@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},
}

@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},
}

@article{3729,
  abstract     = {Measuring the visco-elastic properties of biological macromolecules constitutes an important step towards the understanding of dynamic biological processes, such as cell adhesion, muscle function, or plant cell wall stability. Force spectroscopy techniques based on the atomic force microscope (AFM) are increasingly used to study the complex visco-elastic response of (bio-)molecules on a single-molecule level. These experiments either require that the AFM cantilever is actively oscillated or that the molecule is clamped at constant force to monitor thermal cantilever motion. Here we demonstrate that the visco-elasticity of single bio-molecules can readily be extracted from the Brownian cantilever motion during conventional force-extension measurements. It is shown that the characteristics of the cantilever determine the signal-to-noise (S/N) ratio and time resolution. Using a small cantilever, the visco-elastic properties of single dextran molecules were resolved with a time resolution of 8.3 ms. The presented approach can be directly applied to probe the dynamic response of complex bio-molecular systems or proteins in force-extension experiments.},
  author       = {Bippes, Christian A and Humphris, Andrew D and Stark, Martin and Mueller, Daniel J and Harald Janovjak},
  journal      = {European Biophysics Journal},
  number       = {3},
  pages        = {287 -- 292},
  publisher    = {Springer},
  title        = {{Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments}},
  doi          = {10.1007/s00249-005-0023-9},
  volume       = {35},
  year         = {2006},
}

@article{3750,
  abstract     = {We applied a single-cell assay to characterize how transcription dynamics affects protein expression levels of a tetracycline-inducible gene expression system. Transcriptional activity of the tetracycline promoter in response to a steady level of inducer is steady in ΔacrAB efflux mutant but pulsating in wildtype Escherichia coli cells. We found that the expression level of the green fluorescent protein is several folds higher in ΔacrAB efflux mutant than in wildtype cells.},
  author       = {Le,Thuc T. and Calin Guet and Cluzel,Philippe},
  journal      = {Protein Expression and Purification},
  number       = {1},
  pages        = {28 -- 31},
  publisher    = {Elsevier},
  title        = {{Protein expression enhancement in efflux-deleted mutant bacteria}},
  volume       = {48},
  year         = {2006},
}

@article{3755,
  abstract     = {A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems.},
  author       = {Le,Thuc T. and Emonet,Thierry and Harlepp, Sébastien and Calin Guet and Cluzel,Philippe},
  journal      = {Biophysical Journal},
  number       = {9},
  pages        = {3315 -- 3321},
  publisher    = {Biophysical Society},
  title        = {{Dynamical determinants of drug-inducible gene expression in a single bacterium}},
  doi          = {10.1529/biophysj.105.073353},
  volume       = {90},
  year         = {2006},
}

@inproceedings{3758,
  abstract     = {Control of physical simulation has become a popular topic in the field of computer graphics. Keyframe control has been applied to simulations of rigid bodies, smoke, liquid, flocks, and finite element-based elastic bodies. In this paper, we create a framework for controlling systems of interacting particles -- paying special attention to simulations of cloth and flocking behavior. We introduce a novel integrator-swapping approximation in order to apply the adjoint method to linearized implicit schemes appropriate for cloth simulation. This allows the control of cloth while avoiding computationally infeasible derivative calculations. Meanwhile, flocking control using the adjoint method is significantly more efficient than currently-used methods for constraining group behaviors, allowing the controlled simulation of greater numbers of agents in fewer optimization iterations.},
  author       = {Wojtan, Christopher J and Mucha, Peter and Turk, Greg},
  pages        = {15 -- 23},
  publisher    = {ACM},
  title        = {{Keyframe control of complex particle systems using the adjoint method}},
  year         = {2006},
}

@article{3767,
  abstract     = {Models of RNA secondary structure folding are widely used to study evolution in theory and simulation. However, systematic studies of the parameters involved are rare. In this paper, we study by simulation how RNA evolution is influenced by three different factors, namely the mutation rate, scaling of the fitness function, and distance measure. We found that for low mutation rates the qualitative evolutionary behavior is robust with respect to the scaling of the fitness function. For efficient mutation rates, which are close to the error threshold, scaling and distance measure have a strong influence on the evolutionary behavior. A global distance measure that takes sequence information additively into account lowers the error threshold. When using a local sequence-structure alignment for the distance, we observed a smoother evolution of the fitness over time. Finally, in addition to the well known error threshold, we identify another threshold of the mutation rate, called divergence threshold, where the qualitative transient behavior changes from a localized to an exploratory search.},
  author       = {Anne Kupczok and Dittrich,Peter},
  journal      = {Journal of Theoretical Biology},
  number       = {3},
  pages        = {726 -- 35},
  publisher    = {Elsevier},
  title        = {{Determinants of simulated RNA evolution.}},
  doi          = {10.1016/j.jtbi.2005.06.019},
  volume       = {238},
  year         = {2006},
}

@article{3811,
  abstract     = {Networks of GABAergic neurons are key elements in the generation of gamma oscillations in the brain. Computational studies suggested that the emergence of coherent oscillations requires hyperpolarizing inhibition. Here, we show that GABA(A) receptor-mediated inhibition in mature interneurons of the hippocampal dentate gyrus is shunting rather than hyperpolarizing. Unexpectedly, when shunting inhibition is incorporated into a structured interneuron network model with fast and strong synapses, coherent oscillations emerge. In comparison to hyperpolarizing inhibition, networks with shunting inhibition show several advantages. First, oscillations are generated with smaller tonic excitatory drive. Second, network frequencies are tuned to the gamma band. Finally, robustness against heterogeneity in the excitatory drive is markedly improved. In single interneurons, shunting inhibition shortens the interspike interval for low levels of drive but prolongs it for high levels, leading to homogenization of neuronal firing rates. Thus, shunting inhibition may confer increased robustness to gamma oscillations in the brain.},
  author       = {Vida, Imre and Bartos, Marlene and Peter Jonas},
  journal      = {Neuron},
  number       = {1},
  pages        = {107 -- 17},
  publisher    = {Elsevier},
  title        = {{Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates}},
  doi          = {10.1016/j.neuron.2005.11.036},
  volume       = {49},
  year         = {2006},
}

@article{3813,
  abstract     = {Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed in principal neurons in the central nervous system. However, Ih in inhibitory GABAergic interneurons is less well characterized. We examined the functional properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of 5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent membrane time constant. ZD 7288 blocked a hyperpolarization-activated current in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288 were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of the activation curve of Ih was -83.9 mV, and the activation time constant at -120 mV was 190 ms. Single-cell expression analysis using reverse transcription followed by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD 7288 increased the current threshold for evoking antidromic action potentials by extracellular stimulation, consistent with the expression of Ih in BC axons. Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs, to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged, consistent with the presence of Ih in inhibitory terminals. In conclusion, our results suggest that Ih channels are expressed in the somatodendritic region, axon and presynaptic elements of fast-spiking BCs in the hippocampus.},
  author       = {Aponte, Yexica and Lien, Cheng-Chang and Reisinger, Ellen and Peter Jonas},
  journal      = {Journal of Physiology},
  number       = {Pt 1},
  pages        = {229 -- 43},
  publisher    = {Wiley-Blackwell},
  title        = {{Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus}},
  doi          = {10.1113/jphysiol.2005.104042},
  volume       = {574},
  year         = {2006},
}

@misc{3814,
  abstract     = {The axon terminals (mossy fibers) of hippocampal dentate granule cells form characteristic synaptic connections with large spines or excrescences of both hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled mossy fibers and immunolabeling of target cells with interneuron markers has revealed that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic inhibitory interneurons rather than to excitatory principal cells, although the functional implications of these quantitative differences are unclear. Following a brief description of the "classical" mossy fiber synapse on excrescences of CA3 pyramidal cells, the present review focuses on the contacts formed between granule cells and GABAergic interneurons, both normally and after synaptic reorganization. In response to deafferentation of mossy cell target cells, which include both granule cells and interneurons, mossy fibers "sprout" new axon collaterals that form a band of supragranular mossy fibers in the inner molecular layer of the dentate gyrus. Although most newly formed recurrent mossy fibers establish synapses with granule cells, there is an apparently convergent input of new mossy fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are observed in chronically epileptic rats and may be the structural correlate of the granule cell hyperinhibition observed in these animals in vivo. Together, the findings reviewed here establish mossy fiber synapses as an important component of inhibitory circuits in the hippocampus.},
  author       = {Frotscher, Michael and Peter Jonas and Sloviter, Robert S},
  booktitle    = {Cell and Tissue Research},
  number       = {2},
  pages        = {361 -- 7},
  publisher    = {Springer},
  title        = {{Synapses formed by normal and abnormal hippocampal mossy fibers (Review)}},
  doi          = {10.1007/s00441-006-0269-2},
  volume       = {326},
  year         = {2006},
}

@article{3815,
  abstract     = {It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network.},
  author       = {Bischofberger, Josef and Engel, Dominique and Frotscher, Michael and Peter Jonas},
  journal      = {Pflugers Archiv : European Journal of Physiology},
  number       = {3},
  pages        = {361 -- 72},
  publisher    = {Springer},
  title        = {{Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network}},
  doi          = {10.1007/s00424-006-0093-2},
  volume       = {453},
  year         = {2006},
}