@misc{3594,
author = {Pemberton, Josephine M and Swanson, Graeme M and Nicholas Barton and Livingstone, Suzanne R and Senn, Helen V},
booktitle = {Deer},
number = {9},
pages = {22 -- 26},
publisher = {BDS },
title = {{Hybridisation between red and sika deer in Scotland}},
volume = {13},
year = {2006},
}
@article{3607,
abstract = {We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance–attributable to epistasis rather than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences.},
author = {Turelli, Michael and Nicholas Barton},
journal = {Evolution; International Journal of Organic Evolution},
number = {9},
pages = {1763 -- 1776},
publisher = {Wiley-Blackwell},
title = {{Will population bottlenecks and multilocus epistasis increase additive genetic variance?}},
doi = {10.1111/j.0014-3820.2006.tb00521.x},
volume = {60},
year = {2006},
}
@article{3608,
abstract = {We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests. },
author = {Kirkpatrick, Mark and Nicholas Barton},
journal = {Genetics},
number = {1},
pages = {419 -- 434},
publisher = {Genetics Society of America},
title = {{Chromosome inversions, local adaptation, and speciation}},
doi = {10.1534/genetics.105.047985},
volume = {173},
year = {2006},
}
@article{3609,
abstract = {Bombina bombina and B. variegata are two anciently diverged toad taxa that have adapted to different breeding habitats yet hybridize freely in zones of overlap where their parapatric distributions meet. Here, we report on a joint genetic and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine. We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency clines with a sharp central step occur across a sharp ecotone, where transitions in aquatic habitat, elevation, and terrestrial vegetation coincide. The width of the hybrid zone, estimated as the inverse of the maximum gradient in allele frequency, is 2.3 km. This is the smallest of four estimates derived from different clinal transects across Europe. We argue that the narrow cline near Stryi is mainly due to a combination of habitat distribution and habitat preference. Adult toads show a preference for either ponds (B. bombina) or puddles (B. variegata), which is known to affect the distribution of genotypes within the hybrid zones. At Stryi, it should cause a reduction of the dispersal rate across the ecotone and thus narrow the cline. A detailed comparison of all five intensively studied Bombina transects lends support to the hypothesis that habitat distribution plus habitat preference can jointly affect the structure of hybrid zones and, ultimately, the resulting barriers to gene flow between differentiated gene pools. This study also represents a resampling of an area that was last studied more than 70 years ago. Our allele-frequency clines largely coincide with those that were described then on the basis of morphological variation. However, we found asymmetrical introgression of B. variegata genes into B. bombina territory along the bank of a river.},
author = {Yanchukov, Alexey and Hofman, Sebastian and Szymura, Jacek M and Mezhzherin, Sergey V and Morozov-Leonov, Sviatoslav and Nicholas Barton and Nürnberger, Beate},
journal = {Evolution; International Journal of Organic Evolution},
number = {3},
pages = {583 -- 600},
publisher = {Wiley-Blackwell},
title = {{Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time}},
doi = {10.1111/j.0014-3820.2006.tb01139.x},
volume = {60},
year = {2006},
}
@article{3610,
abstract = {For a model of diallelic loci with arbitrary epistasis, Barton and Turelli [2004. Effects of genetic drift on variance components under a general model of epistasis. Evolution 58, 2111–2132] gave results for variances among and within replicate lines obtained by inbreeding without selection. Here, we discuss the relation between their population genetic methods and classical quantitative genetic arguments. In particular, we consider the case of no dominance using classical identity by descent arguments, which generalizes their results from two alleles to multiple alleles. To clarify the connections between the alternative methods, we obtain the same results using an intermediate method, which explicitly identifies the statistical effects of sets of loci. We also discuss the effects of population bottlenecks on covariances among relatives.},
author = {Hill, William G and Nicholas Barton and Turelli, Michael},
journal = {Theoretical Population Biology},
number = {1},
pages = {56 -- 62},
publisher = {Academic Press},
title = {{Prediction of effects of genetic drift on variance components under a general model of epistasis}},
doi = {10.1016/j.tpb.2005.10.001},
volume = {70},
year = {2006},
}
@inproceedings{3677,
abstract = {We propose a video retrieval framework based on a novel combination of spatiograms and the Jensen-Shannon divergence, and validate its performance in two quantitative experiments on TRECVID BBC Rushes data. In the first experiment, color-based methods are tested by grouping redundant shots in an unsupervised clustering. Results of the second experiment show that motion-based spatiograms make a promising fast, compressed-domain descriptor for the detection of interview scenes.},
author = {Ulges, Adrian and Christoph Lampert and Keysers,Daniel},
pages = {1 -- 10},
publisher = {NIST (National Institute of Standards and Technology, US Department of Commerce)},
title = {{Spatiogram-based shot distances for video retrieval}},
year = {2006},
}
@inproceedings{3679,
abstract = {This paper describes a new system for "Finding Satellite Tracks” in astronomical images based on the modern geometric approach. There is an increasing need of using methods with solid mathematical and statistical foundation in astronomical image processing. Where the computational methods are serving in all disciplines of science, they are becoming popular in the field of astronomy as well. Currently different computational systems are required to be numerically optimized before to get applied on astronomical images. So at present there is no single system which solves the problems of astronomers using computational methods based on modern approaches. The system "Finding Satellite Tracks” is based on geometric matching method "Recognition by Adaptive Subdivision of Transformation Space (RAST)".},
author = {Ali,Haider and Christoph Lampert and Breuel,Thomas M},
pages = {892 -- 901},
publisher = {Springer},
title = {{Satellite tracks removal in astronomical images}},
doi = {10.1007/11892755_92},
volume = {4225},
year = {2006},
}
@inproceedings{3680,
abstract = {The detection of counterfeit in printed documents is currently based mainly on built-in security features or on human expertise. We propose a classification system that supports non-expert users to distinguish original documents from PC-made forgeries by analyzing the printing technique used. Each letter in a document is classified using a support vector machine that has been trained to distinguish laser from inkjet printouts. A color-coded visualization helps the user to interpret the per-letter classification results},
author = {Christoph Lampert and Mei,Lin and Breuel,Thomas M},
pages = {639 -- 634},
publisher = {IEEE},
title = {{Printing technique classification for document counterfeit detection}},
doi = {10.1109/ICCIAS.2006.294214},
volume = {1},
year = {2006},
}
@inproceedings{3683,
abstract = {Many algorithms to remove distortion from document images have be proposed in recent years, but so far there is no reliable method for comparing their performance. In this paper we propose a collection of methods to measure the quality of such restoration algorithms for document image which show a non-linear distortion due to perspective or page curl. For the result from these measurement to be meaningful, a common data set of ground truth is required. We therefore started with the buildup of a document image database that is meant to serve as a common data basis for all kinds of restoration from images of 3D-shaped document. The long term goal would be to establish this database and following extensions in the area of document image dewarping as an as fruitful and indispensable tool as e.g. the NIST database is for OCR, or the Caltech database is for object and face recognition.},
author = {Christoph Lampert and Breuel,Thomas M},
publisher = {Springer},
title = {{Objective quality measurement for geometric document image restoration}},
year = {2006},
}
@inproceedings{3685,
abstract = {Video compression currently is dominated by engineering and fine-tuned heuristic methods. In this paper, we propose to instead apply the well-developed machinery of machine learning in order to support the optimization of existing video encoders and the creation of new ones. Exemplarily, we show how by machine learning we can improve one encoding step that is crucial for the performance of all current video standards: macroblock mode decision. By formulating the problem in a Bayesian setup, we show that macroblock mode decision can be reduced to a classification problem with a cost function for misclassification that is sample dependent. We demonstrate how to apply different machine learning techniques to obtain suitable classifiers and we show in detailed experiments that all of these perform better than the state-of-the-art heuristic method},
author = {Christoph Lampert},
pages = {936 -- 940},
publisher = {IEEE},
title = {{Machine learning for video compression: Macroblock mode decision}},
doi = {10.1109/ICPR.2006.778},
year = {2006},
}
@inproceedings{3692,
author = {Keysers,Daniel and Christoph Lampert and Breuel,Thomas M},
publisher = {SPIE},
title = {{Color image dequantization by constrained diffusion}},
doi = {10.1117/12.648713},
volume = {6058},
year = {2006},
}
@inproceedings{3693,
abstract = {Gaussian filtering in one, two or three dimensions is among the most commonly needed tasks in signal and image processing. Finite impulse response filters in the time domain with Gaussian masks are easy to implement in either floating or fixed point arithmetic, because Gaussian kernels are strictly positive and bounded. But these implementations are slow for large images or kernels. With the recursive IIR-filters and FFT-based methods, there are at least two alternative methods to perform Gaussian filtering in a faster way, but so far they are only applicable when floating-point hardware is available. In this paper, a fixed-point implementation of recursive Gaussian filtering is discussed and applied to isotropic and anisotropic image filtering by making use of a non-orthogonal separation scheme of the Gaussian filter.},
author = {Christoph Lampert and Wirjadi,Oliver},
pages = {1565 -- 1568},
publisher = {IEEE},
title = {{Anisotropic Gaussian filtering using fixed point arithmetic}},
doi = {10.1109/ICIP.2006.312606},
year = {2006},
}
@article{3695,
abstract = {We give an analytical and geometrical treatment of what it means to separate a Gaussian kernel along arbitrary axes in Ropfn, and we present a separation scheme that allows us to efficiently implement anisotropic Gaussian convolution filters for data of arbitrary dimensionality. Based on our previous analysis we show that this scheme is optimal with regard to the number of memory accesses and interpolation operations needed. The proposed method relies on nonorthogonal convolution axes and works completely in image space. Thus, it avoids the need for a fast Fourier transform (FFT)-subroutine. Depending on the accuracy and speed requirements, different interpolation schemes and methods to implement the one-dimensional Gaussian (finite impulse response and infinite impulse response) can be integrated. Special emphasis is put on analyzing the performance and accuracy of the new method. In particular, we show that without any special optimization of the source code, it can perform anisotropic Gaussian filtering faster than methods relying on the FFT.},
author = {Christoph Lampert and Wirjadi,Oliver},
journal = {IEEE Transactions on Image Processing (TIP)},
number = {11},
pages = {3501 -- 3513},
publisher = {IEEE},
title = {{An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter}},
doi = { 10.1109/TIP.2006.877501 },
volume = {15},
year = {2006},
}
@article{9505,
abstract = {Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.},
author = {ZILBERMAN, Daniel and Gehring, Mary and Tran, Robert K. and Ballinger, Tracy and Henikoff, Steven},
issn = {1546-1718},
journal = {Nature Genetics},
number = {1},
pages = {61--69},
publisher = {Nature Publishing Group},
title = {{Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription}},
doi = {10.1038/ng1929},
volume = {39},
year = {2006},
}
@article{2307,
abstract = {The human norepinephrine (NE) transporter (hNET) attenuates neuronal signaling by rapid NE clearance from the synaptic cleft, and NET is a target for cocaine and amphetamines as well as therapeutics for depression, obsessive-compulsive disorder, and post-traumatic stress disorder. In spite of its central importance in the nervous system, little is known about how NET substrates, such as NE, 1-methyl-4-tetrahydropyridinium (MPP+), or amphetamine, interact with NET at the molecular level. Nor do we understand the mechanisms behind the transport rate. Previously we introduced a fluorescent substrate similar to MPP+, which allowed separate and simultaneous binding and transport measurement (Schwartz, J. W., Blakely, R. D., and DeFelice, L. J. (2003) J. Biol. Chem. 278, 9768-9777). Here we use this substrate, 4-(4-(dimethylamino)styrl)-N-methyl-pyridinium (ASP+), in combination with green fluorescent protein-tagged hNETs to measure substrate-transporter stoichiometry and substrate binding kinetics. Calibrated confocal microscopy and fluorescence correlation spectroscopy reveal that hNETs, which are homo-multimers, bind one substrate molecule per transporter subunit. Substrate residence at the transporter, obtained from rapid on-off kinetics revealed in fluorescence correlation spectroscopy, is 526 μs. Substrate residence obtained by infinite dilution is 1000 times slower. This novel examination of substrate-transporter kinetics indicates that a single ASP + molecule binds and unbinds thousands of times before being transported or ultimately dissociated from hNET. Calibrated fluorescent images combined with mass spectroscopy give a transport rate of 0.06 ASP +/hNET-protein/s, thus 36,000 on-off binding events (and 36 actual departures) occur for one transport event. Therefore binding has a low probability of resulting in transport. We interpret these data to mean that inefficient binding could contribute to slow transport rates.},
author = {Schwartz, Joel W and Gaia Novarino and Piston, David W and DeFelice, Louis J},
journal = {Journal of Biological Chemistry},
number = {19},
pages = {19177 -- 19184},
publisher = {American Society for Biochemistry and Molecular Biology},
title = {{Substrate binding stoichiometry and kinetics of the norepinephrine transporter}},
doi = {10.1074/jbc.M412923200},
volume = {280},
year = {2005},
}
@book{2335,
abstract = {This book contains a unique survey of the mathematically rigorous results about the quantum-mechanical many-body problem that have been obtained by the authors in the past seven years. It addresses a topic that is not only rich mathematically, using a large variety of techniques in mathematical analysis, but is also one with strong ties to current experiments on ultra-cold Bose gases and Bose-Einstein condensation. The book provides a pedagogical entry into an active area of ongoing research for both graduate students and researchers. It is an outgrowth of a course given by the authors for graduate students and post-doctoral researchers at the Oberwolfach Research Institute in 2004. The book also provides a coherent summary of the field and a reference for mathematicians and physicists active in research on quantum mechanics.},
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
booktitle = {The mathematics of the Bose gas and its condensation},
publisher = {Birkhäuser},
title = {{The mathematics of the Bose gas and its condensation}},
volume = {34},
year = {2005},
}
@inbook{2336,
abstract = {
Now that the low temperature properties of quantum-mechanical many-body systems (bosons) at low density, ρ, can be examined experimentally it is appropriate to revisit some of the formulas deduced by many authors 4–5 decades ago, and to explore new regimes not treated before. For systems with repulsive (i.e. positive) interaction potentials the experimental low temperature state and the ground state are effectively synonymous — and this fact is used in all modeling. In such cases, the leading term in the energy/particle is 2πħ2 aρ/m where a is the scattering length of the two-body potential. Owing to the delicate and peculiar nature of bosonic correlations (such as the strange N 7/5 law for charged bosons), four decades of research failed to establish this plausible formula rigorously. The only previous lower bound for the energy was found by Dyson in 1957, but it was 14 times too small. The correct asymptotic formula has been obtained by us and this work will be presented. The reason behind the mathematical difficulties will be emphasized. A different formula, postulated as late as 1971 by Schick, holds in two dimensions and this, too, will be shown to be correct. With the aid of the methodology developed to prove the lower bound for the homogeneous gas, several other problems have been successfully addressed. One is the proof by us that the Gross-Pitaevskii equation correctly describes the ground state in the ‘traps’ actually used in the experiments. For this system it is also possible to prove complete Bose condensation and superfluidity as we have shown. On the frontier of experimental developments is the possibility that a dilute gas in an elongated trap will behave like a one-dimensional system; we have proved this mathematically. Another topic is a proof that Foldy’s 1961 theory of a high density Bose gas of charged particles correctly describes its ground state energy; using this we can also prove the N 7/5 formula for the ground state energy of the two-component charged Bose gas proposed by Dyson in 1967. All of this is quite recent work and it is hoped that the mathematical methodology might be useful, ultimately, to solve more complex problems connected with these interesting systems.},
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
booktitle = {Perspectives in Analysis},
editor = {Benedicks, Michael and Jones, Peter W and Smirnov, Stanislav and Winckler, Björn},
pages = {97 -- 183},
publisher = {Springer},
title = {{The quantum-mechanical many-body problem: The Bose gas}},
doi = {10.1007/3-540-30434-7_9},
volume = {27},
year = {2005},
}
@article{2359,
abstract = {The validity of substituting a c-number z for the k = 0 mode operator a0 is established rigorously in full generality, thereby verifying one aspect of Bogoliubov's 1947 theory. This substitution not only yields the correct value of thermodynamic quantities such as the pressure or ground state energy, but also the value of |z|2 that maximizes the partition function equals the true amount of condensation in the presence of a gauge-symmetry-breaking term. This point had previously been elusive.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society},
title = {{Justification of c-number substitutions in bosonic hamiltonians}},
doi = {10.1103/PhysRevLett.94.080401},
volume = {94},
year = {2005},
}
@article{2361,
abstract = {The strong subadditivity of entropy plays a key role in several areas of physics and mathematics. It states that the entropy S[±]=- Tr(Ï±lnÏ±) of a density matrix Ï±123 on the product of three Hilbert spaces satisfies S[Ï±123]- S[Ï±12]≤S[Ï±23]-S[Ï±2]. We strengthen this to S[Ï±123]-S[Ï±12] ≤αnα(S[Ï±23α]-S[Ï±2α]), where the nα are weights and the Ï±23α are partitions of Ï±23. Correspondingly, there is a strengthening of the theorem that the map A|Trexp[L+lnA] is concave. As applications we prove some monotonicity and convexity properties of the Wehrl coherent state entropy and entropy inequalities for quantum gases.},
author = {Lieb, Élliott H and Robert Seiringer},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {6},
publisher = {American Physical Society},
title = {{Stronger subadditivity of entropy}},
doi = {10.1103/PhysRevA.71.062329},
volume = {71},
year = {2005},
}
@article{2362,
abstract = {Recent developments in the physics of low-density trapped gases make it worthwhile to verify old, well-known results that, while plausible, were based on perturbation theory and assumptions about pseudopotentials. We use and extend recently developed techniques to give a rigorous derivation of the asymptotic formula for the ground-state energy of a dilute gas of N fermions interacting with a short-range, positive potential of scattering length a. For spin-12 fermions, this is E∼E0+(22m)2πNa, where E0 is the energy of the noninteracting system and is the density. A similar formula holds in two dimensions (2D), with a replaced by ln(a2). Obviously this 2D energy is not the expectation value of a density-independent pseudopotential.},
author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {5},
publisher = {American Physical Society},
title = {{Ground state energy of the low density Fermi gas}},
doi = {10.1103/PhysRevA.71.053605},
volume = {71},
year = {2005},
}