@article{11975, abstract = {A new method was developed for the quantitative analysis of steryl glycosides in biodiesel (fatty acid methyl esters). This method is much more sensitive than existing methods and has minimum limits of quantification of 50 μg/kg, compared to previously published minimum limits of quantification of about 15 mg/kg. The analysis is based on gas chromatography–mass spectroscopy determination of simple pre-treated and silylated samples via single ion monitoring at 147, 204, 217 m/z, which are specific ions for the silylated sugar moiety. Quantification was carried out using cholesteryl β-d-glucopyranoside as internal standard. The modified synthesis and purification of the internal standard is also presented as well as the characterization by NMR and mass spectroscopy. The advantage of the method compared with other approaches is the simplified sample preparation avoiding extra pre-treatment steps coupled with complete derivatization of the sugar hydroxyl groups by using N,O-bis(trimethylsilyl)acetamide with 5% trimethylchlorosilane as derivatization reagent. On the given conditions high recovery rates ≥89% can be obtained. Evaluation of lab specific variance and intermediate precision underline the robustness of the method which will be further assessed by Round robin tests.}, author = {Pieber, Bartholomäus and Schober, Sigurd and Goebl, Christoph and Mittelbach, Martin}, issn = {0021-9673}, journal = {Journal of Chromatography A}, number = {42}, pages = {6555--6561}, publisher = {Elsevier}, title = {{Novel sensitive determination of steryl glycosides in biodiesel by gas chromatography-mass spectroscopy}}, doi = {10.1016/j.chroma.2010.08.006}, volume = {1217}, 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}, } @article{18022, abstract = {The effect of the partial antiaromaticity of biphenylene on its substitution chemistry, its oxidation potential, and its single-molecule conductance is explored. Biphenylene and fluorene molecules with linkers of two amino groups or two cyclic thioether groups were synthesized and their conduction properties were investigated using scanning tunneling microscopy (STM) break-junction techniques and DFT calculations. Despite the partial antiaromaticity of biphenylene, which causes the biphenylenes to be much more easily oxidizable, no significant increase in molecular conductance was found.}, author = {Schneebeli, Severin and Kamenetska, Maria and Foss, Frank and Vazquez, Hector and Skouta, Rachid and Hybertsen, Mark and Venkataraman, Latha and Breslow, Ronald}, issn = {1523-7052}, journal = {Organic Letters}, number = {18}, pages = {4114--4117}, publisher = {American Chemical Society}, title = {{The electrical properties of biphenylenes}}, doi = {10.1021/ol1017036}, volume = {12}, year = {2010}, } @article{18023, abstract = {We measure the conductance of single Au−molecule−Au junctions with a series of air-stable diphenylphosphine-terminated molecules using the scanning tunneling microscope-based break junction technique. Thousands of conductance versus displacement traces collected for each molecule are used to statistically analyze junction conductance and evolution upon elongation. Measured conductances for a series of alkane-based molecules exhibit an exponential decrease with increasing length, as expected for saturated molecules, with a tunneling decay constant of 0.98 ± 0.04. Measurements of junction elongation indicate strong metal−molecule binding, with a length that increases with the number of methylene groups in the backbone. Measured conductance histograms for four molecules with short, unsaturated backbones (e.g., benzene) are much broader with less well-defined peaks. These measurements are supported by density function theory calculations. The phosphine binds selectively to under-coordinated gold atoms through a donor−acceptor bond with a binding energy of about 1 eV. The calculated tunnel coupling correlates very well with experiment.}, author = {Parameswaran, R. and Widawsky, J. R. and Vázquez, H. and Park, Y. S. and Boardman, B. M. and Nuckolls, C. and Steigerwald, M. L. and Hybertsen, M. S. and Venkataraman, Latha}, issn = {1948-7185}, journal = {The Journal of Physical Chemistry Letters}, number = {14}, pages = {2114--2119}, publisher = {American Chemical Society}, title = {{Reliable formation of single molecule junctions with air-stable diphenylphosphine linkers}}, doi = {10.1021/jz100656s}, volume = {1}, year = {2010}, } @article{18024, abstract = {Using photoemission spectroscopy, we determine the relationship between electronic energy level alignment at a metal−molecule interface and single-molecule junction transport data. We measure the position of the highest occupied molecular orbital (HOMO) relative to the Au metal Fermi level for three 1,4-benzenediamine derivatives on Au(111) and Au(110) with ultraviolet and resonant X-ray photoemission spectroscopy. We compare these results to scanning tunnelling microscope-based break-junction measurements of single molecule conductance and to first-principles calculations. We find that the energy difference between the HOMO and Fermi level for the three molecules adsorbed on Au(111) correlate well with changes in conductance and agree well with quasiparticle energies computed from first-principles calculations incorporating self-energy corrections. On the Au(110) that presents Au atoms with lower-coordination, critical in break-junction conductance measurements, we see that the HOMO level shifts further from the Fermi level. These results provide the first direct comparison of spectroscopic energy level alignment measurements with single molecule junction transport data.}, author = {Dell’Angela, M. and Kladnik, G. and Cossaro, A. and Verdini, A. and Kamenetska, M. and Tamblyn, I. and Quek, S. Y. and Neaton, J. B. and Cvetko, D. and Morgante, A. and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {7}, pages = {2470--2474}, publisher = {American Chemical Society}, title = {{Relating energy level alignment and amine-linked single molecule junction conductance}}, doi = {10.1021/nl100817h}, volume = {10}, year = {2010}, } @article{18027, abstract = {We have measured the conductance and characterized molecule−electrode binding geometries of four pyridine-terminated molecules by elongating and then compressing gold point contacts in a solution of molecules. We have found that all pyridine-terminated molecules exhibit bistable conductance signatures, signifying that the nature of the pyridine−gold bond allows two distinct conductance states that are accessed as the gold−molecule−gold junction is elongated. We have identified the low-conductance state as corresponding to a molecule fully stretched out between the gold electrodes, where the distance between contacts correlates with the length of the molecule; the high-conductance state is due to a molecule bound at an angle. For all molecules, we have found that the distribution of junction elongations in the low-conductance state is the same, while in the high-conductance state, the most likely elongation length increases linearly with molecule length. The results of first-principles conductance calculations for the four molecules in the low-conductance geometry agree well with the experimental results and show that the dominant conducting channel in the conjugated pyridine-linked molecules is through the π* orbital.}, author = {Kamenetska, M. and Quek, Su Ying and Whalley, A. C. and Steigerwald, M. L. and Choi, H. J. and Louie, Steven G. and Nuckolls, C. and Hybertsen, M. S. and Neaton, J. B. and Venkataraman, Latha}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {19}, pages = {6817--6821}, publisher = {American Chemical Society}, title = {{Conductance and geometry of pyridine-linked single-molecule junctions}}, doi = {10.1021/ja1015348}, volume = {132}, year = {2010}, } @inproceedings{18338, abstract = {Invariant image descriptors play an important role in many computer vision and pattern recognition problems such as image search and retrieval. A dominant paradigm today is that of “bags of features”, a representation of images as distributions of primitive visual elements. The main disadvantage of this approach is the loss of spatial relations between features, which often carry important information about the image. In this paper, we show how to construct spatially-sensitive image descriptors in which both the features and their relation are affine-invariant. Our construction is based on a vocabulary of pairs of features coupled with a vocabulary of invariant spatial relations between the features. Experimental results show the advantage of our approach in image retrieval applications.}, author = {Bronstein, Alexander and Bronstein, Michael M.}, booktitle = {11th European Conference on Computer Vision}, isbn = {9783642155512}, issn = {1611-3349}, location = {Heraklion, Greece}, pages = {197–208}, publisher = {Springer Nature}, title = {{Spatially-sensitive affine-invariant image descriptors}}, doi = {10.1007/978-3-642-15552-9_15}, volume = {6312}, year = {2010}, } @inproceedings{18339, abstract = {Automatic detection of symmetries, regularity, and repetitive structures in 3D geometry is a fundamental problem in shape analysis and pattern recognition with applications in computer vision and graphics. Especially challenging is to detect intrinsic regularity, where the repetitions are on an intrinsic grid, without any apparent Euclidean pattern to describe the shape, but rising out of (near) isometric deformation of the underlying surface. In this paper, we employ multidimensional scaling to reduce the problem of intrinsic structure detection to a simpler problem of 2D grid detection. Potential 2D grids are then identified using an autocorrelation analysis, refined using local fitting, validated, and finally projected back to the spatial domain. We test the detection algorithm on a variety of scanned plaster models in presence of imperfections like missing data, noise and outliers. We also present a range of applications including scan completion, shape editing, super-resolution, and structural correspondence.}, author = {Mitra, Niloy J. and Bronstein, Alexander and Bronstein, Michael}, booktitle = {11th European Conference on Computer Vision}, isbn = {9783642155574}, issn = {0302-9743}, location = {Heraklion, Greece}, pages = {398–410}, publisher = {Springer Nature}, title = {{Intrinsic regularity detection in 3D geometry}}, doi = {10.1007/978-3-642-15558-1_29}, volume = {6313}, year = {2010}, } @article{18358, abstract = {In this paper, the problem of non-rigid shape recognition is studied from the perspective of metric geometry. In particular, we explore the applicability of diffusion distances within the Gromov-Hausdorff framework. While the traditionally used geodesic distance exploits the shortest path between points on the surface, the diffusion distance averages all paths connecting the points. The diffusion distance constitutes an intrinsic metric which is robust, in particular, to topological changes. Such changes in the form of shortcuts, holes, and missing data may be a result of natural non-rigid deformations as well as acquisition and representation noise due to inaccurate surface construction. The presentation of the proposed framework is complemented with examples demonstrating that in addition to the relatively low complexity involved in the computation of the diffusion distances between surface points, its recognition and matching performances favorably compare to the classical geodesic distances in the presence of topological changes between the non-rigid shapes.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron and Mahmoudi, Mona and Sapiro, Guillermo}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, number = {2-3}, pages = {266--286}, publisher = {Springer Nature}, title = {{A Gromov-Hausdorff framework with diffusion geometry for topologically-robust non-rigid shape matching}}, doi = {10.1007/s11263-009-0301-6}, volume = {89}, year = {2010}, } @article{18359, abstract = {Symmetry and self-similarity are the cornerstone of Nature, exhibiting themselves through the shapes of natural creations and ubiquitous laws of physics. Since many natural objects are symmetric, the absence of symmetry can often be an indication of some anomaly or abnormal behavior. Therefore, detection of asymmetries is important in numerous practical applications, including crystallography, medical imaging, and face recognition, to mention a few. Conversely, the assumption of underlying shape symmetry can facilitate solutions to many problems in shape reconstruction and analysis. Traditionally, symmetries are described as extrinsic geometric properties of the shape. While being adequate for rigid shapes, such a description is inappropriate for non-rigid ones: extrinsic symmetry can be broken as a result of shape deformations, while its intrinsic symmetry is preserved. In this paper, we present a generalization of symmetries for non-rigid shapes and a numerical framework for their analysis, addressing the problems of full and partial exact and approximate symmetry detection and classification.}, author = {Raviv, Dan and Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, pages = {18--39}, publisher = {Springer Nature}, title = {{Full and partial symmetries of non-rigid shapes}}, doi = {10.1007/s11263-010-0320-3}, volume = {89}, year = {2010}, } @article{18360, abstract = {Many manifold learning procedures try to embed a given feature data into a flat space of low dimensionality while preserving as much as possible the metric in the natural feature space. The embedding process usually relies on distances between neighboring features, mainly since distances between features that are far apart from each other often provide an unreliable estimation of the true distance on the feature manifold due to its non-convexity. Distortions resulting from using long geodesics indiscriminately lead to a known limitation of the Isomap algorithm when used to map non-convex manifolds. Presented is a framework for nonlinear dimensionality reduction that uses both local and global distances in order to learn the intrinsic geometry of flat manifolds with boundaries. The resulting algorithm filters out potentially problematic distances between distant feature points based on the properties of the geodesics connecting those points and their relative distance to the boundary of the feature manifold, thus avoiding an inherent limitation of the Isomap algorithm. Since the proposed algorithm matches non-local structures, it is robust to strong noise. We show experimental results demonstrating the advantages of the proposed approach over conventional dimensionality reduction techniques, both global and local in nature.}, author = {Rosman, Guy and Bronstein, Michael M. and Bronstein, Alexander and Kimmel, Ron}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, pages = {56--68}, publisher = {Springer Nature}, title = {{Nonlinear dimensionality reduction by topologically constrained isometric embedding}}, doi = {10.1007/s11263-010-0322-1}, volume = {89}, year = {2010}, } @inproceedings{18376, abstract = {Visual understanding is often based on measuring similarity between observations. Learning similarities specific to a certain perception task from a set of examples has been shown advantageous in various computer vision and pattern recognition problems. In many important applications, the data that one needs to compare come from different representations or modalities, and the similarity between such data operates on objects that may have different and often incommensurable structure and dimensionality. In this paper, we propose a framework for supervised similarity learning based on embedding the input data from two arbitrary spaces into the Hamming space. The mapping is expressed as a binary classification problem with positive and negative examples, and can be efficiently learned using boosting algorithms. The utility and efficiency of such a generic approach is demonstrated on several challenging applications including cross-representation shape retrieval and alignment of multi-modal medical images.}, author = {Bronstein, Michael M. and Bronstein, Alexander and Michel, Fabrice and Paragios, Nikos}, booktitle = {2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition}, issn = {1063-6919 }, location = {San Francisco, CA, USA}, pages = {3594 -- 3601}, publisher = {IEEE}, title = {{Data fusion through cross-modality metric learning using similarity-sensitive hashing}}, doi = {10.1109/cvpr.2010.5539928}, year = {2010}, } @inproceedings{18432, abstract = {Invariant shape descriptors are instrumental in numerous shape analysis tasks including deformable shape comparison, registration, classification, and retrieval. Most existing constructions model a 3D shape as a two-dimensional surface describing the shape boundary, typically represented as a triangular mesh or a point cloud. Using intrinsic properties of the surface, invariant descriptors can be designed. One such example is the recently introduced heat kernel signature, based on the Laplace-Beltrami operator of the surface. In many applications, however, a volumetric shape model is more natural and convenient. Moreover, modeling shape deformations as approximate isometries of the volume of an object, rather than its boundary, better captures natural behavior of non-rigid deformations in many cases. Here, we extend the idea of heat kernel signature to robust isometry-invariant volumetric descriptors, and show their utility in shape retrieval. The proposed approach achieves state-of-the-art results on the SHREC 2010 large-scale shape retrieval benchmark.}, author = {Raviv, Dan and Bronstein, Michael M. and Bronstein, Alexander and Kimmel, Ron}, booktitle = {Proceedings of the ACM workshop on 3D object retrieval}, isbn = {9781450301602}, location = {Firenze, Italy}, pages = {39 -- 44}, publisher = {ACM}, title = {{Volumetric heat kernel signatures}}, doi = {10.1145/1877808.1877817}, 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}, } @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}, } @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{2095, abstract = {This paper describes a passive stereo system for capturing the 3D geometry of a face in a single-shot under standard light sources. The system is low-cost and easy to deploy. Results are submillimeter accurate and commensurate with those from state-ofthe-art systems based on active lighting, and the models meet the quality requirements of a demanding domain like the movie industry. Recovered models are shown for captures from both high-end cameras in a studio setting and from a consumer binocular-stereo camera, demonstrating scalability across a spectrum of camera deployments, and showing the potential for 3D face modeling to move beyond the professional arena and into the emerging consumer market in stereoscopic photography. Our primary technical contribution is a modification of standard stereo refinement methods to capture pore-scale geometry, using a qualitative approach that produces visually realistic results. The second technical contribution is a calibration method suited to face capture systems. The systemic contribution includes multiple demonstrations of system robustness and quality. These include capture in a studio setup, capture off a consumer binocular-stereo camera, scanning of faces of varying gender and ethnicity and age, capture of highly-transient facial expression, and scanning a physical mask to provide ground-truth validation.}, author = {Beeler, Thabo and Bernd Bickel and Beardsley, Paul A and Sumner, Bob and Groß, Markus S}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{High-quality single-shot capture of facial geometry}}, doi = {10.1145/1778765.1778777}, volume = {29}, year = {2010}, }