News Coverage of the 2008 Presidential Primaries

President George W. Bush was completing his second (and final) term in office and Vice President Dick Cheney decided not to run for president. Thus, the 2008 American presidential primary is the first “open” campaign (with no sitting president or vice president competing) since 1952 with highly competitive primaries for both major political parties. This study uses content analysis to investigate news coverage (national newspapers, network television news, and local newspapers) of the 2008 American presidential primary campaign. Most themes in the news concerned the horse race (66%) with somewhat more emphasis on the candidates’ character (18%) than their policy proposals (15%). The most common topics of horse race comments were campaign strategy (24%), campaign events (19%), polls (17%), and predictions (12%). More news comments were positive (62%) than negative (32%) with few comments about the candidate’s defenses (7%). Most comments were unattributed (statements by journalists: 66%); candidates were quoted or paraphrased in about one in five comments; the remaining comments were from supporters (8%) or others (7%)

Basic tasks of sentiment analysis

Subjectivity detection is the task of identifying objective and subjective sentences. Objective sentences are those which do not exhibit any sentiment. So, it is desired for a sentiment analysis engine to find and separate the objective sentences for further analysis, e.g., polarity detection. In subjective sentences, opinions can often be expressed on one or multiple topics. Aspect extraction is a subtask of sentiment analysis that consists in identifying opinion targets in opinionated text, i.e., in detecting the specific aspects of a product or service the opinion holder is either praising or complaining about

Defects in Chiral Columnar Phases: Tilt Grain Boundaries and Iterated Moire Maps

Biomolecules are often very long with a definite chirality. DNA, xanthan and poly-gamma-benzyl-glutamate (PBLG) can all form columnar crystalline phases. The chirality, however, competes with the tendency for crystalline order. For chiral polymers, there are two sorts of chirality: the first describes the usual cholesteric-like twist of the local director around a pitch axis, while the second favors the rotation of the local bond-orientational order and leads to a braiding of the polymers along an average direction. In the former case chirality can be manifested in a tilt grain boundary phase (TGB) analogous to the Renn-Lubensky phase of smectic-A liquid crystals. In the latter case we are led to a new "moire" state with twisted bond order. In the moire state polymers are simultaneously entangled, crystalline, and aligned, on average, in a common direction. In the moire state polymers are simultaneously entangled, crystalline, and aligned, on average, in a common direction. In this case the polymer trajectories in the plane perpendicular to their average direction are described by iterated moire maps of remarkable complexity, reminiscent of dynamical systems.Comment: plain TeX, (33 pages), 17 figures, some uufiled and included, the remaining available at ftp://ftp.sns.ias.edu/pub/kamien/ or by request to [email protected]

Symmetries of Electrostatic Interaction between DNA Molecules

We study a model for pair interaction $U$ of DNA molecules generated by the discrete dipole moments of base-pairs and the charges of phosphate groups, and find noncommutative group of eighth order ${\cal S}$ of symmetries that leave $U$ invariant. We classify the minima using group ${\cal S}$ and employ numerical methods for finding them. The minima may correspond to several cholesteric phases, as well as phases formed by cross-like conformations of molecules at an angle close to $\rm{90}^{o}$, "snowflake phase". The results depend on the effective charge $Q$ of the phosphate group which can be modified by the polycations or the ions of metals. The snowflake phase could exist for $Q$ above the threshold $Q_C$. Below $Q_C$ there could be several cholesteric phases. Close to $Q_C$ the snowflake phase could change into the cholesteric one at constant distance between adjacent molecules.Comment: 13 pages, 4 figure

Surface Scaling Analysis of a Frustrated Spring-network Model for Surfactant-templated Hydrogels

We propose and study a simplified model for the surface and bulk structures of crosslinked polymer gels, into which voids are introduced through templating by surfactant micelles. Such systems were recently studied by Atomic Force Microscopy [M. Chakrapani et al., e-print cond-mat/0112255]. The gel is represented by a frustrated, triangular network of nodes connected by springs of random equilibrium lengths. The nodes represent crosslinkers, and the springs correspond to polymer chains. The boundaries are fixed at the bottom, free at the top, and periodic in the lateral direction. Voids are introduced by deleting a proportion of the nodes and their associated springs. The model is numerically relaxed to a representative local energy minimum, resulting in an inhomogeneous, ``clumpy'' bulk structure. The free top surface is defined at evenly spaced points in the lateral (x) direction by the height of the topmost spring, measured from the bottom layer, h(x). Its scaling properties are studied by calculating the root-mean-square surface width and the generalized increment correlation functions C_q(x)= . The surface is found to have a nontrivial scaling behavior on small length scales, with a crossover to scale-independent behavior on large scales. As the vacancy concentration approaches the site-percolation limit, both the crossover length and the saturation value of the surface width diverge in a manner that appears to be proportional to the bulk connectivity length. This suggests that a percolation transition in the bulk also drives a similar divergence observed in surfactant templated polyacrylamide gels at high surfactant concentrations.Comment: 17 pages RevTex4, 10 imbedded eps figures. Expanded discussion of multi-affinit

Photonic Analogue of Two-dimensional Topological Insulators and Helical One-Way Edge Transport in Bi-Anisotropic Metamaterials

Recent progress in understanding the topological properties of condensed matter has led to the discovery of time-reversal invariant topological insulators. Because of limitations imposed by nature, topologically non-trivial electronic order seems to be uncommon except in small-band-gap semiconductors with strong spin-orbit interactions. In this Article we show that artificial electromagnetic structures, known as metamaterials, provide an attractive platform for designing photonic analogues of topological insulators. We demonstrate that a judicious choice of the metamaterial parameters can create photonic phases that support a pair of helical edge states, and that these edge states enable one-way photonic transport that is robust against disorder.Comment: 13 pages, 3 figure

Reliability analysis of the Ahringer Caenorhabditis elegans RNAi feeding library: a guide for genome-wide screens

<p>Abstract</p> <p>Background</p> <p>The Ahringer <it>C. elegans </it>RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by direct sequencing, and there are potential errors, including: 1) mis-annotation (the clone with the retired gene name should be remapped to the actual target gene); 2) nonspecific PCR amplification; 3) cross-RNAi; 4) mis-operation such as sample loading error, <it>etc</it>.</p> <p>Results</p> <p>Here we performed a reliability analysis on the Ahringer <it>C. elegans </it>RNAi feeding library, which contains 16,256 bacterial strains, using a bioinformatics approach. Results demonstrated that most (98.3%) of the bacterial strains in the library are reliable. However, we also found that 2,851 (17.54%) bacterial strains need to be re-annotated even they are reliable. Most of these bacterial strains are the clones having the retired gene names. Besides, 28 strains are grouped into unreliable category and 226 strains are marginal because of probably expressing unrelated double-stranded RNAs (dsRNAs). The accuracy of the prediction was further confirmed by direct sequencing analysis of 496 bacterial strains. Finally, a freely accessible database named CelRNAi (<url>http://biocompute.bmi.ac.cn/CelRNAi/</url>) was developed as a valuable complement resource for the feeding RNAi library by providing the predicted information on all bacterial strains. Moreover, submission of the direct sequencing result or any other annotations for the bacterial strains to the database are allowed and will be integrated into the CelRNAi database to improve the accuracy of the library. In addition, we provide five candidate primer sets for each of the unreliable and marginal bacterial strains for users to construct an alternative vector for their own RNAi studies.</p> <p>Conclusions</p> <p>Because of the potential unreliability of the Ahringer <it>C. elegans </it>RNAi feeding library, we strongly suggest the user examine the reliability information of the bacterial strains in the CelRNAi database before performing RNAi experiments, as well as the post-RNAi experiment analysis.</p

Synchronization of coupled limit cycles

A unified approach for analyzing synchronization in coupled systems of autonomous differential equations is presented in this work. Through a careful analysis of the variational equation of the coupled system we establish a sufficient condition for synchronization in terms of the geometric properties of the local limit cycles and the coupling operator. This result applies to a large class of differential equation models in physics and biology. The stability analysis is complemented with a discussion of numerical simulations of a compartmental model of a neuron.Comment: Journal of Nonlinear Science, accepte

The “conscious pilot”—dendritic synchrony moves through the brain to mediate consciousness

Cognitive brain functions including sensory processing and control of behavior are understood as “neurocomputation” in axonal–dendritic synaptic networks of “integrate-and-fire” neurons. Cognitive neurocomputation with consciousness is accompanied by 30- to 90-Hz gamma synchrony electroencephalography (EEG), and non-conscious neurocomputation is not. Gamma synchrony EEG derives largely from neuronal groups linked by dendritic–dendritic gap junctions, forming transient syncytia (“dendritic webs”) in input/integration layers oriented sideways to axonal–dendritic neurocomputational flow. As gap junctions open and close, a gamma-synchronized dendritic web can rapidly change topology and move through the brain as a spatiotemporal envelope performing collective integration and volitional choices correlating with consciousness. The “conscious pilot” is a metaphorical description for a mobile gamma-synchronized dendritic web as vehicle for a conscious agent/pilot which experiences and assumes control of otherwise non-conscious auto-pilot neurocomputation