Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ~2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. Conclusions/Significance These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection

Spectra of magnetic perturbations triggered by pellets in JET plasmas

Aiming at investigating edge localised mode (ELM) pacing for future application on ITER, experiments have been conducted on JET injecting pellets in different plasma configurations, including high confinement regimes with type-I and type-III ELMs, low confinement regimes and Ohmically heated plasmas. The magnetic perturbations spectra and the toroidal mode number, n, of triggered events are compared with those of spontaneous ELMs using a wavelet analysis to provide good time resolution of short-lived coherent modes. It is found that—in all these configurations—triggered events have a coherent mode structure, indicating that pellets can trigger an MHD event basically in every background plasma. Two components have been found in the magnetic perturbations induced by pellets, with distinct frequencies and toroidal mode numbers. In high confinement regimes triggered events have similarities with spontaneous ELMs: both are seen to start from low toroidal mode numbers, then the maximum measured n increases up to about 10 within 0.3 ms before the ELM burst

Automated analysis of atrial late gadolinium enhancement imaging that correlates with endocardial voltage and clinical outcomes: A 2-center study

This work was supported by the British Heart Foundation PG/10/37/28347, RG/10/11/28457, NIHR Biomedical Research Centre funding, and the ElectroCardioMaths Programme of the Imperial BHF Centre of Research Excellence

Microlensing by natural wormholes: theory and simulations

We provide an in depth study of the theoretical peculiarities that arise in effective negative mass lensing, both for the case of a point mass lens and source, and for extended source situations. We describe novel observational signatures arising in the case of a source lensed by a negative mass. We show that a negative mass lens produces total or partial eclipse of the source in the umbra region and also show that the usual Shapiro time delay is replaced with an equivalent time gain. We describe these features both theoretically, as well as through numerical simulations. We provide negative mass microlensing simulations for various intensity profiles and discuss the differences between them. The light curves for microlensing events are presented and contrasted with those due to lensing produced by normal matter. Presence or absence of these features in the observed microlensing events can shed light on the existence of natural wormholes in the Universe.Comment: 16 pages, 24 postscript figures (3 coloured), revtex style, submitted to Phys. Rev.

Strong 3D correlations in vortex system of Bi2212:Pb

The experimental study of magnetic flux penetration under crossed magnetic fields in Bi2212:Pb single crystal performed by magnetooptic technique (MO) reveals remarkable field penetration pattern alteration (flux configuration change) and superconducting current anisotropy enhancement by the in-plane field. The anisotropy increases with the temperature rise up to $T_m = 54 \pm 2 K$. At $T = T_m$ an abrupt change in the flux behavior is found; the correlation between the in-plane magnetic field and the out-of-plane magnetic flux penetration disappears. No correlation is observed for $T > T_m$. The transition temperature $T_m$ does not depend on the magnetic field strength. The observed flux penetration anisotropy is considered as an evidence of a strong 3D - correlation between pancake vortices in different CuO planes at $T < T_m$. This enables understanding of a remarkable pinning observed in Bi2212:Pb at low temperatures.Comment: 8 pages, 9 figure

1053pdgenomics features gf and integration with mri radiomics features rf to develop a prognostic model in oral cavity squamous cell carcinoma oscc

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Fusion product losses due to fishbone instabilities in deuterium JET plasmas

During development of a high-performance hybrid scenario for future deuterium–tritium experiments on the Joint European Torus, an increased level of fast ion losses in the MeV energy range was observed during the instability of high-frequency n  =  1 fishbones. The fishbones are excited during deuterium neutral beam injection combined with ion cyclotron heating. The frequency range of the fishbones, 10–25 kHz, indicates that they are driven by a resonant interaction with the NBI-produced deuterium beam ions in the energy range  ≤120 keV. The fast particle losses in a much higher energy range are measured with a fast ion loss detector, and the data show an expulsion of deuterium plasma fusion products, 1 MeV tritons and 3 MeV protons, during the fishbone bursts. An MHD mode analysis with the MISHKA code combined with the nonlinear wave-particle interaction code HAGIS shows that the loss of toroidal symmetry caused by the n  =  1 fishbones affects strongly the confinement of non-resonant high energy fusion-born tritons and protons by perturbing their orbits and expelling them. This modelling is in a good agreement with the experimental data.This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014-2018 under grant agreement No 633053 and from the RCUK Energy Programme [grant No EP/P012450/1]. To obtain further information on the data and models underlying this paper please contact [email protected] . The views and opinions expressed herein do not necessarily reflect those of the European CommissionPeer ReviewedPostprint (author's final draft

Energy Conditions in f(G)f(G) Modified Gravity with Non-minimal Coupling to Matter

In this paper we study a model of modified gravity with non-minimal coupling between a general function of the Gauss-Bonnet invariant, $f(G)$, and matter Lagrangian from the point of view of the energy conditions. Such model has been introduced in Ref. [21] for description of early inflation and late-time cosmic acceleration. We present the suitable energy conditions for the above mentioned model and then, we use the estimated values of the Hubble, deceleration and jerk parameters to apply the obtained energy conditions to the specific class of modified Gauss-Bonnet models.Comment: 12 pages, no figur, Accepted for publication in Astrophysics and Space Scienc

Origins of the Ambient Solar Wind: Implications for Space Weather

The Sun's outer atmosphere is heated to temperatures of millions of degrees, and solar plasma flows out into interplanetary space at supersonic speeds. This paper reviews our current understanding of these interrelated problems: coronal heating and the acceleration of the ambient solar wind. We also discuss where the community stands in its ability to forecast how variations in the solar wind (i.e., fast and slow wind streams) impact the Earth. Although the last few decades have seen significant progress in observations and modeling, we still do not have a complete understanding of the relevant physical processes, nor do we have a quantitatively precise census of which coronal structures contribute to specific types of solar wind. Fast streams are known to be connected to the central regions of large coronal holes. Slow streams, however, appear to come from a wide range of sources, including streamers, pseudostreamers, coronal loops, active regions, and coronal hole boundaries. Complicating our understanding even more is the fact that processes such as turbulence, stream-stream interactions, and Coulomb collisions can make it difficult to unambiguously map a parcel measured at 1 AU back down to its coronal source. We also review recent progress -- in theoretical modeling, observational data analysis, and forecasting techniques that sit at the interface between data and theory -- that gives us hope that the above problems are indeed solvable.Comment: Accepted for publication in Space Science Reviews. Special issue connected with a 2016 ISSI workshop on "The Scientific Foundations of Space Weather." 44 pages, 9 figure

f(R,L_m) gravity

We generalize the $f(R)$ type gravity models by assuming that the gravitational Lagrangian is given by an arbitrary function of the Ricci scalar $R$ and of the matter Lagrangian $L_m$. We obtain the gravitational field equations in the metric formalism, as well as the equations of motion for test particles, which follow from the covariant divergence of the energy-momentum tensor. The equations of motion for test particles can also be derived from a variational principle in the particular case in which the Lagrangian density of the matter is an arbitrary function of the energy-density of the matter only. Generally, the motion is non-geodesic, and takes place in the presence of an extra force orthogonal to the four-velocity. The Newtonian limit of the equation of motion is also considered, and a procedure for obtaining the energy-momentum tensor of the matter is presented. The gravitational field equations and the equations of motion for a particular model in which the action of the gravitational field has an exponential dependence on the standard general relativistic Hilbert--Einstein Lagrange density are also derived.Comment: 6 pages, no figures; minor modifications, references added; accepted for publication in EPJ