@article{3614,
  abstract     = {We analyze the changes in the mean and variance components of a quantitative trait caused by changes in allele frequencies, concentrating on the effects of genetic drift. We use a general representation of epistasis and dominance that allows an arbitrary relation between genotype and phenotype for any number of diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium in our analyses of drift-induced changes. Random drift generates transient linkage disequilibria that cause correlations between allele frequency fluctuations at different loci. However, we show that these have negligible effects, at least for interactions among small numbers of loci. Our analyses are based on diffusion approximations that summarize the effects of drift in terms of F, the inbreeding coefficient, interpreted as the expected proportional decrease in heterozygosity at each locus. For haploids, the variance of the trait mean after a population bottleneck is var(Δz̄) =inline imagewhere n is the number of loci contributing to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is the kth-order additive epistatic variance. The expected additive genetic variance after the bottleneck, denoted (V*A), is closely related to var(Δz̄); (V*A) (1 –F)inline imageThus, epistasis inflates the expected additive variance above VA(1 –F), the expectation under additivity. For haploids (and diploids without dominance), the expected value of every variance component is inflated by the existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)). This is not true in general with diploidy, because dominance alone can reduce (V*A) below VA(1 –F) (e.g., when dominant alleles are rare). Without dominance, diploidy produces simple expressions: var(Δz̄)=inline image=1 (2F) kVA(k) and (V*A) = (1 –F)inline imagek(2F)k-1VA(k) With dominance (and even without epistasis), var(Δz̄)and (V*A) no longer depend solely on the variance components in the base population. For small F, the expected additive variance simplifies to (V*A)(1 –F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms describing covariances between additive effects and dominance and additive × dominance interactions. Whether population bottlenecks lead to expected increases in additive variance depends primarily on the ratio of nonadditive to additive genetic variance in the base population, but dominance precludes simple predictions based solely on variance components. We illustrate these results using a model in which genotypic values are drawn at random, allowing extreme and erratic epistatic interactions. Although our analyses clarify the conditions under which drift is expected to increase VA, we question the evolutionary importance of such increases.},
  author       = {Barton, Nicholas H and Turelli, Michael},
  issn         = {1558-5646},
  journal      = {Evolution; International Journal of Organic Evolution},
  number       = {10},
  pages        = {2111 -- 2132},
  publisher    = {Wiley-Blackwell},
  title        = {{Effects of allele frequency changes on variance components under a general model of epistasis}},
  doi          = {10.1111/j.0014-3820.2004.tb01591.x},
  volume       = {58},
  year         = {2004},
}

@article{3615,
  abstract     = {We investigate three alternative selection-based scenarios proposed to maintain polygenic variation: pleiotropic balancing selection, G x E interactions (with spatial or temporal variation in allelic effects), and sex-dependent allelic effects. Each analysis assumes an additive polygenic trait with n diallelic loci under stabilizing selection. We allow loci to have different effects and consider equilibria at which the population mean departs from the stabilizing-selection optimum. Under weak selection, each model produces essentially identical, approximate allele-frequency dynamics. Variation is maintained under pleiotropic balancing selection only at loci for which the strength of balancing selection exceeds the effective strength of stabilizing selection. In addition, for all models, polymorphism requires that the population mean be close enough to the optimum that directional selection does not overwhelm balancing selection. This balance allows many simultaneously stable equilibria, and we explore their properties numerically. Both spatial and temporal G x E can maintain variation at loci for which the coefficient of variation (across environments) of the effect of a substitution exceeds a critical value greater than one. The critical value depends on the correlation between substitution effects at different loci. For large positive correlations (e.g., ρ2ij > 3/4), even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly, this constraint on correlations implies that sex-dependent allelic effects cannot maintain polygenic variation. We present numerical results that support our analytical approximations and discuss our results in connection to relevant data and alternative variance-maintaining mechanisms.},
  author       = {Turelli, Michael and Barton, Nicholas H},
  issn         = {1943-2631},
  journal      = {Genetics},
  number       = {2},
  pages        = {1053 -- 1079},
  publisher    = {Genetics Society of America},
  title        = {{Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions}},
  doi          = {10.1534/genetics.166.2.1053},
  volume       = {166},
  year         = {2004},
}

@article{3617,
  abstract     = {The coalescent process can describe the effects of selection at linked loci only if selection is so strong that genotype frequencies evolve deterministically. Here, we develop methods proposed by Kaplan, Darden, and Hudson to find the effects of weak selection. We show that the overall effect is given by an extension to Price's equation: the change in properties such as moments of coalescence times is equal to the covariance between those properties and the fitness of the sample of genes. The distribution of coalescence times differs substantially between allelic classes, even in the absence of selection. However, the average coalescence time between randomly chosen genes is insensitive to the current allele frequency and is affected significantly by purifying selection only if deleterious mutations are common and selection is strong (i.e., the product of population size and selection coefficient, Ns > 3). Balancing selection increases mean coalescence times, but the effect becomes large only when mutation rates between allelic classes are low and when selection is extremely strong. Our analysis supports previous simulations that show that selection has surprisingly little effect on genealogies. Moreover, small fluctuations in allele frequency due to random drift can greatly reduce any such effects. This will make it difficult to detect the action of selection from neutral variation alone.},
  author       = {Barton, Nicholas H and Etheridge, Alison},
  issn         = {1943-2631},
  journal      = {Genetics},
  number       = {2},
  pages        = {1115 -- 1131},
  publisher    = {Genetics Society of America},
  title        = {{The effect of selection on genealogies}},
  doi          = {10.1534/genetics.166.2.1115},
  volume       = {166},
  year         = {2004},
}

@article{3805,
  abstract     = {The operation of neuronal networks crucially depends on a fast time course of signaling in inhibitory interneurons. Synapses that excite interneurons generate fast currents, owing to the expression of glutamate receptors of specific subunit composition. Interneurons generate brief action potentials in response to transient synaptic activation and discharge repetitively at very high frequencies during sustained stimulation. The ability to generate short-duration action potentials at high frequencies depends on the expression of specific voltage-gated K+ channels. Factors facilitating fast action potential initiation following synaptic excitation include depolarized interneuron resting potential, subthreshold conductances and active dendrites. Finally, GABA release at interneuron output synapses is rapid and highly synchronized, leading to a faster inhibition in postsynaptic interneurons than in principal cells. Thus, the expression of distinct transmitter receptors and voltage-gated ion channels ensures that interneurons operate with high speed and temporal precision.},
  author       = {Jonas, Peter M and Bischofberger, Josef and Fricker, Desdemona and Miles, Richard},
  issn         = {1878-108X},
  journal      = {Trends in Neurosciences},
  number       = {1},
  pages        = {30 -- 40},
  publisher    = {Elsevier},
  title        = {{Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons}},
  doi          = {doi:10.1016/j.tins.2003.10.010},
  volume       = {27},
  year         = {2004},
}

@inproceedings{3688,
  abstract     = {Capturing images of documents using handheld digital cameras has a variety of applications in academia, research, knowledge management, retail, and office settings. The ultimate goal of such systems is to achieve image quality comparable to that currently achieved with flatbed scanners even for curved, warped, or curled pages. This can be achieved by high-accuracy 3D modeling of the page surface, followed by a "flattening" of the surface. A number of previous systems have either assumed only perspective distortions, or used techniques like structured lighting, shading, or side-imaging for obtaining 3D shape. This paper describes a system for handheld camera-based document capture using general purpose stereo vision methods followed by a new document dewarping technique. Examples of shape modeling and dewarping of book images is shown.},
  author       = {Ulges, Adrian and Lampert, Christoph and Breuel, Thomas},
  booktitle    = {Proceedings of the 2004 ACM symposium on Document engineering},
  isbn         = {9781581139389},
  location     = {Milwaukee, WI, United States},
  pages        = {198 -- 200},
  publisher    = {ACM},
  title        = {{Document capture using stereo vision}},
  doi          = {10.1145/1030397.1030434},
  year         = {2004},
}

@inbook{3575,
  abstract     = {The Jacobi set of two Morse functions defined on a common - manifold is the set of critical points of the restrictions of one func- tion to the level sets of the other function. Equivalently, it is the set of points where the gradients of the functions are parallel. For a generic pair of Morse functions, the Jacobi set is a smoothly embed- ded 1-manifold. We give a polynomial-time algorithm that com- putes the piecewise linear analog of the Jacobi set for functions specified at the vertices of a triangulation, and we generalize all results to more than two but at most Morse functions.},
  author       = {Edelsbrunner, Herbert and Harer, John},
  booktitle    = {Foundations of Computational Mathematics},
  pages        = {37 -- 57},
  publisher    = {Springer},
  title        = {{Jacobi sets of multiple Morse functions}},
  doi          = {10.1017/CBO9781139106962.003},
  volume       = {312},
  year         = {2004},
}

@inbook{3587,
  author       = {Ulrich, Florian and Heisenberg, Carl-Philipp J},
  booktitle    = {Fish development and genetics : the zebrafish and medaka models},
  editor       = {Korzh, Vladimir and Gong, Zhiyuan},
  isbn         = {9812388214},
  pages        = {39 -- 86},
  publisher    = {World Scientific Publishing},
  title        = {{Gastrulation in zebrafish}},
  volume       = {2},
  year         = {2004},
}

@misc{3595,
  author       = {Charlesworth, Brian and Barton, Nicholas H},
  booktitle    = {Current Biology},
  issn         = {1879-0445},
  number       = {6},
  pages        = {R233 -- R235},
  publisher    = {Cell Press},
  title        = {{Genome size: Does bigger mean worse?}},
  doi          = {10.1016/j.cub.2004.02.054},
  volume       = {14},
  year         = {2004},
}

@misc{3616,
  author       = {Barton, Nicholas H},
  booktitle    = {Current Biology},
  issn         = {1879-0445},
  number       = {15},
  pages        = {R603 -- R604},
  publisher    = {Cell Press},
  title        = {{Speciation: Why, how, where and when?}},
  doi          = {10.1016/j.cub.2004.07.037},
  volume       = {14},
  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 and Pietrzak, Krzysztof Z},
  booktitle    = {First Theory of Cryptography Conference, 2004},
  isbn         = {9783540210009},
  location     = {Cambridge, MA, United},
  pages        = {410 -- 427},
  publisher    = {Springer Nature},
  title        = {{Composition of random systems: When two weak make one strong}},
  doi          = {10.1007/978-3-540-24638-1_23},
  volume       = {2951},
  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 Kolmogorov, Vladimir},
  booktitle    = {Proceedings of the 2004 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2004},
  isbn         = {0769521584},
  issn         = {1063-6919},
  location     = {Washington, DC, United States},
  pages        = {437 -- 444},
  publisher    = {IEEE},
  title        = {{Spatially coherent clustering using graph cuts}},
  doi          = {10.1109/CVPR.2004.1315196},
  volume       = {2},
  year         = {2004},
}

@article{3420,
  abstract     = {Single-molecule force-spectroscopy was employed to unfold and refold single sodium-proton antiporters (NhaA) of Escherichia coli from membrane patches. Although transmembrane α-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, two helices predominantly unfolded pairwise, thereby acting as one structural unit. Many of the potential barriers were detected unfolding NhaA either from the C-terminal or the N-terminal end. It was found that some molecular interactions stabilizing secondary structural elements were directional, while others were not. Additionally, some interactions appeared to occur between the secondary structural elements. After unfolding ten of the 12 helices, the extracted polypeptide was allowed to refold back into the membrane. After five seconds, the refolded polypeptide established all secondary structure elements of the native protein. One helical pair showed a characteristic spring like “snap in” into its folded conformation, while the refolding process of other helices was not detected in particular. Additionally, individual helices required characteristic periods of time to fold. Correlating these results with the primary structure of NhaA allowed us to obtain the first insights into how potential barriers establish and determine the folding kinetics of the secondary structure elements.},
  author       = {Kedrov, Alexej and Ziegler, Christine and Janovjak, Harald L and Kühlbrandt, Werner and Mueller, Daniel},
  issn         = {0022-2836},
  journal      = {Journal of Molecular Biology},
  number       = {5},
  pages        = {1143 -- 1152},
  publisher    = {Elsevier},
  title        = {{Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy}},
  doi          = {10.1016/j.jmb.2004.05.026},
  volume       = {340},
  year         = {2004},
}

@article{3419,
  abstract     = {The folding and stability of transmembrane proteins is a fundamental and unsolved biological problem. Here, single bacteriorhodopsin molecules were mechanically unfolded from native purple membranes using atomic force microscopy and force spectroscopy. The energy landscape of individual transmembrane α helices and polypeptide loops was mapped by monitoring the pulling speed dependence of the unfolding forces and applying Monte Carlo simulations. Single helices formed independently stable units stabilized by a single potential barrier. Mechanical unfolding of the helices was triggered by 3.9–7.7 Å extension, while natural unfolding rates were of the order of 10−3 s−1. Besides acting as individually stable units, helices associated pairwise, establishing a collective potential barrier. The unfolding pathways of individual proteins reflect distinct pulling speed-dependent unfolding routes in their energy landscapes. These observations support the two-stage model of membrane protein folding in which α helices insert into the membrane as stable units and then assemble into the functional protein.},
  author       = {Janovjak, Harald L and Struckmeier, Jens and Hubain, Maurice and Kessler, Max and Kedrov, Alexej and Mueller, Daniel},
  issn         = {1878-4186},
  journal      = {Structure},
  number       = {5},
  pages        = {871 -- 879},
  publisher    = {Cell Press},
  title        = {{Probing the energy landscape of the membrane protein bacteriorhodopsin}},
  doi          = {10.1016/j.str.2004.03.016},
  volume       = {12},
  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 Kolmogorov, Vladimir and Blake, Andrew},
  issn         = {1557-7368},
  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},
}

@inbook{3574,
  author       = {Edelsbrunner, Herbert},
  booktitle    = {Handbook of Discrete and Computational Geometry},
  pages        = {1395 -- 1412},
  publisher    = {CRC Press},
  title        = {{Biological applications of computational topology}},
  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 Kolmogorov, Vladimir},
  issn         = {1939-3539},
  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},
}

@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       = {Kolmogorov, Vladimir and Nguyen, Thành and Nuval, Anthony and Spincemaille, Pascal and Prince, Martin and Zabih, Ramin and Wang, Yusu},
  issn         = {1522-2594},
  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       = {Kolmogorov, Vladimir and Zabih, Ramin},
  issn         = {1939-3539},
  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},
}

@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 Friml, Jirí and Grasser, Klaus},
  issn         = {1365-313X},
  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{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       = {Friml, Jirí and Yang, Xiong and Michniewicz, Marta and Weijers, Dolf and Quint, Ab and Tietz, Olaf and Benjamins, René and Ouwerkerk, Pieter and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul and Palme, Klaus and Offringa, Remko},
  issn         = {1095-9203},
  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},
}