A new metric for probability distributions

We introduce a metric for probability distributions, which is bounded, information-theoretically motivated, and has a natural Bayesian interpretation. The square root of the well-known chi(2) distance is an asymptotic approximation to it. Moreover, it is a close relative of the capacitory discrimination and Jensen-Shannon divergence.Publisher PDFPeer reviewe

The zipper mechanism in phagocytosis: energetic requirements and variability in phagocytic cup shape

Phagocytosis is the fundamental cellular process by which eukaryotic cells bind and engulf particles by their cell membrane. Particle engulfment involves particle recognition by cell-surface receptors, signaling and remodeling of the actin cytoskeleton to guide the membrane around the particle in a zipper-like fashion. Despite the signaling complexity, phagocytosis also depends strongly on biophysical parameters, such as particle shape, and the need for actin-driven force generation remains poorly understood. Here, we propose a novel, three-dimensional and stochastic biophysical model of phagocytosis, and study the engulfment of particles of various sizes and shapes, including spiral and rod-shaped particles reminiscent of bacteria. Highly curved shapes are not taken up, in line with recent experimental results. Furthermore, we surprisingly find that even without actin-driven force generation, engulfment proceeds in a large regime of parameter values, albeit more slowly and with highly variable phagocytic cups. We experimentally confirm these predictions using fibroblasts, transfected with immunoreceptor FcyRIIa for engulfment of immunoglobulin G-opsonized particles. Specifically, we compare the wild-type receptor with a mutant receptor, unable to signal to the actin cytoskeleton. Based on the reconstruction of phagocytic cups from imaging data, we indeed show that cells are able to engulf small particles even without support from biological actin-driven processes. This suggests that biochemical pathways render the evolutionary ancient process of phagocytic highly robust, allowing cells to engulf even very large particles. The particle-shape dependence of phagocytosis makes a systematic investigation of host-pathogen interactions and an efficient design of a vehicle for drug delivery possible.Comment: Accepted for publication in BMC Systems Biology. 17 pages, 6 Figures, + supplementary informatio

Pairwise wave interactions in ideal polytropic gases

We consider the problem of resolving all pairwise interactions of shock waves, contact waves, and rarefaction waves in 1-dimensional flow of an ideal polytropic gas. Resolving an interaction means here to determine the types of the three outgoing (backward, contact, and forward) waves in the Riemann problem defined by the extreme left and right states of the two incoming waves, together with possible vacuum formation. This problem has been considered by several authors and turns out to be surprisingly involved. For each type of interaction (head-on, involving a contact, or overtaking) the outcome depends on the strengths of the incoming waves. In the case of overtaking waves the type of the reflected wave also depends on the value of the adiabatic constant. Our analysis provides a complete breakdown and gives the exact outcome of each interaction.Comment: 39 page

A new proof of the Vorono\"i summation formula

We present a short alternative proof of the Vorono\"i summation formula which plays an important role in Dirichlet's divisor problem and has recently found an application in physics as a trace formula for a Schr\"odinger operator on a non-compact quantum graph \mathfrak{G} [S. Egger n\'e Endres and F. Steiner, J. Phys. A: Math. Theor. 44 (2011) 185202 (44pp)]. As a byproduct we give a new proof of a non-trivial identity for a particular Lambert series which involves the divisor function d(n) and is identical with the trace of the Euclidean wave group of the Laplacian on the infinite graph \mathfrak{G}.Comment: Enlarged version of the published article J. Phys. A: Math. Theor. 44 (2011) 225302 (11pp

A variable neurodegenerative phenotype with polymerase gamma mutation

mtDNA replication and repair, causes mitochondrial diseases including autosomal dominant progressive external ophthalmoplegia (PEO),1 childhood hepato-encephalopathy (Alpers– Huttenlocher syndrome), adult-onset spinocerebellar ataxia, and sensory nerve degeneration with dysarthria and ophthalmoparesis (SANDO)

A learning algorithm with emergent scaling behavior for classifying phase transitions

Machine learning-inspired techniques have emerged as a new paradigm for analysis of phase transitions in quantum matter. In this work, we introduce a supervised learning algorithm for studying critical phenomena from measurement data, which is based on iteratively training convolutional networks of increasing complexity, and test it on the transverse field Ising chain and q = 6 Potts model. At the continuous Ising transition, we identify scaling behavior in the classification accuracy, from which we infer a characteristic classification length scale. It displays a power-law divergence at the critical point, with a scaling exponent that matches with the diverging correlation length. Our algorithm correctly identifies the thermodynamic phase of the system and extracts scaling behavior from projective measurements, independently of the basis in which the measurements are performed. Furthermore, we show the classification length scale is absent for the q=6 Potts model, which has a first order transition and thus lacks a divergent correlation length. The main intuition underlying our finding is that, for measurement patches of sizes smaller than the correlation length, the system appears to be at the critical point, and therefore the algorithm cannot identify the phase from which the data was drawn

SeaWiFS calibration and validation plan, volume 3

The Sea-viewing Wide Field-of-view Sensor (SeaWiFS) will be the first ocean-color satellite since the Nimbus-7 Coastal Zone Color Scanner (CZCS), which ceased operation in 1986. Unlike the CZCS, which was designed as a proof-of-concept experiment, SeaWiFS will provide routine global coverage every 2 days and is designed to provide estimates of photosynthetic concentrations of sufficient accuracy for use in quantitative studies of the ocean's primary productivity and biogeochemistry. A review of the CZCS mission is included that describes that data set's limitations and provides justification for a comprehensive SeaWiFS calibration and validation program. To accomplish the SeaWiFS scientific objectives, the sensor's calibration must be constantly monitored, and robust atmospheric corrections and bio-optical algorithms must be developed. The plan incorporates a multi-faceted approach to sensor calibration using a combination of vicarious (based on in situ observations) and onboard calibration techniques. Because of budget constraints and the limited availability of ship resources, the development of the operational algorithms (atmospheric and bio-optical) will rely heavily on collaborations with the Earth Observing System (EOS), the Moderate Resolution Imaging Spectrometer (MODIS) oceans team, and projects sponsored by other agencies, e.g., the U.S. Navy and the National Science Foundation (NSF). Other elements of the plan include the routine quality control of input ancillary data (e.g., surface wind, surface pressure, ozone concentration, etc.) used in the processing and verification of the level-0 (raw) data to level-1 (calibrated radiances), level-2 (derived products), and level-3 (gridded and averaged derived data) products

Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation

The chemotaxis system in the bacterium Escherichia coli is remarkably sensitive to small relative changes in the concentrations of multiple chemical signals over a broad range of ambient concentrations. Interactions among receptors are crucial to this sensitivity as is precise adaptation, the return of chemoreceptor activity to prestimulus levels in a constant chemoeffector environment. Precise adaptation relies on methylation and demethylation of chemoreceptors by the enzymes CheR and CheB, respectively. Experiments indicate that when transiently bound to one receptor, these enzymes act on small assistance neighborhoods (AN) of five to seven receptor homodimers. In this paper, we model a strongly coupled complex of receptors including dynamic CheR and CheB acting on ANs. The model yields sensitive response and precise adaptation over several orders of magnitude of attractant concentrations and accounts for different responses to aspartate and serine. Within the model, we explore how the precision of adaptation is limited by small AN size as well as by CheR and CheB kinetics (including dwell times, saturation, and kinetic differences among modification sites) and how these kinetics contribute to noise in complex activity. The robustness of our dynamic model for precise adaptation is demonstrated by randomly varying biochemical parameters