SWEEPFINDER2: Increased sensitivity, robustness, and flexibility

SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection, as well as increased flexibility that enables the user to examine genomic regions in greater detail and to specify a fixed distance between test sites. Moreover, SweepFinder2 enables the use of invariant sites for sweep detection, increasing both its power and precision relative to SweepFinder

Ternary cluster decay within the liquid drop model

Longitudinal ternary and binary fission barriers of $^{36}$Ar, $^{56}$Ni and $^{252}$Cf nuclei have been determined within a rotational liquid drop model taking into account the nuclear proximity energy. For the light nuclei the heights of the ternary fission barriers become competitive with the binary ones at high angular momenta since the maximum lies at an outer position and has a much higher moment of inertia.Comment: Talk presented at the 9th International Conference on Clustering Aspects of Nuclear Structure and Dynamics (CLUSTERS'07

Optical extinction, refractive index, and multiple scattering for suspensions of interacting colloidal particles

We provide a general microscopic theory of the scattering cross-section and of the refractive index for a system of interacting colloidal particles, exact at second order in the molecular polarizabilities. In particular: a) we show that the structural features of the suspension are encoded into the forward scattered field by multiple scattering effects, whose contribution is essential for the so-called "optical theorem" to hold in the presence of interactions; b) we investigate the role of radiation reaction on light extinction; c) we discuss our results in the framework of effective medium theories, presenting a general result for the effective refractive index valid, whatever the structural properties of the suspension, in the limit of particles much larger than the wavelength; d) by discussing strongly-interacting suspensions, we unravel subtle anomalous dispersion effects for the suspension refractive index.Comment: Submitted to Journal of Chemical Physics 37 pages, 4 figure

Polyelectrolyte Persistence Length: Attractive Effect of Counterion Correlations and Fluctuations

The persistence length of a single, strongly charged, stiff polyelectrolyte chain is investigated theoretically. Path integral formulation is used to obtain the effective electrostatic interaction between the monomers. We find significant deviations from the classical Odijk, Skolnick and Fixman (OSF) result. An induced attraction between monomers is due to thermal fluctuations and correlations between bound counterions. The electrostatic persistence length is found to be smaller than the OSF value and indicates a possible mechanical instability (collapse) for highly charged polyelectrolytes with multivalent counterions. In addition, we calculate the amount of condensed counterions on a slightly bent polyelectrolyte. More counterions are found to be adsorbed as compared to the Manning condensation on a cylinder.Comment: 5 pages, 1 ps figur

Characterization of anisotropic nano-particles by using depolarized dynamic light scattering in the near field

Light scattering techniques are widely used in many fields of condensed and sof t matter physics. Usually these methods are based on the study of the scattered light in the far field. Recently, a new family of near field detection schemes has been developed, mainly for the study of small angle light scattering. These techniques are based on the detection of the light intensity near to the sample, where light scattered at different directions overlaps but can be distinguished by Fourier transform analysis. Here we report for the first time data obtained with a dynamic near field scattering instrument, measuring both polarized and depolarized scattered light. Advantages of this procedure over the traditional far field detection include the immunity to stray light problems and the possibility to obtain a large number of statistical samples for many different wave vectors in a single instantaneous measurement. By using the proposed technique we have measured the translational and rotational diffusion coefficients of rod-like colloidal particles. The obtained data are in very good agreement with the data acquired with a traditional light scattering apparatus.Comment: Published in Optics Express. This version has changes in bibliograph

Generation of induced Pluripotent Stem Cells as disease modelling of NLSDM

Neutral Lipid Storage Disease with Myopathy (NLSDM) is a rare defect of triacylglycerol metabolism, characterized by the abnormal storage of neutral lipid in organelles known as lipid droplets (LDs). The main clinical features are progressive myopathy and cardiomyopathy. The onset of NLSDM is caused by autosomal recessive mutations in the PNPLA2 gene, which encodes adipose triglyceride lipase (ATGL). Despite its name, this enzyme is present in a wide variety of cell types and catalyzes the first step in triacylglycerol lipolysis and the release of fatty acids. Here, we report the derivation of NLSDM-induced pluripotent stem cells (NLSDM-iPSCs) from fibroblasts of two patients carrying different PNPLA2 mutations. The first patient was homozygous for the c.541delAC, while the second was homozygous for the c.662G>C mutation in the PNPLA2 gene. We verified that the two types of NLSDM-iPSCs possessed properties of embryonic-like stem cells and could differentiate into the three germ layers in vitro. Immunofluorescence analysis revealed that iPSCs had an abnormal accumulation of triglycerides in LDs, the hallmark of NLSDM. Furthermore, NLSDM-iPSCs were deficient in long chain fatty acid lipolysis, when subjected to a pulse chase experiment with oleic acid. Collectively, these results demonstrate that NLSDM-iPSCs are a promising in vitro model to investigate disease mechanisms and screen drug compounds for NLSDM, a rare disease with few therapeutic options

Relationship between dielectric properties and critical behavior of the electric birefringence in binary liquid mixtures

We present experimental results on the critical exponent ψEKE describing the divergence of the Kerr constant of binary liquid mixtures near the critical consolute point. We show that the measured value of ψEKE agrees with the theoretical prediction only if the measurement is performed with a mixture of two liquids presenting a small mismatch in the dielectric constant, and that the measured ψEKE grows as the dielectric constant mismatch increases. Such findings are consistent with a recent model which assumes that the elongation of critical fluctations along the direction of the electric field can become so strong that fluctuations in the direction perpendicular to the electric field may cross over from Ising to mean-field behavior

A QUALITATIVE CHARACTERIZATION OF THE CFTR GENE BY mRNA ANALYSIS

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Quantum computation with linear optics

We present a constructive method to translate small quantum circuits into their optical analogues, using linear components of present-day quantum optics technology only. These optical circuits perform precisely the computation that the quantum circuits are designed for, and can thus be used to test the performance of quantum algorithms. The method relies on the representation of several quantum bits by a single photon, and on the implementation of universal quantum gates using simple optical components (beam splitters, phase shifters, etc.). The optical implementation of Brassard et al.'s teleportation circuit, a non-trivial 3-bit quantum computation, is presented as an illustration.Comment: LaTeX with llncs.cls, 11 pages with 5 postscript figures, Proc. of 1st NASA Workshop on Quantum Computation and Quantum Communication (QCQC 98

Conical-emission and shock-front dynamics in femtosecond laser-pulse filamentation

We investigate both experimentally and numerically the space-time dynamics of an ultrashort laser pulse during self-focusing and nonlinear propagation in water by means of a time-gated angular-spectrum characterization. The results identify the formation of shock fronts on both trailing and leading edges of the wave packet that are due to the formation of subluminal and superluminal group velocity intensity peaks, sustained by conical emission