Discussion

Abstract

Visualization is increasingly being recognized as an effective and efficient way not only to communicate patterns in scientific data, but to discover them as well. In the low dimensions of everyday experience, the human ability to find meaningful order in noisy data may never be matched by automatons. So the introduction of a useful visualization procedure, as provided here by Furnas and Buja, is indeed a welcome development. They show that low-dimensional patterns extracted by a combined projection and section operation (a prosection) can imply the existence of similar higher-dimensional structure. In exploratory or inductive data analyses, then, prosections could be used to generate hypotheses about relationships between sampled variables. However, the familiar curse of dimensionality may confine their practical application to point clouds of only moderate dimension.     

Theory of the statistics of kinetic transitions with application to single-molecule enzyme catalysis

Single-molecule spectroscopy can monitor transitions between two microscopic states when these transitions are associated with the emission of photons. A general formalism is developed for obtaining the statistics of such transitions from a microscopic model when the dynamics is described by master or rate equations or their continuum analog, multidimensional reaction-diffusion equations. The focus is on the distribution of the number of transitions during a fixed observation time, the distribution of times between transitions, and the corresponding correlation functions. It is shown how these quantities are related to each other and how they can be explicitly calculated in a straightforward way for both immobile and diffusing molecules. Our formalism reduces to renewal theory when the monitored transitions either go to or originate from a single state. The influence of dynamics slow compared with the time between monitored transitions is treated in a simple way, and the probability distributions are expressed in terms of Mandel-type formulas. The formalism is illustrated by a detailed analysis of the statistics of catalytic turnovers of enzymes. When the rates of conformational changes are slower than the catalytic rates which are in turn slower than the binding relaxation rate, (1) the mean number of turnovers is shown to have the classical Michaelis-Menten form, (2) the correlation function of the number of turnovers is a direct measure of the time scale of catalytic rate fluctuations, and (3) the distribution of the time between consecutive turnovers is determined by the steady-state distribution.     

Link distance and shortest path problems in the plane

This paper describes algorithms to compute Voronoi diagrams, shortest path maps, the Hausdorff distance, and the Fréchet distance in the plane with polygonal obstacles. The underlying distance measures for these algorithms are either shortest path distances or link distances. The link distance between a pair of points is the minimum number of edges needed to connect the two points with a polygonal path that avoids a set of obstacles. The motivation for minimizing the number of edges on a path comes from robotic motions and wireless communications because turns are more difficult in these settings than straight movements.Link-based Voronoi diagrams are different from traditional Voronoi diagrams because a query point in the interior of a Voronoi face can have multiple nearest sites. Our site-based Voronoi diagram ensures that all points in a face have the same set of nearest sites. Our distance-based Voronoi diagram ensures that all points in a face have the same distance to a nearest site.The shortest path maps in this paper support queries from any source point on a fixed line segment. This is a middle-ground approach because traditional shortest path maps typically support queries from either a fixed point or from all possible points in the plane.The Hausdorff distance and Fréchet distance are fundamental similarity metrics for shape matching. This paper shows how to compute new variations of these metrics using shortest paths or link-based paths that avoid polygonal obstacles in the plane.     

Human Neuroepithelial Cells Express NMDA Receptors

L-glutamate, an excitatory neurotransmitter, binds to both ionotropic and metabotropic glutamate receptors. In certain parts of the brain the BBB contains two normally impermeable barriers: 1) cerebral endothelial barrier and 2) cerebral epithelial barrier. Human cerebral endothelial cells express NMDA receptors; however, to date, human cerebral epithelial cells (neuroepithelial cells) have not been shown to express NMDA receptor message or protein. In this study, human hypothalamic sections were examined for NMDA receptors (NMDAR) expression via immunohistochemistry and murine neuroepithelial cell line (V1) were examined for NMDAR via RT-PCR and Western analysis. We found that human cerebral epithelium express protein and cultured mouse neuroepithelial cells express both mRNA and protein for the NMDA receptor. These findings may have important consequences for neuroepithelial responses during excitotoxicity and in disease.     

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

The correct representation of solute-water interactions is essential for the accurate simulation of most biological phenomena. Several highly accurate quantum methods are available to deal with solvation by using both implicit and explicit solvents. So far, however, most evaluations of those methods were based on a single conformation, which neglects solute entropy. Here, we present the first test of a novel approach to determine hydration free energies that uses molecular mechanics (MM) to sample phase space and quantum mechanics (QM) to evaluate the potential energies. Free energies are determined by using re-weighting with the Non-Boltzmann Bennett (NBB) method. In this context, the method is referred to as QM-NBB. Based on snapshots from MM sampling and accounting for their correct Boltzmann weight, it is possible to obtain hydration free energies that incorporate the effect of solute entropy. We evaluate the performance of several QM implicit solvent models, as well as explicit solvent QM/MM for the blind subset of the SAMPL4 hydration free energy challenge. While classical free energy simulations with molecular dynamics give root mean square deviations (RMSD) of 2.8 and 2.3 kcal/mol, the hybrid approach yields an improved RMSD of 1.6 kcal/mol. By selecting an appropriate functional and basis set, the RMSD can be reduced to 1 kcal/mol for calculations based on a single conformation. Results for a selected set of challenging molecules imply that this RMSD can be further reduced by using NBB to reweight MM trajectories with the SMD implicit solvent model.     

Observation of a two level thermal conductivity in the low-dimensional materials

The recent theoretical one-dimensional models display invariably anomalous thermal conductivity. Thermal conductivity of several low-dimensional crystalline systems has been investigated using our new techniques. The results show that for most of the measured materials in the high temperature range the thermal conductivity is composed of two extremes: a low- and a high-conductive state. The effective thermal conductivity jumps abruptly between these two states giving rise to apparent discontinuities or “spikes”.     

Design and characterization of a directly polarized radioluminescent light source

The properties of several directly polarized radioluminescent light (RL) sources are described. The RL sources are composed of a [small beta]-particle-emitting (90)Sr radioisotope coupled to polarization-oriented light-emitting plastic scintillators. The polarization of the scintillator molecules was achieved through a mechanical stress applied to the polymer matrix. The emission stability of the RL sources is described. It was found that the degree of polarization of light emitted by the sources varied from zero to 26%, depending on the matrix and scintillating material. The RL source with the highest degree of polarization was constructed from polystyrene and anthracene.     

Photon counting histograms for diffusing fluorophores

The theory of photon counting histograms for fluorescent molecules diffusing through a laser spot is presented. Analytic expressions for the factorial cumulants of photon counts are obtained. For an arbitrary counting time window, it is shown how the exact histograms can be obtained by solving an appropriate reaction-diffusion equation. Our formalism reduces correctly when the molecules are immobile. The approximation used in fluorescence intensity multiple distribution analysis (FIMDA) is tested against the exact numerical solution of the problem. FIMDA works very well for a wide range of parameters except for small concentrations and long time windows.     

Advancements in internationally accepted standards for radiation processing

Three subcommittees of the American Society for Testing and Materials (ASTM) are developing standards on various aspects of radiation processing. Subcommittee E10.01 “Dosimetry for Radiation Processing” has published 9 standards on how to select and calibrate dosimeters, where to put them, how many to use, and how to use individual types of dosimeter systems. The group is also developing standards on how to use gamma, electron beam, and x-ray facilities for radiation processing, and a standard on how to treat dose uncertainties. Efforts are underway to promote inclusion of these standards into procedures now being developed by government agencies and by international groups such as the United Nations' International Consultative Group on Food Irradiation (ICGFI) in order to harmonize regulations and help avoid trade barriers.

Subcommittee F10.10 “Food Processing and Packaging” has completed standards on good irradiation practices for meat and poultry and for fresh fruits, and is developing similar standards for the irradiation of seafood and spices. These food-related standards are based on practices previously published by ICGFI.

Subcommittee E10.07 on “Radiation Dosimetry for Radiation Effects on Materials and Devices” principally develops standards for determining doses for radiation hardness testing of electronics. Some, including their standards on the Fricke and TLD dosimetry systems are equally useful in other radiation processing applications.