@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},
}
@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},
}
@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},
}