Identification of Novel Reference Genes Based on MeSH Categories

Cataloged from PDF version of article.Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds. © 2014 Ersahin et al

The New Fat Higgs: Slimmer and More Attractive

In this paper we increase the MSSM tree level higgs mass bound to a value that is naturally larger than the LEP-II search constraint by adding to the superpotential a $\lambda S H_{u}H_{d}$ term, as in the NMSSM, and UV completing with new strong dynamics {\it before} $\lambda$ becomes non-perturbative. Unlike other models of this type the higgs fields remain elementary, alleviating the supersymmetric fine-tuning problem while maintaining unification in a natural way.Comment: 14 pages and 2 figures. Added references and updated argument about constraints from reheating temperatur

Evidence for a dynamical ground state in the frustrated pyrohafnate Tb2Hf2O7

We report the physical properties of Tb2Hf2O7 based on ac magnetic susceptibility \chi_ac(T), dc magnetic susceptibility \chi(T), isothermal magnetization M(H), and heat capacity C_p(T) measurements combined with muon spin relaxation (\muSR) and neutron powder diffraction measurements. No evidence for long-range magnetic order is found down to 0.1 K. However, \chi_ac(T) data present a frequency-dependent broad peak (near 0.9 K at 16 Hz) indicating slow spin dynamics. The slow spin dynamics is further evidenced from the \muSR data (characterized by a stretched exponential behavior) which show persistent spin fluctuations down to 0.3 K. The neutron powder diffraction data collected at 0.1 K show a broad peak of magnetic origin (diffuse scattering) but no magnetic Bragg peaks. The analysis of the diffuse scattering data reveals a dominant antiferromagnetic interaction in agreement with the negative Weiss temperature. The absence of long-range magnetic order and the presence of slow spin dynamics and persistent spin fluctuations together reflect a dynamical ground state in Tb2Hf2O7.Comment: 11 pages and 8 figure

Factors affecting pain and fatigue in females with chronic widespread pain

Purpose: This study was conducted to investigate factors related to pain intensity and global fatigue in females with Chronic Widespread Pain (CWP). Material and methods: One hundred four patients with CWP were included. The mean age was 40.28±10.82 years. Both Pain intensity and global fatigue were assessed using a Visual Analogue Scale (VAS). The Hospital Anxiety and Depression Scale was used to describe anxiety and depression symptoms. Three different questionnaires (leisure time activity, and physical activity at home, at work) were used to determine physical activity levels. Dorsal regression was used to analyze the data. Results: The anxiety score was the most common factor affecting pain intensity (p=0.003). On the other hand, a moderate level of physical activity at home (p=0.027), physical activity level at work (p=0.008), and the anxiety score (p=0.027) were significant factors affecting global fatigue. Conclusion: Our results show that anxiety is the most important factor affecting both pain and global fatigue in women with CWP. These results also support the idea that the characteristics of pain, fatigue and anxiety should be evaluated separately

Linear response theory and transient fluctuation theorems for diffusion processes: a backward point of view

On the basis of perturbed Kolmogorov backward equations and path integral representation, we unify the derivations of the linear response theory and transient fluctuation theorems for continuous diffusion processes from a backward point of view. We find that a variety of transient fluctuation theorems could be interpreted as a consequence of a generalized Chapman-Kolmogorov equation, which intrinsically arises from the Markovian characteristic of diffusion processes

Bi-k-bi clustering: Mining large scale gene expression data using two-level biclustering

Due to the increase in gene expression data sets in recent years, various data mining techniques have been proposed for mining gene expression profiles. However, most of these methods target single gene expression data sets and cannot handle all the available gene expression data in public databases in reasonable amount of time and space. In this paper, we propose a novel framework, bi-k-bi clustering, for finding association rules of gene pairs that can easily operate on large scale and multiple heterogeneous data sets. We applied our proposed framework on the available NCBI GEO Homo sapiens data sets. Our results show consistency and relatedness with the available literature and also provides novel associations. Copyright © 2010 Inderscience Enterprises Ltd

Unconventional pairing in excitonic condensates under spin-orbit coupling

It is shown that the Rashba and Dresselhaus spin orbit couplings enhance the conclusive power in the experiments on the excitonic condensed state by at least three low temperature effects. First, spin orbit coupling facilitates the photoluminescense measurements via enhancing the bright contribution in the otherwise dominantly dark exciton condensed state. The second is the presence of a power law temperature dependence of the thermodynamic observables in low temperatures and the weakening of the second order transition at the critical temperature. The third is the appearance of the nondiagonal elements in the static spin susceptibility.Comment: 4 pages, 4 figures, 1 tabl

A low-complexity lossless image compression for small spacescrafts' on-board computers

In this paper, we present a novel and low-complexity lossless compression for gray-scale images. The gray-scale image is first separated into bit-planes. These bit-planes are then performed a binary wavelet transform (BWT) to obtain an efficient representation for compression. The BWT bits of significant bit-planes are then encoded by the run-length coder that uses Golomb-Rice codes for run-encoding. The experimental results show that the algorithm obtained efficiency in image compression, and low-complexity in implementation that is highly applicable for image compression systems on small spacecraft's on-board computers

How Chaotic is the Stadium Billiard? A Semiclassical Analysis

The impression gained from the literature published to date is that the spectrum of the stadium billiard can be adequately described, semiclassically, by the Gutzwiller periodic orbit trace formula together with a modified treatment of the marginally stable family of bouncing ball orbits. I show that this belief is erroneous. The Gutzwiller trace formula is not applicable for the phase space dynamics near the bouncing ball orbits. Unstable periodic orbits close to the marginally stable family in phase space cannot be treated as isolated stationary phase points when approximating the trace of the Green function. Semiclassical contributions to the trace show an $\hbar$ - dependent transition from hard chaos to integrable behavior for trajectories approaching the bouncing ball orbits. A whole region in phase space surrounding the marginal stable family acts, semiclassically, like a stable island with boundaries being explicitly $\hbar$-dependent. The localized bouncing ball states found in the billiard derive from this semiclassically stable island. The bouncing ball orbits themselves, however, do not contribute to individual eigenvalues in the spectrum. An EBK-like quantization of the regular bouncing ball eigenstates in the stadium can be derived. The stadium billiard is thus an ideal model for studying the influence of almost regular dynamics near marginally stable boundaries on quantum mechanics.Comment: 27 pages, 6 figures, submitted to J. Phys.

Entanglement, local measurements, and symmetry

A definition of entanglement in terms of local measurements is discussed. Viz, the maximum entanglement corresponds to the states that cause the highest level of quantum fluctuations in all local measurements determined by the dynamic symmetry group of the system. A number of examples illustrating this definition is considered.Comment: 10 pages. to be published in Journal of Optics