TY - JOUR
AB - Although the X chromosome is usually similar to the autosomes in size and cytogenetic appearance, theoretical models predict that its hemizygosity in males may cause unusual patterns of evolution. The sequencing of several genomes has indeed revealed differences between the X chromosome and the autosomes in the rates of gene divergence, patterns of gene expression and rates of gene movement between chromosomes. A better understanding of these patterns should provide valuable information on the evolution of genes located on the X chromosome. It could also suggest solutions to more general problems in molecular evolution, such as detecting selection and estimating mutational effects on fitness
AU - Beatriz Vicoso
AU - Charlesworth, Brian
ID - 2066
IS - 8
JF - Nature Reviews Genetics
TI - Evolution on the X chromosome: Unusual patterns and processes
VL - 7
ER -
TY - CONF
AB - We present an adaptive animation method for electrical discharges. Electrical discharges can be simulated using the dielectric breakdown model. Regular discretization of the governing Laplace equation leads to huge equation systems, and the computational cost of solving the equations quickly becomes prohibitive at high resolutions, especially for simulations in 3D. In contrast, our method discretizes the Laplace equation on an adaptive octree, reducing the size of the problem significantly, and making simulations of high resolution 3D datasets and even 3D animations feasible. In order to enhance realism for lightning animations, we propose a particle simulation that animates the residual positive charge. Thus, interaction of electrical discharges with their surroundings
can be simulated.
AU - Bernd Bickel
AU - Wicke, Martin
AU - Gross, Markus
ID - 2077
TI - Adaptive simulation of electrical discharges
ER -
TY - CONF
AB - We have measured 3D face geometry, skin reflectance, and subsurface scattering using custom-built devices for 149 subjects of varying age, gender, and race. We developed a novel skin reflectance model whose parameters can be estimated from measurements. The model decomposes the large amount of measured skin data into a spatially-varying analytic BRDF, a diffuse albedo map, and diffuse subsurface scattering. Our model is intuitive, physically plausible, and - since we do not use the original measured data - easy to edit as well. High-quality renderings come close to reproducing real photographs. The analysis of the model parameters for our sample population reveals variations according to subject age, gender, skin type, and external factors (e.g., sweat, cold, or makeup). Using our statistics, a user can edit the overall appearance of a face (e.g., changing skin type and age) or change small-scale features using texture synthesis (e.g., adding moles and freckles). We are making the collected statistics publicly available to the research community for applications in face synthesis and analysis.
AU - Weyrich, Tim
AU - Matusik, Wojciech
AU - Pfister, Hanspeter
AU - Bernd Bickel
AU - Donner, Craig
AU - Tu, Chien
AU - McAndless, Janet M
AU - Lee, Jinho
AU - Ngan, Addy
AU - Jensen, Henrik W
AU - Groß, Markus S
ID - 2088
TI - Analysis of human faces using a measurement-based skin reflectance model
ER -
TY - JOUR
AB - We have measured 3D face geometry, skin reflectance, and subsurface scattering using custom-built devices for 149 subjects of varying age, gender, and race. We developed a novel skin reflectance model whose parameters can be estimated from measurements. The model decomposes the large amount of measured skin data into a spatially-varying analytic BRDF, a diffuse albedo map, and diffuse subsurface scattering. Our model is intuitive, physically plausible, and - since we do not use the original measured data - easy to edit as well. High-quality renderings come close to reproducing real photographs. The analysis of the model parameters for our sample population reveals variations according to subject age, gender, skin type, and external factors (e.g., sweat, cold, or makeup). Using our statistics, a user can edit the overall appearance of a face (e.g., changing skin type and age) or change small-scale features using texture synthesis (e.g., adding moles and freckles). We are making the collected statistics publicly available to the research community for applications in face synthesis and analysis.
AU - Weyrich, Tim
AU - Matusik, Wojciech
AU - Pfister, Hanspeter
AU - Bernd Bickel
AU - Donner, Craig
AU - Tu, Chien
AU - McAndless, Janet M
AU - Lee, Jinho
AU - Ngan, Addy
AU - Jensen, Henrik W
AU - Groß, Markus S
ID - 2089
IS - 3
JF - ACM Transactions on Graphics
TI - Analysis of human faces using a measurement-based skin reflectance model
VL - 25
ER -
TY - CONF
AU - Bernd Bickel
AU - Weyrich, Tim
AU - Matusik, Wojciech
AU - Pfister, Hanspeter
AU - Donner, Craig
AU - Tu, Chien
AU - McAndless, Janet M
AU - Lee, Jinho
AU - Ngan, Addy
AU - Jensen, Henrik W
AU - Groß, Markus S
ID - 2090
TI - Processing and editing of faces using a measurement-based skin reflectance model
ER -
TY - JOUR
AB - 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).
AU - Timothy Browning
AU - Heath-Brown, Roger
AU - Starr, Jason M
ID - 213
IS - 2
JF - Proceedings of the London Mathematical Society
TI - The density of rational points on non-singular hypersurfaces, II
VL - 93
ER -
TY - JOUR
AB - 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.
AU - Ehresmann, Arno
AU - Werner, Lutz
AU - Klumpp, Stefan
AU - Demekhin, Ph V
AU - Mikhail Lemeshko
AU - Sukhorukov, V. L
AU - Schartner, Karl H
AU - Schmoranzer, Hans P
ID - 2134
IS - 6
JF - Journal of Physics B: Atomic, Molecular and Optical Physics
TI - 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
VL - 39
ER -
TY - JOUR
AB - 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'').
AU - Ehresmann, Arno
AU - Werner, Lutz
AU - Klumpp, Stefan
AU - Lucht, S
AU - Schmoranzer, Hans P
AU - Mickat, Sascha
AU - Schill, Rüdiger H
AU - Schartner, Karl H
AU - Demekhin, Philipp
AU - Mikhail Lemeshko
AU - Sukhorukov, Victor L
ID - 2142
IS - 2
JF - Journal of Physics B: Atomic, Molecular and Optical Physics
TI - Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance
VL - 39
ER -
TY - JOUR
AB - 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.
AU - Vedrinskiǐ, Rostislav V
AU - Nazarenko, Elena S
AU - Mikhail Lemeshko
AU - Nassif, Vivian M
AU - Proux, Olivier
AU - Novakovich, Alexander A
AU - Joly, Yves
ID - 2144
IS - 13
JF - Physical Review B - Condensed Matter and Materials Physics
TI - Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates
VL - 73
ER -
TY - JOUR
AB - 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.*
AU - Timothy Browning
AU - Heath-Brown, Roger
ID - 215
IS - 3
JF - Bulletin of the London Mathematical Society
TI - The density of rational points on non-singular hypersurfaces, I
VL - 38
ER -
TY - JOUR
AB - 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.
AU - Timothy Browning
AU - Heath-Brown, Roger
AU - Salberger, Per
ID - 216
IS - 3
JF - Duke Mathematical Journal
TI - Counting rational points on algebraic varieties
VL - 132
ER -
TY - JOUR
AB - This paper is concerned with the average order of certain arithmetic functions, as they range over the values taken by binary forms.
AU - de la Bretèche, Régis
AU - Timothy Browning
ID - 218
IS - 3
JF - Acta Arithmetica
TI - Sums of arithmetic functions over values of binary forms
VL - 125
ER -
TY - CONF
AU - Lieb, Élliott H
AU - Robert Seiringer
AU - Solovej, Jan P
ID - 2333
TI - Ground-state energy of a dilute Fermi gas
VL - 412
ER -
TY - CONF
AU - Robert Seiringer
AU - Lieb, Élliott H
AU - Yngvason, Jakob
ED - Zambrini, Jean-Claude
ID - 2334
TI - One-dimensional behavior of dilute, trapped Bose gases in traps
ER -
TY - GEN
AB - 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.
AU - Lieb, Élliott H
AU - Robert Seiringer
ID - 2363
IS - 2
T2 - Communications in Mathematical Physics
TI - Derivation of the Gross-Pitaevskii equation for rotating Bose gases
VL - 264
ER -
TY - JOUR
AB - 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.
AU - Robert Seiringer
ID - 2364
IS - 3
JF - Reviews in Mathematical Physics
TI - A correlation estimate for quantum many-body systems at positive temperature
VL - 18
ER -
TY - JOUR
AB - 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.
AU - Robert Seiringer
ID - 2365
IS - 3
JF - Communications in Mathematical Physics
TI - The thermodynamic pressure of a dilute fermi gas
VL - 261
ER -
TY - JOUR
AB - 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.
AU - Frank, Rupert L
AU - Laptev, Ari
AU - Lieb, Élliott H
AU - Robert Seiringer
ID - 2366
IS - 3
JF - Letters in Mathematical Physics
TI - Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials
VL - 77
ER -
TY - CHAP
AB - 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.
AU - Robert Seiringer
ED - Dereziński, Jan
ED - Siedentop, Heinz
ID - 2368
T2 - Large Coulomb Systems
TI - Dilute, trapped Bose gases and Bose-Einstein condensation
VL - 695
ER -
TY - CHAP
AB - 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.
AU - Aizenman, Michael
AU - Lieb, Élliott H
AU - Robert Seiringer
AU - Solovej, Jan P
AU - Yngvason, Jakob
ED - Asch, Joachim
ED - Joye, Alain
ID - 2369
T2 - Mathematical Physics of Quantum Mechanics
TI - Bose-Einstein condensation as a quantum phase transition in an optical lattice
VL - 690
ER -
TY - CHAP
AU - Bang-Jensen, Jørgen
AU - Reed, Bruce
AU - Schacht, Bruce
AU - Šámal, Robert
AU - Toft, Bjarne
AU - Uli Wagner
ID - 2416
T2 - Topics in Discrete Mathematics
TI - On six problems posed by Jarik Nešetřil
VL - 26
ER -
TY - JOUR
AB - 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.
AU - Matoušek, Jiří
AU - Sharir, Micha
AU - Smorodinsky, Shakhar
AU - Uli Wagner
ID - 2429
IS - 2
JF - Discrete & Computational Geometry
TI - K-sets in four dimensions
VL - 35
ER -
TY - JOUR
AB - 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.
AU - Chent, Ke
AU - Fiat, Amos
AU - Kaplan, Haim
AU - Levy, Meital B
AU - Matoušek, Jiří
AU - Mossel, Elchanan
AU - Pach, János
AU - Sharir, Micha
AU - Smorodinsky, Shakhar
AU - Uli Wagner
AU - Welzl, Emo
ID - 2430
IS - 5
JF - SIAM Journal on Computing
TI - Online conflict-free coloring for intervals
VL - 36
ER -
TY - CONF
AB - 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.
AU - Uli Wagner
ID - 2431
TI - On a geometric generalization of the Upper Bound Theorem
ER -
TY - CONF
AB - Often the properties of a single cell are considered as representative for a complete polymer electrolyte fuel cell stack or even a fuel cell system. In some cases this comes close, however, in many real cases differences on several scales become important. Cell interaction phenomena in fuel cell stacks that arise from inequalities between adjacent cells are investigated in detail experimentally. For that, a specialized 2-cell stack with advanced localized diagnostics was developed. The results show that inequalities propagate by electrical coupling, inhomogeneous cell polarization and inducing in-plane current in the common bipolar plate. The effects of the different loss-mechanisms are analyzed and quantified.
AU - Büchi, Felix N.
AU - Freunberger, Stefan Alexander
AU - Santis, Marco
ID - 7326
IS - 1
T2 - ECS Transactions
TI - What is learned beyond the scale of single cells?
VL - 3
ER -
TY - JOUR
AB - Propagation of performance changes to adjacent cells in polymer electrolyte fuel cell stacks is studied by means of voltage monitoring and local current density measurements in peripheral cells of the stack. A technical fuel cell stack has been modified by implementing two independent reactant and coolant supplies in order to deliberately change the performance of one cell (anomalous cell) and study the coupling phenomena to adjacent cells (coupling cells), while keeping the working conditions of the later cell-group unaltered.
Two anomalies are studied: (i) air starvation and (ii) thermal anomaly, in a single anomalous cell in the stack and their coupling to adjacent cells. The results have shown that anomalies inducing considerable changes in the local current density of the anomalous cell (such as air starvation) propagate to adjacent cells affecting their performance. The propagation of local current density changes takes place via the common bipolar plate due to its finite thickness and in-plane conductivity. Consequently, anomalies which do not strongly influence the local current density distribution (such as a thermal anomaly under the studied working conditions) do not propagate to adjacent cells.
AU - Santis, Marco
AU - Freunberger, Stefan Alexander
AU - Papra, Matthias
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7327
IS - 2
JF - Journal of Power Sources
SN - 0378-7753
TI - Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks
VL - 161
ER -
TY - JOUR
AB - An experimental technique for measuring the current density distribution with a resolution smaller than the channel/rib scale of the flow field in polymer electrolyte fuel cells (PEFCs) is presented. The electron conductors in a plane perpendicular to the channel direction are considered as two-dimensional resistors. Hence, the current density is obtained from the solution of Laplace's equation with the potentials at current collector and reaction layer as boundary conditions. Using ohmic drop for calculating the local current, detailed knowledge of all resistances involved is of prime importance. In particular, the contact resistance between the gas diffusion layer (GDL) and flow field rib, as well as GDL bulk conductivity, are strongly dependent on clamping pressure. They represent a substantial amount of the total ohmic drop and therefore require careful consideration. The detailed experimental setup as well as the concise procedure for quantitative data evaluation is described. Finally, the method is applied successfully to a cell operated on pure oxygen and air up to high current densities. The results show that electrical and ionic resistances seem to govern the current distribution at low current regimes, whereas mass transport limitations locally hamper the current production at high loads.
AU - Freunberger, Stefan Alexander
AU - Reum, Mathias
AU - Evertz, Jörg
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7328
IS - 11
JF - Journal of The Electrochemical Society
SN - 0013-4651
TI - Measuring the current distribution in PEFCs with sub-millimeter resolution
VL - 153
ER -
TY - JOUR
AB - A novel measurement principle for measuring the current distribution in polymer electrolyte fuel cells (PEFCs) is introduced. It allows, in contrast to all other known techniques, for the first time for a resolution smaller than the channel/rib scale of the flow field in PEFCs. The current density is obtained by considering the electron conductors in the cell as a two-dimensional resistor with the voltage drop caused by the current. The method was applied to a cell operated on oxygen up to high current densities. The results show that the ohmic resistances govern the current distribution in the low current regime, whereas mass transport limitations hamper the current production under the land at high loads.
AU - Freunberger, Stefan Alexander
AU - Reum, Mathias
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7329
IS - 9
JF - Electrochemistry Communications
SN - 1388-2481
TI - Expanding current distribution measurement in PEFCs to sub-millimeter resolution
VL - 8
ER -
TY - JOUR
AB - Polymer electrolyte fuel cells (PE fuel cells) working with air at low stoichiometries (<2.0) and standard electrochemical components show a high degree of inhomogeneity in the current density distribution over the active area. An inhomogeneous current density distribution leads to a non-uniform utilization of the active area, which could negatively affect the time of life of the cells. Furthermore, it is also believed to lower cell performance. In this work, the homogenization of the current density, realized by means of tailored cathodes with along-the-air-channel redistributed catalyst loadings, is investigated. The air stoichiometry range for which a homogenization of the current density is achieved depends upon the gradient with which the catalyst is redistributed along the air channel. A gentle increasing catalyst loading profile homogenizes the current density at relatively higher air stoichiometries, while a steeper profile is suited better for lower air stoichiometries. The results show that a homogenization of the current density by means of redistributed catalyst loading has negative effects on cell performance. Model calculations corroborate the experimental findings on homogenization of the current density and deliver an explanation for the decrease in cell performance.
AU - Santis, M.
AU - Freunberger, Stefan Alexander
AU - Reiner, A.
AU - Büchi, F.N.
ID - 7330
IS - 25
JF - Electrochimica Acta
SN - 0013-4686
TI - Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients
VL - 51
ER -
TY - JOUR
AB - A previously developed mathematical model for water management and current density distribution in a polymer electrolyte fuel cell (PEFCs) is employed to investigate the effects of cooling strategies on cell performance. The model describes a two-dimensional slice through the cell along the channels and through the entire cell sandwich including the coolant channels and the bipolar plate. Arbitrary flow arrangements of fuel, oxidant, and coolant stream directions can be described. Due to the serious impact of temperature on all processes in the PEFC, both the relative direction of the coolant stream to the gas streams and its mass flow turns out to significantly affect the cell performance. Besides influencing the electrochemical reaction and all kinds of mass transfer temperature, variations predominantly alter the local membrane hydration distribution and subseqently its conductivity.
AU - Freunberger, Stefan Alexander
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7331
IS - 5
JF - Journal of The Electrochemical Society
SN - 0013-4651
TI - In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance
VL - 153
ER -
TY - JOUR
AB - A quasi-two-dimensional, along-the-channel mass and heat-transfer model for a proton exchange membrane fuel cell (PEFC) is described and validated against experimental current distribution data. The model is formulated in a dimensional manner, i.e., local transport phenomena are treated one-dimensional in through-plane direction and coupled in-plane by convective transport in the gas and coolant channels. Thus, a two-dimensional slice running through the repetitive unit of a cell from the anode channel via membrane-electrode assembly (MEA) and cathode channel to the coolant channel and from inlet to outlet is modeled. The aim of the work is to elucidate the influence of operating conditions such as feed gas humidities and stoichiometric ratios on the along-the-channel current density distribution and to identify the distinct underlying voltage loss mechanisms. Furthermore, a complicated technical flow field is modeled by a combination of co- and counterflow subdomains and compared with experimental current densities.
AU - Freunberger, Stefan Alexander
AU - Santis, Marco
AU - Schneider, Ingo A.
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7332
IS - 2
JF - Journal of The Electrochemical Society
SN - 0013-4651
TI - In-plane effects in large-scale PEMFCs
VL - 153
ER -
TY - JOUR
AB - It is commonly believed that both the average length and the frequency of microsatellites correlate with genome size. We have estimated the frequency and the average length for 69 perfect dinucleotide microsatellites in an insect with an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae). Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat arrays are 1.4 to 2 times longer than in other insect species. The average repeat number in C. biguttulus lies in the range of higher vertebrates. Natural populations are highly variable. At least 30 alleles per locus were found and the expected heterozygosity is above 0.95 at all three loci studied. In contrast, the observed heterozygosity is much lower (≤0.51), which could be caused by long null alleles.
AU - Ustinova, Jana
AU - Achmann, Roland
AU - Cremer, Sylvia
AU - Mayer, Frieder
ID - 3908
IS - 2
JF - Journal of Molecular Evolution
TI - Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus
VL - 62
ER -
TY - JOUR
AB - 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.
AU - Cremer, Sylvia
AU - Ugelvig, Line V
AU - Lommen, Suzanne
AU - Petersen, Klaus
AU - Pedersen, Jes
ID - 3912
JF - Myrmecological News
TI - Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain
VL - 9
ER -
TY - JOUR
AB - 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.
AU - Heinze, Jürgen
AU - Cremer, Sylvia
AU - Eckl, Norbert
AU - Schrempf, Alexandra
ID - 3913
IS - 1
JF - Insectes Sociaux
TI - Stealthy invaders: the biology of Cardiocondyla tramp ants
VL - 53
ER -
TY - JOUR
AB - 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.
AU - Moder, Karl
AU - Schlick Steiner, Birgit
AU - Steiner, Florian
AU - Cremer, Sylvia
AU - Christian, Erhard
AU - Seifert, Bernhard
ID - 3914
IS - 1
JF - Journal of Zoological Systematics and Evolutionary Research
TI - Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study
VL - 45
ER -
TY - JOUR
AB - 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.
AU - Henic, Emir
AU - Michael Sixt
AU - Hansson, Stefan
AU - Høyer-Hansen, Gunilla
AU - Casslén, Bertil
ID - 3932
IS - 1
JF - Gynecologic Oncology
TI - EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor
VL - 101
ER -
TY - JOUR
AB - T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla.
AU - Drumea-Mirancea, Mihaela
AU - Wessels, Johannes T
AU - Müller, Claudia A
AU - Essl, Mike
AU - Eble, Johannes A
AU - Tolosa, Eva
AU - Koch, Manuel
AU - Reinhardt, Dieter P
AU - Michael Sixt
AU - Sorokin, Lydia
AU - Stierhof, York-Dieter
AU - Schwarz, Heinz
AU - Klein, Gerd
ID - 3934
IS - Pt 7
JF - Journal of Cell Science
TI - Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules
VL - 119
ER -
TY - JOUR
AB - Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis.
AU - Chu, Haiyan
AU - Thievessen, Ingo
AU - Michael Sixt
AU - Lämmermann, Tim
AU - Waisman, Ari
AU - Braun, Attila
AU - Noegel, Angelika A
AU - Fässler, Reinhard
ID - 3935
IS - 5
JF - Molecular and Cellular Biology
TI - γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response
VL - 26
ER -
TY - JOUR
AB - At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials.
AU - Michael Sixt
AU - Bauer, Martina
AU - Lämmermann, Tim
AU - Fässler, Reinhard
ID - 3936
IS - 5
JF - Current Opinion in Cell Biology
TI - β1 integrins: zip codes and signaling relay for blood cells
VL - 18
ER -
TY - JOUR
AB - 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.
AU - Ban, Yih-En Andrew
AU - Rudolph, Johannes
AU - Zhou, Pei
AU - Herbert Edelsbrunner
ID - 3978
IS - 4
JF - Proteins: Structure, Function and Bioinformatics
TI - Evaluating the quality of NMR structures by local density of protons
VL - 62
ER -
TY - JOUR
AB - 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.
AU - Ban, Yih-En Andrew
AU - Herbert Edelsbrunner
AU - Rudolph, Johannes
ID - 3979
IS - 3
JF - Journal of the ACM
TI - Interface surfaces for protein-protein complexes
VL - 53
ER -
TY - JOUR
AB - 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.
AU - Agarwal, Pankaj K
AU - Herbert Edelsbrunner
AU - Harer, John
AU - Wang, Yusu
ID - 3980
IS - 4
JF - Discrete & Computational Geometry
TI - Extreme elevation on a 2-manifold
VL - 36
ER -
TY - JOUR
AB - Wnt11 is a key signal, determining cell polarization and migration during vertebrate gastrulation. It is known that Wnt11 functionally interacts with several signaling components, the homologues of which control planar cell polarity in Drosophila melanogaster. Although in D. melanogaster these components are thought to polarize cells by asymmetrically localizing at the plasma membrane, it is not yet clear whether their subcellular localization plays a similarly important role in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation.
AU - Witzel, Sabine
AU - Zimyanin, Vitaly
AU - Carreira-Barbosa, Filipa
AU - Tada, Masazumi
AU - Heisenberg, Carl-Philipp
ID - 4140
IS - 5
JF - Journal of Cell Biology
TI - Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane
VL - 175
ER -
TY - JOUR
AB - The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development.
AU - Tonelli, Davide D
AU - Calegari, Frederico
AU - Fei, Ji-Feng
AU - Nomura, Tadashi
AU - Osumi, Noriko
AU - Heisenberg, Carl-Philipp
AU - Huttner, Wieland B
ID - 4145
IS - 6
JF - Biotechniques
TI - Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid
VL - 41
ER -
TY - JOUR
AB - Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.
AU - Link, Vinzenz
AU - Shevchenko, Andrej
AU - Heisenberg, Carl-Philipp
ID - 4173
JF - BMC Developmental Biology
TI - Proteomics of early zebrafish embryos
VL - 6
ER -
TY - JOUR
AB - During vertebrate gastrulation, a well-orchestrated series of morphogenetic changes leads to the formation of the three germ layers: the ectoderm, mesoderm and endoderm. The analysis of gene expression patterns during gastrulation has been central to the identification of genes involved in germ layer formation. However, many proteins are regulated on a translational or post-translational level and are thus undetectable by gene expression analysis. Therefore, we developed a 2D-gel-based comparative proteomic approach to target proteins involved in germ layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and mesendodermal progenitor cells were compared and 35 significantly regulated proteins were identified by mass spectrometry, including several proteins with predicted functions in cytoskeletal organization. A comparison of our proteomic results with data obtained in an accompanying microarray-based gene expression analysis revealed no significant overlap, confirming the complementary nature of proteomics and transcriptomics. The regulation of ezrin2, which was identified based on a reduction in spot intensity in mesendodermal cells, was independently validated. Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal cells and is required for proper germ layer morphogenesis. We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development.
AU - Link, Vinzenz
AU - Carvalho,Lara
AU - Castanon, Irinka
AU - Stockinger, Petra
AU - Shevchenko, Andrej
AU - Heisenberg, Carl-Philipp
ID - 4176
IS - 10
JF - Journal of Cell Science
TI - Identification of regulators of germ layer morphogenesis using proteomics in zebrafish
VL - 119
ER -
TY - JOUR
AB - Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools.
AU - Langenberg, Tobias
AU - Dracz, Tadeusz
AU - Oates, Andrew C
AU - Heisenberg, Carl-Philipp
AU - Brand, Michael
ID - 4178
IS - 4
JF - Developmental Dynamics
TI - Analysis and visualization of cell movement in the developing zebrafish brain
VL - 235
ER -
TY - JOUR
AB - Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis.
AU - Köppen, Mathias
AU - Fernández, Beatriz García
AU - Carvalho,Lara
AU - Jacinto, António
AU - Heisenberg, Carl-Philipp
ID - 4184
IS - 14
JF - Development
TI - Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila
VL - 133
ER -
TY - JOUR
AB - The molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration.
AU - Blaser, Heiko
AU - Reichman-Fried, Michal
AU - Castanon, Irinka
AU - Dumstrei, Karin
AU - Marlow, Florence L
AU - Kawakami, Koichi
AU - Solnica-Krezel, Lilianna
AU - Heisenberg, Carl-Philipp
AU - Raz, Erez
ID - 4218
IS - 5
JF - Developmental Cell
TI - Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow
VL - 11
ER -
TY - JOUR
AU - Harold Vladar
AU - González,J. A
ID - 4235
JF - Journal of Theoretical Biology
TI - Dynamic response of cancer under the influence of immunological activity and therapy
ER -
TY - JOUR
AB - The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the Population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population. (c) 2005 Elsevier Ltd. All rights reserved.
AU - de Vladar,Harold Paul
ID - 4237
IS - 2
JF - Journal of Theoretical Biology
TI - Density-dependence as a size-independent regulatory mechanism
VL - 238
ER -
TY - JOUR
AB - In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson effect” generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.
AU - Roze, Denis
AU - Nicholas Barton
ID - 4248
IS - 3
JF - Genetics
TI - The Hill-Robertson effect and the evolution of recombination
VL - 173
ER -
TY - GEN
AB - A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with ‘hybridisation’ between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation.
AU - Nicholas Barton
ID - 4250
IS - 16
T2 - Current Biology
TI - Evolutionary Biology: How did the human species form?
VL - 16
ER -
TY - JOUR
AB - 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.
AU - Patrick Danowski
AU - Heller,Lambert
ID - 4345
IS - 11
JF - Bibliotheksdienst
TI - Bibliothek 2.0 - Die Bibliothek der Zukunft?
VL - 40
ER -
TY - JOUR
AB - 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.
AU - Jonathan Bollback
ID - 4351
JF - BMC Bioinformatics
TI - SIMMAP: stochastic character mapping of discrete traits on phylogenies
VL - 7
ER -
TY - JOUR
AB - 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.
AU - Conn, Jan E
AU - Vineis, Joseph H
AU - Jonathan Bollback
AU - Onyabe, David Y
AU - Wilkerson, Richard C
AU - Povoa, Marinete M
ID - 4352
IS - 5
JF - The American Journal of Tropical Medicine and Hygiene
TI - Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil
VL - 74
ER -
TY - CONF
AU - Thomas Wies
AU - Kuncak, Viktor
AU - Lam,Patrick
AU - Podelski,Andreas
AU - Rinard,Martin
ID - 4359
TI - Field Constraint Analysis
ER -
TY - CONF
AU - Maler, Oded
AU - Dejan Nickovic
AU - Pnueli,Amir
ID - 4373
TI - Real Time Temporal Logic: Past, Present, Future
ER -
TY - CONF
AU - Maler, Oded
AU - Dejan Nickovic
AU - Pnueli,Amir
ID - 4374
TI - From MITL to Timed Automata
ER -
TY - CONF
AU - Alur, Rajeev
AU - Pavol Cerny
AU - Zdancewic,Steve
ID - 4401
TI - Preserving Secrecy Under Refinement
ER -
TY - CONF
AB - We propose and evaluate a new algorithm for checking the universality of nondeterministic finite automata. In contrast to the standard algorithm, which uses the subset construction to explicitly determinize the automaton, we keep the determinization step implicit. Our algorithm computes the least fixed point of a monotone function on the lattice of antichains of state sets. We evaluate the performance of our algorithm experimentally using the random automaton model recently proposed by Tabakov and Vardi. We show that on the difficult instances of this probabilistic model, the antichain algorithm outperforms the standard one by several orders of magnitude. We also show how variations of the antichain method can be used for solving the language-inclusion problem for nondeterministic finite automata, and the emptiness problem for alternating finite automata.
AU - De Wulf, Martin
AU - Doyen, Laurent
AU - Thomas Henzinger
AU - Raskin, Jean-François
ID - 4406
TI - Antichains: A new algorithm for checking universality of finite automata
VL - 4144
ER -
TY - CONF
AB - We summarize some current trends in embedded systems design and point out some of their characteristics, such as the chasm between analytical and computational models, and the gap between safety-critical and best-effort engineering practices. We call for a coherent scientific foundation for embedded systems design, and we discuss a few key demands on such a foundation: the need for encompassing several manifestations of heterogeneity, and the need for constructivity in design. We believe that the development of a satisfactory Embedded Systems Design Science provides a timely challenge and opportunity for reinvigorating computer science.
AU - Thomas Henzinger
AU - Sifakis, Joseph
ID - 4431
TI - The embedded systems design challenge
VL - 4085
ER -
TY - CONF
AB - We add freeze quantifiers to the game logic ATL in order to specify real-time objectives for games played on timed structures. We define the semantics of the resulting logic TATL by restricting the players to physically meaningful strategies, which do not prevent time from diverging. We show that TATL can be model checked over timed automaton games. We also specify timed optimization problems for physically meaningful strategies, and we show that for timed automaton games, the optimal answers can be approximated to within any degree of precision.
AU - Thomas Henzinger
AU - Prabhu, Vinayak S
ID - 4432
TI - Timed alternating-time temporal logic
VL - 4202
ER -
TY - CONF
AB - We present an assume-guarantee interface algebra for real-time components. In our formalism a component implements a set of task sequences that share a resource. A component interface consists of an arrival rate function and a latency for each task sequence, and a capacity function for the shared resource. The interface specifies that the component guarantees certain task latencies depending on assumptions about task arrival rates and allocated resource capacities. Our algebra defines compatibility and refinement relations on interfaces. Interface compatibility can be checked on partial designs, even when some component interfaces are yet unknown. In this case interface composition computes as new assumptions the weakest constraints on the unknown components that are necessary to satisfy the specified guarantees. Interface refinement is defined in a way that ensures that compatible interfaces can be refined and implemented independently. Our algebra thus formalizes an interface-based design methodology that supports both the incremental addition of new components and the independent stepwise refinement of existing components. We demonstrate the flexibility and efficiency of the framework through simulation experiments.
AU - Thomas Henzinger
AU - Matic, Slobodan
ID - 4436
TI - An interface algebra for real-time components
ER -
TY - CONF
AB - The synthesis of reactive systems requires the solution of two-player games on graphs with ω-regular objectives. When the objective is specified by a linear temporal logic formula or nondeterministic Büchi automaton, then previous algorithms for solving the game require the construction of an equivalent deterministic automaton. However, determinization for automata on infinite words is extremely complicated, and current implementations fail to produce deterministic automata even for relatively small inputs. We show how to construct, from a given nondeterministic Büchi automaton, an equivalent nondeterministic parity automaton that is good for solving games with objective . The main insight is that a nondeterministic automaton is good for solving games if it fairly simulates the equivalent deterministic automaton. In this way, we omit the determinization step in game solving and reactive synthesis. The fact that our automata are nondeterministic makes them surprisingly simple, amenable to symbolic implementation, and allows an incremental search for winning strategies.
AU - Thomas Henzinger
AU - Piterman, Nir
ID - 4437
TI - Solving games without determinization
VL - 4207
ER -
TY - JOUR
AB - One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternation-free fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment.
AU - Thomas Henzinger
AU - Kupferman, Orna
AU - Majumdar, Ritankar S
ID - 4451
IS - 2
JF - Theoretical Computer Science
TI - On the universal and existential fragments of the mu-calculus
VL - 354
ER -
TY - CONF
AB - We consider the problem if a given program satisfies a specified safety property. Interesting programs have infinite state spaces, with inputs ranging over infinite domains, and for these programs the property checking problem is undecidable. Two broad approaches to property checking are testing and verification. Testing tries to find inputs and executions which demonstrate violations of the property. Verification tries to construct a formal proof which shows that all executions of the program satisfy the property. Testing works best when errors are easy to find, but it is often difficult to achieve sufficient coverage for correct programs. On the other hand, verification methods are most successful when proofs are easy to find, but they are often inefficient at discovering errors. We propose a new algorithm, Synergy, which combines testing and verification. Synergy unifies several ideas from the literature, including counterexample-guided model checking, directed testing, and partition refinement.This paper presents a description of the Synergy algorithm, its theoretical properties, a comparison with related algorithms, and a prototype implementation called Yogi.
AU - Gulavani, Bhargav S
AU - Thomas Henzinger
AU - Kannan, Yamini
AU - Nori, Aditya V
AU - Rajamani, Sriram K
ID - 4523
TI - Synergy: A new algorithm for property checking
ER -
TY - CONF
AB - We designed and implemented a new programming language called Hierarchical Timing Language (HTL) for hard realtime systems. Critical timing constraints are specified within the language,and ensured by the compiler. Programs in HTL are extensible in two dimensions without changing their timing behavior: new program modules can be added, and individual program tasks can be refined. The mechanism supporting time invariance under parallel composition is that different program modules communicate at specified instances of time. Time invariance under refinement is achieved by conservative scheduling of the top level. HTL is a coordination language, in that individual tasks can be implemented in "foreign" languages. As a case study, we present a distributed HTL implementation of an automotive steer-by-wire controller.
AU - Ghosal, Arkadeb
AU - Thomas Henzinger
AU - Iercan, Daniel
AU - Kirsch, Christoph M
AU - Sangiovanni-Vincentelli, Alberto
ID - 4526
TI - A hierarchical coordination language for interacting real-time tasks
ER -
TY - CONF
AB - Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models mathematical and computational - according to their different representations of biological phenomena and their diverse potential. We call the approach of constructing computational models of biological systems executable biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline.
AU - Fisher, Jasmin
AU - Thomas Henzinger
ID - 4528
TI - Executable biology
ER -
TY - CONF
AB - A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with ω-regular winning conditions specified as parity objectives. These games lie in NP ∩ coNP. We present a strategy improvement algorithm for stochastic parity games; this is the first non-brute-force algorithm for solving these games. From the strategy improvement algorithm we obtain a randomized subexponential-time algorithm to solve such games.
AU - Krishnendu Chatterjee
AU - Thomas Henzinger
ID - 4538
TI - Strategy improvement and randomized subexponential algorithms for stochastic parity games
VL - 3884
ER -
TY - CONF
AB - Games on graphs with ω-regular objectives provide a model for the control and synthesis of reactive systems. Every ω-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Büchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett (fairness) objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound.
AU - Krishnendu Chatterjee
AU - Thomas Henzinger
ID - 4539
TI - Finitary winning in omega-regular games
VL - 3920
ER -
TY - CONF
AB - We present a compositional theory of system verification, where specifications assign real-numbered costs to systems. These costs can express a wide variety of quantitative system properties, such as resource consumption, price, or a measure of how well a system satisfies its specification. The theory supports the composition of systems and specifications, and the hiding of variables. Boolean refinement relations are replaced by real-numbered distances between descriptions of a system at different levels of detail. We show that the classical Boolean rules for compositional reasoning have quantitative counterparts in our setting. While our general theory allows costs to be specified by arbitrary cost functions, we also consider a class of linear cost functions, which give rise to an instance of our framework where all operations are computable in polynomial time.
AU - Krishnendu Chatterjee
AU - de Alfaro, Luca
AU - Faella, Marco
AU - Thomas Henzinger
AU - Majumdar, Ritankar S
AU - Stoelinga, Mariëlle
ID - 4549
TI - Compositional quantitative reasoning
ER -
TY - JOUR
AB - In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent's payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it sometimes suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of ω-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.
AU - Krishnendu Chatterjee
AU - Thomas Henzinger
AU - Jurdziński, Marcin
ID - 4550
IS - 1-2
JF - Theoretical Computer Science
TI - Games with secure equilibria
VL - 365
ER -
TY - CONF
AB - We consider Markov decision processes (MDPs) with multiple discounted reward objectives. Such MDPs occur in design problems where one wishes to simultaneously optimize several criteria, for example, latency and power. The possible trade-offs between the different objectives are characterized by the Pareto curve. We show that every Pareto-optimal point can be achieved by a memoryless strategy; however, unlike in the single-objective case, the memoryless strategy may require randomization. Moreover, we show that the Pareto curve can be approximated in polynomial time in the size of the MDP. Additionally, we study the problem if a given value vector is realizable by any strategy, and show that it can be decided in polynomial time; but the question whether it is realizable by a deterministic memoryless strategy is NP-complete. These results provide efficient algorithms for design exploration in MDP models with multiple objectives.
This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202.
AU - Krishnendu Chatterjee
AU - Majumdar, Ritankar S
AU - Thomas Henzinger
ID - 4551
TI - Markov decision processes with multiple objectives
VL - 3884
ER -
TY - CONF
AB - A concurrent reachability game is a two-player game played on a graph: at each state, the players simultaneously and independently select moves; the two moves determine jointly a probability distribution over the successor states. The objective for player 1 consists in reaching a set of target states; the objective for player 2 is to prevent this, so that the game is zero-sum. Our contributions are two-fold. First, we present a simple proof of the fact that in concurrent reachability games, for all epsilon > 0, memoryless epsilon-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an epsilon-optimal strategy achieves the objective with probability within epsilon of the value of the game. In contrast to previous proofs of this fact, which rely on the limit behavior of discounted games using advanced Puisieux series analysis, our proof is elementary and combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives.
AU - Krishnendu Chatterjee
AU - de Alfaro, Luca
AU - Thomas Henzinger
ID - 4552
TI - Strategy improvement for concurrent reachability games
ER -
TY - CONF
AB - Many software model checkers are based on predicate abstraction. If the verification goal depends on pointer structures, the approach does not work well, because it is difficult to find adequate predicate abstractions for the heap. In contrast, shape analysis, which uses graph-based heap abstractions, can provide a compact representation of recursive data structures. We integrate shape analysis into the software model checker Blast. Because shape analysis is expensive, we do not apply it globally. Instead, we ensure that, like predicates, shape graphs are computed and stored locally, only where necessary for proving the verification goal. To achieve this, we extend lazy abstraction refinement, which so far has been used only for predicate abstractions, to three-valued logical structures. This approach does not only increase the precision of model checking, but it also increases the efficiency of shape analysis. We implemented the technique by extending Blast with calls to Tvla.
AU - Beyer, Dirk
AU - Thomas Henzinger
AU - Théoduloz, Grégory
ID - 4574
TI - Lazy shape analysis
VL - 4144
ER -
TY - GEN
AB - Mitchison and Jozsa recently suggested that the "chained-Zeno" counterfactual computation protocol recently proposed by Hosten et al. is counterfactual for only one output of the computer. This claim was based on the existing abstract algebraic definition of counterfactual computation, and indeed according to this definition, their argument is correct. However, a more general definition (physically adequate) for counterfactual computation is implicitly assumed by Hosten et. al. Here we explain in detail why the protocol is counterfactual and how the "history tracking" method of the existing description inadequately represents the physics underlying the protocol. Consequently, we propose a modified definition of counterfactual computation. Finally, we comment on one of the most interesting aspects of the error-correcting protocol.
AU - Hosten, Onur
AU - Rakher, Matthew
AU - Barreiro, Julio
AU - Peters, Nicholas
AU - Kwiat, Paul
ID - 573
TI - Counterfactual computation revisited
ER -
TY - GEN
AB - Vaidman, in a recent article adopts the method of 'quantum weak measurements in pre- and postselected ensembles' to ascertain whether or not the chained-Zeno counterfactual computation scheme proposed by Hosten et al. is counterfactual; which has been the topic of a debate on the definition of counterfactuality. We disagree with his conclusion, which brings up some interesting aspects of quantum weak measurements and some concerns about the way they are interpreted.
AU - Hosten, Onur
AU - Kwiat, Paul
ID - 574
TI - Weak measurements and counterfactual computation
ER -
TY - CONF
AB - Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio.
AU - Rangarajan, Radhika
AU - Altepeter, Joseph B
AU - Jeffrey, Evan R
AU - Stoutimore, Micah J
AU - Peters, Nicholas A
AU - Onur Hosten
AU - Kwiat, Paul G
ID - 577
TI - High-efficiency single-photon detectors
VL - 6372
ER -
TY - CONF
AB - A source of single photons allows secure quantum key distribution, in addition, to being a critical resource for linear optics quantum computing. We describe our progress on deterministically creating single photons from spontaneous parametric downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys. Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons by measuring one member of a spontaneously emitted photon pair and storing the remaining conditionally prepared photon until a predetermined time, when it would be "deterministically" released from storage. Our approach attempts to improve upon this by recycling the pump pulse in order to decrease the possibility of multiple-pair generation, while maintaining a high probability of producing a single pair. Many of the challenges we discuss are central to other quantum information technologies, including the need for low-loss optical storage, switching and detection, and fast feed-forward control.
AU - Peters, Nicholas A
AU - Arnold, Keith J
AU - VanDevender, Aaron P
AU - Jeffrey, Evan R
AU - Rangarajan, Radhika
AU - Onur Hosten
AU - Barreiro, Julio T
AU - Altepeter, Joseph B
AU - Kwiat, Paul G
ID - 578
TI - Towards a quasi-deterministic single-photon source
VL - 6305
ER -
TY - JOUR
AB - The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of 'running' and 'not running' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover's search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel 'chained' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence.
AU - Onur Hosten
AU - Rakher, Matthew T
AU - Barreiro, Julio T
AU - Peters, Nicholas A
AU - Kwiat, Paul G
ID - 579
IS - 7079
JF - Nature
TI - Counterfactual quantum computation through quantum interrogation
VL - 439
ER -
TY - CONF
AB - Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) facilitate efficient single-photon detection. We are attempting to improve their efficiency, previously limited to < 88% by coupling losses, via anti-reflection coatings, better electronics and cryogenics.
AU - Rangarajan, Radhika
AU - Peters, Nicholas A
AU - Onur Hosten
AU - Altepeter, Joseph B
AU - Jeffrey, Evan R
AU - Kwiat, Paul G
ID - 583
TI - Improved single-photon detection
ER -
TY - JOUR
AU - Salecker, Iris
AU - Häusser, Michael
AU - de Bono, Mario
ID - 6151
IS - 6
JF - EMBO reports
SN - 1469-221X
TI - On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits
VL - 7
ER -
TY - JOUR
AU - Rogers, Candida
AU - Persson, Annelie
AU - Cheung, Benny
AU - de Bono, Mario
ID - 6152
IS - 7
JF - Current Biology
SN - 0960-9822
TI - Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans
VL - 16
ER -
TY - JOUR
AB - 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.
AU - Luján, Rafael
AU - Ryuichi Shigemoto
ID - 2657
IS - 6
JF - European Journal of Neuroscience
TI - Localization of metabotropic GABA receptor subunits GABAB1 and GABAB2 relative to synaptic sites in the rat developing cerebellum
VL - 23
ER -
TY - JOUR
AB - 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.
AU - Inamura, Mihoko
AU - Itakura, Makoto
AU - Okamoto, Hirotsugu
AU - Hoka, Sumio
AU - Mizoguchi, Akira
AU - Fukazawa, Yugo
AU - Ryuichi Shigemoto
AU - Yamamori, Saori
AU - Takahashi, Masami
ID - 2659
IS - 1
JF - Neuroscience Research
TI - Differential localization and regulation of stargazin-like protein, γ-8 and stargazin in the plasma membrane of hippocampal and cortical neurons
VL - 55
ER -
TY - JOUR
AB - 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.
AU - Shaban, Hamdy
AU - Humeau, Yann
AU - Herry, Cyril
AU - Cassasus, Guillaume
AU - Ryuichi Shigemoto
AU - Ciocchi, Stéphane
AU - Barbieri, Samuel
AU - Van Der Putten, Herman V
AU - Kaupmann, Klemens
AU - Bettler, Bernhard
AU - Lüthi, Andreas
ID - 2660
IS - 8
JF - Nature Neuroscience
TI - Generalization of amygdala LTP and conditioned fear in the absence of presynaptic inhibition
VL - 9
ER -
TY - JOUR
AB - 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.
AU - Vigot, Réjan
AU - Barbieri, Samuel
AU - Bräuner-Osborne, Hans
AU - Tureček, Rostislav
AU - Ryuichi Shigemoto
AU - Zhang, Yan Ping
AU - Luján, Rafael
AU - Jacobson, Laura H
AU - Biermann, Barbara
AU - Fritschy, Jean-Marc
AU - Vacher, Claire-Marie
AU - Müller, Matthias P
AU - Sansig, Gilles
AU - Guetg, Nicole
AU - Cryan, John F
AU - Kaupmann, Klemens
AU - Gassmann, Martin
AU - Oertner, Thomas G
AU - Bettler, Bernhard
ID - 2661
IS - 4
JF - Neuron
TI - Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants
VL - 50
ER -
TY - JOUR
AB - 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.
AU - Kulik, Ákos
AU - Vida, Imre
AU - Fukazawa, Yugo
AU - Guetg, Nicole
AU - Kasugai, Yu
AU - Marker, Cheryl L
AU - Rigato, Franck
AU - Bettler, Bernhard
AU - Wickman, Kevin D
AU - Frotscher, Michael
AU - Ryuichi Shigemoto
ID - 2662
IS - 16
JF - Journal of Neuroscience
TI - Compartment-dependent colocalization of Kir3.2-containing K+ channels and GABAB receptors in hippocampal pyramidal cells
VL - 26
ER -
TY - JOUR
AB - 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.
AU - Kodama, Takashi
AU - Itsukaichi-Nishida, Yuko
AU - Fukazawa, Yugo
AU - Wakamori, Minoru
AU - Miyata, Mariko
AU - Molnár, Elek
AU - Mori, Yasuo
AU - Ryuichi Shigemoto
AU - Imoto, Keiji
ID - 2663
IS - 11
JF - European Journal of Neuroscience
TI - A CaV2.1 calcium channel mutation rocker reduces the number of postsynaptic AMPA receptors in parallel fiber-Purkinje cell synapses
VL - 24
ER -
TY - GEN
AB - 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.
AU - Ferraguti, Francesco
AU - Ryuichi Shigemoto
ID - 2664
IS - 2
T2 - Cell and Tissue Research
TI - Metabotropic glutamate receptors
VL - 326
ER -
TY - JOUR
AB - 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.
AU - Elgart, Alexander
AU - László Erdös
AU - Schlein, Benjamin
AU - Yau, Horng-Tzer
ID - 2745
IS - 2
JF - Archive for Rational Mechanics and Analysis
TI - Gross-Pitaevskii equation as the mean field limit of weakly coupled bosons
VL - 179
ER -
TY - CONF
AB - 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.
AU - László Erdös
AU - Salmhofer, Manfred
AU - Yau, Horng-Tzer
ID - 2746
TI - Towards the quantum Brownian motion
VL - 690
ER -
TY - JOUR
AB - 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.
AU - László Erdös
AU - Schlein, Benjamin
AU - Yau, Horng-Tzer
ID - 2747
IS - 12
JF - Communications on Pure and Applied Mathematics
TI - Derivation of the Gross-Pitaevskii hierarchy for the dynamics of Bose-Einstein condensate
VL - 59
ER -
TY - JOUR
AB - 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.
AU - Björn Hof
AU - Westerweel, Jerry
AU - Schneider, Tobias M
AU - Eckhardt, Bruno
ID - 2791
IS - 7107
JF - Nature
TI - Finite lifetime of turbulence in shear flows
VL - 443
ER -
TY - JOUR
AB - 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].
AU - Björn Hof
AU - van Doorne, Casimir W
AU - Westerweel, Jerry
AU - Nieuwstadt, Frans T
ID - 2792
JF - Fluid Mechanics and its Applications
TI - Observation of nonlinear travelling waves in turbulent pipe flow
VL - 78
ER -
TY - JOUR
AB - 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.
AU - Calado, Dinis P
AU - Tiago Paixao
AU - Holmberg, Dan
AU - Haury, Matthias
ID - 2894
IS - 8
JF - Journal of Immunology
TI - Stochastic Monoallelic Expression of IL 10 in T Cells
VL - 177
ER -
TY - CHAP
AB - 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.
AU - Vladimir Kolmogorov
AU - Zabih, Ramin
ID - 2921
T2 - Handbook of Mathematical Models in Computer Vision
TI - Graph cut algorithms for binocular stereo with occlusions
ER -
TY - CHAP
AB - 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.
AU - Sauer, Michael
AU - Jirí Friml
ED - Mujib, Abdul
ED - Šamaj, Jozef
ID - 3002
T2 - Somatic Embryogenesis
TI - In vitro culture of Arabidopsis embryos
VL - 2
ER -
TY - JOUR
AU - Friml, Jirí
AU - Benfey, Philip
AU - Benková, Eva
AU - Bennett, Malcolm
AU - Berleth, Thomas
AU - Geldner, Niko
AU - Grebe, Markus
AU - Heisler, Marcus
AU - Hejátko, Jan
AU - Jürgens, Gerd
AU - Laux, Thomas
AU - Lindsey, Keith
AU - Lukowitz, Wolfgang
AU - Luschnig, Christian
AU - Offringa, Remko
AU - Scheres, Ben
AU - Swarup, Ranjan
AU - Torres Ruiz, Ramón
AU - Weijers, Dolf
AU - Zažímalová, Eva
ID - 3005
IS - 1
JF - Trends in Plant Science
TI - Apical-basal polarity: Why plant cells don't stand on their heads
VL - 11
ER -