An efficient approach to screening epigenome-wide data

Screening cytosine-phosphate-guanine dinucleotide (CpG) DNA methylation sites in association with some covariate(s) is desired due to high dimensionality. We incorporate surrogate variable analyses (SVAs) into (ordinary or robust) linear regressions and utilize training and testing samples for nested validation to screen CpG sites. SVA is to account for variations in the methylation not explained by the specified covariate(s) and adjust for confounding effects. To make it easier to users, this screening method is built into a user-friendly R package, ttScreening, with efficient algorithms implemented. Various simulations were implemented to examine the robustness and sensitivity of the method compared to the classical approaches controlling for multiple testing: the false discovery rates-based (FDR-based) and the Bonferroni-based methods. The proposed approach in general performs better and has the potential to control both types I and II errors. We applied ttScreening to 383,998 CpG sites in association with maternal smoking, one of the leading factors for cancer risk

Relativistic anisotropic charged fluid spheres with varying cosmological constant

Static spherically symmetric anisotropic source has been studied for the Einstein-Maxwell field equations assuming the erstwhile cosmological constant $\Lambda$ to be a space-variable scalar, viz., $\Lambda = \Lambda(r)$. Two cases have been examined out of which one reduces to isotropic sphere. The solutions thus obtained are shown to be electromagnetic in origin as a particular case. It is also shown that the generally used pure charge condition, viz., $\rho + p_r = 0$ is not always required for constructing electromagnetic mass models.Comment: 15 pages, 3 eps figure

Unification, KK-thresholds and the top Yukawa coupling in F-theory GUTs

In a class of F-theory SU(5) GUTs the low energy chiral mass spectrum is obtained from rank one fermion mass textures with a hierarchical structure organised by U(1) symmetries embedded in the exceptional E_8 group. In these theories chiral fields reside on matter `curves' and the tree level masses are computed from integrals of overlapping wavefuctions of the particles at the triple intersection points. This calculation requires knowledge of the exact form of the wavefuctions. In this work we propose a way to obtain a reliable estimate of the various quantities which determine the strength of the Yukawa couplings. We use previous analysis of KK threshold effects to determine the (ratios of) heavy mass scales of the theory which are involved in the normalization of the wave functions. We consider similar effects from the chiral spectrum of these models and discuss possible constraints on the emerging matter content. In this approach, we find that the Yukawa couplings can be determined solely from the U(1) charges of the states in the `intersection' and the torsion which is a topological invariant quantity. We apply the results to a viable SU(5) model with minimal spectrum which satisfies all the constraints imposed by our analysis. We use renormalization group analysis to estimate the top and bottom masses and find that they are in agreement with the experimental values.Comment: 28 pages, 2 figure

Deceleration and trapping of heavy diatomic molecules using a ring-decelerator

We present an analysis of the deceleration and trapping of heavy diatomic molecules in low-field seeking states by a moving electric potential. This moving potential is created by a 'ring-decelerator', which consists of a series of ring-shaped electrodes to which oscillating high voltages are applied. Particle trajectory simulations have been used to analyze the deceleration and trapping efficiency for a group of molecules that is of special interest for precision measurements of fundamental discrete symmetries. For the typical case of the SrF molecule in the (N,M) = (2, 0) state, the ring-decelerator is shown to outperform traditional and alternate-gradient Stark decelerators by at least an order of magnitude. If further cooled by a stage of laser cooling, the decelerated molecules allow for a sensitivity gain in a parity violation measurement, compared to a cryogenic molecular beam experiment, of almost two orders of magnitude

Functional architecture of the rat parasubiculum

The parasubiculum is a major input structure of layer 2 of medial entorhinal cortex, where most grid cells are found. Here we investigated parasubicular circuits of the rat by anatomical analysis combined with juxtacellular recording/labeling and tetrode recordings during spatial exploration. In tangential sections, the parasubiculum appears as a linear structure flanking the medial entorhinal cortex mediodorsally. With a length of ∼5.2 mm and a width of only ∼0.3 mm (approximately one dendritic tree diameter), the parasubiculum is both one of the longest and narrowest cortical structures. Parasubicular neurons span the height of cortical layers 2 and 3, and we observed no obvious association of deep layers to this structure. The "superficial parasubiculum" (layers 2 and 1) divides into ∼15 patches, whereas deeper parasubicular sections (layer 3) form a continuous band of neurons. Anterograde tracing experiments show that parasubicular neurons extend long "circumcurrent" axons establishing a "global" internal connectivity. The parasubiculum is a prime target of GABAergic and cholinergic medial septal inputs. Other input structures include the subiculum, presubiculum, and anterior thalamus. Functional analysis of identified and unidentified parasubicular neurons shows strong theta rhythmicity of spiking, a large fraction of head-direction selectivity (50%, 34 of 68), and spatial responses (grid, border and irregular spatial cells, 57%, 39 of 68). Parasubicular output preferentially targets patches of calbindin-positive pyramidal neurons in layer 2 of medial entorhinal cortex, which might be relevant for grid cell function. These findings suggest the parasubiculum might shape entorhinal theta rhythmicity and the (dorsoventral) integration of information across grid scales

Channel Coupling in A(e⃗,e′N⃗)BA(\vec{e},e' \vec{N})B Reactions

The sensitivity of momentum distributions, recoil polarization observables, and response functions for nucleon knockout by polarized electrons to channel coupling in final-state interactions is investigated using a model in which both the distorting and the coupling potentials are constructed by folding density-dependent effective interactions with nuclear transition densities. Calculations for $^{16}$O are presented for 200 and 433 MeV ejectile energies, corresponding to proposed experiments at MAMI and TJNAF, and for $^{12}$C at 70 and 270 MeV, corresponding to experiments at NIKHEF and MIT-Bates. The relative importance of charge exchange decreases as the ejectile energy increases, but remains significant for 200 MeV. Both proton and neutron knockout cross sections for large recoil momenta, $p_m > 300$ MeV/c, are substantially affected by inelastic couplings even at 433 MeV. Significant effects on the cross section for neutron knockout are also predicted at smaller recoil momenta, especially for low energies. Polarization transfer for proton knockout is insensitive to channel coupling, even for fairly low ejectile energies, but polarization transfer for neutron knockout retains nonnegligible sensitivity to channel coupling for energies up to about 200 MeV. The present results suggest that possible medium modifications of neutron and proton electromagnetic form factors for $Q^2 \gtrsim 0.5 (GeV/c)^2$ can be studied using recoil polarization with relatively little sensitivity due to final state interactions.Comment: Substantially revised version accepted by Phys. Rev. C; shortened to 49 pages including 21 figure

Generalized quantum Fokker-Planck, diffusion and Smoluchowski equations with true probability distribution functions

Traditionally, the quantum Brownian motion is described by Fokker-Planck or diffusion equations in terms of quasi-probability distribution functions, e.g., Wigner functions. These often become singular or negative in the full quantum regime. In this paper a simple approach to non-Markovian theory of quantum Brownian motion using {\it true probability distribution functions} is presented. Based on an initial coherent state representation of the bath oscillators and an equilibrium canonical distribution of the quantum mechanical mean values of their co-ordinates and momenta we derive a generalized quantum Langevin equation in $c$-numbers and show that the latter is amenable to a theoretical analysis in terms of the classical theory of non-Markovian dynamics. The corresponding Fokker-Planck, diffusion and the Smoluchowski equations are the {\it exact} quantum analogues of their classical counterparts. The present work is {\it independent} of path integral techniques. The theory as developed here is a natural extension of its classical version and is valid for arbitrary temperature and friction (Smoluchowski equation being considered in the overdamped limit).Comment: RevTex, 16 pages, 7 figures, To appear in Physical Review E (minor revision

Bulk-sensitive photoemission spectroscopy of A_2FeMoO_6 double perovskites (A=Sr, Ba)

Electronic structures of Sr_2FeMoO_6 (SFMO) and Ba_2FeMoO_6 (BFMO) double perovskites have been investigated using the Fe 2p->3d resonant photoemission spectroscopy (PES) and the Cooper minimum in the Mo 4d photoionization cross section. The states close to the Fermi level are found to have strongly mixed Mo-Fe t_{2g} character, suggesting that the Fe valence is far from pure 3+. The Fe 2p_{3/2} XAS spectra indicate the mixed-valent Fe^{3+}-Fe^{2+} configurations, and the larger Fe^{2+} component for BFMO than for SFMO, suggesting a kind of double exchange interaction. The valence-band PES spectra reveal good agreement with the LSDA+U calculation.Comment: 4 pages, 3 figure

Bulk Electronic structure of Na0.35_{0.35}CoO2_{2}.1.3H2_{2}O

High-energy (h$\nu$ = 5.95 keV) synchrotron Photoemission spectroscopy (PES) is used to study bulk electronic structure of Na$_{0.35}$CoO$_{2}$.1.3H$_{2}$O, the layered superconductor. In contrast to 3-dimensional doped Co oxides, Co $\it{2p}$ core level spectra show well-separated Co$^{3+}$ and Co$^{4+}$ ions. Cluster calculations suggest low spin Co$^{3+}$ and Co$^{4+}$ character, and a moderate on-site Coulomb correlation energy U$_{dd}\sim$3-5.5 eV. Photon dependent valence band PES identifies Co $\it{3d}$ and O $\it{2p}$ derived states, in near agreement with band structure calculations.Comment: 4 pages 4 figures Revised text added referenc

Enhancing the computation of distributed shortest paths on real dynamic networks

International audienceThe problem of finding and updating shortest paths in distributed networks is considered crucial in today's practical applications. In the recent past, there has been a renewed interest in devising new efficient distance-vector algorithms as an attractive alternative to link-state solutions for large-scale Ethernet networks, in which scalability and reliability are key issues or the nodes can have limited storage capabilities. In this paper we present Distributed Computation Pruning (DCP), a new technique, which can be combined with every distance-vector routing algorithm based on shortest paths, allowing to reduce the total number of messages sent by that algorithm and its space occupancy per node. To check its effectiveness, we combined DCP with DUAL (Diffuse Update ALgorithm), one of the most popular distance-vector algorithm in the literature, which is part of CISCO's widely used EIGRP protocol, and with the recently introduced LFR (Loop Free Routing) which has been shown to have good performances on real networks. We give experimental evidence that these combinations lead to a significant gain both in terms of number of messages sent and memory requirements per node