@article{9524,
abstract = {Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.},
author = {ZILBERMAN, Daniel and Henikoff, Steven},
issn = {1477-9129},
journal = {Development},
number = {22},
pages = {3959--3965},
publisher = {The Company of Biologists},
title = {{Genome-wide analysis of DNA methylation patterns}},
doi = {10.1242/dev.001131},
volume = {134},
year = {2007},
}
@inproceedings{2333,
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P},
pages = {239 -- 248},
publisher = {American Mathematical Society},
title = {{Ground-state energy of a dilute Fermi gas}},
doi = {10.1090/conm/412},
volume = {412},
year = {2006},
}
@inproceedings{2334,
author = {Robert Seiringer and Lieb, Élliott H and Yngvason, Jakob},
editor = {Zambrini, Jean-Claude},
publisher = {World Scientific Publishing},
title = {{One-dimensional behavior of dilute, trapped Bose gases in traps}},
doi = {10.1007/s00220-003-0993-3},
year = {2006},
}
@misc{2363,
abstract = { We prove that the Gross-Pitaevskii equation correctly describes the ground state energy and corresponding one-particle density matrix of rotating, dilute, trapped Bose gases with repulsive two-body interactions. We also show that there is 100% Bose-Einstein condensation. While a proof that the GP equation correctly describes non-rotating or slowly rotating gases was known for some time, the rapidly rotating case was unclear because the Bose (i.e., symmetric) ground state is not the lowest eigenstate of the Hamiltonian in this case. We have been able to overcome this difficulty with the aid of coherent states. Our proof also conceptually simplifies the previous proof for the slowly rotating case. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state. },
author = {Lieb, Élliott H and Robert Seiringer},
booktitle = {Communications in Mathematical Physics},
number = {2},
pages = {505 -- 537},
publisher = {Springer},
title = {{Derivation of the Gross-Pitaevskii equation for rotating Bose gases}},
doi = {10.1007/s00220-006-1524-9},
volume = {264},
year = {2006},
}
@article{2364,
abstract = {We present an inequality that gives a lower bound on the expectation value of certain two-body interaction potentials in a general state on Fock space in terms of the corresponding expectation value for thermal equilibrium states of non-interacting systems and the difference in the free energy. This bound can be viewed as a rigorous version of first-order perturbation theory for many-body systems at positive temperature. As an application, we give a proof of the first two terms in a high density (and high temperature) expansion of the free energy of jellium with Coulomb interactions, both in the fermionic and bosonic case. For bosons, our method works above the transition temperature (for the non-interacting gas) for Bose-Einstein condensation.},
author = {Robert Seiringer},
journal = {Reviews in Mathematical Physics},
number = {3},
pages = {233 -- 253},
publisher = {World Scientific Publishing},
title = {{A correlation estimate for quantum many-body systems at positive temperature}},
doi = {10.1142/S0129055X06002632},
volume = {18},
year = {2006},
}
@article{2365,
abstract = {We consider a gas of fermions with non-zero spin at temperature T and chemical potential μ. We show that if the range of the interparticle interaction is small compared to the mean particle distance, the thermodynamic pressure differs to leading order from the corresponding expression for non-interacting particles by a term proportional to the scattering length of the interparticle interaction. This is true for any repulsive interaction, including hard cores. The result is uniform in the temperature as long as T is of the same order as the Fermi temperature, or smaller.},
author = {Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {3},
pages = {729 -- 757},
publisher = {Springer},
title = {{The thermodynamic pressure of a dilute fermi gas}},
doi = {10.1007/s00220-005-1433-3},
volume = {261},
year = {2006},
}
@article{2366,
abstract = {Inequalities are derived for power sums of the real part and the modulus of the eigenvalues of a Schrödinger operator with a complex-valued potential.},
author = {Frank, Rupert L and Laptev, Ari and Lieb, Élliott H and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {3},
pages = {309 -- 316},
publisher = {Springer},
title = {{Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials}},
doi = {10.1007/s11005-006-0095-1},
volume = {77},
year = {2006},
}
@inbook{2368,
abstract = {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.},
author = {Robert Seiringer},
booktitle = {Large Coulomb Systems},
editor = {Dereziński, Jan and Siedentop, Heinz},
pages = {249 -- 274},
publisher = {Springer},
title = {{Dilute, trapped Bose gases and Bose-Einstein condensation}},
doi = {10.1007/3-540-32579-4_6},
volume = {695},
year = {2006},
}
@inbook{2369,
abstract = {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.},
author = {Aizenman, Michael and Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
booktitle = {Mathematical Physics of Quantum Mechanics},
editor = {Asch, Joachim and Joye, Alain},
pages = {199 -- 215},
publisher = {Springer},
title = {{Bose-Einstein condensation as a quantum phase transition in an optical lattice}},
doi = {10.1007/b11573432},
volume = {690},
year = {2006},
}
@inbook{2416,
author = {Bang-Jensen, Jørgen and Reed, Bruce and Schacht, Bruce and Šámal, Robert and Toft, Bjarne and Uli Wagner},
booktitle = {Topics in Discrete Mathematics},
pages = {613 -- 627},
publisher = {Springer},
title = {{On six problems posed by Jarik Nešetřil}},
doi = {10.1007/3-540-33700-8_30},
volume = {26},
year = {2006},
}
@article{2429,
abstract = {We show, with an elementary proof, that the number of halving simplices in a set of n points in 4 in general position is O(n4-2/45). This improves the previous bound of O(n4-1/134). Our main new ingredient is a bound on the maximum number of halving simplices intersecting a fixed 2-plane. },
author = {Matoušek, Jiří and Sharir, Micha and Smorodinsky, Shakhar and Uli Wagner},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {177 -- 191},
publisher = {Springer},
title = {{K-sets in four dimensions}},
doi = {10.1007/s00454-005-1200-4},
volume = {35},
year = {2006},
}
@article{2430,
abstract = {We consider an online version of the conflict-free coloring of a set of points on the line, where each newly inserted point must be assigned a color upon insertion, and at all times the coloring has to be conflict-free, in the sense that in every interval I there is a color that appears exactly once in I. We present deterministic and randomized algorithms for achieving this goal, and analyze their performance, that is, the maximum number of colors that they need to use, as a function of the number n of inserted points. We first show that a natural and simple (deterministic) approach may perform rather poorly, requiring Ω(√̃) colors in the worst case. We then derive two efficient variants of this simple algorithm. The first is deterministic and uses O(log 2 n) colors, and the second is randomized and uses O(log n) colors with high probability. We also show that the O(log 2 n) bound on the number of colors used by our deterministic algorithm is tight on the worst case. We also analyze the performance of the simplest proposed algorithm when the points are inserted in a random order and present an incomplete analysis that indicates that, with high probability, it uses only O(log n) colors. Finally, we show that in the extension of this problem to two dimensions, where the relevant ranges are disks, n colors may be required in the worst case.},
author = {Chent, Ke and Fiat, Amos and Kaplan, Haim and Levy, Meital B and Matoušek, Jiří and Mossel, Elchanan and Pach, János and Sharir, Micha and Smorodinsky, Shakhar and Uli Wagner and Welzl, Emo},
journal = {SIAM Journal on Computing},
number = {5},
pages = {1342 -- 1359},
publisher = {SIAM},
title = {{Online conflict-free coloring for intervals}},
doi = {10.1137/S0097539704446682},
volume = {36},
year = {2006},
}
@inproceedings{2431,
abstract = {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.},
author = {Uli Wagner},
pages = {635 -- 645},
publisher = {IEEE},
title = {{On a geometric generalization of the Upper Bound Theorem}},
doi = {10.1109/FOCS.2006.53},
year = {2006},
}
@article{2657,
abstract = {The highest densities of the two metabotropic GABA subunits, GABA B1 and GABAB2, have been reported as occurring around the glutamatergic synapses between Purkinje cell spines and parallel fibre varicosities. In order to determine how this distribution is achieved during development, we investigated the expression pattern and the cellular and subcellular localization of the GABAB1 and GABAB2 subunits in the rat cerebellum during postnatal development. At the light microscopic level, immunoreactivity for the GABAB1 and GABAB2 subunits was very prominent in the developing molecular layer, especially in Purkinje cells. Using double immunofluorescence, we demonstrated that GABAB1 was transiently expressed in glial cells. At the electron microscopic level, immunoreactivity for GABAB receptors was always detected both pre- and postsynaptically. Presynaptically, GABAB1 and GABAB2 were localized in the extrasynaptic membrane of parallel fibres at all ages, and only rarely in GABAergic axons. Postsynaptically, GABAB receptors were localized to the extrasynaptic and perisynaptic plasma membrane of Purkinje cell dendrites and spines throughout development. Quantitative analysis and three-dimensional reconstructions further revealed a progressive developmental movement of the GABAB1 subunit on the surface of Purkinje cells from dendritic shafts to its final destination, the dendritic spines. Together, these results indicate that GABAB receptors undergo dynamic regulation during cerebellar development in association with the establishment and maturation of glutamatergic synapses to Purkinje cells.},
author = {Luján, Rafael and Ryuichi Shigemoto},
journal = {European Journal of Neuroscience},
number = {6},
pages = {1479 -- 1490},
publisher = {Wiley-Blackwell},
title = {{Localization of metabotropic GABA receptor subunits GABAB1 and GABAB2 relative to synaptic sites in the rat developing cerebellum}},
doi = {10.1111/j.1460-9568.2006.04669.x},
volume = {23},
year = {2006},
}
@article{2659,
abstract = {Transmembrane AMPA receptor regulatory proteins (TARPs), including stargazin/γ-2, are associated with AMPA receptors and participate in their surface delivery and anchoring at the postsynaptic membrane. TARPs may also act as a positive modulator of the AMPA receptor ion channel function; however, little is known about other TARP members except for stargazin/γ-2. We examined the synaptic localization of stargazin/γ-2 and γ-8 by immunoelectron microscopy and biochemical analysis. The analysis of sodium dodecyl sulfate-digested freeze-fracture replica labeling revealed that stargazin/γ-2 was concentrated in the postsynaptic area, whereas γ-8 was distributed both in synaptic and extra-synaptic plasma membranes of the hippocampal neuron. When a synaptic plasma membrane-enriched brain fraction was treated with Triton X-100 and separated by sucrose density gradient ultracentrifugation, a large proportion of NMDA receptor and stargazin/γ-2 was accumulated in raft-enriched fractions, whereas AMPA receptor and γ-8 were distributed in both the raft-enriched fractions and other Triton-insoluble fractions. Phosphorylation of stargazin/γ-2 and γ-8 was regulated by different sets of kinases and phosphatases in cultured cortical neurons. These results suggested that stargazin/γ-2 and γ-8 have distinct roles in postsynaptic membranes under the regulation of different intracellular signaling pathways.},
author = {Inamura, Mihoko and Itakura, Makoto and Okamoto, Hirotsugu and Hoka, Sumio and Mizoguchi, Akira and Fukazawa, Yugo and Ryuichi Shigemoto and Yamamori, Saori and Takahashi, Masami},
journal = {Neuroscience Research},
number = {1},
pages = {45 -- 53},
publisher = {Elsevier},
title = {{ Differential localization and regulation of stargazin-like protein, γ-8 and stargazin in the plasma membrane of hippocampal and cortical neurons}},
doi = {10.1016/j.neures.2006.01.004},
volume = {55},
year = {2006},
}
@article{2660,
abstract = {Pavlovian fear conditioning, a simple form of associative learning, is thought to involve the induction of associative, NMDA receptor-dependent long-term potentiation (LTP) in the lateral amygdala. Using a combined genetic and electrophysiological approach, we show here that lack of a specific GABAB receptor subtype, GABAB(1a,2), unmasks a nonassociative, NMDA receptor-independent form of presynaptic LTP at cortico-amygdala afferents. Moreover, the level of presynaptic GABA B(1a,2) receptor activation, and hence the balance between associative and nonassociative forms of LTP, can be dynamically modulated by local inhibitory activity. At the behavioral level, genetic loss of GABA B(1a) results in a generalization of conditioned fear to nonconditioned stimuli. Our findings indicate that presynaptic inhibition through GABAB(1a,2) receptors serves as an activity-dependent constraint on the induction of homosynaptic plasticity, which may be important to prevent the generalization of conditioned fear.},
author = {Shaban, Hamdy and Humeau, Yann and Herry, Cyril and Cassasus, Guillaume and Ryuichi Shigemoto and Ciocchi, Stéphane and Barbieri, Samuel and Van Der Putten, Herman V and Kaupmann, Klemens and Bettler, Bernhard and Lüthi, Andreas},
journal = {Nature Neuroscience},
number = {8},
pages = {1028 -- 1035},
publisher = {Nature Publishing Group},
title = {{Generalization of amygdala LTP and conditioned fear in the absence of presynaptic inhibition}},
doi = {10.1038/nn1732},
volume = {9},
year = {2006},
}
@article{2661,
abstract = {GABAB receptors are the G protein-coupled receptors for the main inhibitory neurotransmitter in the brain, γ-aminobutyric acid (GABA). Molecular diversity in the GABAB system arises from the GABAB1a and GABAB1b subunit isoforms that solely differ in their ectodomains by a pair of sushi repeats that is unique to GABAB1a. Using a combined genetic, physiological, and morphological approach, we now demonstrate that GABAB1 isoforms localize to distinct synaptic sites and convey separate functions in vivo. At hippocampal CA3-to-CA1 synapses, GABAB1a assembles heteroreceptors inhibiting glutamate release, while predominantly GABAB1b mediates postsynaptic inhibition. Electron microscopy reveals a synaptic distribution of GABAB1 isoforms that agrees with the observed functional differences. Transfected CA3 neurons selectively express GABAB1a in distal axons, suggesting that the sushi repeats, a conserved protein interaction motif, specify heteroreceptor localization. The constitutive absence of GABAB1a but not GABAB1b results in impaired synaptic plasticity and hippocampus-dependent memory, emphasizing molecular differences in synaptic GABAB functions.},
author = {Vigot, Réjan and Barbieri, Samuel and Bräuner-Osborne, Hans and Tureček, Rostislav and Ryuichi Shigemoto and Zhang, Yan Ping and Luján, Rafael and Jacobson, Laura H and Biermann, Barbara and Fritschy, Jean-Marc and Vacher, Claire-Marie and Müller, Matthias P and Sansig, Gilles and Guetg, Nicole and Cryan, John F and Kaupmann, Klemens and Gassmann, Martin and Oertner, Thomas G and Bettler, Bernhard},
journal = {Neuron},
number = {4},
pages = {589 -- 601},
publisher = {Elsevier},
title = {{Differential Compartmentalization and Distinct Functions of GABAB Receptor Variants}},
doi = {10.1016/j.neuron.2006.04.014},
volume = {50},
year = {2006},
}
@article{2662,
abstract = {G-protein-coupled inwardly rectifying K+ channels (Kir3 channels) coupled to metabotropic GABAB receptors are essential for the control of neuronal excitation. To determine the distribution of Kir3 channels and their spatial relationship to GABAB receptors on hippocampal pyramidal cells, we used a high-resolution immunocytochemical approach. Immunoreactivity for the Kir3.2 subunit was most abundant postsynaptically and localized to the extrasynaptic plasma membrane of dendritic shafts and spines of principal cells. Quantitative analysis of immunogold particles for Kir3.2 revealed an enrichment of the protein around putative glutamatergic synapses on dendritic spines, similar to that of GABA B1. Consistent with this observation, a high degree of coclustering of Kir3.2 and GABAB1 was revealed around excitatory synapses by the highly sensitive SDS-digested freeze-fracture replica immunolabeling. In contrast, in dendritic shafts receptors and channels were found to be mainly segregated. These results suggest that Kir3.2-containing K+ channels on dendritic spines preferentially mediate the effect of GABA, whereas channels on dendritic shafts are likely to be activated by other neurotransmitters as well. Thus, Kir3 channels, localized to different subcellular compartments of hippocampal principal cells, appear to be differentially involved in synaptic integration in pyramidal cell dendrites.},
author = {Kulik, Ákos and Vida, Imre and Fukazawa, Yugo and Guetg, Nicole and Kasugai, Yu and Marker, Cheryl L and Rigato, Franck and Bettler, Bernhard and Wickman, Kevin D and Frotscher, Michael and Ryuichi Shigemoto},
journal = {Journal of Neuroscience},
number = {16},
pages = {4289 -- 4297},
publisher = {Society for Neuroscience},
title = {{Compartment-dependent colocalization of Kir3.2-containing K+ channels and GABAB receptors in hippocampal pyramidal cells}},
doi = {10.1523/JNEUROSCI.4178-05.2006},
volume = {26},
year = {2006},
}
@article{2663,
abstract = {The rocker mice are hereditary ataxic mutants that carry a point mutation in the gene encoding the CaV2.1 (P/Q-type) Ca2+ channel α1 subunit, and show the mildest symptoms among the reported CaV2.1 mutant mice. We studied the basic characteristics of the rocker mutant Ca2+ channel and their impacts on excitatory synaptic transmission in cerebellar Purkinje cells (PCs). In acutely dissociated PC somas, the rocker mutant channel showed a moderate reduction in Ca2+ channel current density, whereas its kinetics and voltage dependency of gating remained nearly normal. Despite the small changes in channel function, synaptic transmission in the parallel fiber (PF)-PC synapses was severely impaired. The climbing fiber inputs onto PCs showed a moderate impairment but could elicit normal complex spikes. Presynaptic function of the PF-PC synapses, however, was unexpectedly almost normal in terms of paired-pulse facilitation, sensitivity to extracellular Ca2+ concentration and glutamate concentration in synaptic clefts. Electron microscopic analyses including freeze-fracture replica labeling revealed that both the number and density of postsynaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors substantially decreased without gross structural changes of the PF-PC synapses. We also observed an abnormal arborization of PC dendrites in young adult rocker mice (∼ 1 month old). These lines of evidence suggest that even a moderate dysfunction of CaV2.1 Ca2+ channel can cause substantial changes in postsynaptic molecular composition of the PF-PC synapses and dendritic structure of PCs.},
author = {Kodama, Takashi and Itsukaichi-Nishida, Yuko and Fukazawa, Yugo and Wakamori, Minoru and Miyata, Mariko and Molnár, Elek and Mori, Yasuo and Ryuichi Shigemoto and Imoto, Keiji},
journal = {European Journal of Neuroscience},
number = {11},
pages = {2993 -- 3007},
publisher = {Wiley-Blackwell},
title = {{A CaV2.1 calcium channel mutation rocker reduces the number of postsynaptic AMPA receptors in parallel fiber-Purkinje cell synapses}},
doi = {10.1111/j.1460-9568.2006.05191.x},
volume = {24},
year = {2006},
}
@misc{2664,
abstract = {Metabotropic glutamate receptors (mGlus) are a family of G-protein-coupled receptors activated by the neurotransmitter glutamate. Molecular cloning has revealed eight different subtypes (mGlu1-8) with distinct molecular and pharmacological properties. Multiplicity in this receptor family is further generated through alternative splicing. mGlus activate a multitude of signalling pathways important for modulating neuronal excitability, synaptic plasticity and feedback regulation of neurotransmitter release. In this review, we summarize anatomical findings (from our work and that of other laboratories) describing their distribution in the central nervous system. Recent evidence regarding the localization of these receptors in peripheral tissues will also be examined. The distinct regional, cellular and subcellular distribution of mGlus in the brain will be discussed in view of their relationship to neurotransmitter release sites and of possible functional implications.},
author = {Ferraguti, Francesco and Ryuichi Shigemoto},
booktitle = {Cell and Tissue Research},
number = {2},
pages = {483 -- 504},
publisher = {Springer},
title = {{Metabotropic glutamate receptors}},
doi = {10.1007/s00441-006-0266-5},
volume = {326},
year = {2006},
}
@article{2745,
abstract = {We consider the dynamics of N boson systems interacting through a pair potential N -1 V a (x i -x j ) where V a (x)=a -3 V(x/a). We denote the solution to the N-particle Schrödinger equation by Ψ N, t . Recall that the Gross-Pitaevskii (GP) equation is a nonlinear Schrödinger equation and the GP hierarchy is an infinite BBGKY hierarchy of equations so that if u t solves the GP equation, then the family of k-particle density matrices [InlineMediaObject not available: see fulltext.] solves the GP hierarchy. Under the assumption that a = Nε for 0 < ε < 3/5, we prove that as N→∞ the limit points of the k-particle density matrices of Ψ N, t are solutions of the GP hierarchy with the coupling constant in the nonlinear term of the GP equation given by ∫ V (x)dx. The uniqueness of the solutions of this hierarchy remains an open question.},
author = {Elgart, Alexander and László Erdös and Schlein, Benjamin and Yau, Horng-Tzer},
journal = {Archive for Rational Mechanics and Analysis},
number = {2},
pages = {265 -- 283},
publisher = {Springer},
title = {{Gross-Pitaevskii equation as the mean field limit of weakly coupled bosons}},
doi = {10.1007/s00205-005-0388-z},
volume = {179},
year = {2006},
}
@inproceedings{2746,
abstract = {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.},
author = {László Erdös and Salmhofer, Manfred and Yau, Horng-Tzer},
pages = {233 -- 257},
publisher = {World Scientific Publishing},
title = {{Towards the quantum Brownian motion}},
doi = {10.1007/3-540-34273-7_18},
volume = {690},
year = {2006},
}
@article{2747,
abstract = {Consider a system of N bosons on the three-dimensional unit torus interacting via a pair potential N 2V(N(x i - x j)) where x = (x i, . . ., x N) denotes the positions of the particles. Suppose that the initial data ψ N,0 satisfies the condition 〈ψ N,0, H 2 Nψ N,0) ≤ C N 2 where H N is the Hamiltonian of the Bose system. This condition is satisfied if ψ N,0 = W Nφ N,t where W N is an approximate ground state to H N and φ N,0 is regular. Let ψ N,t denote the solution to the Schrödinger equation with Hamiltonian H N. Gross and Pitaevskii proposed to model the dynamics of such a system by a nonlinear Schrödinger equation, the Gross-Pitaevskii (GP) equation. The GP hierarchy is an infinite BBGKY hierarchy of equations so that if u t solves the GP equation, then the family of k-particle density matrices ⊗ k |u t?〉 〈 t | solves the GP hierarchy. We prove that as N → ∞ the limit points of the k-particle density matrices of ψ N,t are solutions of the GP hierarchy. Our analysis requires that the N-boson dynamics be described by a modified Hamiltonian that cuts off the pair interactions whenever at least three particles come into a region with diameter much smaller than the typical interparticle distance. Our proof can be extended to a modified Hamiltonian that only forbids at least n particles from coming close together for any fixed n.},
author = {László Erdös and Schlein, Benjamin and Yau, Horng-Tzer},
journal = {Communications on Pure and Applied Mathematics},
number = {12},
pages = {1659 -- 1741},
publisher = {Wiley-Blackwell},
title = {{Derivation of the Gross-Pitaevskii hierarchy for the dynamics of Bose-Einstein condensate}},
doi = {10.1002/cpa.20123},
volume = {59},
year = {2006},
}
@article{2791,
abstract = {Generally, the motion of fluids is smooth and laminar at low speeds but becomes highly disordered and turbulent as the velocity increases. The transition from laminar to turbulent flow can involve a sequence of instabilities in which the system realizes progressively more complicated states, or it can occur suddenly. Once the transition has taken place, it is generally assumed that, under steady conditions, the turbulent state will persist indefinitely. The flow of a fluid down a straight pipe provides a ubiquitous example of a shear flow undergoing a sudden transition from laminar to turbulent motion. Extensive calculations and experimental studies have shown that, at relatively low flow rates, turbulence in pipes is transient, and is characterized by an exponential distribution of lifetimes. They also suggest that for Reynolds numbers exceeding a critical value the lifetime diverges (that is, becomes infinitely large), marking a change from transient to persistent turbulence. Here we present experimental data and numerical calculations covering more than two decades of lifetimes, showing that the lifetime does not in fact diverge but rather increases exponentially with the Reynolds number. This implies that turbulence in pipes is only a transient event (contrary to the commonly accepted view), and that the turbulent and laminar states remain dynamically connected, suggesting avenues for turbulence control.},
author = {Björn Hof and Westerweel, Jerry and Schneider, Tobias M and Eckhardt, Bruno},
journal = {Nature},
number = {7107},
pages = {59 -- 62},
publisher = {Nature Publishing Group},
title = {{Finite lifetime of turbulence in shear flows}},
doi = {10.1038/nature05089},
volume = {443},
year = {2006},
}
@article{2792,
abstract = {Transition to turbulence in pipe flow has posed a riddle in fluid dynamics since the pioneering experiments of Reynolds[1]. Although the laminar flow is linearly stable for all flow rates, practical pipe flows become turbulent at large enough flow speeds. Turbulence arises suddenly and fully without distinct steps and without a clear critical point. The complexity of this problem has puzzled mathematicians, physicists and engineers for more than a century and no satisfactory explanation of this problem has been given. In a very recent theoretical approach it has been suggested that unstable solutions of the Navier Stokes equations may hold the key to understanding this problem. In numerical studies such unstable states have been identified as exact solutions for the idealized case of a pipe with periodic boundary conditions[2, 3]. These solutions have the form of waves extending through the entire pipe and travelling in the streamwise direction at a phase speed close to the bulk velocity of the fluid. With the aid of a recently developed high-speed stereoscopic Particle Image Velocimetry (PIV) system, we were able to observe transients of such unstable solutions in turbulent pipe flow[4].},
author = {Björn Hof and van Doorne, Casimir W and Westerweel, Jerry and Nieuwstadt, Frans T},
journal = {Fluid Mechanics and its Applications},
pages = {109 -- 114},
publisher = {Springer},
title = {{Observation of nonlinear travelling waves in turbulent pipe flow}},
doi = {10.1007/1-4020-4159-4_11},
volume = {78},
year = {2006},
}
@article{2894,
abstract = {IL-10 is a potent anti-inflammatory and immunomodulatory cytokine, exerting major effects in the degree and quality of the immune response. Using a newly generated IL-10 reporter mouse model, which easily allows the study of IL-10 expression from each allele in a single cell, we report here for the first time that IL-10 is predominantly monoallelic expressed in CD4+ T cells. Furthermore, we have compelling evidence that this expression pattern is not due to parental imprinting, allelic exclusion, or strong allelic bias. Instead, our results support a stochastic regulation mechanism, in which the probability to initiate allelic transcription depends on the strength of TCR signaling and subsequent capacity to overcome restrictions imposed by chromatin hypoacetylation. In vivo Ag-experienced T cells show a higher basal probability to transcribe IL-10 when compared with naive cells, yet still show mostly monoallelic IL-10 expression. Finally, statistical analysis on allelic expression data shows transcriptional independence between both alleles. We conclude that CD4+ T cells have a low probability for IL-10 allelic activation resulting in a predominantly monoallelic expression pattern, and that IL-10 expression appears to be stochastically regulated by controlling the frequency of expressing cells, rather than absolute protein levels per cell.},
author = {Calado, Dinis P and Tiago Paixao and Holmberg, Dan and Haury, Matthias},
journal = {Journal of Immunology},
number = {8},
pages = {5358 -- 5364},
publisher = {American Association of Immunologists},
title = {{Stochastic Monoallelic Expression of IL 10 in T Cells}},
doi = {10.4049/jimmunol.177.8.5358 },
volume = {177},
year = {2006},
}
@inbook{2921,
abstract = {Most binocular stereo algorithms assume that all scene elements are visible from both cameras. Scene elements that are visible from only one camera, known as occlusions, pose an important challenge for stereo. Occlusions are important for segmentation, because they appear near discontinuities. However, stereo algorithms tend to ignore occlusions because of their difficulty. One reason is that occlusions require the input images to be treated symmetrically, which complicates the problem formulation. Worse, certain depth maps imply physically impossible scene configurations, and must be excluded from the output. In this chapter we approach the problem of binocular stereo with occlusions from an energy minimization viewpoint. We begin by reviewing traditional stereo methods that do not handle occlusions. If occlusions are ignored, it is easy to formulate the stereo problem as a pixel labeling problem, which leads to an energy function that is common in early vision. This kind of energy function can he minimized using graph cuts, which is a combinatorial optimization technique that has proven to be very effective for low-level vision problems. Motivated by this, we have designed two graph cut stereo algorithms that are designed to handle occlusions. These algorithms produce promising experimental results on real data with ground truth.},
author = {Vladimir Kolmogorov and Zabih, Ramin},
booktitle = {Handbook of Mathematical Models in Computer Vision},
pages = {423 -- 427},
publisher = {Springer},
title = {{Graph cut algorithms for binocular stereo with occlusions}},
doi = {10.1007/0-387-28831-7_26},
year = {2006},
}
@article{8488,
abstract = {We demonstrate for different protein samples that three-dimensional HNCO and HNCA correlation spectra may be recorded in a few minutes acquisition time using the band-selective excitation short-transient sequences presented here. This opens new perspectives for the NMR structural investigation of unstable protein samples and real-time site-resolved studies of protein kinetics.},
author = {Schanda, Paul and Van Melckebeke, Hélène and Brutscher, Bernhard},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
number = {28},
pages = {9042--9043},
publisher = {American Chemical Society},
title = {{Speeding up three-dimensional protein NMR experiments to a few minutes}},
doi = {10.1021/ja062025p},
volume = {128},
year = {2006},
}
@article{8489,
abstract = {Structure elucidation of proteins by either NMR or X‐ray crystallography often requires the screening of a large number of samples for promising protein constructs and optimum solution conditions. For large‐scale screening of protein samples in solution, robust methods are needed that allow a rapid assessment of the folding of a polypeptide under diverse sample conditions. Here we present HET‐SOFAST NMR, a highly sensitive new method for semi‐quantitative characterization of the structural compactness and heterogeneity of polypeptide chains in solution. On the basis of one‐dimensional 1H HET‐SOFAST NMR data, obtained on well‐folded, molten globular, partially‐ and completely unfolded proteins, we define empirical thresholds that can be used as quantitative benchmarks for protein compactness. For 15N‐enriched protein samples, two‐dimensional 1H‐15N HET‐SOFAST correlation spectra provide site‐specific information about the structural heterogeneity along the polypeptide chain.},
author = {Schanda, Paul and Forge, Vincent and Brutscher, Bernhard},
issn = {0749-1581},
journal = {Magnetic Resonance in Chemistry},
number = {S1},
pages = {S177--S184},
publisher = {Wiley},
title = {{HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains}},
doi = {10.1002/mrc.1825},
volume = {44},
year = {2006},
}
@article{8490,
abstract = {We demonstrate the feasibility of recording 1H–15N correlation spectra of proteins in only one second of acquisition time. The experiment combines recently proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved real-time NMR studies of kinetic processes in proteins with an increased time resolution. The sensitivity of the experiment is sufficient to be applicable to a wide range of molecular systems available at millimolar concentration on a high magnetic field spectrometer.},
author = {Schanda, Paul and Brutscher, Bernhard},
issn = {1090-7807},
journal = {Journal of Magnetic Resonance},
keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics},
number = {2},
pages = {334--339},
publisher = {Elsevier},
title = {{Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR}},
doi = {10.1016/j.jmr.2005.10.007},
volume = {178},
year = {2006},
}
@article{8513,
author = {Kaloshin, Vadim and Saprykina, Maria},
issn = {1553-5231},
journal = {Discrete & Continuous Dynamical Systems - A},
number = {2},
pages = {611--640},
publisher = {American Institute of Mathematical Sciences (AIMS)},
title = {{Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits}},
doi = {10.3934/dcds.2006.15.611},
volume = {15},
year = {2006},
}
@article{8514,
abstract = {We study the extent to which the Hausdorff dimension of a compact subset of an infinite-dimensional Banach space is affected by a typical mapping into a finite-dimensional space. It is possible that the dimension drops under all such mappings, but the amount by which it typically drops is controlled by the ‘thickness exponent’ of the set, which was defined by Hunt and Kaloshin (Nonlinearity12 (1999), 1263–1275). More precisely, let $X$ be a compact subset of a Banach space $B$ with thickness exponent $\tau$ and Hausdorff dimension $d$. Let $M$ be any subspace of the (locally) Lipschitz functions from $B$ to $\mathbb{R}^{m}$ that contains the space of bounded linear functions. We prove that for almost every (in the sense of prevalence) function $f \in M$, the Hausdorff dimension of $f(X)$ is at least $\min\{ m, d / (1 + \tau) \}$. We also prove an analogous result for a certain part of the dimension spectra of Borel probability measures supported on $X$. The factor $1 / (1 + \tau)$ can be improved to $1 / (1 + \tau / 2)$ if $B$ is a Hilbert space. Since dimension cannot increase under a (locally) Lipschitz function, these theorems become dimension preservation results when $\tau = 0$. We conjecture that many of the attractors associated with the evolution equations of mathematical physics have thickness exponent zero. We also discuss the sharpness of our results in the case $\tau > 0$.},
author = {OTT, WILLIAM and HUNT, BRIAN and Kaloshin, Vadim},
issn = {0143-3857},
journal = {Ergodic Theory and Dynamical Systems},
number = {3},
pages = {869--891},
publisher = {Cambridge University Press},
title = {{The effect of projections on fractal sets and measures in Banach spaces}},
doi = {10.1017/s0143385705000714},
volume = {26},
year = {2006},
}
@inproceedings{8515,
abstract = {We consider the evolution of a set carried by a space periodic incompressible stochastic flow in a Euclidean space. We
report on three main results obtained in [8, 9, 10] concerning long time behaviour for a typical realization of the stochastic flow. First, at time t most of the particles are at a distance of order √t away from the origin. Moreover, we prove a Central Limit Theorem for the evolution of a measure carried by the flow, which holds for almost every realization of the flow. Second, we show the existence of a zero measure full Hausdorff dimension set of points, which
escape to infinity at a linear rate. Third, in the 2-dimensional case, we study the set of points visited by the original set by time t. Such a set, when scaled down by the factor of t, has a limiting non random shape.},
author = {Kaloshin, Vadim and DOLGOPYAT, D. and KORALOV, L.},
booktitle = {XIVth International Congress on Mathematical Physics},
isbn = {9789812562012},
location = {Lisbon, Portugal},
pages = {290--295},
publisher = {World Scientific},
title = {{Long time behaviour of periodic stochastic flows}},
doi = {10.1142/9789812704016_0026},
year = {2006},
}
@article{854,
abstract = {Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch - the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.},
author = {Rogaev, Evgeny I and Moliaka, Yuri K and Malyarchuk, Boris A and Fyodor Kondrashov and Derenko, Miroslava V and Chumakov, Ilya M and Grigorenko, Anastasia P},
journal = {PLoS Biology},
number = {3},
pages = {0403 -- 0410},
publisher = {Public Library of Science},
title = {{Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius}},
doi = {10.1371/journal.pbio.0040073},
volume = {4},
year = {2006},
}
@article{868,
abstract = {Background: The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results: Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion: The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.},
author = {Fyodor Kondrashov and Koonin, Eugene V and Morgunov, Igor G and Finogenova, Tatiana V and Kondrashova, Marie N},
journal = {Biology Direct},
publisher = {BioMed Central},
title = {{Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation}},
doi = {10.1186/1745-6150-1-31},
volume = {1},
year = {2006},
}
@article{869,
abstract = {The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is ∼10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.},
author = {Fyodor Kondrashov and Ogurtsov, Aleksey Yu and Kondrashov, Alexey S},
journal = {Journal of Theoretical Biology},
number = {4},
pages = {616 -- 626},
publisher = {Elsevier},
title = {{Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites}},
doi = {10.1016/j.jtbi.2005.10.020},
volume = {240},
year = {2006},
}
@article{873,
abstract = {New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10-9-10-10 per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.},
author = {Fyodor Kondrashov and Kondrashov, Alexey S},
journal = {Journal of Theoretical Biology},
number = {2},
pages = {141 -- 151},
publisher = {Elsevier},
title = {{Role of selection in fixation of gene duplications}},
doi = {10.1016/j.jtbi.2005.08.033},
volume = {239},
year = {2006},
}
@article{1715,
abstract = {Background: Cell-to-cell communication at the synapse involves synaptic transmission as well as signaling mediated by growth factors, which provide developmental and plasticity cues. There is evidence that a retrograde, presynaptic transforming growth factor-β (TGF-β) signaling event regulates synapse development and function in Drosophila. Results: Here we show that a postsynaptic TGF-β signaling event occurs during larval development. The type I receptor Thick veins (Tkv) and the R-Smad transcription factor Mothers-against-dpp (Mad) are localized postsynaptically in the muscle. Furthermore, Mad phosphorylation occurs in regions facing the presynaptic active zones of neurotransmitter release within the postsynaptic subsynaptic reticulum (SSR). In order to monitor in real time the levels of TGF-β signaling in the synapse during synaptic transmission, we have established a FRAP assay to measure Mad nuclear import/export in the muscle. We show that Mad nuclear trafficking depends on stimulation of the muscle. Conclusions: Our data suggest a mechanism linking synaptic transmission and postsynaptic TGF-β signaling that may coordinate nerve-muscle development and function.},
author = {Dudu, Veronika and Bittig, Thomas and Entchev, Eugeni V and Anna Kicheva and Julicher, Frank and González-Gaitán, Marcos A},
journal = {Current Biology},
number = {7},
pages = {625 -- 635},
publisher = {Cell Press},
title = {{Postsynaptic mad signaling at the Drosophila neuromuscular junction}},
doi = {10.1016/j.cub.2006.02.061},
volume = {16},
year = {2006},
}
@article{1716,
author = {Dudu, Veronika and Bittig, Thomas and Entchev, Eugeni V and Anna Kicheva and Julicher, Frank and González-Gaitán, Marcos A},
journal = {Current Biology},
number = {12},
publisher = {Cell Press},
title = {{Erratum: Postsynaptic mad signaling at the Drosophila neuromuscular junction}},
doi = {10.1016/j.cub.2006.06.020},
volume = {16},
year = {2006},
}
@article{1745,
abstract = {SiGe islands grown by deposition of 10 monolayers of Ge on Si(0 0 1) at 740 °C were investigated by using a combination of selective wet chemical etching and atomic force microscopy. The used etchant, a solution consisting of ammonium hydroxide and hydrogen peroxide, shows a high selectivity of Ge over SixGe1-x and is characterized by relatively slow etching rates for Si-rich alloys. By performing successive etching experiments on the same sample area, we are able to gain a deeper insight into the lateral displacement the islands undergo during post growth annealing.},
author = {Georgios Katsaros and Rastelli, Armando and Stoffel, Mathieu and Isella, Giovanni and Von Känel, Hans and Bittner, Alexander M and Tersoff, Jerry and Denker, Ulrich and Schmidt, Oliver G and Costantini, Giovanni and Kern, Klaus},
journal = {Surface Science},
number = {12},
pages = {2608 -- 2613},
publisher = {Elsevier},
title = {{Investigating the lateral motion of SiGe islands by selective chemical etching}},
doi = {10.1016/j.susc.2006.04.027},
volume = {600},
year = {2006},
}
@article{1746,
abstract = {A microscopic picture for the GaAs overgrowth of self-organized InAs/GaAs(001) quantum dots is developed. Scanning tunneling microscopy measurements reveal two capping regimes: the first being characterized by a dot shrinking and a backward pyramid-to-dome shape transition. This regime is governed by fast dynamics resulting in island morphologies close to thermodynamic equilibrium. The second regime is marked by a true overgrowth and is controlled by kinetically limited surface diffusion processes. A simple model is developed to describe the observed structural changes which are rationalized in terms of energetic minimization driven by lattice mismatch and alloying.},
author = {Costantini, Giovanni and Rastelli, Armando and Manzano, Carlos and Acosta-Diaz, P and Songmuang, Rudeeson and Georgios Katsaros and Schmidt, Oliver G and Kern, Klaus},
journal = {Physical Review Letters},
number = {22},
publisher = {American Physical Society},
title = {{Interplay between thermodynamics and kinetics in the capping of InAs/GaAs (001) quantum dots}},
doi = {10.1103/PhysRevLett.96.226106},
volume = {96},
year = {2006},
}
@article{1747,
abstract = {We report on recent advances in the understanding of surface processes occurring during growth and post-growth annealing of strained islands which may find application as self-assembled quantum dots. We investigate the model system SiGe/Si(0 0 1) by a new approach based on "reading the footprints" which islands leave on the substrate during their growth and evolution. Such footprints consist of trenches carved in the Si substrate. We distinguish between surface footprints and footprints buried below the islands. The former allow us to discriminate islands which are in the process of growing from those which are shrinking. Islands with steep morphologies grow at the expense of smaller and shallower islands, consistent with the kinetics of anomalous coarsening. While shrinking, islands change their shape according to thermodynamic predictions. Buried footprints are investigated by removing the SiGe epilayer by means of selective wet chemical etching. Their reading shows that: (i) during post-growth annealing islands move laterally because of surface-mediated Si-Ge intermixing; (ii) a tree-ring structure of trenches is created by dislocated islands during their "cyclic" growth. This allows us to distinguish coherent from dislocated islands and to establish whether the latter are the result of island coalescence.},
author = {Rastelli, Armando and Stoffel, Mathieu and Georgios Katsaros and Tersoff, Jerry and Denker, Ulrich and Merdzhanova, Tsvetelina and Kar, Gouranga S and Costantini, Giovanni and Kern, Klaus and Von Känel, Hans and Schmidt, Oliver G},
journal = {Microelectronics Journal},
number = {12},
pages = {1471 -- 1476},
publisher = {Elsevier},
title = {{Reading the footprints of strained islands}},
doi = {10.1016/j.mejo.2006.05.029},
volume = {37},
year = {2006},
}
@article{1748,
abstract = {The authors apply selective wet chemical etching and atomic force microscopy to reveal the three-dimensional shape of SiGeSi (001) islands after capping with Si. Although the "self-assembled quantum dots" remain practically unaffected by capping in the temperature range of 300-450 °C, significant morphological changes take place on the Si surface. At 450 °C, the morphology of the capping layer (Si matrix) evolves toward an intriguing semifacetted structure, which we call a "ziggurat," giving the misleading impression of a stepped SiGe island shape.},
author = {Georgios Katsaros and Rastelli, Armando and Stoffel, Mathieu and Costantini, Giovanni and Schmidt, Oliver G and Kern, Klaus and Tersoff, Jerry and Müller, Elisabeth and Von Känel, Hans},
journal = {Applied Physics Letters},
number = {25},
publisher = {American Institute of Physics},
title = {{Evolution of buried semiconductor nanostructures and origin of stepped surface mounds during capping}},
doi = {10.1063/1.2405876},
volume = {89},
year = {2006},
}
@article{1796,
abstract = {Drugs that block the entry of human immunodeficiency virus type 1 (HIV-1) into host cells abrogate the establishment of a productive infection and should ideally diminish the chances of HIV-1 developing resistance. This review will give an overview of the mechanism by which the envelope glycoprotein mediates HIV-1 entry and will summarize current drug developments.},
author = {Sandra Siegert and Schnierle, Peter and Schnierle, Barbara S},
journal = {Mini-Reviews in Medicinal Chemistry},
number = {5},
pages = {557 -- 562},
publisher = {Bentham Science Publishers},
title = {{Novel anti-viral therapy: Drugs that block HIV entry at different target sites}},
doi = {10.2174/138955706776876267},
volume = {6},
year = {2006},
}
@article{1961,
abstract = {Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster Nia, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.
},
author = {Leonid Sazanov and Hinchliffe, Philip },
journal = {Science},
number = {5766},
pages = {1430 -- 1436},
publisher = {American Association for the Advancement of Science},
title = {{Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus}},
doi = {10.1126/science.1123809},
volume = {311},
year = {2006},
}
@article{1966,
abstract = {The hydrophilic domain (peripheral arm) of the proton-translocating NADH:quinone oxidoreductase (complex I) from the thermophilic organism Thermus thermophilus HB8 has been purified and characterized. The subcomplex is stable in sodium dodecyl sulfate up to 80 °C. Of nine iron-sulfur clusters, four to five (one or two binuclear and three tetranuclear) could be detected by EPR in the NADH-reduced enzyme. The preparation consists of eight different polypeptides. Seven of them have been positively identified by peptide mass mapping and N-terminal sequencing as known hydrophilic subunits of T. thermophilus complex I. The eighth polypeptide copurified with the subcomplex at all stages, is strongly associated with the other subunits, and is present in crystals of the subcomplex, used for X-ray data collection. Therefore, it has been identified as a novel complex I subunit and named Nqo15. It is encoded in a locus separate from the nqo operon, containing the 14 other known complex I genes. ORFs encoding Nqo15 homologues are present in the genomes of the closest relatives of T. thermophilus. Our data show that, contrary to previous assumptions, bacterial complex I can contain proteins in addition to a "core" complement of 14 subunits.},
author = {Hinchliffe, Philip and Carroll, Joe D and Leonid Sazanov},
journal = {Biochemistry},
number = {14},
pages = {4413 -- 4420},
publisher = {ACS},
title = {{Identification of a novel subunit of respiratory complex I from Thermus thermophilus}},
doi = {10.1021/bi0600998},
volume = {45},
year = {2006},
}
@article{2066,
abstract = {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},
author = {Beatriz Vicoso and Charlesworth, Brian},
journal = {Nature Reviews Genetics},
number = {8},
pages = {645 -- 653},
publisher = {Nature Publishing Group},
title = {{Evolution on the X chromosome: Unusual patterns and processes}},
doi = {10.1038/nrg1914},
volume = {7},
year = {2006},
}
@inproceedings{2077,
abstract = {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.},
author = {Bernd Bickel and Wicke, Martin and Gross, Markus},
publisher = {IOS Press},
title = {{Adaptive simulation of electrical discharges}},
year = {2006},
}
@inproceedings{2088,
abstract = {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. },
author = {Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Bernd Bickel and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
pages = {1013 -- 1024},
publisher = {ACM},
title = {{Analysis of human faces using a measurement-based skin reflectance model}},
doi = {10.1145/1179352.1141987},
year = {2006},
}
@article{2089,
abstract = {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.},
author = {Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Bernd Bickel and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
journal = {ACM Transactions on Graphics},
number = {3},
pages = {1013 -- 1024},
publisher = {ACM},
title = {{Analysis of human faces using a measurement-based skin reflectance model}},
doi = {10.1145/1141911.1141987},
volume = {25},
year = {2006},
}