Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.
Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from “seed” lists of human Entrez gene names. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is available at http://actin.pharm.mssm.edu/genes2networks.
Genes2Network is a powerful web-based software application tool that can help experimental biologists to interpret high-throughput experimental results used in genomics and proteomics studies where the output of these experiments is a list of significantly changing genes or proteins. The system can be used to find relationships between nodes from the seed list, and predict novel nodes that play a key role in a common function

Numerical solution of the nonlinear evolution equation at small x with impact parameter and beyond the LL approximation

Nonlinear evolution equation at small x with impact parameter dependence is analyzed numerically. Saturation scales and the radius of expansion in impact parameter are extracted as functions of rapidity. Running coupling is included in this evolution, and it is found that the solution is sensitive to the infrared regularization. Kinematical effects beyond leading logarithmic approximation are taken partially into account by modifying the kernel which includes the rapidity dependent cuts. While the local nonlinear evolution is not very sensitive to these effects, the kinematical constraints cannot be neglected in the evolution with impact parameter.Comment: 22 pages, 37 figures, RevTe

Slow magnetic dynamics and hysteresis loops of a bulk ferromagnet

Magnetic dynamics of a bulk ferromagnet, a new single crystalline compound Co7(TeO3)4Br6, was studied by ac susceptibility and the related techniques. Very large Arrhenius activation energy of 17.2 meV (201 K) and long attempt time (2x10^(-4)s) span the full spectrum of magnetic dynamics inside a convenient frequency window, offering a rare opportunity for general studies of magnetic dynamics. Within the experimental window the ac susceptibility data build almost ideally semicircular Cole-Cole plots. Comprehensive study of experimental dynamic hysteresis loops of the compound is presented and interpreted within a simple thermal-activation-assisted spin lattice relaxation model for spin reversal. Quantitative agreement between the experimental results and the model's prediction for dynamic coercive field is achieved by assuming the central physical quantity, the Debye relaxation rate, to depend on frequency, as well as on the applied field strength and sample temperature. Cross-over between minor- to major hysteresis loops is carefully analyzed. Low-frequency limitations of the model, relying on domain wall pinning effects, are experimentally detected and appropriately discussed.Comment: A paragraph on dynamical-hysteresis assymetry added, text partially revised; Accepted in Physical Review

Ferrimagnetism of the magnetoelectric compound Cu2_2OSeO3_3 probed by 77^{77}Se NMR

We present a thorough $^{77}$Se NMR study of a single crystal of the magnetoelectric compound Cu$_2$OSeO$_3$. The temperature dependence of the local electronic moments extracted from the NMR data is fully consistent with a magnetic phase transition from the high-T paramagnetic phase to a low-T ferrimagnetic state with 3/4 of the Cu$^{2+}$ ions aligned parallel and 1/4 aligned antiparallel to the applied field of 14.09 T. The transition to this 3up-1down magnetic state is not accompanied by any splitting of the NMR lines or any abrupt modification in their broadening, hence there is no observable reduction of the crystalline symmetry from its high-T cubic \textit{P}2$_1$3 space group. These results are in agreement with high resolution x-ray diffraction and magnetization data on powder samples reported previously by Bos {\it et al.} [Phys. Rev. B, {\bf 78}, 094416 (2008)]. We also develop a mean field theory description of the problem based on a microscopic spin Hamiltonian with one antiferromagnetic ($J_\text{afm}\simeq 68$ K) and one ferromagnetic ($J_\text{fm}\simeq -50$ K) nearest-neighbor exchange interaction

Small x nonlinear evolution with impact parameter and the structure function data

The nonlinear Balitsky-Kovchegov equation at small x is solved numerically, incorporating impact parameter dependence. Confinement is modeled by including effective gluon mass in the dipole evolution kernel, which regulates the splitting of dipoles with large sizes. It is shown, that the solution is sensitive to different implementations of the mass in the kernel. In addition, running coupling effects are taken into account in this analysis. Finally, a comparison of the calculations using the dipole framework with the inclusive data from HERA on the structure functions F2 and FL is performed.Comment: 19 pages, 11 figures. Minor revision. One reference added, two figures update

Hunting Local Mixmaster Dynamics in Spatially Inhomogeneous Cosmologies

Heuristic arguments and numerical simulations support the Belinskii et al (BKL) claim that the approach to the singularity in generic gravitational collapse is characterized by local Mixmaster dynamics (LMD). Here, one way to identify LMD in collapsing spatially inhomogeneous cosmologies is explored. By writing the metric of one spacetime in the standard variables of another, signatures for LMD may be found. Such signatures for the dynamics of spatially homogeneous Mixmaster models in the variables of U(1)-symmetric cosmologies are reviewed. Similar constructions for U(1)-symmetric spacetimes in terms of the dynamics of generic $T^2$-symmetric spacetime are presented.Comment: 17 pages, 5 figures. Contribution to CQG Special Issue "A Spacetime Safari: Essays in Honour of Vincent Moncrief

A new route towards uniformly functionalized single-layer graphene

It is shown, by DFT calculations, that the uniform functionalization of upper layer of graphite by hydrogen or fluorine does not change essentially its bonding energy with the underlying layers, whereas the functionalization by phenyl groups decreases the bonding energy by a factor of approximately ten. This means that the functionalized monolayer in the latter case can be easily separated by mild sonication. According to our computational results, such layers can be cleaned up to pure graphene, as well as functionalized further up to 25% coverage, without essential difficulties. The energy gap within the interval from 0.5 to 3 eV can be obtained by such one-side funtionalization using different chemical species.Comment: 15 pages, 3 figures, to appear in J. Phys. D: Applied Physic

The canonical 8-form on manifolds with holonomy group Spin(9)

An explicit expression of the canonical 8-form on a Riemannian manifold with a Spin(9)-structure, in terms of the nine local symmetric involutions involved, is given. The list of explicit expressions of all the canonical forms related to Berger's list of holonomy groups is thus completed. Moreover, some results on Spin(9)-structures as G-structures defined by a tensor and on the curvature tensor of the Cayley planes, are obtained