Assessing the effectiveness of pen-based input queries

In this poster, we describe an experiment exploring the effectiveness of a pen based text input device for use in query construction. Standard TREC queries were written, recognised, and subsequently retrieved upon. Comparisons between retrieval effectiveness based on the recognised writing and a typed text baseline were made. On average, effectiveness was 75% of the baseline. Other statistics on the quality and nature of recognition are also reported

Population connectivity shifts at high frequency within an open-coast marine protected area network.

A complete understanding of population connectivity via larval dispersal is of great value to the effective design and management of marine protected areas (MPA). However empirical estimates of larval dispersal distance, self-recruitment, and within season variability of population connectivity patterns and their influence on metapopulation structure remain rare. We used high-resolution otolith microchemistry data from the temperate reef fish Hypsypops rubicundus to explore biweekly, seasonal, and annual connectivity patterns in an open-coast MPA network. The three MPAs, spanning 46 km along the southern California coastline were connected by larval dispersal, but the magnitude and direction of connections reversed between 2008 and 2009. Self-recruitment, i.e. spawning, dispersal, and settlement to the same location, was observed at two locations, one of which is a MPA. Self-recruitment to this MPA ranged from 50-84%; within the entire 60 km study region, self-recruitment accounted for 45% of all individuals settling to study reefs. On biweekly time scales we observed directional variability in alongshore current data and larval dispersal trajectories; if viewed in isolation these data suggest the system behaves as a source-sink metapopulation. However aggregate biweekly data over two years reveal a reef network in which H. rubicundus behaves more like a well-mixed metapopulation. As one of the few empirical studies of population connectivity within a temperate open coast reef network, this work can inform the MPA design process, implementation of ecosystem based management plans, and facilitate conservation decisions

Electrostatics of ions inside the nanopores and trans-membrane channels

A model of a finite cylindrical ion channel through a phospholipid membrane of width $L$ separating two electrolyte reservoirs is studied. Analytical solution of the Poisson equation is obtained for an arbitrary distribution of ions inside the trans-membrane pore. The solution is asymptotically exact in the limit of large ionic strength of electrolyte on the two sides of membrane. However, even for physiological concentrations of electrolyte, the electrostatic barrier sizes found using the theory are in excellent agreement with the numerical solution of the Poisson equation. The analytical solution is used to calculate the electrostatic potential energy profiles for pores containing charged protein residues. Availability of a semi-exact interionic potential should greatly facilitate the study of ionic transport through nanopores and ion channels

Dynamical study of the empty Bianchi type I model in generalised scalar-tensor theory

A dynamical study of the generalised scalar-tensor theory in the empty Bianchi type I model is made. We use a method from which we derive the sign of the first and second derivatives of the metric functions and examine three different theories that can all tend towards relativistic behaviours at late time. We determine conditions so that the dynamic be in expansion and decelerated at late time.Comment: 18 pages, 3 figures, to appear in General Relativity and Gravitatio

A Neutral Polyampholyte in an ionic solution

The behavior of a neutral polyampholyte ($PA$) chain with $N$ monomers, in an ionic solution, is analyzed in the framework of the full Debye-H$\ddot u$ckel-Bjerrum-Flory $(DHBjF)$ theory. A $PA$ chain, that in addition to the neutral monomers, also contains an equal number of positively and negatively charged monomers, is dissolved in an ionic solution. For \underline{high} concentrations of salt and at high temperatures, the $PA$ exists in an extended state. As the temperature is decreased, the electrostatic energy becomes more relevant and at a $T=T_{\theta}$ the system collapses into a dilute globular state, or microelectrolyte. This state contains a concentration of salt higher than the surrounding medium. As the temperature is decreased even further, association between the monomers of the polymer and the ions of the salt becomes relevant and there is a crossover from this globular state to a low temperature extended state. For \underline{low} densities of salt, the system is collapsed for almost all temperatures and exhibits a first-order phase transition to an extended state at an unphysical low temperature.Comment: 10 pages, Revtex with epsf, 9 Postscript figures. Submitted to PR

Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues

We undertake an extensive numerical investigation of the graph spectra of thousands regular graphs, a set of random Erd\"os-R\'enyi graphs, the two most popular types of complex networks and an evolving genetic network by using novel conceptual and experimental tools. Our objective in so doing is to contribute to an understanding of the meaning of the Eigenvalues of a graph relative to its topological and information-theoretic properties. We introduce a technique for identifying the most informative Eigenvalues of evolving networks by comparing graph spectra behavior to their algorithmic complexity. We suggest that extending techniques can be used to further investigate the behavior of evolving biological networks. In the extended version of this paper we apply these techniques to seven tissue specific regulatory networks as static example and network of a na\"ive pluripotent immune cell in the process of differentiating towards a Th17 cell as evolving example, finding the most and least informative Eigenvalues at every stage.Comment: Forthcoming in 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Lecture Notes in Bioinformatics, 201

Application of Monte Carlo Algorithms to the Bayesian Analysis of the Cosmic Microwave Background

Power spectrum estimation and evaluation of associated errors in the presence of incomplete sky coverage; non-homogeneous, correlated instrumental noise; and foreground emission is a problem of central importance for the extraction of cosmological information from the cosmic microwave background. We develop a Monte Carlo approach for the maximum likelihood estimation of the power spectrum. The method is based on an identity for the Bayesian posterior as a marginalization over unknowns. Maximization of the posterior involves the computation of expectation values as a sample average from maps of the cosmic microwave background and foregrounds given some current estimate of the power spectrum or cosmological model, and some assumed statistical characterization of the foregrounds. Maps of the CMB are sampled by a linear transform of a Gaussian white noise process, implemented numerically with conjugate gradient descent. For time series data with N_{t} samples, and N pixels on the sphere, the method has a computational expense $KO[N^{2} +- N_{t} +AFw-log N_{t}], where K is a prefactor determined by the convergence rate of conjugate gradient descent. Preconditioners for conjugate gradient descent are given for scans close to great circle paths, and the method allows partial sky coverage for these cases by numerically marginalizing over the unobserved, or removed, region.Comment: submitted to Ap

Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel

Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchet-like mechanism. For an aquaglyceroporin that conducts water and glycerol we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev. Let

Charge reversal of colloidal particles

A theory is presented for the effective charge of colloidal particles in suspensions containing multivalent counterions. It is shown that if colloids are sufficiently strongly charged, the number of condensed multivalent counterion can exceed the bare colloidal charge leading to charge reversal. Charge renormalization in suspensions with multivalent counterions depends on a subtle interplay between the solvation energies of the multivalent counterions in the bulk and near the colloidal surface. We find that the effective charge is {\it not} a monotonically decreasing function of the multivalent salt concentration. Furthermore, contrary to the previous theories, it is found that except at very low concentrations, monovalent salt hinders the charge reversal. This conclusion is in agreement with the recent experiments and simulations