@inproceedings{4437,
abstract = {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.},
author = {Thomas Henzinger and Piterman, Nir},
pages = {395 -- 410},
publisher = {Springer},
title = {{Solving games without determinization}},
doi = {10.1007/11874683_26},
volume = {4207},
year = {2006},
}
@article{4451,
abstract = {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.},
author = {Thomas Henzinger and Kupferman, Orna and Majumdar, Ritankar S},
journal = {Theoretical Computer Science},
number = {2},
pages = {173 -- 186},
publisher = {Elsevier},
title = {{On the universal and existential fragments of the mu-calculus}},
doi = {10.1016/j.tcs.2005.11.015},
volume = {354},
year = {2006},
}
@inproceedings{4526,
abstract = {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.},
author = {Ghosal, Arkadeb and Thomas Henzinger and Iercan, Daniel and Kirsch, Christoph M and Sangiovanni-Vincentelli, Alberto},
pages = {132 -- 141},
publisher = {ACM},
title = {{A hierarchical coordination language for interacting real-time tasks}},
doi = {10.1145/1176887.1176907},
year = {2006},
}
@inproceedings{4552,
abstract = {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.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Thomas Henzinger},
pages = {291 -- 300},
publisher = {IEEE},
title = {{Strategy improvement for concurrent reachability games}},
doi = {10.1109/QEST.2006.48},
year = {2006},
}
@inproceedings{4401,
author = {Alur, Rajeev and Pavol Cerny and Zdancewic,Steve},
pages = {107 -- 118},
publisher = {Springer},
title = {{Preserving Secrecy Under Refinement}},
doi = {1543},
year = {2006},
}
@inproceedings{4538,
abstract = {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.},
author = {Krishnendu Chatterjee and Thomas Henzinger},
pages = {512 -- 523},
publisher = {Springer},
title = {{Strategy improvement and randomized subexponential algorithms for stochastic parity games}},
doi = {10.1007/11672142_42},
volume = {3884},
year = {2006},
}
@inproceedings{578,
abstract = {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.},
author = {Peters, Nicholas A and Arnold, Keith J and VanDevender, Aaron P and Jeffrey, Evan R and Rangarajan, Radhika and Onur Hosten and Barreiro, Julio T and Altepeter, Joseph B and Kwiat, Paul G},
publisher = {SPIE},
title = {{Towards a quasi-deterministic single-photon source}},
doi = {10.1117/12.684702},
volume = {6305},
year = {2006},
}
@article{903,
abstract = {Background: Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. Methods: A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues. Results: We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. Conclusion: The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during tumorigenic somatic evolution.},
author = {Babenko, Vladimir N and Basu, Malay K and Fyodor Kondrashov and Rogozin, Igor B and Koonin, Eugene V},
journal = {BMC Cancer},
publisher = {BioMed Central},
title = {{Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis}},
doi = {10.1186/1471-2407-6-36},
volume = {6},
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{7328,
abstract = {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.},
author = {Freunberger, Stefan Alexander and Reum, Mathias and Evertz, Jörg and Wokaun, Alexander and Büchi, Felix N.},
issn = {0013-4651},
journal = {Journal of The Electrochemical Society},
number = {11},
publisher = {The Electrochemical Society},
title = {{Measuring the current distribution in PEFCs with sub-millimeter resolution}},
doi = {10.1149/1.2345591},
volume = {153},
year = {2006},
}
@article{7330,
abstract = {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.},
author = {Santis, M. and Freunberger, Stefan Alexander and Reiner, A. and Büchi, F.N.},
issn = {0013-4686},
journal = {Electrochimica Acta},
number = {25},
pages = {5383--5393},
publisher = {Elsevier},
title = {{Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients}},
doi = {10.1016/j.electacta.2006.02.008},
volume = {51},
year = {2006},
}
@unpublished{573,
abstract = {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. },
author = {Hosten, Onur and Rakher, Matthew and Barreiro, Julio and Peters, Nicholas and Kwiat, Paul},
pages = {12},
publisher = {ArXiv},
title = {{Counterfactual computation revisited}},
year = {2006},
}
@article{2134,
abstract = {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.},
author = {Ehresmann, Arno and Werner, Lutz and Klumpp, Stefan and Demekhin, Ph V and Mikhail Lemeshko and Sukhorukov, V. L and Schartner, Karl H and Schmoranzer, Hans P},
journal = {Journal of Physics B: Atomic, Molecular and Optical Physics},
number = {6},
pages = {L119 -- L126},
publisher = {IOP Publishing Ltd.},
title = {{Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule}},
doi = {10.1088/0953-4075/39/6/L03},
volume = {39},
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},
}
@inproceedings{2090,
author = {Bernd Bickel and Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
publisher = {ACM},
title = {{Processing and editing of faces using a measurement-based skin reflectance model}},
doi = {10.1145/1179849.1180059},
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{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{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{3005,
author = {Friml, Jirí and Benfey, Philip and Benková, Eva and Bennett, Malcolm and Berleth, Thomas and Geldner, Niko and Grebe, Markus and Heisler, Marcus and Hejátko, Jan and Jürgens, Gerd and Laux, Thomas and Lindsey, Keith and Lukowitz, Wolfgang and Luschnig, Christian and Offringa, Remko and Scheres, Ben and Swarup, Ranjan and Torres Ruiz, Ramón and Weijers, Dolf and Zažímalová, Eva},
journal = {Trends in Plant Science},
number = {1},
pages = {12 -- 14},
publisher = {Cell Press},
title = {{Apical-basal polarity: Why plant cells don't stand on their heads}},
doi = {10.1016/j.tplants.2005.11.010},
volume = {11},
year = {2006},
}
@article{3012,
abstract = {Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux.},
author = {Petrášek, Jan and Mravec, Jozef and Bouchard, Rodolphe and Blakeslee, Joshua and Melinda Abas and Seifertová, Daniela and Wiśniewska, Justyna and Tadele, Zerihun and Kubeš, Martin and Čovanová, Milada and Dhonukshe, Pankaj and Skůpa, Petr and Eva Benková and Perry, Lucie and Křeček, Pavel and Lee, Ok Ran and Fink, Gerald R and Geisler, Markus and Murphy, Angus S and Luschnig, Christian and Zažímalová, Eva and Jirí Friml},
journal = {Science},
number = {5775},
pages = {914 -- 918},
publisher = {American Association for the Advancement of Science},
title = {{PIN proteins perform a rate-limiting function in cellular auxin efflux}},
doi = {10.1126/science.1123542},
volume = {312},
year = {2006},
}
@article{3017,
abstract = {The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events.},
author = {Tanaka, Hirokazu and Dhonukshe, Pankaj and Brewer, Philip and Friml, Jirí},
journal = {Cellular and Molecular Life Sciences},
number = {23},
pages = {2738 -- 2754},
publisher = {Birkhäuser},
title = {{Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development}},
doi = {10.1007/s00018-006-6116-5},
volume = {63},
year = {2006},
}
@inproceedings{3214,
abstract = {The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key.
Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers.
But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation.},
author = {Maurer, Ueli M and Oswald, Yvonne A and Krzysztof Pietrzak and Sjödin, Johan},
pages = {391 -- 408},
publisher = {Springer},
title = {{Luby Rackoff ciphers from weak round functions }},
doi = {10.1007/11761679_24},
volume = {4004},
year = {2006},
}
@inbook{3404,
author = {Harald Janovjak and Sawhney, Ravi K and Stark, Martin and Mueller, Daniel J},
booktitle = {Techniques in Microscopy for Biomedical Applications},
pages = {213 -- 284},
publisher = {World Scientific Publishing},
title = {{Atomic force microscopy}},
volume = {2},
year = {2006},
}
@misc{3512,
abstract = {Methods, apparatus and computer program products provide efficient techniques for reconstructing surfaces from data point sets. These techniques include reconstructing surfaces from sets of scanned data points that have preferably undergone preprocessing operations to improve their quality by, for example, reducing noise and removing outliers. These techniques include reconstructing a dense and locally two-dimensionally distributed 3D point set (e.g., point cloud) by merging stars in two-dimensional weighted Delaunay triangulations within estimated tangent planes. The techniques include determining a plurality of stars from a plurality of points p.sub.i in a 3D point set S that at least partially describes the 3D surface, by projecting the plurality of points p.sub.i onto planes T.sub.i that are each estimated to be tangent about a respective one of the plurality of points p.sub.i. The plurality of stars are then merged into a digital model of the 3D surface.},
author = {Fletcher, Yates G and Gloth, Tobias and Herbert Edelsbrunner and Fu, Ping},
publisher = {Elsevier},
title = {{Method, apparatus and computer products that reconstruct surfaces from data points}},
doi = {US 7,023,432 B2},
year = {2006},
}
@article{3815,
abstract = {It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network.},
author = {Bischofberger, Josef and Engel, Dominique and Frotscher, Michael and Peter Jonas},
journal = {Pflugers Archiv : European Journal of Physiology},
number = {3},
pages = {361 -- 72},
publisher = {Springer},
title = {{Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network}},
doi = {10.1007/s00424-006-0093-2},
volume = {453},
year = {2006},
}
@inproceedings{3500,
abstract = {The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n).},
author = {Krishnendu Chatterjee and Thomas Henzinger and Piterman, Nir},
publisher = {ACM},
title = {{Algorithms for Büchi Games}},
year = {2006},
}
@inproceedings{3889,
abstract = {We study observation-based strategies for two-player turn-based games on graphs with omega-regular objectives. An observation-based strategy relies on imperfect information about the history of a play, namely, on the past sequence of observations. Such games occur in the synthesis of a controller that does not see the private state of the plant. Our main results are twofold. First, we give a fixed-point algorithm for computing the set of states from which a player can win with a deterministic observation-based strategy for any omega-regular objective. The fixed point is computed in the lattice of antichains of state sets. This algorithm has the advantages of being directed by the objective and of avoiding an explicit subset construction on the game graph. Second, we give an algorithm for computing the set of states from which a player can win with probability 1 with a randomized observation-based strategy for a Buchi objective. This set is of interest because in the absence of perfect information, randomized strategies are more powerful than deterministic ones. We show that our algorithms are optimal by proving matching lower bounds.},
author = {Krishnendu Chatterjee and Doyen, Laurent and Thomas Henzinger and Raskin, Jean-François},
pages = {287 -- 302},
publisher = {Springer},
title = {{Algorithms for omega-regular games with imperfect information}},
doi = {10.1007/11874683_19},
volume = {4207},
year = {2006},
}
@inproceedings{3891,
abstract = {We study infinite stochastic games played by two-players over a finite state space, with objectives specified by sets of infinite traces. The games are concurrent (players make moves simultaneously and independently), stochastic (the next state is determined by a probability distribution that depends on the current state and chosen moves of the players) and infinite (proceeds for infinite number of rounds). The analysis of concurrent stochastic games can be classified into: quantitative analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing the set of states with optimum value 1. We consider concurrent games with tail objectives, i.e., objectives that are independent of the finite-prefix of traces, and show that the class of tail objectives are strictly richer than the omega-regular objectives. We develop new proof techniques to extend several properties of concurrent games with omega-regular objectives to concurrent games with tail objectives. We prove the positive limit-one property for tail objectives, that states for all concurrent games if the optimum value for a player is positive for a tail objective Phi at some state, then there is a state where the optimum value is 1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly conflicting objectives) games with tail objectives can be related to equilibrium values of nonzero-sum (not strictly conflicting objectives) games with simpler reachability objectives. A consequence of our analysis presents a polynomial time reduction of the quantitative analysis of tail objectives to the qualitative analysis for the sub-class of one-player stochastic games (Markov decision processes).},
author = {Krishnendu Chatterjee},
pages = {256 -- 270},
publisher = {Springer},
title = {{Concurrent games with tail objectives}},
doi = {10.1007/11874683_17},
volume = {4207},
year = {2006},
}
@article{3935,
abstract = {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.},
author = {Chu, Haiyan and Thievessen, Ingo and Michael Sixt and Lämmermann, Tim and Waisman, Ari and Braun, Attila and Noegel, Angelika A and Fässler, Reinhard},
journal = {Molecular and Cellular Biology},
number = {5},
pages = {1817 -- 1825},
publisher = {American Society for Microbiology},
title = {{γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response}},
doi = {10.1128/MCB.26.5.1817-1825.2006},
volume = {26},
year = {2006},
}
@article{3978,
abstract = {Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures.},
author = {Ban, Yih-En Andrew and Rudolph, Johannes and Zhou, Pei and Herbert Edelsbrunner},
journal = {Proteins: Structure, Function and Bioinformatics},
number = {4},
pages = {852 -- 864},
publisher = {Wiley-Blackwell},
title = {{Evaluating the quality of NMR structures by local density of protons}},
doi = {10.1002/prot.20811},
volume = {62},
year = {2006},
}
@article{3980,
abstract = {Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking.},
author = {Agarwal, Pankaj K and Herbert Edelsbrunner and Harer, John and Wang, Yusu},
journal = {Discrete & Computational Geometry},
number = {4},
pages = {553 -- 572},
publisher = {Springer},
title = {{Extreme elevation on a 2-manifold}},
doi = {10.1007/s00454-006-1265-8},
volume = {36},
year = {2006},
}
@article{4173,
abstract = {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.},
author = {Link, Vinzenz and Shevchenko, Andrej and Heisenberg, Carl-Philipp},
journal = {BMC Developmental Biology},
pages = {1 -- 9},
publisher = {BioMed Central},
title = {{Proteomics of early zebrafish embryos}},
doi = {10.1186/1471-213X-6-1},
volume = {6},
year = {2006},
}
@article{4178,
abstract = {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.},
author = {Langenberg, Tobias and Dracz, Tadeusz and Oates, Andrew C and Heisenberg, Carl-Philipp and Brand, Michael},
journal = {Developmental Dynamics},
number = {4},
pages = {928 -- 933},
publisher = {Wiley-Blackwell},
title = {{Analysis and visualization of cell movement in the developing zebrafish brain}},
doi = {10.1002/dvdy.20692},
volume = {235},
year = {2006},
}
@misc{4250,
abstract = {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.},
author = {Nicholas Barton},
booktitle = {Current Biology},
number = {16},
pages = {647 -- 650},
publisher = {Cell Press},
title = {{Evolutionary Biology: How did the human species form?}},
doi = {10.1016/j.cub.2006.07.032},
volume = {16},
year = {2006},
}
@article{4351,
abstract = {BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.},
author = {Jonathan Bollback},
journal = {BMC Bioinformatics},
publisher = {BioMed Central},
title = {{SIMMAP: stochastic character mapping of discrete traits on phylogenies}},
doi = {10.1186/1471-2105-7-88},
volume = {7},
year = {2006},
}
@article{4248,
abstract = {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.},
author = {Roze, Denis and Nicholas Barton},
journal = {Genetics},
number = {3},
pages = {1793 -- 1811},
publisher = {Genetics Society of America},
title = {{The Hill-Robertson effect and the evolution of recombination}},
doi = {10.1534/genetics.106.058586 },
volume = {173},
year = {2006},
}
@inproceedings{4539,
abstract = {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.},
author = {Krishnendu Chatterjee and Thomas Henzinger},
pages = {257 -- 271},
publisher = {Springer},
title = {{Finitary winning in omega-regular games}},
doi = {10.1007/11691372_17},
volume = {3920},
year = {2006},
}
@article{579,
abstract = {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. },
author = {Onur Hosten and Rakher, Matthew T and Barreiro, Julio T and Peters, Nicholas A and Kwiat, Paul G},
journal = {Nature},
number = {7079},
pages = {949 -- 952},
publisher = {Nature Publishing Group},
title = {{Counterfactual quantum computation through quantum interrogation}},
doi = {10.1038/nature04523},
volume = {439},
year = {2006},
}
@article{7331,
abstract = {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.},
author = {Freunberger, Stefan Alexander and Wokaun, Alexander and Büchi, Felix N.},
issn = {0013-4651},
journal = {Journal of The Electrochemical Society},
number = {5},
publisher = {The Electrochemical Society},
title = {{In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance}},
doi = {10.1149/1.2185282},
volume = {153},
year = {2006},
}
@article{7329,
abstract = {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.},
author = {Freunberger, Stefan Alexander and Reum, Mathias and Wokaun, Alexander and Büchi, Felix N.},
issn = {1388-2481},
journal = {Electrochemistry Communications},
number = {9},
pages = {1435--1438},
publisher = {Elsevier},
title = {{Expanding current distribution measurement in PEFCs to sub-millimeter resolution}},
doi = {10.1016/j.elecom.2006.05.032},
volume = {8},
year = {2006},
}
@unpublished{574,
abstract = {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. },
author = {Hosten, Onur and Kwiat, Paul},
pages = {2},
publisher = {ArXiv},
title = {{Weak measurements and counterfactual computation}},
year = {2006},
}
@article{1461,
abstract = {This note proves combinatorially that the intersection pairing on the middle-dimensional compactly supported cohomology of a toric hyperkähler variety is always definite, providing a large number of non-trivial L 2 harmonic forms for toric hyperkähler metrics on these varieties. This is motivated by a result of Hitchin about the definiteness of the pairing of L 2 harmonic forms on complete hyperkähler manifolds of linear growth.},
author = {Tamas Hausel and Swartz, Edward},
journal = {Proceedings of the American Mathematical Society},
number = {8},
pages = {2403 -- 2409},
publisher = {American Mathematical Society},
title = {{Intersection forms of toric hyperkähler varieties}},
doi = {10.1090/S0002-9939-06-08248-7},
volume = {134},
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{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{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},
}
@article{2142,
abstract = {Fluorescence from fragments formed after the de-excitation of the N*2(1s−1π*) resonance has been measured in the spectral range of 135–190 nm. This range is dominated by lines in atomic nitrogen and lines formed by overlapping C2Σ+u(v') → X2Σ+g(v'') bands with Δv = const in the N+2 molecular ion which result from the spectator Auger decays of the N*2(1s−1π*(vr)) resonances. Ab initio calculations of the corresponding potential curves and transition probabilities showed that the observed irregular intensity dependence of the C2Σ+u(v') → X2Σ+g(v'')(Δv = const) fluorescence lines on the vibrational quantum number vr is due to transitions between vibrational levels during the reaction N2(v0 = 0)→ N*2(1s−1π*(vr)) Longrightarrow C2Σ+u(v') → X2Σ+g(v'').},
author = {Ehresmann, Arno and Werner, Lutz and Klumpp, Stefan and Lucht, S and Schmoranzer, Hans P and Mickat, Sascha and Schill, Rüdiger H and Schartner, Karl H and Demekhin, Philipp and Mikhail Lemeshko and Sukhorukov, Victor L},
journal = {Journal of Physics B: Atomic, Molecular and Optical Physics},
number = {2},
pages = {283 -- 304},
publisher = {IOP Publishing Ltd.},
title = {{Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance}},
doi = {10.1088/0953-4075/39/2/006},
volume = {39},
year = {2006},
}
@article{215,
abstract = {For any n≥3, let F ∈ Z[X0,...,Xn ] be a form of degree d *≥5 that defines a non-singular hypersurface X ⊂ Pn . The main result in this paper is a proof of the fact that the number N (F ; B) of Q-rational points on X which have height at most B satisfiesN (F ; B) = Od,ε,n (Bn −1+ε ), for any ε > 0. The implied constant in this estimate depends at most upon d, ε and n. New estimates are also obtained for the number of representations of a positive integer as the sum of three dth powers, and for the paucity of integer solutions to equal sums of like polynomials.*},
author = {Timothy Browning and Heath-Brown, Roger},
journal = {Bulletin of the London Mathematical Society},
number = {3},
pages = {401 -- 410},
publisher = {Wiley-Blackwell},
title = {{The density of rational points on non-singular hypersurfaces, I}},
doi = {10.1112/S0024609305018412},
volume = {38},
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},
}
@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},
}