@inproceedings{3237, abstract = {Blinding is a popular and well-known countermeasure to protect public-key cryptosystems against side-channel attacks. The high level idea is to randomize an exponentiation in order to prevent multiple measurements of the same operation on different data, as such measurements might allow the adversary to learn the secret exponent. Several variants of blinding have been proposed in the literature, using additive or multiplicative secret-sharing to blind either the base or the exponent. These countermeasures usually aim at preventing particular side-channel attacks (mostly power analysis) and come without any formal security guarantee. In this work we investigate to which extend blinding can provide provable security against a general class of side-channel attacks. Surprisingly, it turns out that in the context of public-key encryption some blinding techniques are more suited than others. In particular, we consider a multiplicatively blinded version of ElGamal public-key encryption where - we prove that the scheme, instantiated over bilinear groups of prime order p (where p - 1 is not smooth) is leakage resilient in the generic-group model. Here we consider the model of chosen-ciphertext security in the presence of continuous leakage, i.e., the scheme remains chosen-ciphertext secure even if with every decryption query the adversary can learn a bounded amount (roughly log(p)/2 bits) of arbitrary, adversarially chosen information about the computation. - we conjecture that the scheme, instantiated over arbitrary groups of prime order p (where p - 1 is not smooth) is leakage resilient. Previous to this work no encryption scheme secure against continuous leakage was known. Constructing a scheme that can be proven secure in the standard model remains an interesting open problem. }, author = {Kiltz, Eike and Krzysztof Pietrzak}, pages = {595 -- 612}, publisher = {Springer}, title = {{Leakage resilient ElGamal encryption}}, doi = {10.1007/978-3-642-17373-8_34}, volume = {6477}, year = {2010}, } @article{3294, abstract = {Olfactory responses of Drosophila undergo pronounced changes after eclosion. The flies develop attraction to odors to which they are exposed and aversion to other odors. Behavioral adaptation is correlated with changes in the firing pattern of olfactory receptor neurons (ORNs). In this article, we present an information-theoretic analysis of the firing pattern of ORNs. Flies reared in a synthetic odorless medium were transferred after eclosion to three different media: (i) a synthetic medium relatively devoid of odor cues, (ii) synthetic medium infused with a single odorant, and (iii) complex cornmeal medium rich in odors. Recordings were made from an identified sensillum (type II), and the Jensen-Shannon divergence (D(JS)) was used to assess quantitatively the differences between ensemble spike responses to different odors. Analysis shows that prolonged exposure to ethyl acetate and several related esters increases sensitivity to these esters but does not improve the ability of the fly to distinguish between them. Flies exposed to cornmeal display varied sensitivity to these odorants and at the same time develop greater capacity to distinguish between odors. Deprivation of odor experience on an odorless synthetic medium leads to a loss of both sensitivity and acuity. Rich olfactory experience thus helps to shape the ORNs response and enhances its discriminative power. The experiments presented here demonstrate an experience-dependent adaptation at the level of the receptor neuron.}, author = {Iyengar, Atulya and Chakraborty Tuhin, Subhra and Sarit Goswami and Wu, Chun Fang and Siddiqi, Obaid}, journal = {PNAS}, number = {21}, pages = {9855 -- 60}, publisher = {National Academy of Sciences}, title = {{Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila}}, doi = {10.1073/pnas.1003856107}, volume = {107}, year = {2010}, } @phdthesis{3296, abstract = {Accurate computational representations of highly deformable surfaces are indispensable in the fields of computer animation, medical simulation, computer vision, digital modeling, and computational physics. The focus of this dissertation is on the animation of physics-based phenomena with highly detailed deformable surfaces represented by triangle meshes. We first present results from an algorithm that generates continuum mechanics animations with intricate surface features. This method combines a finite element method with a tetrahedral mesh generator and a high resolution surface mesh, and it is orders of magnitude more efficient than previous approaches. Next, we present an efficient solution for the challenging problem of computing topological changes in detailed dynamic surface meshes. We then introduce a new physics-inspired surface tracking algorithm that is capable of preserving arbitrarily thin features and reproducing realistic fine-scale topological changes like Rayleigh-Plateau instabilities. This physics-inspired surface tracking technique also opens the door for a unique coupling between surficial finite element methods and volumetric finite difference methods, in order to simulate liquid surface tension phenomena more efficiently than any previous method. Due to its dramatic increase in computational resolution and efficiency, this method yielded the first computer simulations of a fully developed crown splash with droplet pinch off.}, author = {Wojtan, Christopher J}, pages = {1 -- 175}, publisher = {Georgia Institute of Technology}, title = {{Animating physical phenomena with embedded surface meshes}}, year = {2010}, } @article{3303, abstract = {Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. }, author = {Weissman, Daniel and Feldman, Marcus and Fisher, Daniel}, journal = {Genetics}, number = {4}, pages = {1389 -- 1410}, publisher = {Genetics Society of America}, title = {{The rate of fitness-valley crossing in sexual populations}}, doi = {10.1534/genetics.110.123240}, volume = {186}, year = {2010}, } @article{3306, abstract = {We use methods from combinatorics and algebraic statistics to study analogues of birth-and-death processes that have as their state space a finite subset of the m-dimensional lattice and for which the m matrices that record the transition probabilities in each of the lattice directions commute pairwise. One reason such processes are of interest is that the transition matrix is straightforward to diagonalize, and hence it is easy to compute n step transition probabilities. The set of commuting birth-and-death processes decomposes as a union of toric varieties, with the main component being the closure of all processes whose nearest neighbor transition probabilities are positive. We exhibit an explicit monomial parametrization for this main component, and we explore the boundary components using primary decomposition.}, author = {Evans, Steven N and Sturmfels, Bernd and Caroline Uhler}, journal = {The Annals of Applied Probability}, pages = {238 -- 266}, publisher = {Institute of Mathematical Statistics}, title = {{Commuting birth and death processes}}, doi = {10.1214/09-AAP615}, volume = {20}, year = {2010}, } @article{3308, abstract = {We study multivariate normal models that are described by linear constraints on the inverse of the covariance matrix. Maximum likelihood estimation for such models leads to the problem of maximizing the determinant function over a spectrahedron, and to the problem of characterizing the image of the positive definite cone under an arbitrary linear projection. These problems at the interface of statistics and optimization are here examined from the perspective of convex algebraic geometry.}, author = {Sturmfels, Bernd and Caroline Uhler}, journal = {Annals of the Institute of Statistical Mathematics}, number = {4}, pages = {603 -- 638}, publisher = {Springer}, title = {{Multivariate Gaussians, semidefinite matrix completion, and convex algebraic geometry}}, doi = {10.1007/s10463-010-0295-4}, volume = {62}, year = {2010}, } @article{3402, abstract = {Model checking transactional memories (TMs) is difficult because of the unbounded number, length, and delay of concurrent transactions, as well as the unbounded size of the memory. We show that, under certain conditions satisfied by most TMs we know of, the model checking problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several TMs, including two-phase locking, DSTM, and TL2. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom. Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the TMs mentioned above. In a first step we show that every TM that enjoys certain structural properties either violates a requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step, we use a model checker to prove the requirement for the TM applied to a most general program with two threads and two variables. In the safety case, the model checker checks language inclusion between two finite-state transition systems, a nondeterministic transition system representing the given TM applied to a most general program, and a deterministic transition system representing a most liberal safe TM applied to the same program. The given TM transition system is nondeterministic because a TM can be used with different contention managers, which resolve conflicts differently. In the liveness case, the model checker analyzes fairness conditions on the given TM transition system.}, author = {Guerraoui, Rachid and Thomas Henzinger and Vasu Singh}, journal = {Distributed Computing}, number = {3}, pages = {129 -- 145}, publisher = {Springer}, title = {{Model checking transactional memories}}, doi = {10.1007/s00446-009-0092-6}, volume = {22}, year = {2010}, } @misc{3403, abstract = {Rate remapping is a conjunctive code that potentially enables hippocampal place cells to jointly represent spatial and nonspatial information. In this issue of Neuron, Rennó-Costa et al. introduce a theoretical model wherein the convergence of the medial and lateral entorhinal excitatory inputs, combined with local inhibition, explains hippocampal rate remapping. © 2010 Elsevier Inc.}, author = {Pleydell-Bouverie, Barty and Jozsef Csicsvari}, booktitle = {Neuron}, number = {6}, pages = {1015 -- 1016}, publisher = {Elsevier}, title = {{Rate remapping: When the code goes beyond space (preview)}}, doi = {10.1016/j.neuron.2010.12.011}, volume = {68}, year = {2010}, } @misc{3406, abstract = {The impact of structural biology on the design of ligands (agonists, antagonists and modulators) for ionotropic glutamate receptors is reviewed.}, author = {Stawski, Philipp and Harald Janovjak and Trauner, Dirk}, booktitle = {Bioorganic and Medicinal Chemistry}, number = {22}, pages = {7759 -- 7772}, publisher = {Elsevier}, title = {{Pharmacology of ionotropic glutamate receptors: a structural perspective}}, doi = {10.1016/j.bmc.2010.09.012}, volume = {18}, year = {2010}, } @article{3407, abstract = {Genetically targeted light-activated ion channels and pumps make it possible to determine the role of specific neurons in neuronal circuits, information processing and behavior. We developed a K+-selective ionotropic glutamate receptor that reversibly inhibits neuronal activity in response to light in dissociated neurons and brain slice and also reversibly suppresses behavior in zebrafish. The receptor is a chimera of the pore region of a K+-selective bacterial glutamate receptor and the ligand-binding domain of a light-gated mammalian kainate receptor. This hyperpolarizing light-gated channel, HyLighter, is turned on by a brief light pulse at one wavelength and turned off by a pulse at a second wavelength. The control is obtained at moderate intensity. After optical activation, the photocurrent and optical silencing of activity persists in the dark for extended periods. The low light requirement and bi-stability of HyLighter represent advantages for the dissection of neural circuitry.}, author = {Harald Janovjak and Szobota, Stephanie and Wyart, Claire and Trauner, Dirk and Isacoff, Ehud Y}, journal = {Nature Neuroscience}, pages = {1027 -- 1032}, publisher = {Nature Publishing Group}, title = {{A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing}}, doi = {10.1038/nn.2589}, volume = {13}, year = {2010}, } @article{1465, abstract = {We prove a generating function formula for the Betti numbers of Nakajima quiver varieties. We prove that it is a q-deformation of the Weyl-Kac character formula. In particular this implies that the constant term of the polynomial counting the number of absolutely indecomposable representations of a quiver equals the multiplicity of a certain weight in the corresponding Kac-Moody algebra, which was conjectured by Kac in 1982.}, author = {Tamas Hausel}, journal = {Inventiones Mathematicae}, number = {1}, pages = {21 -- 37}, publisher = {Springer}, title = {{Kac's conjecture from Nakajima quiver varieties}}, doi = {10.1007/s00222-010-0241-3}, volume = {181}, year = {2010}, } @article{1466, abstract = {In Hausel et al. (2008) [10] we presented a conjecture generalizing the Cauchy formula for Macdonald polynomial. This conjecture encodes the mixed Hodge polynomials of the character varieties of representations of the fundamental group of a punctured Riemann surface of genus g. We proved several results which support this conjecture. Here we announce new results which are consequences of those in Hausel et al. (2008) [10].}, author = {Tamas Hausel and Letellier, Emmanuel and Rodríguez Villegas, Fernando}, journal = {Comptes Rendus Mathematique}, number = {3-4}, pages = {131 -- 135}, publisher = {Elsevier}, title = {{Topology of character varieties and representations of quivers}}, doi = {10.1016/j.crma.2010.01.025}, volume = {348}, year = {2010}, } @inbook{1468, abstract = {This chapter surveys the motivations, related results, and progress made towards the following problem, raised by Hitchin in 1995: What is the space of L2 harmonic forms on the moduli space of Higgs bundles on a Riemann surface?}, author = {Tamas Hausel}, booktitle = {The Many Facets of Geometry: A Tribute to Nigel Hitchin}, publisher = {Oxford University Press}, title = {{S-Duality in HyperkäHler Hodge Theory}}, doi = {10.1093/acprof:oso/9780199534920.003.0016}, year = {2010}, } @article{1800, abstract = {Retinitis pigmentosa refers to a diverse group of hereditary diseases that lead to incurable blindness, affecting two million people worldwide. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. It is unknown if these cones are accessible for therapeutic intervention. Here, we show that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. Resensitized photoreceptors activate all retinal cone pathways, drive sophisticated retinal circuit functions (including directional selectivity), activate cortical circuits, and mediate visually guided behaviors. Using human ex vivo retinas, we show that halorhodopsin can reactivate light-insensitive human photoreceptors. Finally, we identified blind patients with persisting, light-insensitive cones for potential halorhodopsin-based therapy.}, author = {Busskamp, Volker and Duebel, Jens and Bálya, Dávid and Fradot, Mathias and Viney, Tim J and Sandra Siegert and Groner, Anna C and Cabuy, Erik and Forster, Valérie and Seeliger, Mathias W and Biel, Martin and Humphries, Peter and Pâques, Michel and Mohand-Saïd, Saddek and Trono, Didier and Deisseroth, Karl A and Sähel, José A and Picaud, Serge A and Roska, Botond M}, journal = {Science}, number = {5990}, pages = {413 -- 417}, publisher = {American Association for the Advancement of Science}, title = {{Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa}}, doi = {10.1126/science.1190897}, volume = {329}, year = {2010}, } @article{1300, abstract = {Motion vision is a major function of all visual systems, yet the underlying neural mechanisms and circuits are still elusive. In the lamina, the first optic neuropile of Drosophila melanogaster, photoreceptor signals split into five parallel pathways, L1-L5. Here we examine how these pathways contribute to visual motion detection by combining genetic block and reconstitution of neural activity in different lamina cell types with whole-cell recordings from downstream motion-sensitive neurons. We find reduced responses to moving gratings if L1 or L2 is blocked; however, reconstitution of photoreceptor input to only L1 or L2 results in wild-type responses. Thus, the first experiment indicates the necessity of both pathways, whereas the second indicates sufficiency of each single pathway. This contradiction can be explained by electrical coupling between L1 and L2, allowing for activation of both pathways even when only one of them receives photoreceptor input. A fundamental difference between the L1 pathway and the L2 pathway is uncovered when blocking L1 or L2 output while presenting moving edges of positive (ON) or negative (OFF) contrast polarity: blocking L1 eliminates the response to moving ON edges, whereas blocking L2 eliminates the response to moving OFF edges. Thus, similar to the segregation of photoreceptor signals in ON and OFF bipolar cell pathways in the vertebrate retina, photoreceptor signals segregate into ON-L1 and OFF-L2 channels in the lamina of Drosophila.}, author = {Maximilian Jösch and Schnell, Bettina and Raghu, Shamprasad V and Reiff, Dierk F and Borst, Alexander}, journal = {Nature}, number = {7321}, pages = {300 -- 304}, publisher = {Nature Publishing Group}, title = {{ON and off pathways in Drosophila motion vision}}, doi = {10.1038/nature09545}, volume = {468}, year = {2010}, } @article{1301, abstract = {Motion vision is essential for navigating through the environment. Due to its genetic amenability, the fruit fly Drosophila has been serving for a lengthy period as a model organism for studying optomotor behavior as elicited by large-field horizontal motion. However, the neurons underlying the control of this behavior have not been studied in Drosophila so far. Here we report the first whole cell recordings from three cells of the horizontal system (HSN, HSE, and HSS) in the lobula plate of Drosophila. All three HS cells are tuned to large-field horizontal motion in a direction-selective way; they become excited by front-to-back motion and inhibited by back-to-front motion in the ipsilateral field of view. The response properties of HS cells such as contrast and velocity dependence are in accordance with the correlation-type model of motion detection. Neurobiotin injection suggests extensive coupling among ipsilateral HS cells and additional coupling to tangential cells that have their dendrites in the contralateral hemisphere of the brain. This connectivity scheme accounts for the complex layout of their receptive fields and explains their sensitivity both to ipsilateral and to contralateral motion. Thus the main response properties of Drosophila HS cells are strikingly similar to the responses of their counterparts in the blowfly Calliphora, although we found substantial differences with respect to their dendritic structure and connectivity. This long-awaited functional characterization of HS cells in Drosophila provides the basis for the future dissection of optomotor behavior and the underlying neural circuitry by combining genetics, physiology, and behavior.}, author = {Schnell, Bettina and Jösch, Maximilian A and Förstner, Friedrich and Raghu, Shamprasad and Otsuna, Hideo and Ito, Kei and Borst, Alexander and Reiff, Dierk}, issn = {1522-1598}, journal = {Journal of Neurophysiology}, number = {3}, pages = {1646 -- 1657}, publisher = {American Physiological Society}, title = {{Processing of horizontal optic flow in three visual interneurons of the Drosophila brain}}, doi = {10.1152/jn.00950.2009}, volume = {103}, year = {2010}, } @article{2071, abstract = {The X or Z chromosome has several characteristics that distinguish it from the autosomes, namely hemizygosity in the heterogametic sex, and a potentially different effective population size, both of which may influence the rate and nature of evolution. In particular, there may be an accelerated rate of adaptive change for X-linked compared to autosomal coding sequences, often referred to as the Faster-X effect. Empirical studies have indicated that the strength of Faster-X evolution varies among different species, and theoretical treatments have shown that demography and mating system can substantially affect the degree of Faster-X evolution. Here we integrate genomic data on Faster-X evolution from a variety of animals with the demographic factors, mating system, and sex chromosome regulatory characteristics that may influence it. Our results suggest that differences in effective population size and mechanisms of dosage compensation may influence the perceived extent of Faster-X evolution, and help to explain several clade-specific patterns that we observe.}, author = {Mank, Judith E and Beatriz Vicoso and Berlin, Sofia and Charlesworth, Brian}, journal = {Evolution}, number = {3}, pages = {663 -- 674}, publisher = {Wiley-Blackwell}, title = {{Effective population size and the Faster-X effect: Empirical results and their interpretation}}, doi = {10.1111/j.1558-5646.2009.00853.x}, volume = {64}, year = {2010}, } @phdthesis{2075, abstract = {This thesis investigates the combination of data-driven and physically based techniques for acquiring, modeling, and animating deformable materials, with a special focus on human faces. Furthermore, based on these techniques, we introduce a data-driven process for designing and fabricating materials with desired deformation behavior. Realistic simulation behavior, surface details, and appearance are still demanding tasks. Neither pure data-driven, pure procedural, nor pure physical methods are best suited for accurate synthesis of facial motion and details (both for appearance and geometry), due to the difficulties in model design, parameter estimation, and desired controllability for animators. Capturing of a small but representative amount of real data, and then synthesizing diverse on-demand examples with physically-based models and real data as input benefits from both sides: Highly realistic model behavior due to real-world data and controllability due to physically-based models. To model the face and its behavior, hybrid physically-based and data-driven approaches are elaborated. We investigate surface-based representations as well as a solid representation based on FEM. To achieve realistic behavior, we propose to build light-weighted data capture devices to acquire real-world data to estimate model parameters and to employ concepts from data-driven modeling techniques and machine learning. The resulting models support simple acquisition systems, offer techniques to process and extract model parameters from real-world data, provide a compact representation of the facial geometry and its motion, and allow intuitive editing. We demonstrate applications such as capture of facial geometry and motion and real-time animation and transfer of facial details, and show that our soft tissue model can react to external forces and produce realistic deformations beyond facial expressions. Based on this model, we furthermore introduce a data-driven process for designing and fabricating materials with desired deformation behavior. The process starts with measuring deformation properties of base materials. Each material is represented as a non-linear stress-strain relationship in a finite-element model. For material design and fabrication, we introduce an optimization process that finds the best combination of base materials that meets a user’s criteria specified by example deformations. Our algorithm employs a number of strategies to prune poor solutions from the combinatorial search space. We finally demonstrate the complete process by designing and fabricating objects with complex heterogeneous materials using modern multi-material 3D printers. }, author = {Bernd Bickel}, booktitle = {Unknown}, number = {7458}, publisher = {Unknown}, title = {{Measurement-based modeling and fabrication of deformable materials for human faces}}, doi = {dx.doi.org/10.3929/ethz-a-006354908}, volume = {499}, year = {2010}, } @article{1970, abstract = {Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the α-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 Å resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-Å long amphipathic α-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 Å resolution. The L-shaped assembly consists of the α-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic α-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.}, author = {Efremov, Rouslan G and Baradaran, Rozbeh and Leonid Sazanov}, journal = {Nature}, number = {7297}, pages = {441 -- 445}, publisher = {Nature Publishing Group}, title = {{The architecture of respiratory complex I}}, doi = {10.1038/nature09066}, volume = {465}, year = {2010}, } @inbook{14983, abstract = {This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data.}, author = {Schlögl, Alois and Vidaurre, Carmen and Müller, Klaus-Robert}, booktitle = {Brain-Computer Interfaces}, editor = {Graimann, Bernhard and Pfurtscheller, Gert and Allison, Brendan}, isbn = {9783642020902}, issn = {1612-3018}, pages = {331--355}, publisher = {Springer}, title = {{Adaptive Methods in BCI Research - An Introductory Tutorial}}, doi = {10.1007/978-3-642-02091-9_18}, year = {2010}, }