Previously Unidentified Changes in Renal Cell Carcinoma Gene Expression Identified by Parametric Analysis of Microarray Data

BACKGROUND. Renal cell carcinoma is a common malignancy that often presents as a metastatic-disease for which there are no effective treatments. To gain insights into the mechanism of renal cell carcinogenesis, a number of genome-wide expression profiling studies have been performed. Surprisingly, there is very poor agreement among these studies as to which genes are differentially regulated. To better understand this lack of agreement we profiled renal cell tumor gene expression using genome-wide microarrays (45,000 probe sets) and compare our analysis to previous microarray studies. METHODS. We hybridized total RNA isolated from renal cell tumors and adjacent normal tissue to Affymetrix U133A and U133B arrays. We removed samples with technical defects and removed probesets that failed to exhibit sequence-specific hybridization in any of the samples. We detected differential gene expression in the resulting dataset with parametric methods and identified keywords that are overrepresented in the differentially expressed genes with the Fisher-exact test. RESULTS. We identify 1,234 genes that are more than three-fold changed in renal tumors by t-test, 800 of which have not been previously reported to be altered in renal cell tumors. Of the only 37 genes that have been identified as being differentially expressed in three or more of five previous microarray studies of renal tumor gene expression, our analysis finds 33 of these genes (89%). A key to the sensitivity and power of our analysis is filtering out defective samples and genes that are not reliably detected. CONCLUSIONS. The widespread use of sample-wise voting schemes for detecting differential expression that do not control for false positives likely account for the poor overlap among previous studies. Among the many genes we identified using parametric methods that were not previously reported as being differentially expressed in renal cell tumors are several oncogenes and tumor suppressor genes that likely play important roles in renal cell carcinogenesis. This highlights the need for rigorous statistical approaches in microarray studies.National Institutes of Healt

Remarks on monopole charge properties within the Generalized Coherent State Model

The Generalized Coherent State Model, proposed previously for a unified description of magnetic and electric collective properties of nuclear systems, is used to study the ground state band charge density as well as the E0 transitions from $0^+_{\beta}$ to $0^+_g$. The influence of the nuclear deformation and of angular momentum projection on the charge density is investigated. The monopole transition amplitude has been calculated for ten nuclei. The results are compared with some previous theoretical studies and with the available experimental data. Our results concerning angular momentum projection are consistent with those of previous microscopic calculations for the ground state density. The calculations for the E0 transitions agree quite well with the experimental data. Issues like how the shape transitions or shape coexistence are reflected in the $\rho(E0)$ behavior are also addressed.Comment: 32 pages, 7 figure

Constraining H0 from Chandra Observations of Q0957+561

We report the detection of the lens cluster of the gravitational lens (GL) system Q0957+561 from a deep observation with the Advanced CCD Imaging Spectrometer on-board the Chandra X-ray Observatory. Intracluster X-ray emission is found to be centered 4.3 +/- 1.3 arcsec east and 3.5(-0.6,+1.3) arcsec north of image B, nearer than previous estimates. Its spectrum can be modeled well with a thermal plasma model consistent with the emission originating from a cluster at a redshift of 0.36. Our best-fit estimates of the cluster temperature of T_e = 2.09(-0.54,+0.83) keV (90 percent confidence) and mass distribution of the cluster are used to derive the convergence parameter kappa, the ratio of the cluster surface mass density to the critical density required for lensing. We estimate the convergence parameter at the location of the lensed images A and B to be kappa_A = 0.22(+0.14,-0.07) and kappa_B = 0.21(+0.12,-0.07), respectively (90 percent confidence levels). The observed cluster center, mass distribution and convergence parameter kappa provide additional constraints to lens models of this system. Our new results break a mass-sheet degeneracy in GL models of this system and provide better constraints of ~ 29 percent (90 percent confidence levels) on the Hubble constant. We also present results from the detection of the most distant X-ray jet (z = 1.41) detected to date. The jet extends approximately 8 arcsec NE of image A and three knots are resolved along the X-ray jet with flux densities decreasing with distance from the core. The observed radio and optical flux densities of the knots are fitted well with a synchrotron model and the X-ray emission is modeled well with inverse Compton scattering of Cosmic Microwave Background photons by synchrotron-emitting electrons in the jet.Comment: 18 pages, includes 7 figures, Accepted for publication in Ap

Economic inequalities in the effectiveness of a primary care intervention for depression and suicidal ideation.

BACKGROUND: Economic disadvantage is associated with depression and suicide. We sought to determine whether economic disadvantage reduces the effectiveness of depression treatments received in primary care. METHODS: We conducted differential-effects analyses of the Prevention of Suicide in Primary Care Elderly: Collaborative Trial, a primary-care-based randomized, controlled trial for late-life depression and suicidal ideation conducted between 1999 and 2001, which included 514 patients with major depression or clinically significant minor depression. RESULTS: The intervention effect, defined as change in depressive symptoms from baseline, was stronger among persons reporting financial strain at baseline (differential effect size = -4.5 Hamilton Depression Rating Scale points across the study period [95% confidence interval = -8.6 to -0.3]). We found similar evidence for effect modification by neighborhood poverty, although the intervention effect weakened after the initial 4 months of the trial for participants residing in poor neighborhoods. There was no evidence of substantial differences in the effectiveness of the intervention on suicidal ideation and depression remission by economic disadvantage. CONCLUSIONS: Economic conditions moderated the effectiveness of primary-care-based treatment for late-life depression. Financially strained individuals benefited more from the intervention; we speculate this was because of the enhanced treatment management protocol, which led to a greater improvement in the care received by these persons. People living in poor neighborhoods experienced only temporary benefit from the intervention. Thus, multiple aspects of economic disadvantage affect depression treatment outcomes; additional work is needed to understand the underlying mechanisms

Deep Imaging of AXJ2019+112: The Luminosity of a ``Dark Cluster''

We detect a distant cluster of galaxies centered on the QSO lens and luminous X-ray source AXJ2019+112, a.k.a. ``The Dark Cluster'' (Hattori et al 1997). Using deep V,I Keck images and wide-field K_s imaging from the NTT, a tight red sequence of galaxies is identified within a radius of 0.2 h^{-1} Mpc of the known z=1.01 elliptical lensing galaxy. The sequence, which includes the central elliptical galaxy, has a slope in good agreement with the model predictions of Kodama et al (1998) for z~1. We estimate the integrated rest-frame luminosity of the cluster to be L_V > 3.2 x 10^{11}h^{-2}L_{\sun} (after accounting for significant extinction at the low latitude of this field), more than an order of magnitude higher than previous estimates. The central region of the cluster is deconvolved using the technique of Magain, Courbin & Sohy (1998), revealing a thick central arc coincident with an extended radio source. All the observed lensing features are readily explained by differential magnification of a radio loud AGN by a shallow elliptical potential. The QSO must lie just outside the diamond caustic, producing two images, and the arc is a highly magnified image formed from a region close to the center of the host galaxy, projecting inside the caustic. The mass--to--light ratio within an aperture of 0.4 h ^{-1} Mpc is M_x/L_V= 224^{+112}_{-78}h(M/L_V)_{\sun}, using the X-ray temperature. The strong lens model yields a compatible value, M/L_V= 372^{+94}_{-94}h(M/L_V)_{\sun}, whereas an independent weak lensing analysis sets an upper limit of M/L_V <520 h(M/L_V)_{\sun}, typical of massive clusters.Comment: AAS Latex format, 24 pages, 9 figures. Fig 1a,b available at http://astro.berkeley.edu/~benitezn/cluster.html . Submitted to ApJ on August 15t

Macroscopic models for superconductivity

This paper reviews the derivation of some macroscopic models for superconductivity and also some of the mathematical challenges posed by these models. The paper begins by exploring certain analogies between phase changes in superconductors and those in solidification and melting. However, it is soon found that there are severe limitations on the range of validity of these analogies and outside this range many interesting open questions can be posed about the solutions to the macroscopic models

Anharmonic double-phonon excitations in the interacting boson model

Double-$\gamma$ vibrations in deformed nuclei are analyzed in the context of the interacting boson model. A simple extension of the original version of the model towards higher-order interactions is required to explain the observed anharmonicities of nuclear vibrations. The influence of three- and four-body interactions on the moments of inertia of ground- and $\gamma$-bands, and on the relative position of single-$\gamma$ and double-$\gamma$ bands is studied in detail. As an example of a realistic calculation, spectra and transitions of the highly $\gamma$-anharmonic nuclei $^{164}$Dy, $^{166}$Er, and $^{168}$Er are interpreted in this approach.Comment: 38 pages, TeX (ReVTeX). 15 ps figures. Submitted to Phys. Rev.

Force distributions in a triangular lattice of rigid bars

We study the uniformly weighted ensemble of force balanced configurations on a triangular network of nontensile contact forces. For periodic boundary conditions corresponding to isotropic compressive stress, we find that the probability distribution for single-contact forces decays faster than exponentially. This super-exponential decay persists in lattices diluted to the rigidity percolation threshold. On the other hand, for anisotropic imposed stresses, a broader tail emerges in the force distribution, becoming a pure exponential in the limit of infinite lattice size and infinitely strong anisotropy.Comment: 11 pages, 17 figures Minor text revisions; added references and acknowledgmen