Exact Asymptotic Results for a Model of Sequence Alignment

Finding analytically the statistics of the longest common subsequence (LCS) of a pair of random sequences drawn from c alphabets is a challenging problem in computational evolutionary biology. We present exact asymptotic results for the distribution of the LCS in a simpler, yet nontrivial, variant of the original model called the Bernoulli matching (BM) model which reduces to the original model in the large c limit. We show that in the BM model, for all c, the distribution of the asymptotic length of the LCS, suitably scaled, is identical to the Tracy-Widom distribution of the largest eigenvalue of a random matrix whose entries are drawn from a Gaussian unitary ensemble. In particular, in the large c limit, this provides an exact expression for the asymptotic length distribution in the original LCS problem.Comment: 4 pages Revtex, 2 .eps figures include

The impact of health communication and enhanced laboratory-based surveillance on detection of cyclosporiasis outbreaks in California.

We investigated the timing of diagnosis, influence of media information on testing for Cyclospora, and the method used to identify cases during eight cyclosporiasis outbreaks in California in spring of 1997. We found that Internet information, media reports, and enhanced laboratory surveillance improved detection of these outbreaks

The Fall and Rise of US Inequities in Premature Mortality: 1960–2002

Nancy Krieger and colleagues found evidence of decreasing, and then increasing or stagnating, socioeconomic and racial inequities in US premature mortality and infant death from 1960 to 2002

Thermodynamics of protein folding: a random matrix formulation

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows however that the evolution of the statistical measures e.g Gibbs free energy, heat capacity, entropy is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies.Comment: 21 Pages, no figure

Formation and Interaction of Membrane Tubes

We show that the formation of membrane tubes (or membrane tethers), which is a crucial step in many biological processes, is highly non-trivial and involves first order shape transitions. The force exerted by an emerging tube is a non-monotonic function of its length. We point out that tubes attract each other, which eventually leads to their coalescence. We also show that detached tubes behave like semiflexible filaments with a rather short persistence length. We suggest that these properties play an important role in the formation and structure of tubular organelles.Comment: 4 pages, 3 figure

Parental bonding and identity style as correlates of self-esteem among adult adoptees and nonadoptees

Adult adoptees (n equals 100) and non-adoptees (n equals 100) were compared with regard to selfesteem, identity processing style, and parental bonding. While some differences were found with regard to self-esteem, maternal care, and maternal overprotection, these differences were qualified by reunion status such that only reunited adoptees differed significantly from nonadoptees. Moreover, hierarchical regression analyses indicated that parental bonding and identity processing style were more important than adoptive status per se in predicting self esteem. Implications for practitioners who work with adoptees are discussed

The secret world of shrimps: polarisation vision at its best

Animal vision spans a great range of complexity, with systems evolving to detect variations in optical intensity, distribution, colour, and polarisation. Polarisation vision systems studied to date detect one to four channels of linear polarisation, combining them in opponent pairs to provide intensity-independent operation. Circular polarisation vision has never been seen, and is widely believed to play no part in animal vision. Polarisation is fully measured via Stokes' parameters--obtained by combined linear and circular polarisation measurements. Optimal polarisation vision is the ability to see Stokes' parameters: here we show that the crustacean \emph{Gonodactylus smithii} measures the exact components required. This vision provides optimal contrast-enhancement, and precise determination of polarisation with no confusion-states or neutral-points--significant advantages. We emphasise that linear and circular polarisation vision are not different modalities--both are necessary for optimal polarisation vision, regardless of the presence of strongly linear or circularly polarised features in the animal's environment.Comment: 10 pages, 6 figures, 2 table

Polarized light field under dynamic ocean surfaces: Numerical modeling compared with measurements

As part of the Radiance in a Dynamic Ocean (RaDyO) program, we have developed a numerical model for efficiently simulating the polarized light field under highly dynamic ocean surfaces. Combining the advantages of the three-dimensional Monte Carlo and matrix operator methods, this hybrid model has proven to be computationally effective for simulations involving a dynamic air-sea interface. Given water optical properties and ocean surface wave slopes obtained from RaDyO field measurements, model-simulated radiance and polarization fields under a dynamic surface are found to be qualitatively comparable to their counterparts from field measurements and should be quantitatively comparable if the light field measurement and the wave slope/water optical property measurements are appropriately collocated and synchronized. This model serves as a bridge to connect field measurements of water optical properties, wave slopes and polarized light fields. It can also be used as a powerful yet convenient tool to predict the temporal underwater polarized radiance in a real-world situation. When appropriate surface measurements are available, model simulation is shown to reveal more dynamic features in the underwater light field than direct measurements