Linear fuzzy gene network models obtained from microarray data by exhaustive search

BACKGROUND: Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are needed to interpret the resulting large and complex data sets. Rationally designed perturbations (e.g., gene knock-outs) can be used to iteratively refine hypothetical models, suggesting an approach for high-throughput biological system analysis. We introduce an approach to gene network modeling based on a scalable linear variant of fuzzy logic: a framework with greater resolution than Boolean logic models, but which, while still semi-quantitative, does not require the precise parameter measurement needed for chemical kinetics-based modeling. RESULTS: We demonstrated our approach with exhaustive search for fuzzy gene interaction models that best fit transcription measurements by microarray of twelve selected genes regulating the yeast cell cycle. Applying an efficient, universally applicable data normalization and fuzzification scheme, the search converged to a small number of models that individually predict experimental data within an error tolerance. Because only gene transcription levels are used to develop the models, they include both direct and indirect regulation of genes. CONCLUSION: Biological relationships in the best-fitting fuzzy gene network models successfully recover direct and indirect interactions predicted from previous knowledge to result in transcriptional correlation. Fuzzy models fit on one yeast cell cycle data set robustly predict another experimental data set for the same system. Linear fuzzy gene networks and exhaustive rule search are the first steps towards a framework for an integrated modeling and experiment approach to high-throughput "reverse engineering" of complex biological systems

Vertex-corrected tunneling inversion in superconductors: Pb

The McMillan-Rowell tunneling inversion program, which extracts the electron-phonon spectral function $\alpha^2F(\Omega)$ and the Coulomb pseudopotential $\mu^*$ from experimental tunneling data, is generalized to include the lowest-order vertex correction. We neglect the momentum dependence of the electron-phonon matrix elements, which is equivalent to using a local approximation. The perturbation theory is performed on the imaginary axis and then an exact analytic continuation is employed to produce the density of states on the real axis. Comparison is made with the experimental data for Pb.Comment: 14 pages, typeset in ReVTeX, including three encapsulated postscript figure

Density-functional-based predictions of Raman and IR spectra for small Si clusters

We have used a density-functional-based approach to study the response of silicon clusters to applied electric fields. For the dynamical response, we have calculated the Raman activities and infrared (IR) intensities for all of the vibrational modes of several clusters (SiN with N=3-8, 10, 13, 20, and 21) using the local density approximation (LDA). For the smaller clusters (N=3-8) our results are in good agreement with previous quantum-chemical calculations and experimental measurements, establishing that LDA-based IR and Raman data can be used in conjunction with measured spectra to determine the structure of clusters observed in experiment. To illustrate the potential of the method for larger clusters, we present calculated IR and Raman data for two low-energy isomers of Si10 and for the lowest-energy structure of Si13 found to date. For the static response, we compare our calculated polarizabilities for N=10, 13, 20, and 21 to recent experimental measurements. The calculated results are in rough agreement with experiment, but show less variation with cluster size than the measurements. Taken together, our results show that LDA calculations can offer a powerful means for establishing the structures of experimentally fabricated clusters and nanoscale systems

The Effective Particle-Hole Interaction and the Optical Response of Simple Metal Clusters

Following Sham and Rice [L. J. Sham, T. M. Rice, Phys. Rev. 144 (1966) 708] the correlated motion of particle-hole pairs is studied, starting from the general two-particle Greens function. In this way we derive a matrix equation for eigenvalues and wave functions, respectively, of the general type of collective excitation of a N-particle system. The interplay between excitons and plasmons is fully described by this new set of equations. As a by-product we obtain - at least a-posteriori - a justification for the use of the TDLDA for simple-metal clusters.Comment: RevTeX, 15 pages, 5 figures in uufiles format, 1 figure avaible from [email protected]

Electronic interactions in fullerene spheres

The electron-phonon and Coulomb interactions inC$_{60}$, and larger fullerene spheres are analyzed. The coupling between electrons and intramolecular vibrations give corrections $\sim 1 - 10$ meV to the electronic energies for C$_{60}$, and scales as $R^{-4}$ in larger molecules. The energies associated with electrostatic interactions are of order $\sim 1 - 4$ eV, in C$_{60}$ and scale as $R^{-1}$. Charged fullerenes show enhanced electron-phonon coupling, $\sim 10$ meV, which scales as $R^{-2}$. Finally, it is argued that non only C$_{60}^{-}$, but also C$_{60}^{--}$ are highly polarizable molecules. The polarizabilities scale as $R^3$ and $R^4$, respectively. The role of this large polarizability in mediating intermolecular interactions is also discussed.Comment: 12 pages. No figure

Plasmon Lifetime in K: A Case Study of Correlated Electrons in Solids Amenable to Ab Initio Theory

On the basis of a new ab initio, all-electron response scheme, formulated within time-dependent density-functional theory, we solve the puzzle posed by the anomalous dispersion of the plasmon linewidth in K. The key damping mechanism is shown to be decay into particle-hole pairs involving empty states of d-symmetry. While the effect of many-particle correlations is small, the correlations built into the "final-state" -d-bands play an important, and novel, role ---which is related to the phase-space complexity associated with these flat bands. Our case study of plasmon lifetime in K illustrates the importance of ab initio paradigms for the study of excitations in correlated-electron systems.Comment: 12 pages, 4 figures, for html browsing see http://web.utk.edu/~weik

Stone-Wales Transformation Paths in Fullerene C60

The mechanisms of formation of a metastable defect isomer of fullerene C60 due to the Stone-Wales transformation are theoretically studied. It is demonstrated that the paths of the "dynamic" Stone-Wales transformation at a high sufficient for overcoming potential barriers) temperature can differ from the two "adiabatic" transformation paths discussed in the literature. This behavior is due to the presence of a great near-flat segment of the potential-energy surface in the neighborhood of metastable states. Besides, the sequence of rupture and formation of interatomic bonds is other than that in the case of the adiabatictransformation.Comment: 10 pages, 6 figure

How to Identify Disadvantage: Taking the Envy Test Seriously

In this paper, I am concerned with the comparative disadvantage an individual suffers in having less valuable opportunities than another individual. The dominant approach with respect to this topic proceeds by identifying a metric by which to determine whether an individual?s opportunities are less valuable than another?s. Let?s call this the Metric Test. However, there is another way in which to proceed. Rather than appealing to a metric by which to determine disadvantage, we could instead allow an individual to determine for herself whether or not she is disadvantaged. On the version of this view that I shall defend, we should treat an individual as disadvantaged if and only if that individual envies another?s opportunities. Let?s call this the Envy Test. My overall aim is to illuminate the appeal of the Envy Test and, in particular, to explain its superiority over the Metric Test

MRI scans significantly change target coverage decisions in radical radiotherapy for prostate cancer

INTRODUCTION: Conventional clinical staging for prostate cancer has many limitations. This study evaluates the impact of adding MRI scans to conventional clinical staging for guiding decisions about radiotherapy target coverage. METHODS: This was a retrospective review of 115 patients who were treated between February 2002 and September 2005 with radical radiotherapy for prostate cancer. All patients had MRI scans approximately 2 weeks before the initiation of radiotherapy. The T stage was assessed by both conventional clinical methods (cT-staging) as well as by MRI (mT-staging). The radiotherapy target volumes were determined first based on cT-staging and then taking the additional mT staging into account. The number of times extracapsular extension or seminal vesicle invasion was incorporated into target volumes was quantified based on both cT-staging and the additional mT-staging. RESULTS: Extracapsular extension was incorporated into target volumes significantly more often with the addition of mT-staging (46 patients (40%) ) compared with cT-staging alone (37 patients (32%) ) (P = 0.002). Seminal vesicle invasion was incorporated into target volumes significantly more often with the addition of mT-staging (21 patients (18%) ) compared with cT-staging alone (three patients (3%) ) (P < 0.001). A total of 23 patients (20%) had changes to their target coverage based on the mT-staging. CONCLUSIONS: MRI scans can significantly change decisions about target coverage in radical radiotherapy for prostate cancer.Joe H. Chang, Daryl Lim Joon, Brandon T. Nguyen, Chee-Yan Hiew, Stephen Esler, David Angus, Michael Chao, Morikatsu Wada, George Quong, and Vincent Kho

Beyond Eliashberg superconductivity in MgB2: anharmonicity, two-phonon scattering, and multiple gaps

Density-functional calculations of the phonon spectrum and electron-phonon coupling in MgB$_2$ are presented. The $E_{2g}$ phonons, which involve in-plane B displacements, couple strongly to the $p_{x,y}$ electronic bands. The isotropic electron-phonon coupling constant is calculated to be about 0.8. Allowing for different order parameters in different bands, the superconducting $\lambda$ in the clean limit is calculated to be significantly larger. The $E_{2g}$ phonons are strongly anharmonic, and the non-linear contribution to the coupling between the $E_{2g}$ modes and the p$_{x,y}$ bands is significant.Comment: 4 pages, 3 figure