@inproceedings{3213, abstract = {We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case. In this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.}, author = {Krzysztof Pietrzak}, pages = {55 -- 65}, publisher = {Springer}, title = {{Composition does not imply adaptive security}}, doi = {10.1007/11535218_4}, volume = {3621}, year = {2005}, } @article{3416, abstract = {In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins.}, author = {Harald Janovjak and Sapra, Tanuj K and Mueller, Daniel J}, journal = {Biophysical Journal}, number = {5}, pages = {37 -- 39}, publisher = {Biophysical Society}, title = {{Complex stability of single proteins explored by forced unfolding experiments}}, doi = {10.1529/biophysj.105.059774}, volume = {88}, year = {2005}, } @article{3417, abstract = {Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.}, author = {Kuhn, Michael and Harald Janovjak and Hubain, Maurice and Mueller, Daniel J}, journal = {Journal of Microscopy}, number = {2}, pages = {125 -- 132}, publisher = {Wiley-Blackwell}, title = {{Automated alignment and pattern recognition of single-molecule force spectroscopy data}}, doi = {10.1111/j.1365-2818.2005.01478.x}, volume = {218}, year = {2005}, } @article{3418, abstract = {Atomic force microscopy (AFM) allows the critical forces that unfold single proteins and rupture individual receptor–ligand bonds to be measured. To derive the shape of the energy landscape, the dynamic strength of the system is probed at different force loading rates. This is usually achieved by varying the pulling speed between a few nm/s and a few mgrm/s, although for a more complete investigation of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic drag force acting on the AFM cantilever reaches the same order of magnitude as the molecular forces. This has limited the maximum pulling speed in AFM single-molecule force spectroscopy experiments. Here, we present an approach for considering these hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements recorded over an extended range of pulling speeds (and thus loading rates). To support and illustrate our theoretical considerations, we experimentally evaluated the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling speed.}, author = {Harald Janovjak and Struckmeier, Jens and Mueller, Daniel J}, journal = {European Biophysics Journal}, number = {1}, pages = {91 -- 96}, publisher = {Springer}, title = {{Hydrodynamic effects in fast AFM single molecule force measurements}}, doi = {10.1007/s00249-004-0430-3}, volume = {34}, year = {2005}, } @article{13431, abstract = {Hydrogel stamps can microstructure solid surfaces, i.e., modify the surface topology of metals, glasses, and crystals. It is demonstrated that stamps soaked in an appropriate etchant can remove material with micrometer-scale precision. The Figure shows an array of concentric circles etched in glass using the immersion wet stamping process described (scale bar: 500 μm).}, author = {Smoukov, S. K. and Bishop, K. J. M. and Klajn, Rafal and Campbell, C. J. and Grzybowski, B. A.}, issn = {1521-4095}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {11}, pages = {1361--1365}, publisher = {Wiley}, title = {{Cutting into solids with micropatterned gels}}, doi = {10.1002/adma.200402086}, volume = {17}, year = {2005}, } @article{13432, abstract = {A new experimental technique is described that uses reaction−diffusion phenomena as a means of one-step microfabrication of complex, multilevel surface reliefs. Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically micropatterned with a solution of silver nitrate delivered from an agarose stamp. Precipitation reaction between the two salts causes the surface to deform. The mechanism of surface deformation is shown to involve a sequence of reactions, diffusion, and gel swelling/contraction. This mechanism is established experimentally and provides a basis of a theoretical lattice-gas model that allows prediction surface topographies emerging from arbitrary geometries of the stamped features. The usefulness of the technique is demonstrated by using it to rapidly prepare two types of mold for passive microfluidic mixers.}, author = {Campbell, Christopher J. and Klajn, Rafal and Fialkowski, Marcin and Grzybowski, Bartosz A.}, issn = {1520-5827}, journal = {Langmuir}, keywords = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science}, number = {1}, pages = {418--423}, publisher = {American Chemical Society}, title = {{One-step multilevel microfabrication by reaction−diffusion}}, doi = {10.1021/la0487747}, volume = {21}, year = {2005}, } @article{13433, abstract = {Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals are versatile constructs with which to study interfacial phenomena and reactions at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse environments, propensity to interact with or to resist adsorption of macromolecules -- depend on and can be controlled flexibly by the properties of the functional (head) groups in the w position of the alkyl chain. SAMs provide a basis for many important scientific and technological applications, ranging from micropatterning methods, through sensing, to biological recognition. Despite their importance, the literature on SAMs and the synthesis of molecules that constitute them remains scattered and often conflicting. The purpose of this Review is (i) to summarize the applications and physical properties of SAMs and (ii) to systematize the strategies of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme is developed that allows efficient synthetic planning. Issues related to the selection of appropriate protecting groups and the ways of introduction of the thiol functionality are discussed in detail, and illustrated with examples of syntheses of several complex alkane thiols.}, author = {Witt, Dariusz and Klajn, Rafal and Barski, Piotr and Grzybowski, Bartosz}, issn = {1875-5348}, journal = {Current Organic Chemistry}, keywords = {Organic Chemistry}, number = {18}, pages = {1763--1797}, publisher = {Bentham Science}, title = {{Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers}}, doi = {10.2174/1385272043369421}, volume = {8}, year = {2005}, } @inbook{1444, abstract = {The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat connections and character varieties for curves, respectively. Several new results and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman and Earl-Kirwan are explained. These use the representation theory of finite groups of Lie-type via the arithmetic of character varieties and lead to an unexpected conjecture for a Hard Lefschetz theorem for their cohomology.}, author = {Tamas Hausel}, booktitle = {Geometric Methods in Algebra and Number Theory}, pages = {193 -- 217}, publisher = {Springer}, title = {{Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a curve}}, doi = {10.1007/0-8176-4417-2_9}, volume = {235}, year = {2005}, } @article{1447, abstract = {Building on a recent paper [8], here we argue that the combinatorics of matroids are intimately related to the geometry and topology of toric hyperkähler varieties. We show that just like toric varieties occupy a central role in Stanley’s proof for the necessity of McMullen’s conjecture (or g-inequalities) about the classification of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties leads to new restrictions on face vectors of matroid complexes. Namely in this paper we will give two proofs that the injectivity part of the Hard Lefschetz theorem survives for toric hyperkähler varieties. We explain how this implies the g-inequalities for rationally representable matroids. We show how the geometrical intuition in the first proof, coupled with results of Chari [3], leads to a proof of the g-inequalities for general matroid complexes, which is a recent result of Swartz [20]. The geometrical idea in the second proof will show that a pure O-sequence should satisfy the g-inequalities, thus showing that our result is in fact a consequence of a long-standing conjecture of Stanley.}, author = {Tamas Hausel}, journal = {Open Mathematics}, number = {1}, pages = {26 -- 38}, publisher = {Central European Science Journals}, title = {{Quaternionic geometry of matroids}}, doi = {10.2478/BF02475653}, volume = {3}, year = {2005}, } @article{1463, abstract = {We study an integration theory in circle equivariant cohomology in order to prove a theorem relating the cohomology ring of a hyperkähler quotient to the cohomology ring of the quotient by a maximal abelian subgroup, analogous to a theorem of Martin for symplectic quotients. We discuss applications of this theorem to quiver varieties, and compute as an example the ordinary and equivariant cohomology rings of a hyperpolygon space.}, author = {Tamas Hausel and Proudfoot, Nicholas J}, journal = {Topology}, number = {1}, pages = {231 -- 248}, publisher = {Elsevier}, title = {{Abelianization for hyperkähler quotients}}, doi = {10.1016/j.top.2004.04.002}, volume = {44}, year = {2005}, } @article{17810, abstract = {Large future galaxy cluster surveys, combined with cosmic microwave background observations, can achieve a high sensitivity to the masses of cosmologically important neutrinos. We show that a weak lensing selected sample of ≳100 000 clusters could tighten the current upper bound on the sum of masses of neutrino species by an order of magnitude, to a level of 0.03 eV. Since this statistical sensitivity is below the best existing lower limit on the mass of at least one neutrino species, a future detection is likely, provided that systematic errors can be controlled to a similar level.}, author = {Wang, Sheng and Haiman, Zoltán and Hu, Wayne and Khoury, Justin and May, Morgan}, issn = {1079-7114}, journal = {Physical Review Letters}, publisher = {American Physical Society}, title = {{Weighing neutrinos with galaxy cluster surveys}}, doi = {10.1103/physrevlett.95.011302}, volume = {95}, year = {2005}, } @article{17811, abstract = {The z = 10 galaxy recently discovered by Pello and coworkers has a strong Lyα emission line that does not appear to have the expected asymmetry with more transmission on the red side. The blue wing of a Lyα line originating at high redshift should be strongly suppressed by resonant hydrogen absorption along the line of sight, an expectation borne out by the observed asymmetric shapes of the existing sample of Lyα-emitting sources at lower redshifts (3 < z < 6.7). The observed line is inconsistent with the galaxy being embedded in a fully neutral intergalactic medium (IGM) and having no receding peculiar velocity relative to the surrounding absorbing gas at the 95.0%-98.8% confidence level. Absorption on the blue side of the line of the Pello et al. source could be reduced if the IGM in the vicinity of the galaxy is highly ionized, but we show that this requires an unrealistically high ionizing emissivity. We suggest instead that the Lyα-emitting gas is receding relative to the surrounding gas with a velocity of ≳35 km s-1, which reduces the inconsistency confidence level to less than 76.0%-94.5%. We find that with this velocity shift, the observed strength and shape of the line is more consistent with the galaxy being surrounded by its own Strömgren sphere embedded in a fully neutral IGM. More generally, we predict that at any given redshift, the bright Lyα emitters with broader lines would exhibit stronger asymmetry than fainter ones. Bright galaxies with symmetric Lyα lines may be signposts for groups and clusters of galaxies, within which they can acquire random velocities comparable to or larger than their line widths.}, author = {Cen, Renyue and Haiman, Zoltán and Mesinger, Andrei}, issn = {1538-4357}, journal = {The Astrophysical Journal}, number = {1}, pages = {89--94}, publisher = {American Astronomical Society}, title = {{Implications of the Lyα Emission Line from a Candidate z = 10 Galaxy}}, doi = {10.1086/425243}, volume = {621}, year = {2005}, } @article{1795, abstract = {Background: Murine leukemia virus (MLV) vector particles can be pseudotyped with a truncated variant of the human immunodeficiency virus type 1 (HIV-1) envelope protein (Env) and selectively target gene transfer to human cells expressing both CD4 and an appropriate co-receptor. Vector transduction mimics the HIV-1 entry process and is therefore a safe tool to study HIV-1 entry. Results: Using FLY cells, which express the MLV gag and pol genes, we generated stable producer cell lines that express the HIV-1 envelope gene and a retroviral vector genome encoding the green fluorescent protein (GFP). The BH10 or 89.6 P HIV-1 Env was expressed from a bicistronic vector which allowed the rapid selection of stable cell lines. A codon-usage-optimized synthetic env gene permitted high, Rev-independent Env expression. Vectors generated by these producer cells displayed different sensitivity to entry inhibitors. Conclusion: These data illustrate that MLV/HIV-1 vectors are a valuable screening system for entry inhibitors or neutralizing antisera generated by vaccines.}, author = {Sandra Siegert and Thaler, Sonja and Wagner, Ralf and Schnierle, Barbara S}, journal = {AIDS Research and Therapy}, number = {1}, publisher = {BioMed Central}, title = {{Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors}}, doi = {10.1186/1742-6405-2-7}, volume = {2}, year = {2005}, } @article{18317, abstract = {We address the problem of recovering a scene recorded through a semireflecting medium (i.e. planar lens), with a virtual reflected image being superimposed on the image of the scene transmitted through the semirefelecting lens. Recent studies propose imaging through a linear polarizer at several orientations to estimate the reflected and the transmitted components in the scene. In this study we extend the sparse ICA (SPICA) technique and apply it to the problem of separating the image of the scene without having any a priori knowledge about its structure or statistics. Recent novel advances in the SPICA approach are discussed. Simulation and experimental results demonstrate the efficacy of the proposed methods.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Zibulevsky, Michael and Zeevi, Yehoshua Y.}, issn = {1098-1098}, journal = {International Journal of Imaging Systems and Technology}, number = {1}, pages = {84--91}, publisher = {Wiley}, title = {{Sparse ICA for blind separation of transmitted and reflected images}}, doi = {10.1002/ima.20042}, volume = {15}, year = {2005}, } @inproceedings{18319, abstract = {The problem of isometry-invariant representation and comparison of surfaces is of cardinal importance in pattern recognition applications dealing with deformable objects. Particularly, in three-dimensional face recognition treating facial expressions as isometries of the facial surface allows to perform robust recognition insensitive to expressions. Isometry-invariant representation of surfaces can be constructed by isometrically embedding them into some convenient space, and carrying out the comparison in that space. Presented here is a discussion on isometric embedding into S3, which appears to be superior over the previously used Euclidean space in sense of the representation accuracy.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, booktitle = {5th International Conference on Scale-Space Theories in Computer Vision}, isbn = {9783540255475}, issn = {1611-3349}, location = {Hofgeismar, Germany}, pages = {622--631}, publisher = {Springer Berlin Heidelberg}, title = {{Isometric embedding of facial surfaces into S3}}, doi = {10.1007/11408031_53}, volume = {3459}, year = {2005}, } @article{18354, abstract = {An expression-invariant 3D face recognition approach is presented. Our basic assumption is that facial expressions can be modelled as isometries of the facial surface. This allows to construct expression-invariant representations of faces using the bending-invariant canonical forms approach. The result is an efficient and accurate face recognition algorithm, robust to facial expressions, that can distinguish between identical twins (the first two authors). We demonstrate a prototype system based on the proposed algorithm and compare its performance to classical face recognition methods. The numerical methods employed by our approach do not require the facial surface explicitly. The surface gradients field, or the surface metric, are sufficient for constructing the expression-invariant representation of any given face. It allows us to perform the 3D face recognition task while avoiding the surface reconstruction stage.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, number = {1}, pages = {5--30}, publisher = {Springer Nature}, title = {{Three-dimensional face recognition}}, doi = {10.1007/s11263-005-1085-y}, volume = {64}, year = {2005}, } @inproceedings{18398, abstract = {We pose the problem of tissue classification in MRI as a blind source separation (BSS) problem and solve it by means of sparse component analysis (SCA). Assuming that most MR images can be sparsely represented, we consider their optimal sparse representation. Sparse components define a physically-meaningful feature space for classification. We demonstrate our approach on simulated and real multi-contrast MRI data. The proposed framework is general in that it is applicable to other modalities of medical imaging as well, whenever the linear mixing model is applicable.}, author = {Bronstein, Alexander and Bronstein, M.M. and Zibulevsky, M. and Zeevi, Y.Y.}, booktitle = {IEEE International Conference on Image Processing}, isbn = {0780391349}, location = {Genova, Italy}, pages = {1279--1282}, publisher = {IEEE}, title = {{"Unmixing" tissues: Sparse component analysis in multi-contrast MRI}}, doi = {10.1109/icip.2005.1530297}, volume = {2}, year = {2005}, } @inproceedings{18399, abstract = {Recently, it was proven empirically that facial expressions can be modelled as isometries, that is, geodesic distances on the facial surface were shown to be significantly less sensitive to facial expressions compared to Euclidean ones. Based on this assumption, the 3DFACE face recognition system was built. The system efficiently computes expression invariant signatures based on isometry-invariant representation of the facial surface. One of the crucial steps in the recognition system was embedding of the face geometric structure into a Euclidean (flat) space. Here, we propose to replace the flat embedding by a spherical one to construct isometric invariant representations of the facial image. We refer to these new invariants as spherical canonical images. Compared to its Euclidean counterpart, spherical embedding leads to notably smaller metric distortion. We demonstrate experimentally that representations with lower embedding error lead to better recognition. In order to efficiently compute the invariants we introduce a dissimilarity measure between the spherical canonical images based on the spherical harmonic transform.}, author = {Bronstein, Alexander and Bronstein, M.M. and Kimmel, R.}, booktitle = {International Conference on Image Processing}, isbn = {0780391349}, location = {Genova, Italy}, pages = {756--759}, publisher = {IEEE}, title = {{Expression-invariant face recognition via spherical embedding}}, doi = {10.1109/icip.2005.1530502}, volume = {3}, year = {2005}, } @article{18407, abstract = {The relative Newton algorithm, previously proposed for quasi-maximum likelihood blind source separation and blind deconvolution of one-dimensional signals is generalized for blind deconvolution of images. Smooth approximation of the absolute value is used as the nonlinear term for sparse sources. In addition, we propose a method of sparsification, which allows blind deconvolution of arbitrary sources, and show how to find optimal sparsifying transformations by supervised learning.}, author = {Bronstein, M.M. and Bronstein, Alexander and Zibulevsky, M. and Zeevi, Y.Y.}, issn = {1057-7149}, journal = {IEEE Transactions on Image Processing}, number = {6}, pages = {726--736}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Blind deconvolution of images using optimal sparse representations}}, doi = {10.1109/tip.2005.847322}, volume = {14}, year = {2005}, } @article{18417, abstract = {We propose a relative optimization framework for quasi-maximum likelihood (QML) blind deconvolution and the relative Newton method as its particular instance. Special Hessian structure allows fast Newton system construction and solution, resulting in a fast-convergent algorithm with iteration complexity comparable to that of gradient methods. We also propose the use of rational infinite impulse response (IIR) restoration kernels, which constitute a richer family of filters than the traditionally used finite impulse response (FIR) kernels. We discuss different choices of nonlinear functions that are suitable for deconvolution of super- and sub-Gaussian sources and formulate the conditions under which the QML estimation is stable. Simulation results demonstrate the efficiency of the proposed methods.}, author = {Bronstein, Alexander and Bronstein, M.M. and Zibulevsky, M.}, issn = {1053-587X}, journal = {IEEE Transactions on Signal Processing}, number = {6}, pages = {2018--2026}, publisher = {Institute of Electrical and Electronics Engineers (IEEE)}, title = {{Relative optimization for blind deconvolution}}, doi = {10.1109/tsp.2005.847822}, volume = {53}, year = {2005}, }