ADGO 2.0: interpreting microarray data and list of genes using composite annotations

ADGO 2.0 is a web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate composite annotations solely for interpreting lists of genes but usually provide highly redundant information. This new version has the following additional features: first, it provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. Second, it screens redundant composite annotations when generating and prioritizing them. Third, it incorporates union and subtracted sets as well as intersection sets. Lastly, users can upload their own gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. The first two features are unique to ADGO 2.0. Using our tool, we demonstrate analyses of a microarray dataset and a list of genes for T-cell differentiation. The new ADGO is available at http://www.btool.org/ADGO2

Cluster Analysis of Extremely High Energy Cosmic Rays in the Northern Sky

The arrival directions of extremely high energy cosmic rays (EHECR) above $4\times10^{19}$ eV, observed by four surface array experiments in the northern hemisphere,are examined for coincidences from similar directions in the sky. The total number of cosmic rays is 92.A significant number of double coincidences (doublet) and triple coincidences (triplet) are observed on the supergalactic plane within the experimental angular resolution. The chance probability of such multiplets from a uniform distribution is less than 1 % if we consider a restricted region within $\pm 10^{\circ}$ of the supergalactic plane. Though there is still a possibility of chance coincidence, the present results on small angle clustering along the supergalactic plane may be important in interpreting EHECR enigma. An independent set of data is required to check our claims.Comment: 9 pages, 6 tables, 8 figures. submitted to Astroparticle Physic

Deficiency of Phosphoinositide 3-Kinase Enhancer Protects Mice From Diet-Induced Obesity and Insulin Resistance

OBJECTIVE: Phosphoinositide 3-kinase enhancer A (PIKE-A) is a proto-oncogene that promotes tumor growth and transformation by enhancing Akt activity. However, the physiological functions of PIKE-A in peripheral tissues are unknown. Here, we describe the effect of PIKE deletion in mice and explore the role of PIKE-A in obesity development. RESEARCH DESIGN AND METHODS: Whole-body PIKE knockout mice were generated and subjected to high-fat–diet feeding for 20 weeks. The glucose tolerance, tissue-specific insulin sensitivity, adipocyte differentiation, and lipid oxidation status were determined. The molecular mechanism of PIKE in the insulin signaling pathway was also studied. RESULTS: We show that PIKE-A regulates obesity development by modulating AMP-activated protein kinase (AMPK) phosphorylation. PIKE-A is important for insulin to suppress AMPK phosphorylation. The expression of PIKE-A is markedly increased in adipose tissue of obese mice, whereas depletion of PIKE-A inhibits adipocyte differentiation. PIKE knockout mice exhibit a prominent phenotype of lipoatrophy and are resistant to high-fat diet–induced obesity, liver steatosis, and diabetes. PIKE knockout mice also have augmented lipid oxidation, which is accompanied by enhanced AMPK phosphorylation in both muscle and adipose tissue. Moreover, insulin sensitivity is improved in PIKE-A–deficient muscle and fat, thus protecting the animals from diet-induced diabetes. CONCLUSIONS: Our results suggest that PIKE-A is implicated in obesity and associated diabetes development by negatively regulating AMPK activity

Magnetic field tuning of antiferromagnetic Yb3_{3}Pt4_{4}

We present measurements of the specific heat, magnetization, magnetocaloric effect and magnetic neutron diffraction carried out on single crystals of antiferromagnetic Yb$_{3}$Pt$_{4}$, where highly localized Yb moments order at $T_{\rm N}=2.4$ K in zero field. The antiferromagnetic order was suppressed to $T_{\rm N}\rightarrow 0$ by applying a field of 1.85 T in the $ab$ plane. Magnetocaloric effect measurements show that the antiferromagnetic phase transition is always continuous for $T_{\rm N}>0$, although a pronounced step in the magnetization is observed at the critical field in both neutron diffraction and magnetization measurements. These steps sharpen with decreasing temperature, but the related divergences in the magnetic susceptibility are cut off at the lowest temperatures, where the phase line itself becomes vertical in the field-temperature plane. As $T_{\rm N}\rightarrow0$, the antiferromagnetic transition is increasingly influenced by a quantum critical endpoint, where $T_{\rm N}$ ultimately vanishes in a first order phase transition.Comment: 9 pages, 6 figure

Direct measurement of the spin gaps in a gated GaAs two-dimensional electron gas.

We have performed magnetotransport measurements on gated GaAs two-dimensional electron gases in which electrons are confined in a layer of the nanoscale. From the slopes of a pair of spin-split Landau levels (LLs) in the energy-magnetic field plane, we can perform direct measurements of the spin gap for different LLs. The measured g-factor g is greatly enhanced over its bulk value in GaAs (0.44) due to electron-electron (e-e) interactions. Our results suggest that both the spin gap and g determined from conventional activation energy studies can be very different from those obtained by direct measurements.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are