional digital model of a shell surface in a manner that eliminates self-intersections and results in a thickened model having an internal volume that is a high percentage of an external volume of the model. ' acknowledgement: sold to Siemens and Phonak applicant: - Phonak AG article_processing_charge: No author: - first_name: Ping full_name: Fu, Ping last_name: Fu - first_name: Dmitry full_name: Nekhayev, Dmitry last_name: Nekhayev - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Fu P, Nekhayev D, Edelsbrunner H. Manufacturing methods and systems for rapid production of hearing-aid shells. 2006. apa: Fu, P., Nekhayev, D., & Edelsbrunner, H. (2006). Manufacturing methods and systems for rapid production of hearing-aid shells. chicago: Fu, Ping, Dmitry Nekhayev, and Herbert Edelsbrunner. “Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells,” 2006. ieee: P. Fu, D. Nekhayev, and H. Edelsbrunner, “Manufacturing methods and systems for rapid production of hearing-aid shells.” 2006. ista: Fu P, Nekhayev D, Edelsbrunner H. 2006. Manufacturing methods and systems for rapid production of hearing-aid shells. mla: Fu, Ping, et al. Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells. 2006. short: P. Fu, D. Nekhayev, H. Edelsbrunner, (2006). date_created: 2018-12-11T12:03:43Z date_published: 2006-05-23T00:00:00Z date_updated: 2022-01-05T13:03:56Z day: '23' extern: '1' ipc: G06F 9/00 ipn: US7050876B1 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US7050876B1 month: '05' oa: 1 oa_version: Published Version publication_date: 2006-05-23 publist_id: '2876' status: public title: Manufacturing methods and systems for rapid production of hearing-aid shells type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3512' abstract: - lang: eng text: Methods, apparatus and computer program products provide efficient techniques for reconstructing surfaces from data point sets. These techniques include reconstructing surfaces from sets of scanned data points that have preferably undergone preprocessing operations to improve their quality by, for example, reducing noise and removing outliers. These techniques include reconstructing a dense and locally two-dimensionally distributed 3D point set (e.g., point cloud) by merging stars in two-dimensional weighted Delaunay triangulations within estimated tangent planes. The techniques include determining a plurality of stars from a plurality of points p.sub.i in a 3D point set S that at least partially describes the 3D surface, by projecting the plurality of points p.sub.i onto planes T.sub.i that are each estimated to be tangent about a respective one of the plurality of points p.sub.i. The plurality of stars are then merged into a digital model of the 3D surface. applicant: - Geomagic Inc. article_processing_charge: No author: - first_name: Yates full_name: Fletcher, Yates last_name: Fletcher - first_name: Tobias full_name: Gloth, Tobias last_name: Gloth - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu citation: ama: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. Method, apparatus and computer products that reconstruct surfaces from data points. 2006. apa: Fletcher, Y., Gloth, T., Edelsbrunner, H., & Fu, P. (2006). Method, apparatus and computer products that reconstruct surfaces from data points. chicago: Fletcher, Yates, Tobias Gloth, Herbert Edelsbrunner, and Ping Fu. “Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points,” 2006. ieee: Y. Fletcher, T. Gloth, H. Edelsbrunner, and P. Fu, “Method, apparatus and computer products that reconstruct surfaces from data points.” 2006. ista: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. 2006. Method, apparatus and computer products that reconstruct surfaces from data points. mla: Fletcher, Yates, et al. Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points. 2006. short: Y. Fletcher, T. Gloth, H. Edelsbrunner, P. Fu, (2006). date_created: 2018-12-11T12:03:43Z date_published: 2006-04-04T00:00:00Z date_updated: 2022-01-05T14:00:00Z day: '04' extern: '1' ipc: ' G06T17/20 ; B33Y50/00' ipn: US7023432B2 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US7023432B2 month: '04' oa: 1 oa_version: Published Version publication_date: 2006-04-04 publist_id: '2875' status: public title: Method, apparatus and computer products that reconstruct surfaces from data points type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3545' abstract: - lang: eng text: The functional organization of the basal ganglia ( BG) is often defined according to one of two opposing schemes. The first proposes multiple, essentially independent channels of information processing. The second posits convergence and lateral integration of striatal channels at the level of the globus pallidus ( GP). We tested the hypothesis that these proposed aspects of functional connectivity within the striatopallidal axis are dynamic and related to brain state. Local field potentials ( LFPs) were simultaneously recorded from multiple sites in striatum and GP in anesthetized rats during slow-wave activity( SWA) and during global activation evoked by sensory stimulation. Functional connectivity was inferred from comparative analyses of the internuclear and intranuclear coherence between bipolar derivations of LFPs. During prominent SWA, as shown in the electrocorticogram and local field potentials in the basal ganglia, intranuclear coherence, and, thus, lateral functional connectivity within striatum or globus pallidus was relatively weak. Furthermore, the temporal coupling of LFPs recorded across these two nuclei involved functional convergence at the level of GP. Global activation, indicated by a loss of SWA, was accompanied by a rapid functional reorganization of the striatopallidal axis. Prominent lateral functional connectivity developed within GP and, to a significantly more constrained spatial extent, striatum. Additionally, functional convergence on GP was no longer apparent, despite increased internuclear coherence. These data demonstrate that functional connectivity within the BG is highly dynamic and suggest that the relative expression of organizational principles, such as parallel, independent processing channels, striatopallidal convergence, and lateral integration within BG nuclei, is dependent on brain state. author: - first_name: Peter full_name: Magill,Peter J last_name: Magill - first_name: Alek full_name: Pogosyan,Alek last_name: Pogosyan - first_name: Andrew full_name: Sharott,Andrew last_name: Sharott - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: John full_name: Bolam, John Paul last_name: Bolam - first_name: Peter full_name: Brown,Peter last_name: Brown citation: ama: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. 2006;26(23):6318-6329. doi:10.1523/​JNEUROSCI.0620-06.2006 apa: Magill, P., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., & Brown, P. (2006). Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/​JNEUROSCI.0620-06.2006 chicago: Magill, Peter, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John Bolam, and Peter Brown. “Changes in Functional Connectivity within the Rat Striatopallidal Axis during Global Brain Activation in Vivo.” Journal of Neuroscience. Society for Neuroscience, 2006. https://doi.org/10.1523/​JNEUROSCI.0620-06.2006. ieee: P. Magill, A. Pogosyan, A. Sharott, J. L. Csicsvari, J. Bolam, and P. Brown, “Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo,” Journal of Neuroscience, vol. 26, no. 23. Society for Neuroscience, pp. 6318–6329, 2006. ista: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. 2006. Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. 26(23), 6318–6329. mla: Magill, Peter, et al. “Changes in Functional Connectivity within the Rat Striatopallidal Axis during Global Brain Activation in Vivo.” Journal of Neuroscience, vol. 26, no. 23, Society for Neuroscience, 2006, pp. 6318–29, doi:10.1523/​JNEUROSCI.0620-06.2006. short: P. Magill, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, Journal of Neuroscience 26 (2006) 6318–6329. date_created: 2018-12-11T12:03:53Z date_published: 2006-06-07T00:00:00Z date_updated: 2021-01-12T07:44:13Z day: '07' doi: 10.1523/​JNEUROSCI.0620-06.2006 extern: 1 intvolume: ' 26' issue: '23' month: '06' page: 6318 - 6329 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '2840' quality_controlled: 0 status: public title: Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo type: journal_article volume: 26 year: '2006' ... --- _id: '3559' abstract: - lang: eng text: Persistent homology is the mathematical core of recent work on shape, including reconstruction, recognition, and matching. Its per- tinent information is encapsulated by a pairing of the critical values of a function, visualized by points forming a diagram in the plane. The original algorithm in [10] computes the pairs from an ordering of the simplices in a triangulation and takes worst-case time cubic in the number of simplices. The main result of this paper is an algorithm that maintains the pairing in worst-case linear time per transposition in the ordering. A side-effect of the algorithm’s anal- ysis is an elementary proof of the stability of persistence diagrams [7] in the special case of piecewise-linear functions. We use the algorithm to compute 1-parameter families of diagrams which we apply to the study of protein folding trajectories. acknowledgement: Partially supported by NSF under grant CCR- 00-86013, by DARPA under grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under grant B543154. author: - first_name: David full_name: Cohen-Steiner, David last_name: Cohen Steiner - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov citation: ama: 'Cohen Steiner D, Edelsbrunner H, Morozov D. Vines and vineyards by updating persistence in linear time. In: ACM; 2006:119-126. doi:10.1145/1137856.1137877' apa: 'Cohen Steiner, D., Edelsbrunner, H., & Morozov, D. (2006). Vines and vineyards by updating persistence in linear time (pp. 119–126). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137877' chicago: Cohen Steiner, David, Herbert Edelsbrunner, and Dmitriy Morozov. “Vines and Vineyards by Updating Persistence in Linear Time,” 119–26. ACM, 2006. https://doi.org/10.1145/1137856.1137877. ieee: 'D. Cohen Steiner, H. Edelsbrunner, and D. Morozov, “Vines and vineyards by updating persistence in linear time,” presented at the SCG: Symposium on Computational Geometry, 2006, pp. 119–126.' ista: 'Cohen Steiner D, Edelsbrunner H, Morozov D. 2006. Vines and vineyards by updating persistence in linear time. SCG: Symposium on Computational Geometry, 119–126.' mla: Cohen Steiner, David, et al. Vines and Vineyards by Updating Persistence in Linear Time. ACM, 2006, pp. 119–26, doi:10.1145/1137856.1137877. short: D. Cohen Steiner, H. Edelsbrunner, D. Morozov, in:, ACM, 2006, pp. 119–126. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:03:58Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:44:18Z day: '01' doi: 10.1145/1137856.1137877 extern: 1 month: '06' page: 119 - 126 publication_status: published publisher: ACM publist_id: '2826' quality_controlled: 0 status: public title: Vines and vineyards by updating persistence in linear time type: conference year: '2006' ... --- _id: '3560' abstract: - lang: eng text: We continue the study of topological persistence [5] by investigat- ing the problem of simplifying a function f in a way that removes topological noise as determined by its persistence diagram [2]. To state our results, we call a function g an ε-simplification of another function f if ∥f − g∥∞ ≤ ε, and the persistence diagrams of g are the same as those of f except all points within L1-distance at most ε from the diagonal have been removed. We prove that for func- tions f on a 2-manifold such ε-simplification exists, and we give an algorithm to construct them in the piecewise linear case. acknowledgement: Partially supported by NSF under grant CCR-00-86013, by DARPA under grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under grant B543154. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Edelsbrunner H, Morozov D, Pascucci V. Persistence-sensitive simplification of functions on 2-manifolds. In: ACM; 2006:127-134. doi:10.1145/1137856.1137878' apa: 'Edelsbrunner, H., Morozov, D., & Pascucci, V. (2006). Persistence-sensitive simplification of functions on 2-manifolds (pp. 127–134). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137878' chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Valerio Pascucci. “Persistence-Sensitive Simplification of Functions on 2-Manifolds,” 127–34. ACM, 2006. https://doi.org/10.1145/1137856.1137878. ieee: 'H. Edelsbrunner, D. Morozov, and V. Pascucci, “Persistence-sensitive simplification of functions on 2-manifolds,” presented at the SCG: Symposium on Computational Geometry, 2006, pp. 127–134.' ista: 'Edelsbrunner H, Morozov D, Pascucci V. 2006. Persistence-sensitive simplification of functions on 2-manifolds. SCG: Symposium on Computational Geometry, 127–134.' mla: Edelsbrunner, Herbert, et al. Persistence-Sensitive Simplification of Functions on 2-Manifolds. ACM, 2006, pp. 127–34, doi:10.1145/1137856.1137878. short: H. Edelsbrunner, D. Morozov, V. Pascucci, in:, ACM, 2006, pp. 127–134. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:03:58Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:44:19Z day: '01' doi: 10.1145/1137856.1137878 extern: 1 main_file_link: - open_access: '0' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.4465 month: '06' page: 127 - 134 publication_status: published publisher: ACM publist_id: '2825' quality_controlled: 0 status: public title: Persistence-sensitive simplification of functions on 2-manifolds type: conference year: '2006' ... --- _id: '3594' author: - first_name: Josephine full_name: Pemberton, Josephine M last_name: Pemberton - first_name: Graeme full_name: Swanson, Graeme M last_name: Swanson - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Suzanne full_name: Livingstone, Suzanne R last_name: Livingstone - first_name: Helen full_name: Senn, Helen V last_name: Senn citation: ama: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. Hybridisation between red and sika deer in Scotland. Deer. 2006;13(9):22-26. apa: Pemberton, J., Swanson, G., Barton, N. H., Livingstone, S., & Senn, H. (2006). Hybridisation between red and sika deer in Scotland. Deer. BDS . chicago: Pemberton, Josephine, Graeme Swanson, Nicholas H Barton, Suzanne Livingstone, and Helen Senn. “Hybridisation between Red and Sika Deer in Scotland.” Deer. BDS , 2006. ieee: J. Pemberton, G. Swanson, N. H. Barton, S. Livingstone, and H. Senn, “Hybridisation between red and sika deer in Scotland,” Deer, vol. 13, no. 9. BDS , pp. 22–26, 2006. ista: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. 2006. Hybridisation between red and sika deer in Scotland. Deer. 13(9), 22–26. mla: Pemberton, Josephine, et al. “Hybridisation between Red and Sika Deer in Scotland.” Deer, vol. 13, no. 9, BDS , 2006, pp. 22–26. short: J. Pemberton, G. Swanson, N.H. Barton, S. Livingstone, H. Senn, Deer 13 (2006) 22–26. date_created: 2018-12-11T12:04:08Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:31Z day: '01' extern: 1 intvolume: ' 13' issue: '9' month: '01' page: 22 - 26 publication: Deer publication_status: published publisher: 'BDS ' publist_id: '2789' quality_controlled: 0 status: public title: Hybridisation between red and sika deer in Scotland type: review volume: 13 year: '2006' ...