Diffusion and Velocity Auto-Correlation in Shearing Granular Media

We perform numerical simulations to examine particle diffusion at steady shear in a model granular material in two dimensions at the jamming density and zero temperature. We confirm findings by others that the diffusion constant depends on shear rate as $D\sim\dot\gamma^{q_D}$ with $q_D<1$, and set out to determine a relation between $q_D$ and other exponents that characterize the jamming transition. We then examine the the velocity auto-correlation function, note that it is governed by two processes with different time scales, and identify a new fundamental exponent, $\lambda$, that characterizes an algebraic decay of correlations with time

Asymmetric velocity correlations in shearing media

A model of soft frictionless disks in two dimensions at zero temperature is simulated with a shearing dynamics to study various kinds of asymmetries in sheared systems. We examine both single particle properties, the spatial velocity correlation function, and a correlation function designed to separate clockwise and counter-clockwise rotational fields from one another. Among the rich and interesting behaviors we find that the velocity correlation along the two different diagonals corresponding to compression and dilation, respectively, are almost identical and, furthermore, that a feature in one of the correlation functions is directly related to irreversible plastic events

The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication

Most RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1–1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sensitive to exogenously added interferon-β, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of high CpG and UpA mutants, potentially through inhibition of currently uncharacterized pattern recognition receptors that respond to RNA composition. Generating viruses with enhanced replication kinetics has applications in vaccine production and reporter gene construction. More fundamentally, the findings introduce a new evolutionary paradigm where dinucleotide composition of viral genomes is subjected to selection pressures independently of coding capacity and profoundly influences host–pathogen interactions

Vision and Reading Difficulties Part 5: Clinical protocol and the role of the eye-care practitioner

This series of articles has described various aspects of visual characteristics of reading difficulties and the background behind techniques such as the use of coloured filters in helping to reduce the difficulties that are experienced. The present article, which is the last in series, aims to describe a clinical protocol that can be used by the busy eye care practitioner for the investigation and management of such patients. It also describes the testing techniques that can be used for the various assessments. Warning: DO NOT LOOK AT FIGURE 7 IF YOU HAVE MIGRAINE OR EPILEPSY

Vision and Reading Difficulties Part 4: Coloured filters - how do they work?

This article is the fourth in a series of five about vision and reading difficulties. The first article provided a general overview and the second covered conventional optometric correlates of reading difficulties (e.g. binocular vision problems). The present article continues on from the third article by describing the use of coloured filters in treating a condition now known as visual stress. Visual stress is often associated with reading difficulties, but also a variety of other neurological conditions. This article concentrates on the possible mechanisms for the benefit from coloured filters, beginning with obvious peripheral factors. The terminology for this condition has changed over the years (e.g. Scotopic Sensitivity Syndrome, and Meares-Irlen Syndrome) and the issue of terminology is discussed at the end of this article. Warning: DO NOT LOOK AT FIGURE 6 ON PAGE 33 IF YOU HAVE A MIGRAINE OR EPILEPSY

Vision and Reading Difficulties Part 1: Specific learning difficulties and vision

This article is the first in a series of five about vision and reading difficulties, and provides an introduction and an overview of learning disabilities and specific learning difficulties. It outlines the role of the optometrist in helping people with such problems; it describes the symptoms that optometrists should look for and it provides an introduction of the evidence-based approach. The second article in this series will cover the optometric and orthoptic correlates of reading difficulties. Articles three and four will describe the use of coloured filters, including background, techniques, evidence, and mechanism. The final article will draw together the themes in the series of articles and discuss the clinical protocol and the role of the eye care practitioner in managing visual factors associated with reading difficulties

Vision and Reading Difficulties Part 3: Coloured filters - do they work?

This is the third article in a series of five on Vision and Reading Difficulties. The first article provided a general overview of learning disabilities and specific learning difficulties (SpLD). It outlined the role of the optometrist in helping people with SpLD. The second article covered conventional optometric correlates of reading difficulties (e.g. binocular vision problems) This article and the next will describe the use of coloured filters to treat a condition now know as "visual stress", which is often associated with reading difficulties; the symptoms of visual stress were described in Part 1. The terminology for this condition has changed over the years (e.g. Scotopic Sensitivity syndrome, Meares-Irlen syndrome). Terminology is discussed more in Part 4

Vision and Reading Difficulties Part 2: Optometric correlates of reading difficulties

In this second article of the series on vision and reading difficulties, the optometric factors (for example refractive error and orthoptic function) that may be associated with reading problems are discussed in detail. The first article of this series introduced the correlates of, and interventions for, reading difficulties that have been supported by evidence-based research. This present article describes the optometric correlates more specifically, providing details of the aspects of visual function that ought to be considered for further investigation

Distributional Equivalence and Structure Learning for Bow-free Acyclic Path Diagrams

We consider the problem of structure learning for bow-free acyclic path diagrams (BAPs). BAPs can be viewed as a generalization of linear Gaussian DAG models that allow for certain hidden variables. We present a first method for this problem using a greedy score-based search algorithm. We also prove some necessary and some sufficient conditions for distributional equivalence of BAPs which are used in an algorithmic ap- proach to compute (nearly) equivalent model structures. This allows us to infer lower bounds of causal effects. We also present applications to real and simulated datasets using our publicly available R-package

Duality in Shearing Rheology Near the Athermal Jamming Transition

We consider the rheology of soft-core frictionless disks in two dimensions in the neighborhood of the athermal jamming transition. From numerical simulations of bidisperse, overdamped, particles, we argue that the divergence of the viscosity below jamming is characteristic of the hard-core limit, independent of the particular soft-core interaction. We develop a mapping from soft-core to hard-core particles that recovers all the critical behavior found in earlier scaling analyses. Using this mapping we derive a duality relation that gives the exponent of the non-linear Herschel-Bulkley rheology above jamming in terms of the exponent of the diverging viscosity below jamming.Comment: 5 pages, 4 figures. Manuscript revisions: new title, additional text concerning connections to experiment, revised Fig. 4, other minor changes and clarifications in text. Conclusions remain essentially unchanged. Accepted for publication in Phys. Rev. Let