TY - JOUR AB - 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. AU - Dupret, David AU - Joseph O'Neill AU - Pleydell-Bouverie, Barty AU - Jozsef Csicsvari ID - 3441 IS - 8 JF - Nature Neuroscience TI - The reorganization and reactivation of hippocampal maps predict spatial memory performance VL - 13 ER - TY - JOUR AB - 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. AU - Joseph O'Neill AU - Pleydell-Bouverie, Barty AU - Dupret, David AU - Jozsef Csicsvari ID - 3442 IS - 5 JF - Trends in Neurosciences TI - Play it again: reactivation of waking experience and memory VL - 33 ER - TY - CHAP AU - Fakler, Bernd AU - Peter Jonas ED - Schmidt, R. F. ED - Heckmann, M. ED - Lang, Florian ID - 3459 T2 - Physiologie Des Menschen TI - Grundlagen zellulärer Erregbarkeit ER - TY - JOUR AB - 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. AU - Jiruska, Premysl AU - Csicsvari, Jozsef L AU - Powell, Andrew AU - Fox, John AU - Chang, Wei AU - Vreugdenhil, Martin AU - Li, Xiaoli AU - Palus, Milan AU - Bujan, Alejandro AU - Dearden, Richard AU - Jefferys, John ID - 3538 IS - 16 JF - Journal of Neuroscience TI - High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro VL - 30 ER - TY - JOUR AB - 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. AU - Senn, Helen AU - Goodman, Simon AU - Swanson, Graeme AU - Barton, Nicholas H AU - Pemberton, Josephine ID - 3604 IS - 5 JF - Molecular Ecology TI - Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland VL - 19 ER - TY - JOUR AB - 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. AU - Nicholas Barton AU - Kelleher, Jerome AU - Etheridge, Alison M ID - 3603 IS - 9 JF - Evolution; International Journal of Organic Evolution TI - A new model for large-scale population dynamics: quantifying phylogeography VL - 64 ER - TY - JOUR AB - 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. AU - Nowozin, Sebastian AU - Christoph Lampert ID - 3686 IS - 4 (Special Section on Optimization in Imaging Sciences) JF - SIAM Journal on Imaging Sciences TI - Global interactions in random field models: A potential function ensuring connectedness VL - 3 ER - TY - CONF AB - 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. AU - Tang, Kevin D AU - Tappen, Marshall F AU - Sukthankar,Rahul AU - Christoph Lampert ID - 3682 TI - Optimizing one-shot recognition with micro-set learning ER - TY - CONF AB - Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al. [1]) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation. We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements. All experiments were carried out on a Barrett WAM using a four camera vision system. AU - Kober,Jens AU - Mülling,Katharina AU - Krömer,Oliver AU - Christoph Lampert AU - Schölkopf,Bernhard AU - Peters, Jan ID - 3702 TI - Movement templates for learning of hitting and batting ER - TY - CONF AB - The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk. AU - Feret, Jérôme AU - Henzinger, Thomas A AU - Koeppl, Heinz AU - Petrov, Tatjana ID - 3719 TI - Lumpability abstractions of rule-based systems VL - 40 ER - TY - JOUR AB - Long-term depression (LTD) is a form of synaptic plasticity that may contribute to information storage in the central nervous system. Here we report that LTD can be elicited in layer 5 pyramidal neurons of the rat prefrontal cortex by pairing low frequency stimulation with a modest postsynaptic depolarization. The induction of LTD required the activation of both metabotropic glutamate receptors of the mGlu1 subtype and voltage-sensitive Ca(2+) channels (VSCCs) of the T/R, P/Q and N types, leading to the stimulation of intracellular inositol trisphosphate (IP3) receptors by IP3 and Ca(2+). The subsequent release of Ca(2+) from intracellular stores activated the protein phosphatase cascade involving calcineurin and protein phosphatase 1. The activation of purinergic P2Y(1) receptors blocked LTD. This effect was prevented by P2Y(1) receptor antagonists and was absent in mice lacking P2Y(1) but not P2Y(2) receptors. We also found that activation of P2Y(1) receptors inhibits Ca(2+) transients via VSCCs in the apical dendrites and spines of pyramidal neurons. In addition, we show that the release of ATP under hypoxia is able to inhibit LTD by acting on postsynaptic P2Y(1) receptors. In conclusion, these data suggest that the reduction of Ca(2+) influx via VSCCs caused by the activation of P2Y(1) receptors by ATP is the possible mechanism for the inhibition of LTD in prefrontal cortex. AU - Guzmán, José AU - Schmidt, Hartmut AU - Franke, Heike AU - Krügel, Ute AU - Eilers, Jens AU - Illes, Peter AU - Gerevich, Zoltan ID - 3718 IS - 6 JF - Neuropharmacology TI - P2Y1 receptors inhibit long-term depression in the prefrontal cortex. VL - 59 ER - TY - JOUR AB - The visual system is challenged with extracting and representing behaviorally relevant information contained in natural inputs of great complexity and detail. This task begins in the sensory periphery: retinal receptive fields and circuits are matched to the first and second-order statistical structure of natural inputs. This matching enables the retina to remove stimulus components that are predictable (and therefore uninformative), and primarily transmit what is unpredictable (and therefore informative). Here we show that this design principle applies to more complex aspects of natural scenes, and to central visual processing. We do this by classifying high-order statistics of natural scenes according to whether they are uninformative vs. informative. We find that the uninformative ones are perceptually nonsalient, while the informative ones are highly salient, and correspond to previously identified perceptual mechanisms whose neural basis is likely central. Our results suggest that the principle of efficient coding not only accounts for filtering operations in the sensory periphery, but also shapes subsequent stages of sensory processing that are sensitive to high-order image statistics. AU - Gasper Tkacik AU - Prentice, Jason S AU - Victor,Jonathan D AU - Balasubramanian, Vijay ID - 3735 IS - 42 JF - PNAS TI - Local statistics in natural scenes predict the saliency of synthetic textures VL - 107 ER - TY - JOUR AB - In retina and in cortical slice the collective response of spiking neural populations is well described by "maximum-entropy" models in which only pairs of neurons interact. We asked, how should such interactions be organized to maximize the amount of information represented in population responses? To this end, we extended the linear-nonlinear-Poisson model of single neural response to include pairwise interactions, yielding a stimulus-dependent, pairwise maximum-entropy model. We found that as we varied the noise level in single neurons and the distribution of network inputs, the optimal pairwise interactions smoothly interpolated to achieve network functions that are usually regarded as discrete–stimulus decorrelation, error correction, and independent encoding. These functions reflected a trade-off between efficient consumption of finite neural bandwidth and the use of redundancy to mitigate noise. Spontaneous activity in the optimal network reflected stimulus-induced activity patterns, and single-neuron response variability overestimated network noise. Our analysis suggests that rather than having a single coding principle hardwired in their architecture, networks in the brain should adapt their function to changing noise and stimulus correlations. AU - Gasper Tkacik AU - Prentice, Jason S AU - Balasubramanian, Vijay AU - Schneidman, Elad ID - 3736 IS - 32 JF - PNAS TI - Optimal population coding by noisy spiking neurons VL - 107 ER - TY - JOUR AB - Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes. As the concentration of the transcription factor varies, the target genes thus undergo correlated changes, and this redundancy limits the ability of the cell to transmit information about input signals. We explore how interactions among the target genes can reduce this redundancy and optimize information transmission. Our discussion builds on recent work [Tkacik, Phys. Rev. E 80, 031920 (2009)], and there are connections to much earlier work on the role of lateral inhibition in enhancing the efficiency of information transmission in neural circuits; for simplicity we consider here the case where the interactions have a feed forward structure, with no loops. Even with this limitation, the networks that optimize information transmission have a structure reminiscent of the networks found in real biological systems. AU - Walczak, Aleksandra M AU - Gasper Tkacik AU - Bialek, William S ID - 3738 IS - 4 JF - Physical Review E Statistical Nonlinear and Soft Matter Physics TI - Optimizing information flow in small genetic networks. II. Feed-forward interactions VL - 81 ER - TY - JOUR AB - The chemotaxis signalling network in Escherichia coli that controls the locomotion of bacteria is a classic model system for signal transduction1, 2. This pathway modulates the behaviour of flagellar motors to propel bacteria towards sources of chemical attractants. Although this system relaxes to a steady state in response to environmental changes, the signalling events within the chemotaxis network are noisy and cause large temporal variations of the motor behaviour even in the absence of stimulus3. That the same signalling network governs both behavioural variability and cellular response raises the question of whether these two traits are independent. Here, we experimentally establish a fluctuation–response relationship in the chemotaxis system of living bacteria. Using this relationship, we demonstrate the possibility of inferring the cellular response from the behavioural variability measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour of individual bacterial motors, we found that variability scales linearly with the response time for different functioning states of the cell. This study highlights that the fundamental relationship between fluctuation and response is not constrained to physical systems at thermodynamic equilibrium4 but is extensible to living cells5. Such a relationship not only implies that behavioural variability and cellular response can be coupled traits, but it also provides a general framework within which we can examine how the selection of a network design shapes this interdependence AU - Park, Heungwon AU - Pontius, William AU - Calin Guet AU - Marko, John F AU - Emonet,Thierry AU - Cluzel,Philippe ID - 3748 JF - Nature TI - Interdependence of behavioural variability and response to small stimuli in bacteria VL - 468 ER - TY - JOUR AB - In E. coli, chemotactic behavior exhibits perfect adaptation that is robust to changes in the intracellular concentration of the chemotactic proteins, such as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly imply a robust chemotactic response. Previous studies on the robustness of the chemotactic response relied on swarming assays, which can be confounded by processes besides chemotaxis, such as cellular growth and depletion of nutrients. Here, using a high-throughput capillary assay that eliminates the effects of growth, we experimentally studied how the chemotactic response depends on the relative concentration of the chemotactic proteins. We simultaneously measured both the chemotactic response of E. coli cells to L: -aspartate and the concentrations of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable to the chemotactic response of wild-type behavior. In contrast to adaptation in chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB] ratio. AU - Park, Heungwon AU - Calin Guet AU - Emonet,Thierry AU - Cluzel,Philippe ID - 3749 IS - 3 JF - Current Microbiology TI - Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay VL - 62 ER - TY - JOUR AB - We present an approach to simulate flows driven by surface tension based on triangle meshes. Our method consists of two simulation layers: the first layer is an Eulerian method for simulating surface tension forces that is free from typical strict time step constraints. The second simulation layer is a Lagrangian finite element method that simulates sub-grid scale wave details on the fluid surface. The surface wave simulation employs an unconditionally stable, symplectic time integration method that allows for a high propagation speed due to strong surface tension. Our approach can naturally separate the grid-and sub-grid scales based on a volumepreserving mean curvature flow. As our model for the sub-grid dynamics enforces a local conservation of mass, it leads to realistic pinch off and merging effects. In addition to this method for simulating dynamic surface tension effects, we also present an efficient non-oscillatory approximation for capturing damped surface tension behavior. These approaches allow us to efficiently simulate complex phenomena associated with strong surface tension, such as Rayleigh-Plateau instabilities and crown splashes, in a short amount of time. AU - Thürey, Nils AU - Wojtan, Christopher J AU - Gross, Markus AU - Turk, Greg ID - 3766 IS - 4 JF - ACM Transactions on Graphics TI - A multiscale approach to mesh-based surface tension flows VL - 29 ER - TY - JOUR AB - MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/. AU - Palero, Ferran AU - González Candelas, Fernando AU - Pascual, Marta ID - 3783 IS - 2 JF - Journal of Heredity TI - Microsatelight – Pipeline to expedite microsatellite analysis VL - 102 ER - TY - CONF AB - In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically. AU - Chen, Chao AU - Freedman, Daniel ID - 3782 T2 - Conference proceedings MCV 2010 TI - Topology noise removal for curve and surface evolution VL - 6533 ER - TY - CHAP AB - The (apparent) contour of a smooth mapping from a 2-manifold to the plane, f: M → R2 , is the set of critical values, that is, the image of the points at which the gradients of the two component functions are linearly dependent. Assuming M is compact and orientable and measuring difference with the erosion distance, we prove that the contour is stable. AU - Edelsbrunner, Herbert AU - Morozov, Dmitriy AU - Patel, Amit ID - 3795 T2 - Topological Data Analysis and Visualization: Theory, Algorithms and Applications TI - The stability of the apparent contour of an orientable 2-manifold ER -