31 research outputs found
Analysis of Gene Sets Based on the Underlying Regulatory Network
Networks are often used to represent the interactions among genes and proteins. These interactions are known to play an important role in vital cell functions and should be included in the analysis of genes that are differentially expressed. Methods of gene set analysis take advantage of external biological information and analyze a priori defined sets of genes. These methods can potentially preserve the correlation among genes; however, they do not directly incorporate the information about the gene network. In this paper, we propose a latent variable model that directly incorporates the network information. We then use the theory of mixed linear models to present a general inference framework for the problem of testing the significance of subnetworks. Several possible test procedures are introduced and a network based method for testing the changes in expression levels of genes as well as the structure of the network is presented. The performance of the proposed method is compared with methods of gene set analysis using both simulation studies, as well as real data on genes related to the galactose utilization pathway in yeast.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78147/1/cmb.2008.0081.pd
Numerical evidence for `multi-scalar stars'
We present a class of general relativistic soliton-like solutions composed of
multiple minimally coupled, massive, real scalar fields which interact only
through the gravitational field. We describe a two-parameter family of
solutions we call ``phase-shifted boson stars'' (parameterized by central
density rho_0 and phase delta), which are obtained by solving the ordinary
differential equations associated with boson stars and then altering the phase
between the real and imaginary parts of the field. These solutions are similar
to boson stars as well as the oscillating soliton stars found by Seidel and
Suen [E. Seidel and W.M. Suen, Phys. Rev. Lett. 66, 1659 (1991)]; in
particular, long-time numerical evolutions suggest that phase-shifted boson
stars are stable. Our results indicate that scalar soliton-like solutions are
perhaps more generic than has been previously thought.Comment: Revtex. 4 pages with 4 figures. Submitted to Phys. Rev.
Evolution of the Schr\"odinger--Newton system for a self--gravitating scalar field
Using numerical techniques, we study the collapse of a scalar field
configuration in the Newtonian limit of the spherically symmetric
Einstein--Klein--Gordon (EKG) system, which results in the so called
Schr\"odinger--Newton (SN) set of equations. We present the numerical code
developed to evolve the SN system and topics related, like equilibrium
configurations and boundary conditions. Also, we analyze the evolution of
different initial configurations and the physical quantities associated to
them. In particular, we readdress the issue of the gravitational cooling
mechanism for Newtonian systems and find that all systems settle down onto a
0--node equilibrium configuration.Comment: RevTex file, 19 pages, 26 eps figures. Minor changes, matches version
to appear in PR
Classical and Quantum Decay of Oscillatons: Oscillating Self-Gravitating Real Scalar Field Solitons
The oscillating gravitational field of an oscillaton of finite mass M causes
it to lose energy by emitting classical scalar field waves, but at a rate that
is non-perturbatively tiny for small GMm, where m is the scalar field mass:
d(GM)/dt ~ -3797437.776333015 e^[-39.433795197160163/(GMm)]/(GMm)^2.
Oscillatons also decay by the quantum process of the annihilation of scalarons
into gravitons, which is only perturbatively small in GMm, giving by itself
d(GM)/dt ~ - 0.008513223934732692 G m^2 (GMm)^5. Thus the quantum decay is
faster than the classical one for Gmm < 39.4338/[ln(1/Gm^2)}-7ln(GMm)+19.9160].
The time for an oscillaton to decay away completely into free scalarons and
gravitons is ~ 2/(G^5 m^11) ~ 10^324 yr (1 meV/m)^11. Oscillatons of more than
one real scalar field of the same mass generically asymptotically approach a
static-geometry U(1) boson star configuration with GMm = GM_0 m, at the rate
d(GM/c^3)/dt ~ [(C/(GMm)^4)e^{-alpha/(GMm)}+Q(m/m_{Pl})^2(GMm)^3]
[(GMm)^2-(GM_0 m)^2], with GM_0 m depending on the magnitudes and relative
phases of the oscillating fields, and with the same constants C, alpha, and Q
given numerically above for the single-field case that is equivalent to GM_0 m
= 0.Comment: 75 pages, LaTe
Cellular and molecular mechanisms involved in the neurotoxicity of opioid and psychostimulant drugs
Substance abuse and addiction are the most costly of all the neuropsychiatric disorders. In the last decades, much progress has been achieved in understanding the effects of the drugs of abuse in the brain. However, efficient treatments that prevent relapse have not been developed. Drug addiction is now considered a brain disease, because the abuse of drugs affects several brain functions. Neurological impairments observed in drug addicts may reflect drug-induced neuronal dysfunction and neurotoxicity. The drugs of abuse directly or indirectly affect neurotransmitter systems, particularly dopaminergic and glutamatergic neurons. This review explores the literature reporting cellular and molecular alterations reflecting the cytotoxicity induced by amphetamines, cocaine and opiates in neuronal systems. The neurotoxic effects of drugs of abuse are often associated with oxidative stress, mitochondrial dysfunction, apoptosis and inhibition of neurogenesis, among other mechanisms. Understanding the mechanisms that underlie brain dysfunction observed in drug-addicted individuals may contribute to improve the treatment of drug addiction, which may have social and economic consequences.http://www.sciencedirect.com/science/article/B6SYS-4S50K2J-1/1/7d11c902193bfa3f1f57030572f7034