@article{2741,
  abstract     = {The Pauli operator describes the energy of a nonrelativistic quantum particle with spin 1/2 in a magnetic field and an external potential. A new Lieb-Thirring type inequality on the sum of the negative eigenvalues is presented. The main feature compared to earlier results is that in the large field regime the present estimate grows with the optimal (first) power of the strength of the magnetic field. As a byproduct of the method, we also obtain an optimal upper bound on the pointwise density of zero energy eigenfunctions of the Dirac operator. The main technical tools are: (i) a new localization scheme for the square of the resolvent of a general class of second order elliptic operators; (ii) a geometric construction of a Dirac operator with a constant magnetic field that approximates the original Dirac operator in a tubular neighborhood of a fixed field line. The errors may depend on the regularity of the magnetic field but they are uniform in the field strength.},
  author       = {László Erdös and Solovej, Jan P},
  journal      = {Annales Henri Poincare},
  number       = {4},
  pages        = {671 -- 741},
  publisher    = {Birkhäuser},
  title        = {{Uniform Lieb-Thirring inequality for the three-dimensional Pauli operator with a strong non-homogeneous magnetic field}},
  doi          = {10.1007/s00023-004-0180-x},
  volume       = {5},
  year         = {2004},
}

@article{2742,
  abstract     = {We consider a system of N weakly interacting fermions with a real analytic pair interaction. We prove that for a general class of initial data there exists a fixed time T such that the difference between the one particle density matrix of this system and the solution of the nonlinear Hartree equation is of order N−1 for any time t⩽T.},
  author       = {Elgart, Alexander and László Erdös and Schlein, Benjamin and Yau, Horng-Tzer},
  journal      = {Journal de Mathématiques Pures et Appliquées},
  number       = {10},
  pages        = {1241 -- 1273},
  publisher    = {Elsevier},
  title        = {{Nonlinear Hartree equation as the mean field limit of weakly coupled fermions}},
  doi          = {10.1016/j.matpur.2004.03.006},
  volume       = {83},
  year         = {2004},
}

@article{2786,
  abstract     = {Transition to turbulence in pipe flow is one of the most fundamental and longest- standing problems in fluid dynamics. Stability theory suggests that the flow remains laminar for all flow rates, but in practice pipe flow becomes turbulent even at moderate speeds. This transition drastically affects the transport efficiency of mass, momentum, and heat. On the basis of the recent discovery of unstable traveling waves in computational studies of the Navier-Stokes equations and ideas from dynamical systems theory, a model for the transition process has been suggested. We report experimental observation of these traveling waves in pipe flow, confirming the proposed transition scenario and suggesting that the dynamics associated with these unstable states may indeed capture the nature of fluid turbulence.},
  author       = {Björn Hof and van Doorne, Casimir W and Westerweel, Jerry and Nieuwstadt, Frans T and Faisst, Holger and Eckhardt, Bruno and Wedin, Håkan and Kersweli, Richard R and Waleffe, Fabian},
  journal      = {Science},
  number       = {5690},
  pages        = {1594 -- 1598},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Experimental observation of nonlinear traveling waves in turbulent pipe flow}},
  doi          = {10.1126/science.1100393},
  volume       = {305},
  year         = {2004},
}

@article{2787,
  abstract     = {The results of experimental and numerical investigations of the onset of oscillatory convection in a sidewall heated rectangular cavity of molten gallium are reported. Detailed comparisons are made between experimental observations and calculations from numerical simulations of a three-dimensional Boussinesq model. The onset of time-dependence takes place through supercritical Hopf bifurcations and the loci of critical points in the (Gr, Pr)-plane are qualitatively similar with excellent agreement between the frequencies of the oscillatory motion. This provides a severe test of the control of the experiment since the mode of oscillation is extremely sensitive to imperfections. Detailed numerical investigations reveal that there are a pair of Hopf bifurcations which exist on two asymmetric states which themselves arise at a subcritical pitchfork from the symmetric state. There is no evidence for this in the experiment and this qualitative difference is attributed to non-Boussinesq perturbations which increase with Gr. However, the antisymmetric spatial structure of the oscillatory state is robust and is present in both the experiment and the numerical model. Moreover, the detailed analysis of the numerical results reveals the origins of the oscillatory instability.},
  author       = {Björn Hof and Juel, Anne and Zhao, Li and Henry, Daniel  and Ben Hadid, Hamda and Mullin, Tom P},
  journal      = {Journal of Fluid Mechanics},
  pages        = {391 -- 413},
  publisher    = {Cambridge University Press},
  title        = {{On the onset of oscillatory convection in molten gallium}},
  doi          = {10.1017/S0022112004000527},
  volume       = {515},
  year         = {2004},
}

@article{2997,
  abstract     = {Polar transport-dependent local accumulation of auxin provides positional cues for multiple plant patterning processes. This directional auxin flow depends on the polar subcellular localization of the PIN auxin efflux regulators. Overexpression of the PINOID protein kinase induces a basal-to-apical shift in PIN localization, resulting in the loss of auxin gradients and strong defects in embryo and seedling roots. Conversely, pid loss of function induces an apical-to-basal shift in PIN1 polar targeting at the inflorescence apex, accompanied by defective organogenesis. Our results show that a PINOID-dependent binary switch controls PIN polarity and mediates changes in auxin flow to create local gradients for patterning processes.},
  author       = {Jirí Friml and Yang, Xiong and Michniewicz, Marta and Weijers, Dolf and Quint, Ab and Tietz, Olaf and Benjamins, René and Ouwerkerk, Pieter B and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul J and Palme, Klaus and Offringa, Remko},
  journal      = {Science},
  number       = {5697},
  pages        = {862 -- 865},
  publisher    = {American Association for the Advancement of Science},
  title        = {{A PINOID-dependent binary switch in apical-basal PIN polar targeting directs auxin efflux}},
  doi          = {10.1126/science.1100618},
  volume       = {306},
  year         = {2004},
}

@article{2998,
  abstract     = {The packaging of the genomic DNA into chromatin in the cell nucleus requires machineries that facilitate DNA-dependent processes such as transcription in the presence of repressive chromatin structures. Using co-immunoprecipitation we have identified in Arabidopsis thaliana cells the FAcilitates Chromatin Transcription (FACT) complex, consisting of the 120-kDa Spt16 and the 71-kDa SSRP1 proteins. Indirect immunofluorecence analyses revealed that both FACT subunits co-localize to nuclei of the majority of cell types in embryos, shoots and roots, whereas FACT is not present in terminally differentiated cells such as mature trichoblasts or cells of the root cap. In the nucleus, Spt16 and SSRP1 are found in the cytologically defined euchromatin of interphase cells independent of the status of DNA replication, but the proteins are not associated with heterochromatic chromocentres and condensed mitotic chromosomes. FACT can be detected by chromatin immunoprecipitation over the entire transcribed region (5′-UTR, coding sequence, 3′-UTR) of actively transcribed genes, whereas it does not occur at transcriptionally inactive heterochromatic regions and intergenic regions. FACT localizes to inducible genes only after induction of transcription, and the association of the complex with the genes correlates with the level of transcription. Collectively, these results indicate that FACT assists transcription elongation through plant chromatin.},
  author       = {Duroux, Meg and Houben, Andreas and Růžička, Kamil and Jirí Friml and Grasser, Klaus D},
  journal      = {Plant Journal},
  number       = {5},
  pages        = {660 -- 671},
  publisher    = {Wiley-Blackwell},
  title        = {{The chromatin remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome}},
  doi          = {10.1111/j.1365-313X.2004.02242.x},
  volume       = {40},
  year         = {2004},
}

@article{2999,
  abstract     = {Embryogenesis of flowering plants establishes a basic body plan with apical-basal, radial and bilateral patterns from the single-celled zygote. Arabidopsis embryogenesis exhibits a nearly invariant cell division pattern and therefore is an ideal system for studies of early plant development. However, plant embryos are difficult to access for experimental manipulation, as they develop deeply inside maternal tissues. Here we present a method for the culture of zygotic Arabidopsis embryos in vitro. The technique omits excision of the embryo by culturing the entire ovule, thus greatly facilitating the time and effort involved. It enables external manipulation of embryo development and culture from the earliest developmental stages up to maturity. Administration of various chemical treatments as well as the use of different molecular markers is demonstrated together with standard techniques for visualizing gene expression and protein localization in in vitro cultivated embryos. The presented set of techniques allows for so far unavailable molecular physiology approaches in the study of early plant development.},
  author       = {Sauer, Michael and Jirí Friml},
  journal      = {Plant Journal},
  number       = {5},
  pages        = {835 -- 843},
  publisher    = {Wiley-Blackwell},
  title        = {{In vitro culture of Arabidopsis embryos within their ovules}},
  doi          = {10.1111/j.1365-313X.2004.02248.x},
  volume       = {40},
  year         = {2004},
}

@misc{3142,
  abstract     = {Assembly of neuronal circuits is controlled by the sequential acquisition of neuronal subpopulation-specific identities at progressive developmental steps. Whereas neuronal features involved in initial phases of differentiation are already established at cell-cycle exit, recent findings, based mainly on work in the peripheral nervous system, suggest that the timely integration of signals encountered en route to targets and from the target region itself is essential to control late steps in connectivity. As neurons project towards their targets they require target-derived signals to establish mature axonal projections and acquire neuronal traits such as the expression of distinct combinations of neurotransmitters. Recent evidence presented in this review shows that this principle, of a signaling interplay between target-derived signals and neuronal cell bodies, is often mediated through transcriptional events and is evolutionarily conserved.},
  author       = {Simon Hippenmeyer and Kramer, Ina and Arber, Silvia},
  booktitle    = {Trends in Neurosciences},
  number       = {8},
  pages        = {482 -- 488},
  publisher    = {Elsevier},
  title        = {{Control of neuronal phenotype: What targets tell the cell bodies}},
  doi          = {10.1016/j.tins.2004.05.012},
  volume       = {27},
  year         = {2004},
}

@article{3172,
  abstract     = {The simultaneous multiple volume (SMV) approach in navigator-gated MRI allows the use of the whole motion range or the entire scan time for the reconstruction of final images by simultaneously acquiring different image volumes at different motion states. The motion tolerance range for each volume is kept small, thus SMV substantially increases the scan efficiency of navigator methods while maintaining the effectiveness of motion suppression. This article reports a general implementation of the SMV approach using a multiprocessor scheduling algorithm. Each motion state is regarded as a processor and each volume is regarded as a job. An efficient scheduling that completes all jobs in minimal time is maintained even when the motion pattern changes. Initial experiments demonstrated that SMV significantly increased the scan efficiency of navigatorgated MRI.},
  author       = {Vladimir Kolmogorov and Nguyen, Thành D and Nuval, Anthony and Spincemaille, Pascal and Prince, Martin R and Zabih, Ramin and Wang, Yusu},
  journal      = {Magnetic Resonance in Medicine},
  number       = {2},
  pages        = {362 -- 367},
  publisher    = {Wiley-Blackwell},
  title        = {{Multiprocessor scheduling implementation of the simultaneous multiple volume SMV navigator method}},
  doi          = {10.1002/mrm.20162},
  volume       = {52},
  year         = {2004},
}

@article{3173,
  abstract     = {In the last few years, several new algorithms based on graph cuts have been developed to solve energy minimization problems in computer vision. Each of these techniques constructs a graph such that the minimum cut on the graph also minimizes the energy. Yet, because these graph constructions are complex and highly specific to a particular energy function, graph cuts have seen limited application to date. In this paper, we give a characterization of the energy functions that can be minimized by graph cuts. Our results are restricted to functions of binary variables. However, our work generalizes many previous constructions and is easily applicable to vision problems that involve large numbers of labels, such as stereo, motion, image restoration, and scene reconstruction. We give a precise characterization of what energy functions can be minimized using graph cuts, among the energy functions that can be written as a sum of terms containing three or fewer binary variables. We also provide a general-purpose construction to minimize such an energy function. Finally, we give a necessary condition for any energy function of binary variables to be minimized by graph cuts. Researchers who are considering the use of graph cuts to optimize a particular energy function can use our results to determine if this is possible and then follow our construction to create the appropriate graph. A software implementation is freely available.},
  author       = {Vladimir Kolmogorov and Zabih, Ramin},
  journal      = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  number       = {2},
  pages        = {147 -- 159},
  publisher    = {IEEE},
  title        = {{What energy functions can be minimized via graph cuts? }},
  doi          = {10.1109/TPAMI.2004.1262177},
  volume       = {26},
  year         = {2004},
}

@inproceedings{3177,
  abstract     = {Feature space clustering is a popular approach to image segmentation, in which a feature vector of local properties (such as intensity, texture or motion) is computed at each pixel. The feature space is then clustered, and each pixel is labeled with the cluster that contains its feature vector. A major limitation of this approach is that feature space clusters generally lack spatial coherence (i.e., they do not correspond to a compact grouping of pixels). In this paper, we propose a segmentation algorithm that operates simultaneously in feature space and in image space. We define an energy function over both a set of clusters and a labeling of pixels with clusters. In our framework, a pixel is labeled with a single cluster (rather than, for example, a distribution over clusters). Our energy function penalizes clusters that are a poor fit to the data in feature space, and also penalizes clusters whose pixels lack spatial coherence. The energy function can be efficiently minimized using graph cuts. Our algorithm can incorporate both parametric and non-parametric clustering methods. It can be applied to many optimization-based clustering methods, including k-means and k-medians, and can handle models which are very close in feature space. Preliminary results are presented on segmenting real and synthetic images, using both parametric and non-parametric clustering.},
  author       = {Zabih, Ramin and Vladimir Kolmogorov},
  pages        = {437 -- 444},
  publisher    = {IEEE},
  title        = {{Spatially coherent clustering using graph cuts}},
  doi          = {10.1109/CVPR.2004.1315196},
  volume       = {2},
  year         = {2004},
}

@article{3178,
  abstract     = {Minimum cut/maximum flow algorithms on graphs have emerged as an increasingly useful tool for exactor approximate energy minimization in low-level vision. The combinatorial optimization literature provides many min-cut/max-flow algorithms with different polynomial time complexity. Their practical efficiency, however, has to date been studied mainly outside the scope of computer vision. The goal of this paper is to provide an experimental comparison of the efficiency of min-cut/max flow algorithms for applications in vision. We compare the running times of several standard algorithms, as well as a new algorithm that we have recently developed. The algorithms we study include both Goldberg-Tarjan style "push -relabel" methods and algorithms based on Ford-Fulkerson style "augmenting paths." We benchmark these algorithms on a number of typical graphs in the contexts of image restoration, stereo, and segmentation. In many cases, our new algorithm works several times faster than any of the other methods, making near real-time performance possible. An implementation of our max-flow/min-cut algorithm is available upon request for research purposes.},
  author       = {Boykov, Yuri and Vladimir Kolmogorov},
  journal      = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  number       = {9},
  pages        = {1124 -- 1137},
  publisher    = {IEEE},
  title        = {{An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision}},
  doi          = {10.1109/TPAMI.2004.60},
  volume       = {26},
  year         = {2004},
}

@inproceedings{3179,
  abstract     = {The problem of efficient, interactive foreground/background segmentation in still images is of great practical importance in image editing. Classical image segmentation tools use either texture (colour) information, e.g. Magic Wand, or edge (contrast) information, e.g. Intelligent Scissors. Recently, an approach based on optimization by graph-cut has been developed which successfully combines both types of information. In this paper we extend the graph-cut approach in three respects. First, we have developed a more powerful, iterative version of the optimisation. Secondly, the power of the iterative algorithm is used to simplify substantially the user interaction needed for a given quality of result. Thirdly, a robust algorithm for "border matting" has been developed to estimate simultaneously the alpha-matte around an object boundary and the colours of foreground pixels. We show that for moderately difficult examples the proposed method outperforms competitive tools.},
  author       = {Rother, Carsten and Vladimir Kolmogorov and Blake, Andrew},
  number       = {3},
  pages        = {309 -- 314},
  publisher    = {ACM},
  title        = {{"GrabCut" - Interactive foreground extraction using iterated graph cuts }},
  doi          = {10.1145/1015706.1015720},
  volume       = {23},
  year         = {2004},
}

@inproceedings{3208,
  abstract     = {A new technique for proving the adaptive indistinguishability of two systems, each composed of some component systems, is presented, using only the fact that corresponding component systems are non-adaptively indistinguishable. The main tool is the definition of a special monotone condition for a random system F, relative to another random system G, whose probability of occurring for a given distinguisher D is closely related to the distinguishing advantage ε of D for F and G, namely it is lower and upper bounded by ε and (1+ln1), respectively.
A concrete instantiation of this result shows that the cascade of two random permutations (with the second one inverted) is indistinguishable from a uniform random permutation by adaptive distinguishers which may query the system from both sides, assuming the components’ security only against non-adaptive one-sided distinguishers.
As applications we provide some results in various fields as almost k-wise independent probability spaces, decorrelation theory and computational indistinguishability (i.e., pseudo-randomness).},
  author       = {Maurer, Ueli M and Krzysztof Pietrzak},
  pages        = {410 -- 427},
  publisher    = {Springer},
  title        = {{Composition of random systems: When two weak make one strong}},
  doi          = {10.1007/978-3-540-24638-1_23},
  volume       = {2951},
  year         = {2004},
}

@article{11762,
  abstract     = {In this paper, we describe six algorithmic problems that arise in web search engines and that are not or only partially solved: (1) Uniformly sampling of web pages; (2) modeling the web graph; (3) finding duplicate hosts; (4) finding top gainers and losers in data streams; (5) finding large dense bipartite graphs; and (6) understanding how eigenvectors partition the web.},
  author       = {Henzinger, Monika H},
  issn         = {1944-9488},
  journal      = {Internet Mathematics},
  number       = {1},
  pages        = {115--123},
  publisher    = {Internet Mathematics},
  title        = {{Algorithmic challenges in web search engines}},
  doi          = {10.1080/15427951.2004.10129079},
  volume       = {1},
  year         = {2004},
}

@article{8517,
  abstract     = {We consider the evolution of a connected set on the plane carried by a space periodic incompressible stochastic flow. While for almost every realization of the stochastic flow at time t most of the particles are at a distance of order equation image away from the origin, there is a measure zero set of points that escape to infinity at the linear rate. We study the set of points visited by the original set by time t and show that such a set, when scaled down by the factor of t, has a limiting nonrandom shape.},
  author       = {Dolgopyat, Dmitry and Kaloshin, Vadim and Koralov, Leonid},
  issn         = {0010-3640},
  journal      = {Communications on Pure and Applied Mathematics},
  keywords     = {Applied Mathematics, General Mathematics},
  number       = {9},
  pages        = {1127--1158},
  publisher    = {Wiley},
  title        = {{A limit shape theorem for periodic stochastic dispersion}},
  doi          = {10.1002/cpa.20032},
  volume       = {57},
  year         = {2004},
}

@article{8518,
  author       = {Koralov, Leonid and Kaloshin, Vadim and Dolgopyat, Dmitry},
  issn         = {0091-1798},
  journal      = {The Annals of Probability},
  number       = {1A},
  pages        = {1--27},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Sample path properties of the stochastic flows}},
  doi          = {10.1214/aop/1078415827},
  volume       = {32},
  year         = {2004},
}

@article{864,
  abstract     = {We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.},
  author       = {Panchenko, Anna R and Fyodor Kondrashov and Bryant, Stephen H},
  journal      = {Protein Science},
  number       = {4},
  pages        = {884 -- 892},
  publisher    = {Wiley-Blackwell},
  title        = {{Prediction of functional sites by analysis of sequence and structure conservation}},
  doi          = {10.1110/ps.03465504},
  volume       = {13},
  year         = {2004},
}

@article{870,
  abstract     = {Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates.},
  author       = {Fyodor Kondrashov and Ogurtsov, Aleksey Yu and Kondrashov, Alexey S},
  journal      = {Nucleic Acids Research},
  number       = {5},
  pages        = {1731 -- 1737},
  publisher    = {Oxford University Press},
  title        = {{Bioinformatical assay of human gene morbidity}},
  doi          = {10.1093/nar/gkh330},
  volume       = {32},
  year         = {2004},
}

@article{875,
  abstract     = {The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis.},
  author       = {Fyodor Kondrashov and Koonin, Eugene V},
  journal      = {Trends in Genetics},
  number       = {7},
  pages        = {287 -- 291},
  publisher    = {Elsevier},
  title        = {{A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications}},
  doi          = {10.1016/j.tig.2004.05.001},
  volume       = {20},
  year         = {2004},
}