@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}, } @inproceedings{3430, abstract = {These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.}, author = {Gasper Tkacik}, publisher = {Elsevier}, title = {{Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics}}, year = {2010}, } @article{3441, abstract = {The hippocampus is an important brain circuit for spatial memory and the spatially selective spiking of hippocampal neuronal assemblies is thought to provide a mnemonic representation of space. We found that remembering newly learnt goal locations required NMDA receptorĝ€"dependent stabilization and enhanced reactivation of goal-related hippocampal assemblies. During spatial learning, place-related firing patterns in the CA1, but not CA3, region of the rat hippocampus were reorganized to represent new goal locations. Such reorganization did not occur when goals were marked by visual cues. The stabilization and successful retrieval of these newly acquired CA1 representations of behaviorally relevant places was NMDAR dependent and necessary for subsequent memory retention performance. Goal-related assembly patterns associated with sharp wave/ripple network oscillations, during both learning and subsequent rest periods, predicted memory performance. Together, these results suggest that the reorganization and reactivation of assembly firing patterns in the hippocampus represent the formation and expression of new spatial memory traces. © 2010 Nature America, Inc. All rights reserved.}, author = {Dupret, David and Joseph O'Neill and Pleydell-Bouverie, Barty and Jozsef Csicsvari}, journal = {Nature Neuroscience}, number = {8}, pages = {995 -- 1002}, publisher = {Nature Publishing Group}, title = {{The reorganization and reactivation of hippocampal maps predict spatial memory performance}}, doi = {10.1038/nn.2599}, volume = {13}, year = {2010}, } @article{3442, abstract = {Episodic and spatial memories each involve the encoding of complex associations in hippocampal neuronal circuits. Such memory traces could be stabilised from short- to long-term forms by consolidation processes involving the 'reactivation' of the original network firing patterns during sleep and rest. Waking experience can be replayed in many different brain areas, but an important role for the hippocampus lies in the organisation of the 'reactivation' process. Emerging evidence suggests that sharp wave/ripple (SWR) events in the hippocampus could coordinate the reactivation of memory traces and direct their reinstatement in cortical circuits. Although the mechanisms remain uncertain, there is a growing consensus that such SWR-directed reactivation of brain-wide memory traces could underlie memory consolidation. © 2010 Elsevier Ltd.}, author = {Joseph O'Neill and Pleydell-Bouverie, Barty and Dupret, David and Jozsef Csicsvari}, journal = {Trends in Neurosciences}, number = {5}, pages = {220 -- 229}, publisher = {Elsevier}, title = {{Play it again: reactivation of waking experience and memory}}, doi = {10.1016/j.tins.2010.01.006}, volume = {33}, year = {2010}, } @inbook{3459, author = {Fakler, Bernd and Peter Jonas}, booktitle = {Physiologie Des Menschen}, editor = {Schmidt, R. F. and Heckmann, M. and Lang, Florian}, publisher = {Springer}, title = {{Grundlagen zellulärer Erregbarkeit}}, year = {2010}, } @article{3498, abstract = {Purpose Calcifying tendinitis is a common condition of the shoulder. In many cases, arthroscopic reduction in the deposit is indicated. The localization of the deposit is sometimes challenging and time-consuming. Pre-operative ultrasound (US)-guided needle placement in the deposit and pre-operative US marking of the deposit at the skin with a ballpoint are described and recommended methods to alleviate the procedure without using ionizing radiation by fluoroscopy. Methods Intra-operative sonography of the shoulder is introduced as a new method to localize the calcific deposit with high accuracy. After standard arthroscopic buresectomy, the surgeon performs an ultrasound examination under sterile conditions to localize the deposits. A ventral longitudinal US section is recommended, and the upper arm is rotated until the deposit is visible. Subsequently, perpendicular to the skin at the position of the transducer, a needle is introduced under arthroscopic and ultrasound visualization to puncture the deposit. Results The presence of snow-white crystals at the tip of the needle proves the exact localization. Consecutively, the curettage can be accomplished. Another intra-operative sonography evaluates possible calcific remnants and the tendon structure. Conclusion This new technique may alleviate arthroscopic calcific deposit curettage by visualizing the deposit without using ionizing radiation. Additionally, soft tissue damage due to decreased number of punctures to detect the deposit may be achieved. Both factors may contribute to reduced operation time.}, author = {Sabeti Aschraf, M. and Gonano, C. and Nemecek, E. and Cichocki, Lisa and Schueller Weidekamm, C.}, journal = {Knee Surgery, Sports Traumatology, Arthroscopy}, number = {12}, pages = {1792 -- 1794}, publisher = {Springer}, title = {{Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis}}, doi = {10.1007/s00167-010-1227-9}, volume = {18}, year = {2010}, } @article{3538, abstract = {How seizures start is a major question in epilepsy research. Preictal EEG changes occur in both human patients and animal models, but their underlying mechanisms and relationship with seizure initiation remain unknown. Here we demonstrate the existence, in the hippocampal CA1 region, of a preictal state characterized by the progressive and global increase in neuronal activity associated with a widespread buildup of low-amplitude high-frequency activity (HFA) (> 100 Hz) and reduction in system complexity. HFA is generated by the firing of neurons, mainly pyramidal cells, at much lower frequencies. Individual cycles of HFA are generated by the near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization; the presence of very similar HFA in the high-potassium model shows that it does not depend on an absence of synaptic transmission. Immediately before seizure onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing perturbations can trigger seizures. Transition to seizure is characterized by a rapid expansion and fusion of the neuronal populations responsible for HFA, associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous cluster generating the high-amplitude low-frequency activity of the seizure.}, author = {Jiruska, Premysl and Csicsvari, Jozsef L and Powell, Andrew and Fox, John and Chang, Wei and Vreugdenhil, Martin and Li, Xiaoli and Palus, Milan and Bujan, Alejandro and Dearden, Richard and Jefferys, John}, journal = {Journal of Neuroscience}, number = {16}, pages = {5690 -- 5701}, publisher = {Society for Neuroscience}, title = {{High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro}}, doi = {10.1523/JNEUROSCI.0535-10.2010}, volume = {30}, year = {2010}, } @article{3592, abstract = {The zebrafish is a favorite model organism to study tissue morphogenesis during development at a subcellular level. This largely results from the fact that zebrafish embryos are transparent and thus accessible to various imaging techniques, such as confocal and two-photon excitation (2PE) microscopy. In particular, 2PE microscopy has been shown to be useful for imaging deep cell layers within the embryo and following tissue morphogenesis over long periods. This chapter describes how to use 2PE microscopy to study morphogenetic movements during early zebrafish embryonic development, providing a general blueprint for its use in zebrafish.}, author = {Carvalho, Lara and Heisenberg, Carl-Philipp J}, journal = {Methods in Molecular Biology}, number = {Part 5}, pages = {273 -- 287}, publisher = {Springer}, title = {{Imaging zebrafish embryos by two-photon excitation time-lapse microscopy}}, doi = {10.1007/978-1-60327-977-2_17}, volume = {546}, year = {2010}, } @article{3603, abstract = {Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.}, author = {Nicholas Barton and Kelleher, Jerome and Etheridge, Alison M}, journal = {Evolution; International Journal of Organic Evolution}, number = {9}, pages = {2701 -- 2715}, publisher = {Wiley-Blackwell}, title = {{A new model for large-scale population dynamics: quantifying phylogeography }}, doi = {10.1111/j.1558-5646.2010.01019.x}, volume = {64}, year = {2010}, } @article{3604, abstract = {We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales.}, author = {Senn, Helen and Goodman, Simon and Swanson, Graeme and Barton, Nicholas H and Pemberton, Josephine}, journal = {Molecular Ecology}, number = {5}, pages = {910 -- 924}, publisher = {Wiley-Blackwell}, title = {{Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland}}, doi = {10.1111/j.1365-294X.2009.04497.x}, volume = {19}, year = {2010}, } @inproceedings{3676, abstract = {Most state-of-the-art systems for content-based video understanding tasks require video content to be represented as collections of many low-level descriptors, e.g. as histograms of the color, texture or motion in local image regions. In order to preserve as much of the information contained in the original video as possible, these representations are typically high-dimensional, which conflicts with the aim for compact descriptors that would allow better efficiency and lower storage requirements. In this paper, we address the problem of semantic com- pression of video, i.e. the reduction of low-level descriptors to a small number of dimensions while preserving most of the semantic information. For this, we adapt topic models – which have previously been used as compact representations of still images – to take into account the temporal structure of a video, as well as multi-modal components such as motion information. Experiments on a large-scale collection of YouTube videos show that we can achieve a compression ratio of 20 : 1 compared to ordinary histogram representations and at least 2 : 1 compared to other dimensionality reduction techniques without significant loss of prediction accuracy. Also, improvements are demonstrated for our video-specific extensions modeling temporal structure and multiple modalities.}, author = {Wanke,Jörn and Ulges, Adrian and Christoph Lampert and Breuel,Thomas M}, pages = {275 -- 284}, publisher = {ACM}, title = {{Topic models for semantic video compression}}, doi = {10.1145/1743384.1743433}, year = {2010}, } @inproceedings{3682, abstract = {For object category recognition to scale beyond a small number of classes, it is important that algorithms be able to learn from a small amount of labeled data per additional class. One-shot recognition aims to apply the knowledge gained from a set of categories with plentiful data to categories for which only a single exemplar is available for each. As with earlier efforts motivated by transfer learning, we seek an internal representation for the domain that generalizes across classes. However, in contrast to existing work, we formulate the problem in a fundamentally new manner by optimizing the internal representation for the one-shot task using the notion of micro-sets. A micro-set is a sample of data that contains only a single instance of each category, sampled from the pool of available data, which serves as a mechanism to force the learned representation to explicitly address the variability and noise inherent in the one-shot recognition task. We optimize our learned domain features so that they minimize an expected loss over micro-sets drawn from the training set and show that these features generalize effectively to previously unseen categories. We detail a discriminative approach for optimizing one-shot recognition using micro-sets and present experiments on the Animals with Attributes and Caltech-101 datasets that demonstrate the benefits of our formulation.}, author = {Tang, Kevin D and Tappen, Marshall F and Sukthankar,Rahul and Christoph Lampert}, pages = {3027 -- 3034}, publisher = {IEEE}, title = {{Optimizing one-shot recognition with micro-set learning}}, doi = {10.1109/CVPR.2010.5540053}, year = {2010}, } @article{3686, abstract = {Markov random field (MRF) models, including conditional random field models, are popular in computer vision. However, in order to be computationally tractable, they are limited to incorporating only local interactions and cannot model global properties such as connectedness, which is a potentially useful high-level prior for object segmentation. In this work, we overcome this limitation by deriving a potential function that forces the output labeling to be connected and that can naturally be used in the framework of recent maximum a posteriori (MAP)-MRF linear program (LP) relaxations. Using techniques from polyhedral combinatorics, we show that a provably strong approximation to the MAP solution of the resulting MRF can still be found efficiently by solving a sequence of max-flow problems. The efficiency of the inference procedure also allows us to learn the parameters of an MRF with global connectivity potentials by means of a cutting plane algorithm. We experimentally evaluate our algorithm on both synthetic data and on the challenging image segmentation task of the PASCAL Visual Object Classes 2008 data set. We show that in both cases the addition of a connectedness prior significantly reduces the segmentation error. }, author = {Nowozin, Sebastian and Christoph Lampert}, journal = {SIAM Journal on Imaging Sciences}, number = {4 (Special Section on Optimization in Imaging Sciences)}, pages = {1048 -- 1074}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Global interactions in random field models: A potential function ensuring connectedness}}, doi = {10.1137/090752614}, volume = {3}, year = {2010}, }