Evolutionary History and Phylodynamics of Influenza A and B Neuraminidase (NA) Genes Inferred from Large- Scale Sequence Analyses

Background: Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking. Methodology/Principal findings: Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A NA subtypes. Twenty-three lineages were identified within influenza A, two lineages were classified within influenza B, and most lineages were specific to host, subtype or geographical location. Interestingly, evolutionary rates vary not only among lineages but also among branches within lineages. The estimated tMRCAs of influenza lineages suggest that the viruses of different lineages emerge several months or even years before their initial detection. The dN/dS ratios ranged from 0.062 to 0.313 for influenza A lineages, and 0.257 to 0.259 for influenza B lineages. Structural analyses revealed that all positively selected sites are at the surface of the NA protein, with a number of sites found to be important for host antibody and drug binding. Conclusions/Significance: The divergence into influenza type A and B from a putative ancestral NA was followed by the divergence of type A into nine NA subtypes, of which 23 lineages subsequently diverged. This study provides a better understanding of influenza NA lineages and their evolutionary dynamics, which may facilitate early detection of newly emerging influenza viruses and thus improve influenza surveillance

A General Catalogue of Molecular Hydrogen Emission-Line Objects (MHOs) in Outflows from Young Stars

We present a catalogue of Molecular Hydrogen emission-line Objects (MHOs) in outflows from young stars, most of which are embedded. All objects are identified in the near-infrared lines of molecular hydrogen, all reside in the Milky Way, and all are associated with jets or molecular outflows from young stars. Objects in both low and high-mass star forming regions are included. This catalogue complements the existing database of Herbig-Haro objects; indeed, for completeness, HH objects that are detected in H2 emission are included in the MHO catalogue.Comment: 8 Pages, 5 figures. Accepted for publication in A&A. Searchable catalogue/Data tables available from http://www.jach.hawaii.edu/UKIRT/MHCat

Random Walks for Spike-Timing Dependent Plasticity

Random walk methods are used to calculate the moments of negative image equilibrium distributions in synaptic weight dynamics governed by spike-timing dependent plasticity (STDP). The neural architecture of the model is based on the electrosensory lateral line lobe (ELL) of mormyrid electric fish, which forms a negative image of the reafferent signal from the fish's own electric discharge to optimize detection of sensory electric fields. Of particular behavioral importance to the fish is the variance of the equilibrium postsynaptic potential in the presence of noise, which is determined by the variance of the equilibrium weight distribution. Recurrence relations are derived for the moments of the equilibrium weight distribution, for arbitrary postsynaptic potential functions and arbitrary learning rules. For the case of homogeneous network parameters, explicit closed form solutions are developed for the covariances of the synaptic weight and postsynaptic potential distributions.Comment: 18 pages, 8 figures, 15 subfigures; uses revtex4, subfigure, amsmat

Genetic Stasis of Dominant West Nile Virus Genotype, Houston, Texas

The accumulation and fixation of mutations in West Nile virus (WNV) led to the emergence of a dominant genotype throughout North America. Subsequent analysis of 44 isolates, including 19 new sequences, from Houston, Texas, suggests that WNV has reached relative genetic stasis at the local level in recent years

Unconfined Specimens

ABSTRACT: Effective diffusion coefficients, D*, of chloride and zinc diffusing in saturated, unconfined specimens of a compacted sandclay mixture are measured for three specimen lengths, L (2.91, 5.83, and 11.60 cm) and three test durations (7, 14, and 21 days). For a specimen length of 2.91 cm, both the chloride and zinc D* values tend to decrease with increasing test duration, possibly due to the measurement of concentration-dependent D* values. For a 14-day test duration, no consistent trend in D* with specimen length is observed, but the overall effect of specimen length on D* is minor relative to the range of measured D* values. A 21-day test duration provides the best correlation between the D* values based on reservoir concentrations, DiScs, and the D* values based on soil concentrations, D~oil, for chloride for a given test regardless of the specimen length. The effect of test duration on the correlation between D~cs and D~oit for zinc is minor based on the relatively narrow range of measured zinc D* values. The observed effects of specimen length on the correlation between D~¢s and D~oil for a given test are consistent with the more uniform final porosity distributions in the shorter specimens and the contrasting effects of the non-linear distributions in porosity and dry density that become less significant as the specimen length increases. KEYWORDS: adsorption, attapulgite clay, batch equilibrium, chloride diffusion, contaminant transport, diffusion testing, Freundlich isotherm, sand-clay mixture, swelling, zinc diffusion Over the past -30 years, diffusion testing has been performed in several different disciplines (e.g., soil science, geology, oceanography, geotechnical engineering) for several different purposes, including diffusion of nutrients to plant roots (Olsen and Kemper 1968), characterization of pore water in geologic deposits Several different types of diffusion testing procedures can be used, test durations have ranged from a few hours to several months, and the specimen volumes have ranged from as small as 10 cm 3 to more than 944 cm 3 (Shacketford 1991). Practical limitations to some, if not all, of the different test methods undoubtedly exist, and variability in test duration and specimen size may have an effect on determination of the measured diffusion coefficients. As a result, an evaluation of the factors potentially affecting the measurement of effective diffusion coefficients is needed. Such an evaluation is particularly of interest to geotechnical engineers associated with the design and evaluation of waste containment barriers because of the increasing importance placed on contaminant transport, in general, and diffusive transport, in particular, in such applications. The primary objective of this study is to evaluate the potential influence of test duration and specimen length on the diffusion of chloride and zinc in compacted, unconfined specimens of a sandclay mixture. The evaluation is based on the single reservoir, decreasing source concentration method that has been used extensively in the measurement of effective diffusion coefficients associated with waste disposal applications Materials and Methods Soil The soil used in this study is a mixture of 75% sand and 25% attapulgite clay (dry weight basis). Physical and chemical properties of the sand and attapulgite clay are provided i