@article{3185,
abstract = {This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.},
author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {9},
pages = {1480 -- 1492},
publisher = {IEEE},
title = {{Probabilistic fusion of stereo with color and contrast for bilayer segmentation}},
doi = {10.1109/TPAMI.2006.193},
volume = {28},
year = {2006},
}
@inproceedings{3186,
abstract = {We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion.},
author = {Boykov, Yuri and Vladimir Kolmogorov and Cremers, Daniel and Delong, Andrew},
pages = {409 -- 422},
publisher = {Springer},
title = {{An integral solution to surface evolution PDEs via geo cuts}},
doi = {10.1007/11744078_32},
volume = {3953},
year = {2006},
}
@inproceedings{3188,
abstract = {We introduce the term cosegmentation which denotes the task of segmenting simultaneously the common parts of an image pair. A generative model for cosegmentation is presented. Inference in the model leads to minimizing an energy with an MRF term encoding spatial coherency and a global constraint which attempts to match the appearance histograms of the common parts. This energy has not been proposed previously and its optimization is challenging and NP-hard. For this problem a novel optimization scheme which we call trust region graph cuts is presented. We demonstrate that this framework has the potential to improve a wide range of research: Object driven image retrieval, video tracking and segmentation, and interactive image editing. The power of the framework lies in its generality, the common part can be a rigid/non-rigid object (or scene), observed from different viewpoints or even similar objects of the same class.},
author = {Rother, Carsten and Vladimir Kolmogorov and Minka, Thomas P and Blake, Andrew},
pages = {993 -- 1000},
publisher = {IEEE},
title = {{Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs}},
doi = {10.1109/CVPR.2006.91},
year = {2006},
}
@inproceedings{3189,
abstract = {This paper presents an algorithm capable of real-time separation of foreground from background in monocular video sequences. Automatic segmentation of layers from colour/contrast or from motion alone is known to be error-prone. Here motion, colour and contrast cues are probabilistically fused together with spatial and temporal priors to infer layers accurately and efficiently. Central to our algorithm is the fact that pixel velocities are not needed, thus removing the need for optical flow estimation, with its tendency to error and computational expense. Instead, an efficient motion vs non-motion classifier is trained to operate directly and jointly on intensity-change and contrast. Its output is then fused with colour information. The prior on segmentation is represented by a second order, temporal, Hidden Markov Model, together with a spatial MRF favouring coherence except where contrast is high. Finally, accurate layer segmentation and explicit occlusion detection are efficiently achieved by binary graph cut. The segmentation accuracy of the proposed algorithm is quantitatively evaluated with respect to existing ground-truth data and found to be comparable to the accuracy of a state of the art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated in the application of live background substitution and shown to generate convincingly good quality composite video.},
author = {Criminisi, Antonio and Cross, Geoffrey and Blake, Andrew and Vladimir Kolmogorov},
pages = {53 -- 60},
publisher = {IEEE},
title = {{Bilayer segmentation of live video}},
doi = {10.1109/CVPR.2006.69},
volume = {1},
year = {2006},
}
@article{3190,
abstract = {Algorithms for discrete energy minimization are of fundamental importance in computer vision. In this paper, we focus on the recent technique proposed by Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW). It was inspired by the problem of maximizing a lower bound on the energy. However, the algorithm is not guaranteed to increase this bound - it may actually go down. In addition, TRW does not always converge. We develop a modification of this algorithm which we call sequential tree-reweighted message passing. Its main property is that the bound is guaranteed not to decrease. We also give a weak tree agreement condition which characterizes local maxima of the bound with respect to TRW algorithms. We prove that our algorithm has a limit point that achieves weak tree agreement. Finally, we show that, our algorithm requires half as much memory as traditional message passing approaches. Experimental results demonstrate that on certain synthetic and real problems, our algorithm outperforms both the ordinary belief propagation and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition, on stereo problems with Potts interactions, we obtain a lower energy than graph cuts.},
author = {Vladimir Kolmogorov},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {10},
pages = {1568 -- 1583},
publisher = {IEEE},
title = {{Convergent tree reweighted message passing for energy minimization}},
doi = {10.1109/TPAMI.2006.200},
volume = {28},
year = {2006},
}
@inproceedings{3214,
abstract = {The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key.
Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers.
But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation.},
author = {Maurer, Ueli M and Oswald, Yvonne A and Krzysztof Pietrzak and Sjödin, Johan},
pages = {391 -- 408},
publisher = {Springer},
title = {{Luby Rackoff ciphers from weak round functions }},
doi = {10.1007/11761679_24},
volume = {4004},
year = {2006},
}
@inproceedings{3215,
abstract = {Most cryptographic primitives such as encryption, authentication or secret sharing require randomness. Usually one assumes that perfect randomness is available, but those primitives might also be realized under weaker assumptions. In this work we continue the study of building secure cryptographic primitives from imperfect random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows that there exists a (high-entropy) source of randomness allowing for perfect encryption of a bit, and yet from which one cannot extract even a single weakly random bit, separating encryption from extraction. Our main result separates encryption from 2-out-2 secret sharing (both in the information-theoretic and in the computational settings): any source which can be used to achieve one-bit encryption also can be used for 2-out-2 secret sharing of one bit, but the converse is false, even for high-entropy sources. Therefore, possibility of extraction strictly implies encryption, which in turn strictly implies 2-out-2 secret sharing.},
author = {Dodis, Yevgeniy and Krzysztof Pietrzak and Przydatek, Bartosz},
pages = {601 -- 616},
publisher = {Springer},
title = {{Separating sources for encryption and secret sharing}},
doi = {10.1007/11681878_31},
volume = {3876},
year = {2006},
}
@inproceedings{3216,
abstract = {We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04].
The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found.},
author = {Krzysztof Pietrzak},
pages = {168 -- 179},
publisher = {Springer},
title = {{A tight bound for EMAC}},
doi = {10.1007/11787006_15},
volume = {4052},
year = {2006},
}
@inproceedings{3217,
abstract = {To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true.
To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not.},
author = {Krzysztof Pietrzak},
pages = {328 -- 338},
publisher = {Springer},
title = {{Composition implies adaptive security in minicrypt}},
doi = {10.1007/11761679_20},
volume = {4004},
year = {2006},
}
@inbook{3404,
author = {Harald Janovjak and Sawhney, Ravi K and Stark, Martin and Mueller, Daniel J},
booktitle = {Techniques in Microscopy for Biomedical Applications},
pages = {213 -- 284},
publisher = {World Scientific Publishing},
title = {{Atomic force microscopy}},
volume = {2},
year = {2006},
}
@article{3413,
abstract = {Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.
Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.
We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.},
author = {Kessler, Max and Gottschalk, Kay E and Harald Janovjak and Mueller, Daniel J and Gaub, Hermann},
journal = {Journal of Molecular Biology},
number = {2},
pages = {644 -- 654},
publisher = {Elsevier},
title = {{Bacteriorhodopsin folds into the membrane against an external force}},
doi = {10.1016/j.jmb.2005.12.065},
volume = {357},
year = {2006},
}
@article{3414,
abstract = {Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter.},
author = {Kedrov, Alexej and Harald Janovjak and Ziegler, Christine and Kühlbrandt, Werner and Mueller, Daniel J},
journal = {Journal of Molecular Biology},
number = {1},
pages = {2 -- 8},
publisher = {Elsevier},
title = {{Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli}},
doi = {10.1016/j.jmb.2005.10.028},
volume = {355},
year = {2006},
}
@misc{3415,
author = {Harald Janovjak and Kedrov, Alexej and Cisneros, David and Sapra, Tanuj K and Struckmeier, Jens and Mueller, Daniel J},
booktitle = {Neurobiology of Aging},
pages = {546 -- 561},
publisher = {Elsevier},
title = {{Imaging and detecting molecular interactions of single membrane proteins}},
doi = {10.1016/j.neurobiolaging.2005.03.031},
volume = {27},
year = {2006},
}
@unpublished{3431,
abstract = {Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses.},
author = {Gasper Tkacik and Schneidman, E. and Berry, M. J. and Bialek, William S},
booktitle = {ArXiv},
pages = {1 -- 4},
publisher = {ArXiv},
title = {{Ising models for networks of real neurons}},
year = {2006},
}
@article{3437,
abstract = {The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models.},
author = {Betancourt, Andrea J and Jonathan Bollback},
journal = {Current Opinion in Genetics & Development},
number = {6},
pages = {618 -- 623},
publisher = {Elsevier},
title = {{Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution}},
doi = {10.1016/j.gde.2006.10.006},
volume = {16},
year = {2006},
}
@inproceedings{3449,
abstract = {We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control.},
author = {Krishnendu Chatterjee and Jagadeesan, Rhada and Pitcher, Corin},
pages = {70 -- 82},
publisher = {IEEE},
title = {{Games for controls}},
doi = {10.1109/CSFW.2006.14},
year = {2006},
}
@misc{3463,
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, Joseph and Engel, Dominique and Frotscher, Michael and Peter Jonas},
booktitle = {Pflugers Archiv : European Journal of Physiology},
number = {3},
pages = {361 -- 372},
publisher = {Springer},
title = {{Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review)}},
doi = {10.1007/s00424-006-0093-2},
volume = {453},
year = {2006},
}
@misc{3510,
abstract = {Embodiments automatically generate an accurate network of watertight NURBS patches from polygonal models of objects while automatically detecting and preserving character lines thereon. These embodiments generate from an initial triangulation of the surface, a hierarchy of progressively coarser triangulations of the surface by performing a sequence of edge contractions using a greedy algorithm that selects edge contractions by their numerical properties. Operations are also performed to connect the triangulations in the hierarchy using homeomorphisms that preserve the topology of the initial triangulation in the coarsest triangulation. A desired quadrangulation of the surface can then be generated by homeomorphically mapping edges of a coarsest triangulation in the hierarchy back to the initial triangulation. This quadrangulation is topologically consistent with the initial triangulation and is defined by a plurality of quadrangular patches. These quadrangular patches are linked together by a (U, V) mesh that is guaranteed to be continuous at patch boundaries. A grid is then preferably fit to each of the quadrangles in the resulting quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles. A watertight NURBS model may be generated from the resulting quadrangulation.},
author = {Herbert Edelsbrunner and Fu, Ping and Nekhayev, Dmitry V and Facello, Michael and Williams, Steven P},
publisher = {Elsevier},
title = {{Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism}},
doi = {US 6,996,505 B1},
year = {2006},
}
@misc{3511,
abstract = {Methods, apparatus and computer program products provide efficient techniques for designing and printing shells of hearing-aid devices with a high degree of quality assurance and reliability and with a reduced number of manual and time consuming production steps and operations. These techniques also preferably provide hearing-aid shells having internal volumes that can approach a maximum allowable ratio of internal volume relative to external volume. These high internal volumes facilitate the inclusion of hearing-aid electrical components having higher degrees of functionality and/or the use of smaller and less conspicuous hearing-aid shells. A preferred method includes operations to generate a watertight digital model of a hearing-aid shell by thickening a three-dimensional digital model of a shell surface in a manner that eliminates self-intersections and results in a thickened model having an internal volume that is a high percentage of an external volume of the model. },
author = {Fu, Ping and Nekhayev, Dmitry V and Herbert Edelsbrunner},
publisher = {Elsevier},
title = {{Manufacturing methods and systems for rapid production of hearing-aid shells}},
doi = {US 7,050,876 B1},
year = {2006},
}
@misc{3512,
abstract = {Methods, apparatus and computer program products provide efficient techniques for reconstructing surfaces from data point sets. These techniques include reconstructing surfaces from sets of scanned data points that have preferably undergone preprocessing operations to improve their quality by, for example, reducing noise and removing outliers. These techniques include reconstructing a dense and locally two-dimensionally distributed 3D point set (e.g., point cloud) by merging stars in two-dimensional weighted Delaunay triangulations within estimated tangent planes. The techniques include determining a plurality of stars from a plurality of points p.sub.i in a 3D point set S that at least partially describes the 3D surface, by projecting the plurality of points p.sub.i onto planes T.sub.i that are each estimated to be tangent about a respective one of the plurality of points p.sub.i. The plurality of stars are then merged into a digital model of the 3D surface.},
author = {Fletcher, Yates G and Gloth, Tobias and Herbert Edelsbrunner and Fu, Ping},
publisher = {Elsevier},
title = {{Method, apparatus and computer products that reconstruct surfaces from data points}},
doi = {US 7,023,432 B2},
year = {2006},
}
@article{3522,
abstract = {We observed sharp wave/ripples (SWR) during exploration within brief (< 2.4 s) interruptions of or during theta oscillations. CA1 network responses of SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility or sleep were similar. However, neuronal activity during eSWR was location dependent, and eSWR-related firing was stronger inside the place field than outside. The eSPW-related firing increase was stronger than the baseline increase inside compared to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs. Pairs of cells with similar place fields and/or correlated firing during exploration showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential activation of place cells was not required for the reactivation of waking co-firing patterns; cell pairs with symmetrical cross-correlations still showed reactivated waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing during eSWRs facilitates initial associations between cells with similar place fields that enable place-related ensemble patterns to recur during subsequent sleep-SWRs.},
author = {Joseph O'Neill and Senior,Timothy and Jozsef Csicsvari},
journal = {Neuron},
number = {1},
pages = {143 -- 155},
publisher = {Elsevier},
title = {{Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior}},
doi = {10.1016/j.neuron.2005.10.037},
volume = {49},
year = {2006},
}
@article{3545,
abstract = {The functional organization of the basal ganglia ( BG) is often defined according to one of two opposing schemes. The first proposes multiple, essentially independent channels of information processing. The second posits convergence and lateral integration of striatal channels at the level of the globus pallidus ( GP). We tested the hypothesis that these proposed aspects of functional connectivity within the striatopallidal axis are dynamic and related to brain state. Local field potentials ( LFPs) were simultaneously recorded from multiple sites in striatum and GP in anesthetized rats during slow-wave activity( SWA) and during global activation evoked by sensory stimulation. Functional connectivity was inferred from comparative analyses of the internuclear and intranuclear coherence between bipolar derivations of LFPs. During prominent SWA, as shown in the electrocorticogram and local field potentials in the basal ganglia, intranuclear coherence, and, thus, lateral functional connectivity within striatum or globus pallidus was relatively weak. Furthermore, the temporal coupling of LFPs recorded across these two nuclei involved functional convergence at the level of GP. Global activation, indicated by a loss of SWA, was accompanied by a rapid functional reorganization of the striatopallidal axis. Prominent lateral functional connectivity developed within GP and, to a significantly more constrained spatial extent, striatum. Additionally, functional convergence on GP was no longer apparent, despite increased internuclear coherence. These data demonstrate that functional connectivity within the BG is highly dynamic and suggest that the relative expression of organizational principles, such as parallel, independent processing channels, striatopallidal convergence, and lateral integration within BG nuclei, is dependent on brain state.},
author = {Magill,Peter J and Pogosyan,Alek and Sharott,Andrew and Jozsef Csicsvari and Bolam, John Paul and Brown,Peter},
journal = {Journal of Neuroscience},
number = {23},
pages = {6318 -- 6329},
publisher = {Society for Neuroscience},
title = {{Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo}},
doi = {10.1523/JNEUROSCI.0620-06.2006},
volume = {26},
year = {2006},
}
@inproceedings{3559,
abstract = {Persistent homology is the mathematical core of recent work on shape, including reconstruction, recognition, and matching. Its per- tinent information is encapsulated by a pairing of the critical values of a function, visualized by points forming a diagram in the plane. The original algorithm in [10] computes the pairs from an ordering of the simplices in a triangulation and takes worst-case time cubic in the number of simplices. The main result of this paper is an algorithm that maintains the pairing in worst-case linear time per transposition in the ordering. A side-effect of the algorithm’s anal- ysis is an elementary proof of the stability of persistence diagrams [7] in the special case of piecewise-linear functions. We use the algorithm to compute 1-parameter families of diagrams which we apply to the study of protein folding trajectories.},
author = {Cohen-Steiner, David and Herbert Edelsbrunner and Morozov, Dmitriy},
pages = {119 -- 126},
publisher = {ACM},
title = {{Vines and vineyards by updating persistence in linear time}},
doi = {10.1145/1137856.1137877},
year = {2006},
}
@inproceedings{3560,
abstract = {We continue the study of topological persistence [5] by investigat- ing the problem of simplifying a function f in a way that removes topological noise as determined by its persistence diagram [2]. To state our results, we call a function g an ε-simplification of another function f if ∥f − g∥∞ ≤ ε, and the persistence diagrams of g are the same as those of f except all points within L1-distance at most ε from the diagonal have been removed. We prove that for func- tions f on a 2-manifold such ε-simplification exists, and we give an algorithm to construct them in the piecewise linear case.},
author = {Herbert Edelsbrunner and Morozov, Dmitriy and Pascucci, Valerio},
pages = {127 -- 134},
publisher = {ACM},
title = {{Persistence-sensitive simplification of functions on 2-manifolds}},
doi = {10.1145/1137856.1137878},
year = {2006},
}
@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},
}
@inproceedings{3499,
abstract = {We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. },
author = {Krishnendu Chatterjee},
pages = {271 -- 286},
publisher = {Springer},
title = {{Nash equilibrium for upward-closed objectives}},
doi = {10.1007/11874683_18},
volume = {4207},
year = {2006},
}
@inproceedings{3500,
abstract = {The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n).},
author = {Krishnendu Chatterjee and Thomas Henzinger and Piterman, Nir},
publisher = {ACM},
title = {{Algorithms for Büchi Games}},
year = {2006},
}
@inproceedings{4549,
abstract = {We present a compositional theory of system verification, where specifications assign real-numbered costs to systems. These costs can express a wide variety of quantitative system properties, such as resource consumption, price, or a measure of how well a system satisfies its specification. The theory supports the composition of systems and specifications, and the hiding of variables. Boolean refinement relations are replaced by real-numbered distances between descriptions of a system at different levels of detail. We show that the classical Boolean rules for compositional reasoning have quantitative counterparts in our setting. While our general theory allows costs to be specified by arbitrary cost functions, we also consider a class of linear cost functions, which give rise to an instance of our framework where all operations are computable in polynomial time.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Faella, Marco and Thomas Henzinger and Majumdar, Ritankar S and Stoelinga, Mariëlle},
pages = {179 -- 188},
publisher = {IEEE},
title = {{Compositional quantitative reasoning}},
doi = {10.1109/QEST.2006.11},
year = {2006},
}
@article{4550,
abstract = {In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent's payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it sometimes suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of ω-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.},
author = {Krishnendu Chatterjee and Thomas Henzinger and Jurdziński, Marcin},
journal = {Theoretical Computer Science},
number = {1-2},
pages = {67 -- 82},
publisher = {Elsevier},
title = {{Games with secure equilibria}},
doi = {10.1016/j.tcs.2006.07.032},
volume = {365},
year = {2006},
}
@inproceedings{4551,
abstract = {We consider Markov decision processes (MDPs) with multiple discounted reward objectives. Such MDPs occur in design problems where one wishes to simultaneously optimize several criteria, for example, latency and power. The possible trade-offs between the different objectives are characterized by the Pareto curve. We show that every Pareto-optimal point can be achieved by a memoryless strategy; however, unlike in the single-objective case, the memoryless strategy may require randomization. Moreover, we show that the Pareto curve can be approximated in polynomial time in the size of the MDP. Additionally, we study the problem if a given value vector is realizable by any strategy, and show that it can be decided in polynomial time; but the question whether it is realizable by a deterministic memoryless strategy is NP-complete. These results provide efficient algorithms for design exploration in MDP models with multiple objectives.
This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202. },
author = {Krishnendu Chatterjee and Majumdar, Ritankar S and Thomas Henzinger},
pages = {325 -- 336},
publisher = {Springer},
title = {{Markov decision processes with multiple objectives}},
doi = {10.1007/11672142_26},
volume = {3884},
year = {2006},
}
@inproceedings{4552,
abstract = {A concurrent reachability game is a two-player game played on a graph: at each state, the players simultaneously and independently select moves; the two moves determine jointly a probability distribution over the successor states. The objective for player 1 consists in reaching a set of target states; the objective for player 2 is to prevent this, so that the game is zero-sum. Our contributions are two-fold. First, we present a simple proof of the fact that in concurrent reachability games, for all epsilon > 0, memoryless epsilon-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an epsilon-optimal strategy achieves the objective with probability within epsilon of the value of the game. In contrast to previous proofs of this fact, which rely on the limit behavior of discounted games using advanced Puisieux series analysis, our proof is elementary and combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Thomas Henzinger},
pages = {291 -- 300},
publisher = {IEEE},
title = {{Strategy improvement for concurrent reachability games}},
doi = {10.1109/QEST.2006.48},
year = {2006},
}
@inproceedings{4574,
abstract = {Many software model checkers are based on predicate abstraction. If the verification goal depends on pointer structures, the approach does not work well, because it is difficult to find adequate predicate abstractions for the heap. In contrast, shape analysis, which uses graph-based heap abstractions, can provide a compact representation of recursive data structures. We integrate shape analysis into the software model checker Blast. Because shape analysis is expensive, we do not apply it globally. Instead, we ensure that, like predicates, shape graphs are computed and stored locally, only where necessary for proving the verification goal. To achieve this, we extend lazy abstraction refinement, which so far has been used only for predicate abstractions, to three-valued logical structures. This approach does not only increase the precision of model checking, but it also increases the efficiency of shape analysis. We implemented the technique by extending Blast with calls to Tvla.},
author = {Beyer, Dirk and Thomas Henzinger and Théoduloz, Grégory},
pages = {532 -- 546},
publisher = {Springer},
title = {{Lazy shape analysis}},
doi = {10.1007/11817963_48},
volume = {4144},
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{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},
}
@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},
}