Does biased gene conversion influence polymorphism in the circumsporozoite protein-encoding gene of Plasmodium vivax?

Variation between North Korean and Latin American isolates in the circumsporozoite (CS) protein encoding gene of the human malaria parasite Plasmodium vivax was studied. Polymorphic positions are confined to the central tandemly repeated sequences. Nucleotide substitutions in the tandem repeats produce variants; these substituted positions within the repeat array tend to be conserved between genes. The North Korean CS gene has a short insertion after the repeats encoding a 4-amino acid repeat (Ala-Gly-Gly-Asn) not found in the New World P. vivax genes. This sequence is found both flanking and within the tandem repeats of the CS genes of several strains of the Southeast Asian simian malaria parasite, Plasmodium cynomolgi. The intraspecific conservation of positions of variants within tandem repeat arrays and the interspecific conservation of probably ancestral repeat motifs at the end of these arrays are consistent with the occurrence of nonreciprocal genetic exchanges between the tandem repeats of these genes. However, a striking asymmetry in strand nucleotide composition within the tandem repeats of all CS genes leads us to suggest that biased correction of heteroduplexes formed during recombination plays a role in the evolution of these genes

Phase-field approach to heterogeneous nucleation

We consider the problem of heterogeneous nucleation and growth. The system is described by a phase field model in which the temperature is included through thermal noise. We show that this phase field approach is suitable to describe homogeneous as well as heterogeneous nucleation starting from several general hypotheses. Thus we can investigate the influence of grain boundaries, localized impurities, or any general kind of imperfections in a systematic way. We also put forward the applicability of our model to study other physical situations such as island formation, amorphous crystallization, or recrystallization.Comment: 8 pages including 7 figures. Accepted for publication in Physical Review

Spin dynamics in a structurally ordered non-Fermi liquid compound: YbRh_2Si_2

Muon spin relaxation (muSR) experiments have been carried out at low temperatures in the non-Fermi-liquid heavy-fermion compound YbRh_2Si_2. The longitudinal-field muSR relaxation function is exponential, indicative that the dynamic spin fluctuations are homogeneous. The relaxation rate 1/T_1 varies with applied field as H^{-y}, y = 1.0 \pm 0.1, which implies a scaling law of the form \chi''(\omega) \propto \omega^{-y} f(\omega/T), \lim_{x\to0} f(x) = x for the dynamic spin susceptibility.Comment: 5 pages, 2 figures. To be published in proceedings of musr2002 (Physica B

Volcanic air pollution and human health: recent advances and future directions

Volcanic air pollution from both explosive and effusive activity can affect large populations as far as thousands of kilometers away from the source, for days to decades or even centuries. Here, we summarize key advances and prospects in the assessment of health hazards, effects, risk, and management. Recent advances include standardized ash assessment methods to characterize the multiple physicochemical characteristics that might influence toxicity; the rise of community-based air quality monitoring networks using low-cost gas and particulate sensors; the development of forecasting methods for ground-level concentrations and associated public advisories; the development of risk and impact assessment methods to explore health consequences of future eruptions; and the development of evidence-based, locally specific measures for health protection. However, it remains problematic that the health effects of many major and sometimes long-duration eruptions near large populations have gone completely unmonitored. Similarly, effects of prolonged degassing on exposed populations have received very little attention relative to explosive eruptions. Furthermore, very few studies have longitudinally followed populations chronically exposed to volcanic emissions; thus, knowledge gaps remain about whether chronic exposures can trigger development of potentially fatal diseases. Instigating such studies will be facilitated by continued co-development of standardized protocols, supporting local study teams and procuring equipment, funding, and ethical permissions. Relationship building between visiting researchers and host country academic, observatory, and agency partners is vital and can, in turn, support the effective communication of health impacts of volcanic air pollution to populations, health practitioners, and emergency managers

Development of a simulated lung fluid leaching method to assess the release of potentially toxic elements from volcanic ash

Freshly erupted volcanic ash contains a range of soluble elements, some of which can generate harmful effects in living cells and are considered potentially toxic elements (PTEs). This work investigates the leaching dynamics of ash-associated PTEs in order to optimize a method for volcanic ash respiratory hazard assessment. Using three pristine (unaffected by precipitation) ash samples, we quantify the release of PTEs (Al, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, V, Zn) and major cations typical of ash leachates (Mg, Na, Ca, K) in multiple simulated lung fluid (SLF) preparations and under varying experimental parameters (contact time and solid to liquid ratio). Data are compared to a standard water leach (WL) to ascertain whether the WL can be used as a simple proxy for SLF leaching. The main findings are: PTE concentrations reach steady-state dissolution by 24 h, and a relatively short contact time (10 min) approximates maximum dissolution; PTE dissolution is comparatively stable at low solid to liquid ratios (1:100 to 1:1000); inclusion of commonly used macromolecules has element-specific effects, and addition of a lung surfactant has little impact on extraction efficiency. These observations indicate that a WL can be used to approximate lung bioaccessible PTEs in an eruption response situation. This is a useful step towards standardizing in vitro methods to determine the soluble-element hazard from inhaled ash

Virus shapes and buckling transitions in spherical shells

We show that the icosahedral packings of protein capsomeres proposed by Caspar and Klug for spherical viruses become unstable to faceting for sufficiently large virus size, in analogy with the buckling instability of disclinations in two-dimensional crystals. Our model, based on the nonlinear physics of thin elastic shells, produces excellent one parameter fits in real space to the full three-dimensional shape of large spherical viruses. The faceted shape depends only on the dimensionless Foppl-von Karman number \gamma=YR^2/\kappa, where Y is the two-dimensional Young's modulus of the protein shell, \kappa is its bending rigidity and R is the mean virus radius. The shape can be parameterized more quantitatively in terms of a spherical harmonic expansion. We also investigate elastic shell theory for extremely large \gamma, 10^3 < \gamma < 10^8, and find results applicable to icosahedral shapes of large vesicles studied with freeze fracture and electron microscopy.Comment: 11 pages, 12 figure

Detecting Current Noise with a Josephson Junction in the Macroscopic Quantum Tunneling Regime

We discuss the use of a hysteretic Josephson junction to detect current fluctuations with frequencies below the plasma frequency of the junction. These adiabatic fluctuations are probed by switching measurements observing the noise-affected average rate of macroscopic quantum tunneling of the detector junction out of its zero-voltage state. In a proposed experimental scheme, frequencies of the noise are limited by an on-chip filtering circuit. The third cumulant of current fluctuations at the detector is related to an asymmetry of the switching rates.Comment: 26 pages, 10 figures. To appear in Journal of Low Temperature Physics in the proceedings of the ULTI conference organized in Lammi, Finland (2006

Structure of Fat Jets at the Tevatron and Beyond

Boosted resonances is a highly probable and enthusiastic scenario in any process probing the electroweak scale. Such objects when decaying into jets can easily blend with the cornucopia of jets from hard relative light QCD states. We review jet observables and algorithms that can contribute to the identification of highly boosted heavy jets and the possible searches that can make use of such substructure information. We also review previous studies by CDF on boosted jets and its measurements on specific jet shapes.Comment: invited review for a special "Top and flavour physics in the LHC era" issue of The European Physical Journal C, we invite comments regarding contents of the review; v2 added references and institutional preprint number

Nonlinear Viscous Vortex Motion in Two-Dimensional Josephson-Junction Arrays

When a vortex in a two-dimensional Josephson junction array is driven by a constant external current it may move as a particle in a viscous medium. Here we study the nature of this viscous motion. We model the junctions in a square array as resistively and capacitively shunted Josephson junctions and carry out numerical calculations of the current-voltage characteristics. We find that the current-voltage characteristics in the damped regime are well described by a model with a {\bf nonlinear} viscous force of the form $F_D=\eta(\dot y)\dot y={{A}\over {1+B\dot y}}\dot y$, where $\dot y$ is the vortex velocity, $\eta(\dot y)$ is the velocity dependent viscosity and $A$ and $B$ are constants for a fixed value of the Stewart-McCumber parameter. This result is found to apply also for triangular lattices in the overdamped regime. Further qualitative understanding of the nature of the nonlinear friction on the vortex motion is obtained from a graphic analysis of the microscopic vortex dynamics in the array. The consequences of having this type of nonlinear friction law are discussed and compared to previous theoretical and experimental studies.Comment: 14 pages RevTex, 9 Postscript figure

Hard Scattering Factorization from Effective Field Theory

In this paper we show how gauge symmetries in an effective theory can be used to simplify proofs of factorization formulae in highly energetic hadronic processes. We use the soft-collinear effective theory, generalized to deal with back-to-back jets of collinear particles. Our proofs do not depend on the choice of a particular gauge, and the formalism is applicable to both exclusive and inclusive factorization. As examples we treat the pi-gamma form factor (gamma gamma* -> pi^0), light meson form factors (gamma* M -> M), as well as deep inelastic scattering (e- p -> e- X), Drell-Yan (p pbar -> X l+ l-), and deeply virtual Compton scattering (gamma* p -> gamma(*) p).Comment: 35 pages, 4 figures, typos corrected, journal versio