@article{3193,
abstract = {Optimization techniques based on graph cuts have become a standard tool for many vision applications. These techniques allow to minimize efficiently certain energy functions corresponding to pairwise Markov Random Fields (MRFs). Currently, there is an accepted view within the computer vision community that graph cuts can only be used for optimizing a limited class of MRF energies (e.g., submodular functions). In this survey, we review some results that show that graph cuts can be applied to a much larger class of energy functions (in particular, nonsubmodular functions). While these results are well-known in the optimization community, to our knowledge they were not used in the context of computer vision and MRF optimization. We demonstrate the relevance of these results to vision on the problem of binary texture restoration. },
author = {Vladimir Kolmogorov and Rother, Carsten},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {7},
pages = {1274 -- 1279},
publisher = {IEEE},
title = {{Minimizing nonsubmodular functions with graph cuts - A review}},
doi = {10.1109/TPAMI.2007.1031},
volume = {29},
year = {2007},
}
@inproceedings{3218,
abstract = {A (k, ℓ)-robust combiner for collision-resistant hash-functions is a construction which from ℓ hash-functions constructs a hash-function which is collision-resistant if at least k of the components are collision-resistant. One trivially gets a (k, ℓ)-robust combiner by concatenating the output of any ℓ - k + 1 of the components, unfortunately this is not very practical as the length of the output of the combiner is quite large. We show that this is unavoidable as no black-box (k, ℓ)-robust combiner whose output is significantly shorter than what can be achieved by concatenation exists. This answers a question of Boneh and Boyen (Crypto'06). },
author = {Krzysztof Pietrzak},
pages = {23 -- 33},
publisher = {Springer},
title = {{Non-trivial black-box combiners for collision-resistant hash-functions don't exist}},
doi = {10.1007/978-3-540-72540-4_2},
volume = {4515},
year = {2007},
}
@inproceedings{3219,
abstract = {Many aspects of cryptographic security proofs can be seen as the proof that a certain system (e.g. a block cipher) is indistinguishable from an ideal system (e.g. a random permutation), for different types of distinguishers. This paper presents a new generic approach to proving upper bounds on the information-theoretic distinguishing advantage (from an ideal system) for a combined system, assuming upper bounds of certain types for the component systems. For a general type of combination operation of systems, including the XOR of functions or the cascade of permutations, we prove two amplification theorems. The first is a product theorem, in the spirit of XOR-lemmas: The distinguishing advantage of the combination of two systems is at most twice the product of the individual distinguishing advantages. This bound is optimal. The second theorem states that the combination of systems is secure against some strong class of distinguishers, assuming only that the components are secure against some weaker class of distinguishers. A key technical tool of the paper is the proof of a tight two-way correspondence, previously only known to hold in one direction, between the distinguishing advantage of two systems and the probability of winning an appropriately defined game. © International Association for Cryptologic Research 2007.},
author = {Maurer, Ueli M and Krzysztof Pietrzak and Renner, Renato},
pages = {130 -- 149},
publisher = {Springer},
title = {{Indistinguishability amplification}},
doi = {10.1007/978-3-540-74143-5_8},
volume = {4622},
year = {2007},
}
@inproceedings{3220,
abstract = {We introduce a new primitive called intrusion-resilient secret sharing (IRSS), whose security proof exploits the fact that there exist functions which can be efficiently computed interactively using low communication complexity in k, but not in k-1 rounds. IRSS is a means of sharing a secret message amongst a set of players which comes with a very strong security guarantee. The shares in an IRSS are made artificially large so that it is hard to retrieve them completely, and the reconstruction procedure is interactive requiring the players to exchange k short messages. The adversaries considered can attack the scheme in rounds, where in each round the adversary chooses some player to corrupt and some function, and retrieves the output of that function applied to the share of the corrupted player. This model captures for example computers connected to a network which can occasionally he infected by malicious software like viruses, which can compute any function on the infected machine, but cannot sent out a huge amount of data. Using methods from the bounded-retrieval model, we construct an IRSS scheme which is secure against any computationally unbounded adversary as long as the total amount of information retrieved by the adversary is somewhat less than the length of the shares, and the adversary makes at most k-1 corruption rounds (as described above, where k rounds are necessary for reconstruction). We extend our basic scheme in several ways in order to allow the shares sent by the dealer to be short (the players then blow them up locally) and to handle even stronger adversaries who can learn some of the shares completely. As mentioned, there is an obvious connection between IRSS schemes and the fact that there exist functions with an exponential gap in their communication complexity for k and k-1 rounds. Our scheme implies such a separation which is in several aspects stronger than the previously known ones.},
author = {Dziembowski, Stefan and Krzysztof Pietrzak},
pages = {227 -- 237},
publisher = {IEEE},
title = {{Intrusion resilient secret sharing}},
doi = {10.1109/FOCS.2007.63},
year = {2007},
}
@inproceedings{3221,
abstract = {We investigate a general class of (black-box) constructions for range extension of weak pseudorandom functions: a construction based on m independent functions F 1,...,F m is given by a set of strings over {1,...,m}*, where for example {〈2〉, 〈1,2〉} corresponds to the function X ↦[F 2(X),F 2(F 1(X))]. All efficient constructions for range expansion of weak pseudorandom functions that we are aware of are of this form.
We completely classify such constructions as good, bad or ugly, where the good constructions are those whose security can be proven via a black-box reduction, the bad constructions are those whose insecurity can be proven via a black-box reduction, and the ugly constructions are those which are neither good nor bad.
Our classification shows that the range expansion from [10] is optimal, in the sense that it achieves the best possible expansion (2 m − 1 when using m keys).
Along the way we show that for weak quasirandom functions (i.e. in the information theoretic setting), all constructions which are not bad – in particular all the ugly ones – are secure.},
author = {Krzysztof Pietrzak and Sjödin, Johan},
pages = {517 -- 533},
publisher = {Springer},
title = {{Range extension for weak PRFs the good the bad and the ugly}},
doi = {10.1007/978-3-540-72540-4_30},
volume = {4515},
year = {2007},
}
@inproceedings{3222,
abstract = {Parallel repetition is well known to reduce the error probability at an exponential rate for single- and multi-prover interactive proofs.
Bellare, Impagliazzo and Naor (1997) show that this is also true for protocols where the soundness only holds against computationally bounded provers (e.g. interactive arguments) if the protocol has at most three rounds.
On the other hand, for four rounds they give a protocol where this is no longer the case: the error probability does not decrease below some constant even if the protocol is repeated a polynomial number of times. Unfortunately, this protocol is not very convincing as the communication complexity of each instance of the protocol grows linearly with the number of repetitions, and for such protocols the error does not even decrease for some types of interactive proofs. Noticing this, Bellare et al. construct (a quite artificial) oracle relative to which a four round protocol exists whose communication complexity does not depend on the number of parallel repetitions. This shows that there is no “black-box” error reduction theorem for four round protocols.
In this paper we give the first computationally sound protocol where k-fold parallel repetition does not decrease the error probability below some constant for any polynomial k (and where the communication complexity does not depend on k). The protocol has eight rounds and uses the universal arguments of Barak and Goldreich (2001). We also give another four round protocol relative to an oracle, unlike the artificial oracle of Bellare et al., we just need a generic group. This group can then potentially be instantiated with some real group satisfying some well defined hardness assumptions (we do not know of any candidate for such a group at the moment).},
author = {Krzysztof Pietrzak and Wikström, Douglas},
pages = {86 -- 102},
publisher = {Springer},
title = {{Parallel repetition of computationally sound protocols revisited}},
doi = {10.1007/978-3-540-70936-7_5},
volume = {4392},
year = {2007},
}
@inproceedings{3223,
abstract = {“Hash then encrypt” is an approach to message authentication, where first the message is hashed down using an ε-universal hash function, and then the resulting k-bit value is encrypted, say with a block-cipher. The security of this scheme is proportional to εq2, where q is the number of MACs the adversary can request. As ε is at least 2−k, the best one can hope for is O(q2/2k) security. Unfortunately, such small ε is not achieved by simple hash functions used in practice, such as the polynomial evaluation or the Merkle-Damg ̊ard construction, where ε grows with the message length L.
The main insight of this work comes from the fact that, by using ran- domized message preprocessing via a short random salt p (which must then be sent as part of the authentication tag), we can use the “hash then encrypt” paradigm with suboptimal “practical” ε-universal hash func- tions, and still improve its exact security to optimal O(q2/2k). Specif- ically, by using at most an O(logL)-bit salt p, one can always regain the optimal exact security O(q2/2k), even in situations where ε grows polynomially with L. We also give very simple preprocessing maps for popular “suboptimal” hash functions, namely polynomial evaluation and the Merkle-Damg ̊ard construction.
Our results come from a general extension of the classical Carter- Wegman paradigm, which we believe is of independent interest. On a high level, it shows that public randomization allows one to use the potentially much smaller “average-case” collision probability in place of the “worst-case” collision probability ε.},
author = {Dodis, Yevgeniy and Krzysztof Pietrzak},
pages = {414 -- 433},
publisher = {Springer},
title = {{Improving the security of MACs via randomized message preprocessing}},
doi = {10.1007/978-3-540-74619-5_26},
volume = {4593},
year = {2007},
}
@article{3305,
abstract = {The accumulation of deleterious mutations plays a major role in evolution, and key to this are the interactions between their fitness effects, known as epistasis. Whether mutations tend to interact synergistically (with multiple mutations being more deleterious than would be expected from their individual fitness effects) or antagonistically is important for a variety of evolutionary questions, particularly the evolution of sex. Unfortunately, the experimental evidence on the prevalence and strength of epistasis is mixed and inconclusive. Here we study theoretically whether synergistic or antagonistic epistasis is likely to be favored by evolution and by how much. We find that in the presence of recombination, evolution favors less synergistic or more antagonistic epistasis whenever mutations that change the epistasis in this direction are possible. This is because evolution favors increased buffering against the effects of deleterious mutations. This suggests that we should not expect synergistic epistasis to be widespread in nature and hence that the mutational deterministic hypothesis for the advantage of sex may not apply widely.},
author = {Desai, Michael M and Daniel Weissman and Feldman, Marcus W},
journal = {Genetics},
number = {2},
pages = {1001 -- 10},
publisher = {Genetics Society of America},
title = {{Evolution can favor antagonistic epistasis}},
doi = {10.1534/genetics.107.075812},
volume = {177},
year = {2007},
}
@article{3411,
abstract = {Mechanical single-molecule techniques offer exciting possibilities to investigate protein folding and stability in native environments at submolecular resolution. By applying a free-energy reconstruction procedure developed by Hummer and Szabo, which is based on a statistical theorem introduced by Jarzynski, we determined the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin, and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium unfolding free energy was independent of pulling rate and temperature ranging between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties in individual transmembrane helices. In halorhodopsin, the stabilization of a short helical segment yielded a characteristic signature in the energy profile. In NhaA, a pronounced peak was observed at a functionally important site in the protein. Since a large variety of single- and multispan membrane proteins can be tackled in mechanical unfolding experiments, our approach provides a basis for systematically elucidating energetic properties of membrane proteins with the resolution of individual secondary-structure elements.},
author = {Preiner, Johannes and Harald Janovjak and Rankl, Christian and Knaus, Helene and Cisneros, David A and Kedrov, Alexej and Kienberger, Ferry and Mueller, Daniel J and Hinterdorfer, Peter},
journal = {Biophysical Journal},
number = {3},
pages = {930 -- 937},
publisher = {Biophysical Society},
title = {{Free energy of membrane protein unfolding derived from single-molecule force measurements}},
doi = {10.1529/biophysj.106.096982},
volume = {93},
year = {2007},
}
@misc{3412,
abstract = {Molecular interactions are the basic language of biological processes.
They establish the forces interacting between the building blocks of
proteins and other macromolecules, thus determining their functional
roles. Because molecular interactions trigger virtually every
biological process, approaches to decipher their language are needed.
Single-molecule force spectroscopy (SMFS) has been used to detect
and characterize different types of molecular interactions that occur
between and within native membrane proteins. The first experiments
detected and localized molecular interactions that stabilized
membrane proteins, including how these interactions were established
during folding of α-helical secondary structure elements into
the native protein and how they changed with oligomerization, temperature,
and mutations. SMFS also enables investigators to detect
and locate molecular interactions established during ligand and inhibitor
binding. These exciting applications provide opportunities
for studying the molecular forces of life. Further developments will
elucidate the origins of molecular interactions encoded in their lifetimes,
interaction ranges, interplay, and dynamics characteristic of biological systems.},
author = {Kedrov, Alexej and Harald Janovjak and Sapra, Tanuj K and Mueller, Daniel J},
booktitle = {Annual Review of Biophysics},
pages = {233 -- 260},
publisher = {Annual Reviews},
title = {{Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy}},
doi = {10.1146/annurev.biophys.36.040306.132640},
volume = {36},
year = {2007},
}
@article{3427,
abstract = {We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the wing disk of the fruit fly Drosophila.
© 2007 The American Physical Society},
author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and Gonzalez Gaitan, Marcos and Julicher, Frank},
journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
number = {1},
publisher = {American Institute of Physics},
title = {{Morphogen transport in epithelia}},
doi = {10.1103/PhysRevE.75.011901},
volume = {75},
year = {2007},
}
@inbook{3432,
abstract = {Evolution has left its signature on the molecules and morphology of living organisms. Ancestral reconstruction offers an excellent tool for understanding the process of evolution using comparative information. Methods for ancestral reconstruction have generally focused on reconstructing the ancestral states at the internal nodes of a phylogeny. Often, we are not interested in particular nodes of the phylogeny but the whole history of a character. This chapter focuses on a Bayesian method for estimating these histories, or mutational paths, on phylogenies. Mutational path methods differ most notably from other approaches in their ability to estimate not only the ancestral states at the internal nodes of a phylogeny, but also the order and timing of mutational changes across the phylogeny. The chapter provides a concise introduction to the statistical tools needed for sampling mutational paths on a phylogeny.},
author = {Jonathan Bollback and Gardner, Paul P and Nielsen, Rasmus},
booktitle = {Ancestral Sequence Reconstruction},
editor = {Liberles, David A},
pages = {69 -- 79},
publisher = {Oxford University Press},
title = {{Estimating the history of mutations on a phylogeny}},
doi = {10.1093/acprof:oso/9780199299188.003.0006},
year = {2007},
}
@article{3436,
abstract = {he potential for di? erences between genetic paternity and paternity inferred from behavioral observation has long been recognized. These di? erences are associated with the challenge for females of seeking both genetic and material bene? ts; this challenge is less severe in species with polygynous, non-resource-based mating systems (such as leks) than in those with resource-based systems. We pres- ent the ? rst study of paternity patt erns in a non-resource-based species that does not form true leks. We compared paternity inferred from observed mating behavior to genetically assigned paternity in the Satin Bowerbird (Ptilonorhynchus violaceus) using eight microsatellite markers. Mating behavior was observed and recorded via automated video-cameras positioned at all bowers (29?34 bowers each year) in the study site throughout each mating season. We obtained blood samples and identi- ? ed mothers for 11 chicks in 9 nests. For all chicks, the most likely genetic father had been observed to mate with the mother in the year the chick was sampled. All most likely genetic fathers were assigned with high con? dence and all were bower- holding males. These results demonstrate that genetic paternity can be inferred from observed mating behavior with reasonable con? dence in Satin Bowerbirds. Observed male mating-success is therefore a reliable predictor of reproductive success, and this suggests that high skew in observed male mating-success translates directly to high skew in reproductive success. },
author = {Reynolds, Sheila M and Dryer, Katie and Jonathan Bollback and Uy, J Albert and Patricelli, Gail L and Robson, Timothy and Borgia, Gerald and Braun, Michael J},
journal = {The Auk},
number = {3},
pages = {857 -- 867},
publisher = {University of California Press},
title = {{Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system}},
doi = {10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2},
volume = {124},
year = {2007},
}
@article{3450,
author = {Peter Jonas and Buzsáki, György},
journal = {Scholarpedia},
publisher = {Scholarpedia},
title = {{Neural inhibition}},
doi = {10.4249/scholarpedia.3286},
volume = {2},
year = {2007},
}
@article{3523,
abstract = {On the linear track, the recent firing sequences of CA1 place cells recur during sharp wave/ripple patterns (SWRs) in a reverse temporal order [Foster & Wilson (2006) Nature, 440, 680-683]. We have found similar reverse-order reactivation during SWRs in open-field exploration where the firing sequence of cells varied before each SWR. Both the onset times and the firing patterns of cells showed a tendency for reversed sequences during SWRs. These effects were observed for SWRs that occurred during exploration, but not for those during longer immobility periods. Additionally, reverse reactivation was stronger when it was preceded by higher speed (> 5 cm/s) run periods. The trend for reverse-order SWR reactivation was not significantly different in familiar and novel environments, even though SWR-associated firing rates of both pyramidal cells and interneurons were reduced in novel environments as compared with familiar. During exploration-associated SWRs (eSWR) place cells retain place-selective firing [O'Neill et al. (2006) Neuron, 49, 143-155]. Here, we have shown that each cell's firing onset was more delayed and firing probability more reduced during eSWRs the further the rat was from the middle of the cell's place field; that is, cells receiving less momentary place-related excitatory drive fired later during SWR events. However, even controlling for place field distance, the recent firing of cells was still significantly correlated with SWR reactivation sequences. We therefore propose that both place-related drive and the firing history of cells contribute to reverse reactivation during eSWRs.},
author = {Jozsef Csicsvari and Joseph O'Neill and Allen, Kevin and Senior,Timothy},
journal = {European Journal of Neuroscience},
number = {3},
pages = {704 -- 716},
publisher = {Wiley-Blackwell},
title = {{Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration}},
doi = {10.1111/j.1460-9568.2007.05684.x},
volume = {26},
year = {2007},
}
@inproceedings{3561,
abstract = {The main result of this paper is an extension of de Silva's Weak Delaunay Theorem to smoothly embedded curves and surfaces in Euclidean space. Assuming a sufficiently fine sampling, we prove that i + 1 points in the sample span an i-simplex in the restricted Delaunay triangulation iff every subset of the i + 1 points has a weak witness.},
author = {Attali, Dominique and Herbert Edelsbrunner and Mileyko, Yuriy},
pages = {143 -- 150},
publisher = {ACM},
title = {{Weak witnesses for Delaunay triangulations of submanifolds}},
doi = {10.1145/1236246.1236267},
year = {2007},
}
@inproceedings{3601,
abstract = {In this paper, the multiobjective optimal design of space-based reconfigurable sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II) is employed to obtain multi-criteria Pareto-optimal solutions, which allows system designers to easily make a reasonable trade-off choice from the set of non-dominated solutions according to their preferences and system requirements. As a case study, a cluster-based satellite sensing network is simulated under multiple objectives. Most importantly, this paper also presents the application of our newly designed adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal design of space-based reconfigurable sensor networks.},
author = {Yang, Erfu and Haridas, Nakul and El-Rayis, Ahmed O and Erdogan, Ahmet T and Arslan, Tughrul and Nicholas Barton},
pages = {27 -- 34},
publisher = {IEEE},
title = {{Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications}},
doi = {10.1109/AHS.2007.76},
year = {2007},
}
@book{3674,
abstract = {Evolution permeates all of biology. But researchers in molecular and cellular biology, genetics, developmental biology, microbiology, and neuroscience have only recently begun to think seriously in terms of evolution. The chief reasons for this shift are the growing list of organisms with sequenced genomes; the increasingly sophisticated ways of interpreting those sequences; and the ever more powerful experimental techniques (and wider range of model organisms) with which to ask questions about evolution as well as mechanism.
Evolution serves as a primary text for undergraduate and graduate courses in evolution. It is also a text working scientists can use to educate themselves on how evolution affects their fields. It differs from currently available alternatives in containing more molecular biology than is traditionally the case. But this is not at the expense of traditional evolutionary theory. Indeed, a glance at the Table of Contents and the authors' interests reveals the range of material covered in this book. The authors are world-renowned in population genetics, bacterial genomics, paleontology, human genetics, and developmental biology. The integration of molecular biology and evolutionary biology reflects the current direction of much research among evolutionary scientists.},
author = {Barton, Nicholas H and Briggs, Derek and Eisen, Jonathan and Goldstein, David and Patel, Nipam},
publisher = {Wiley-Blackwell},
title = {{Evolution}},
year = {2007},
}
@inproceedings{3681,
abstract = {The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.
Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.},
author = {Ulges, Adrian and Christoph Lampert and Keysers,Daniel and Breuel,Thomas M},
pages = {204 -- 213},
publisher = {Springer},
title = {{Optimal dominant motion estimation using adaptive search of transformation space}},
doi = {10.1007/978-3-540-74936-3_21},
volume = {4713},
year = {2007},
}
@techreport{3687,
abstract = {Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image.
We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem.
We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.},
author = {Blaschko,Matthew B and Hofmann,Thomas and Christoph Lampert},
booktitle = {Unknown},
number = {164},
publisher = {Max-Planck-Institute for Biological Cybernetics},
title = {{Efficient subwindow search for object localization}},
year = {2007},
}
@inproceedings{3701,
abstract = {The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms.
Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.},
author = {Ulges, Adrian and Christoph Lampert and Keysers,Daniel and Breuel,Thomas M},
pages = {204 -- 213},
publisher = {Springer},
title = {{Optimal dominant motion estimation using adaptive search of transformation space}},
doi = {10.1007/978-3-540-74936-3_21},
volume = {4713},
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},
}
@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{213,
abstract = {For any integers d,n ≥2, let X ⊂ Pn be a non‐singular hypersurface of degree d that is defined over the rational numbers. The main result in this paper is a proof that the number of rational points on X which have height at most B is O(Bn − 1 + ɛ), for any ɛ > 0. The implied constant in this estimate depends at most upon d, ɛ and n. 2000 Mathematics Subject Classification 11D45 (primary), 11G35, 14G05 (secondary).},
author = {Timothy Browning and Heath-Brown, Roger and Starr, Jason M},
journal = {Proceedings of the London Mathematical Society},
number = {2},
pages = {273 -- 303},
publisher = {John Wiley and Sons Ltd},
title = {{The density of rational points on non-singular hypersurfaces, II}},
doi = {https://doi.org/10.1112/S0024611506015784},
volume = {93},
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},
}
@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{2144,
abstract = {Temperature dependent preedge and extended x-ray absorption fine structure measurements at the Zr K edge for the perovskite-type zirconates Pb Zr0.515 Ti0.485 O3 (PZT), PbZr O3 (PZ), and BaZr O3 are performed. To carry out a more accurate study of the weak reconstruction of the local atomic structure we employed a combination of two techniques: (i) analysis of the preedge fine structure, and (ii) analysis of the Fourier transform of the difference between χ (k) functions obtained at different temperatures. A detailed investigation of local atomic structure in the cubic phase for all the crystals is also performed. It is shown that neither the displacive nor the order-disorder model can describe correctly the changes of local atomic structure during phase transitions in PZ and PZT. A spherical model describing the local atomic structure of perovskite-type crystals suffering structural phase transitions is proposed.},
author = {Vedrinskiǐ, Rostislav V and Nazarenko, Elena S and Mikhail Lemeshko and Nassif, Vivian M and Proux, Olivier and Novakovich, Alexander A and Joly, Yves},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {13},
publisher = {American Physical Society},
title = {{Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates}},
doi = {10.1103/PhysRevB.73.134109},
volume = {73},
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},
}
@article{216,
abstract = {For any N ≥ 2, let Z ⊂ ℙN be a geometrically integral algebraic variety of degree d. This article is concerned with the number Nz(B) of ℚ-rational points on Z which have height at most B. For any ε > 0, we establish the estimate NZ(B) = O d,ε,N(Bdim Z+ε), provided that d ≥ 6. As indicated, the implied constant depends at most on d, ε, and N.},
author = {Timothy Browning and Heath-Brown, Roger and Salberger, Per},
journal = {Duke Mathematical Journal},
number = {3},
pages = {545 -- 578},
publisher = {Unknown},
title = {{Counting rational points on algebraic varieties}},
doi = {10.1215/S0012-7094-06-13236-2},
volume = {132},
year = {2006},
}
@article{218,
abstract = {This paper is concerned with the average order of certain arithmetic functions, as they range over the values taken by binary forms.},
author = {de la Bretèche, Régis and Timothy Browning},
journal = {Acta Arithmetica},
number = {3},
pages = {291 -- 304},
publisher = {Instytut Matematyczny},
title = {{Sums of arithmetic functions over values of binary forms}},
doi = {10.4064/aa125-3-6},
volume = {125},
year = {2006},
}
@inproceedings{7326,
abstract = {Often the properties of a single cell are considered as representative for a complete polymer electrolyte fuel cell stack or even a fuel cell system. In some cases this comes close, however, in many real cases differences on several scales become important. Cell interaction phenomena in fuel cell stacks that arise from inequalities between adjacent cells are investigated in detail experimentally. For that, a specialized 2-cell stack with advanced localized diagnostics was developed. The results show that inequalities propagate by electrical coupling, inhomogeneous cell polarization and inducing in-plane current in the common bipolar plate. The effects of the different loss-mechanisms are analyzed and quantified. },
author = {Büchi, Felix N. and Freunberger, Stefan Alexander and Santis, Marco},
booktitle = {ECS Transactions},
location = {Cancun, Mexico},
number = {1},
pages = {963--968},
publisher = {ECS},
title = {{What is learned beyond the scale of single cells?}},
doi = {10.1149/1.2356215},
volume = {3},
year = {2006},
}
@article{7327,
abstract = {Propagation of performance changes to adjacent cells in polymer electrolyte fuel cell stacks is studied by means of voltage monitoring and local current density measurements in peripheral cells of the stack. A technical fuel cell stack has been modified by implementing two independent reactant and coolant supplies in order to deliberately change the performance of one cell (anomalous cell) and study the coupling phenomena to adjacent cells (coupling cells), while keeping the working conditions of the later cell-group unaltered.
Two anomalies are studied: (i) air starvation and (ii) thermal anomaly, in a single anomalous cell in the stack and their coupling to adjacent cells. The results have shown that anomalies inducing considerable changes in the local current density of the anomalous cell (such as air starvation) propagate to adjacent cells affecting their performance. The propagation of local current density changes takes place via the common bipolar plate due to its finite thickness and in-plane conductivity. Consequently, anomalies which do not strongly influence the local current density distribution (such as a thermal anomaly under the studied working conditions) do not propagate to adjacent cells.},
author = {Santis, Marco and Freunberger, Stefan Alexander and Papra, Matthias and Wokaun, Alexander and Büchi, Felix N.},
issn = {0378-7753},
journal = {Journal of Power Sources},
number = {2},
pages = {1076--1083},
publisher = {Elsevier},
title = {{Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks}},
doi = {10.1016/j.jpowsour.2006.06.007},
volume = {161},
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{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},
}
@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},
}
@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{7332,
abstract = {A quasi-two-dimensional, along-the-channel mass and heat-transfer model for a proton exchange membrane fuel cell (PEFC) is described and validated against experimental current distribution data. The model is formulated in a dimensional manner, i.e., local transport phenomena are treated one-dimensional in through-plane direction and coupled in-plane by convective transport in the gas and coolant channels. Thus, a two-dimensional slice running through the repetitive unit of a cell from the anode channel via membrane-electrode assembly (MEA) and cathode channel to the coolant channel and from inlet to outlet is modeled. The aim of the work is to elucidate the influence of operating conditions such as feed gas humidities and stoichiometric ratios on the along-the-channel current density distribution and to identify the distinct underlying voltage loss mechanisms. Furthermore, a complicated technical flow field is modeled by a combination of co- and counterflow subdomains and compared with experimental current densities.},
author = {Freunberger, Stefan Alexander and Santis, Marco and Schneider, Ingo A. and Wokaun, Alexander and Büchi, Felix N.},
issn = {0013-4651},
journal = {Journal of The Electrochemical Society},
number = {2},
publisher = {The Electrochemical Society},
title = {{In-plane effects in large-scale PEMFCs}},
doi = {10.1149/1.2150150},
volume = {153},
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},
}
@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},
}
@inproceedings{577,
abstract = {Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio.},
author = {Rangarajan, Radhika and Altepeter, Joseph B and Jeffrey, Evan R and Stoutimore, Micah J and Peters, Nicholas A and Onur Hosten and Kwiat, Paul G},
publisher = {SPIE},
title = {{High-efficiency single-photon detectors}},
doi = {10.1117/12.686117},
volume = {6372},
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{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},
}
@inproceedings{583,
abstract = {Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) facilitate efficient single-photon detection. We are attempting to improve their efficiency, previously limited to < 88% by coupling losses, via anti-reflection coatings, better electronics and cryogenics.},
author = {Rangarajan, Radhika and Peters, Nicholas A and Onur Hosten and Altepeter, Joseph B and Jeffrey, Evan R and Kwiat, Paul G},
publisher = {IEEE},
title = {{Improved single-photon detection}},
doi = {10.1109/CLEO.2006.4628641},
year = {2006},
}
@article{6151,
author = {Salecker, Iris and Häusser, Michael and de Bono, Mario},
issn = {1469-221X},
journal = {EMBO reports},
number = {6},
pages = {585--589},
publisher = {Wiley},
title = {{On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits}},
doi = {10.1038/sj.embor.7400713},
volume = {7},
year = {2006},
}
@article{6152,
author = {Rogers, Candida and Persson, Annelie and Cheung, Benny and de Bono, Mario},
issn = {0960-9822},
journal = {Current Biology},
number = {7},
pages = {649--659},
publisher = {Elsevier},
title = {{Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans}},
doi = {10.1016/j.cub.2006.03.023},
volume = {16},
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{1462,
abstract = {A Fourier transform technique is introduced for counting the number of solutions of holomorphic moment map equations over a finite field. This technique in turn gives information on Betti numbers of holomorphic symplectic quotients. As a consequence, simple unified proofs are obtained for formulas of Poincaré polynomials of toric hyperkähler varieties (recovering results of Bielawski-Dancer and Hausel-Sturmfels), Poincaré polynomials of Hubert schemes of points and twisted Atiyah-Drinfeld-Hitchin-Manin (ADHM) spaces of instantons on ℂ2 (recovering results of Nakajima-Yoshioka), and Poincaré polynomials of all Nakajima quiver varieties. As an application, a proof of a conjecture of Kac on the number of absolutely indecomposable representations of a quiver is announced.},
author = {Tamas Hausel},
journal = {PNAS},
number = {16},
pages = {6120 -- 6124},
publisher = {National Academy of Sciences},
title = {{Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform}},
doi = {10.1073/pnas.0601337103},
volume = {103},
year = {2006},
}
@article{1033,
abstract = {Systems of three interacting particles are notorious for their complex physical behaviour. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction1,2 of a universal set of bound trimer states appearing for three identical bosons with a resonant two-body interaction. Counterintuitively, these states even exist in the absence of a corresponding two-body bound state. Since the formulation of Efimov\'s problem in the context of nuclear physics 35 years ago, it has attracted great interest in many areas of physics3-8. However, the observation of Efimov quantum states has remained an elusive goal3,5. Here we report the observation of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs in the range of large negative two-body scattering lengths, arising from the coupling of three free atoms to an Efimov trimer. Experimentally, we observe its signature as a giant three-body recombination loss9,10 when the strength of the two-body interaction is varied. We also detect a minimum 9,11,12 in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point with which to explore the universal properties of resonantly interacting few-body systems7. While Feshbach resonances13,14 have provided the key to control quantum-mechanical interactions on the two-body level, Efimov resonances connect ultracold matter15 to the world of few-body quantum phenomena.},
author = {Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Chin, Cheng and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Nägerl, Hanns and Grimm, Rudolf},
journal = {Nature},
number = {7082},
pages = {315 -- 318},
publisher = {Nature Publishing Group},
title = {{Evidence for Efimov quantum states in an ultracold gas of caesium atoms}},
doi = {10.1038/nature04626},
volume = {440},
year = {2006},
}
@inproceedings{1034,
abstract = {Three interacting particles form a system which is well known for its complex physical behavior. A landmark theoretical result in few-body quantum physics is Efimov\'s prediction of a universal set of weakly bound trimer states appearing for three identical bosons with a resonant two-body interaction [1, 2]. Surprisingly, these states even exist in the absence of a corresponding two-body bound state and their precise nature is largely independent of the particular type of the two-body interaction potential. Efimov\'s scenario has attracted great interest in many areas of physics; an experimental test however has not been achieved. We report the observation of an Efimov resonance in an ultracold thermal gas of cesium atoms [3]. The resonance occurs in the range of large negative two-body scattering lengths and arises from the coupling of three free atoms to an Efimov trimer. We observe its signature as a giant three-body recombination loss when the strength of the two-body interaction is varied near a Feshbach resonance. This resonance develops into a continuum resonance at non-zero collision energies, and we observe a shift of the resonance position as a function of temperature. We also report on a minimum in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point from which to explore the universal properties of resonantly interacting few-body systems.},
author = {Nägerl, Hanns and Kraemer, Tobias and Mark, Michael and Waldburger, Philipp and Danzl, Johann G and Engeser, Bastian and Lange, Adam and Pilch, Karl and Jaakkola, Antti and Chin, Cheng and Grimm, Rudolf},
pages = {269 -- 277},
publisher = {AIP},
title = {{Experimental evidence for Efimov quantum states}},
doi = {10.1063/1.2400657},
volume = {869},
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},
}
@inbook{3722,
author = {Harald Janovjak and Mueller, Daniel J},
booktitle = {Bioanalytik},
publisher = {Spektrum Akademischer Verlag},
title = {{Rastersondenmikroskopie}},
year = {2006},
}
@article{3728,
abstract = {Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard–Jones contact interactions is applied to model the protein–membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins.},
author = {Cieplak, Marek and Filipek, Sławomir and Harald Janovjak and Krzysko, Krystiana A},
journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes},
number = {4},
pages = {537 -- 544},
publisher = {Elsevier},
title = {{Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment}},
doi = {10.1016/j.bbamem.2006.03.028},
volume = {1758},
year = {2006},
}