Dirac quasinormal frequencies of Reissner-Nordstr\"om black hole in Anti-de Sitter spacetime

The quasinormal modes (QNMs) of Dirac field perturbations of a Reissner-Nordstr\"om black hole in an asymptotically Anti-de Sitter spacetime are investigated. We find that both the real and imaginary parts of the fundamental quasinormal frequencies for large black holes are the linear functions of the Hawking temperature, and the slope of the lines for the real parts decreases while that for the magnitude of the imaginary parts increases as the black hole charge increases. According to the Anti-de Sitter/Conformal Field Theory (AdS/CFT) correspondence, the fact shows that different charge presents different time scale in three-dimensional CFT. Another interesting result is that the quasinormal frequencies become evenly spaced for high overtone number, and in the spacing expressions the real part decreases while the magnitude of the imaginary part increases as the charge increases. We also study the relation between quasinormal frequencies and angular quantum number and find that the real part increases while the magnitude of the imaginary part decreases as the angular quantum number increases.Comment: 16 pages, 4 figure

Jetset: selecting the optimal microarray probe set to represent a gene

<p>Abstract</p> <p>Background</p> <p>Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver inconsistent or even contradictory measurements. Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be a nontrivial but essential task.</p> <p>Results</p> <p>We developed scoring methods to assess each probe set for specificity, splice isoform coverage, and robustness against transcript degradation. We used these scores to select a single representative probe set for each gene, thus creating a simple one-to-one mapping between gene and probe set. To test this method, we evaluated concordance between protein measurements and gene expression values, and between sets of genes whose expression is known to be correlated. For both test cases, we identified genes that were nominally detected by multiple probe sets, and we found that the probe set chosen by our method showed stronger concordance.</p> <p>Conclusions</p> <p>This method provides a simple, unambiguous mapping to allow assessment of the expression levels of specific genes of interest.</p

Holographic Superconductors in Gauss-Bonnet gravity with Born-Infeld electrodynamics

We investigate the holographic superconductors in Gauss-Bonnet gravity with Born-Infeld electrodynamics. We find that the Gauss-Bonnet constant, the model parameters and the Born-Infeld coupling parameter will affect the formation of the scalar hair, the transition point of the phase transition from the second order to the first order, and the relation connecting the gap frequency in conductivity with the critical temperature. The combination of the Gauss-Bonnet gravity and the Born-Infeld electrodynamics provides richer physics in the phase transition and the condensation of the scalar hair.Comment: 11 pages, 2 figures, 2 table

Degradation of non-maximal entanglement of scalar and Dirac fields in non-inertial frames

The entanglement between two modes of the free scalar and Dirac fields as seen by two relatively accelerated observers has been investigated. It is found that the same initial entanglement for an initial state parameter $\alpha$ and its "normalized partner" $\sqrt{1-\alpha^{2}}$ will be degraded by the Unruh effect along two different trajectories except for the maximally entangled state, which just shows the inequivalence of the quantization for a free field in the Minkowski and Rindler coordinates. In the infinite acceleration limit the state doesn't have the distillable entanglement for any $\alpha$ for the scalar field but always remains entangled to a degree which is dependent of $\alpha$ for the Dirac field. It is also interesting to note that in this limit the mutual information equals to just half of the initially mutual information, which is independent of $\alpha$ and the type of field.Comment: 9 pages, 4 figure

Holographic Superconductors with Power-Maxwell field

With the Sturm-Liouville analytical and numerical methods, we investigate the behaviors of the holographic superconductors by introducing a complex charged scalar field coupled with a Power-Maxwell field in the background of $d$-dimensional Schwarzschild AdS black hole. We note that the Power-Maxwell field takes the special asymptotical solution near boundary which is different from all known cases. We find that the larger power parameter $q$ for the Power-Maxwell field makes it harder for the scalar hair to be condensated. We also find that, for different $q$, the critical exponent of the system is still 1/2, which seems to be an universal property for various nonlinear electrodynamics if the scalar field takes the form of this paper.Comment: 14 pages, 1 figure, and 2 table

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response

Genome scale expression profiling of human tumor samples is likely to yield improved cancer treatment decisions. However, identification of clinically predictive or prognostic classifiers can be challenging when a large number of genes are measured in a small number of tumors.Journal ArticleResearch Support, N.I.H. ExtramuralResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

The vast majority of disease-associated single nucleotide polymorphisms (SNPs) mapped by genome-wide association studies (GWAS) are located in the non-protein coding genome, but establishing the functional and mechanistic roles of these sequence variants has proven challenging. Here, we describe a general pipeline in which candidate functional SNPs are first evaluated by fine-mapping, epigenomic profiling, and epigenome editing and then interrogated for causal function by using genome editing to create isogenic cell lines. To validate this approach, we analyzed the 6q22.1 prostate cancer risk locus and identified rs339331 as the top scoring SNP. Epigenome editing confirmed that rs339331 possessed regulatory potential. Using transcription activator-like effector nuclease (TALEN)-mediated genome-editing, we created a panel of isogenic 22Rv1 prostate cancer cell lines representing all three genotypes (TT, TC, CC) at rs339331. Introduction of the “T” risk allele increased transcription of the RFX6 gene, increased HOXB13 binding at the rs339331 region, and increased deposition of the enhancer-associated H3K4me2 histone mark at the rs339331 region. The cell lines also differed in cellular morphology and adhesion, and pathway analysis of differentially expressed genes suggested an influence of androgens. In summary, we have developed and validated a widely accessible approach to establish functional causality for non-coding sequence variants identified by GWAS

Bayesian Estimation of Pneumonia Etiology: Epidemiologic Considerations and Applications to the Pneumonia Etiology Research for Child Health Study.

In pneumonia, specimens are rarely obtained directly from the infection site, the lung, so the pathogen causing infection is determined indirectly from multiple tests on peripheral clinical specimens, which may have imperfect and uncertain sensitivity and specificity, so inference about the cause is complex. Analytic approaches have included expert review of case-only results, case-control logistic regression, latent class analysis, and attributable fraction, but each has serious limitations and none naturally integrate multiple test results. The Pneumonia Etiology Research for Child Health (PERCH) study required an analytic solution appropriate for a case-control design that could incorporate evidence from multiple specimens from cases and controls and that accounted for measurement error. We describe a Bayesian integrated approach we developed that combined and extended elements of attributable fraction and latent class analyses to meet some of these challenges and illustrate the advantage it confers regarding the challenges identified for other methods

Differential modes of DNA binding by mismatch uracil DNA glycosylase from Escherichia coli: implications for abasic lesion processing and enzyme communication in the base excision repair pathway

Mismatch uracil DNA glycosylase (Mug) from Escherichia coli is an initiating enzyme in the base-excision repair pathway. As with other DNA glycosylases, the abasic product is potentially more harmful than the initial lesion. Since Mug is known to bind its product tightly, inhibiting enzyme turnover, understanding how Mug binds DNA is of significance when considering how Mug interacts with downstream enzymes in the base-excision repair pathway. We have demonstrated differential binding modes of Mug between its substrate and abasic DNA product using both band shift and fluorescence anisotropy assays. Mug binds its product cooperatively, and a stoichiometric analysis of DNA binding, catalytic activity and salt-dependence indicates that dimer formation is of functional significance in both catalytic activity and product binding. This is the first report of cooperativity in the uracil DNA glycosylase superfamily of enzymes, and forms the basis of product inhibition in Mug. It therefore provides a new perspective on abasic site protection and the findings are discussed in the context of downstream lesion processing and enzyme communication in the base excision repair pathway