Annotation-based meta-analysis of microarray experiments

We are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments

Cervical Cancer-Associated Human Papillomavirus 16 E7 Oncoprotein Inhibits Induction of Anti-Cancer Immunity by a CD4+ T Cell Dependent Mechanism

Attempts to develop therapeutic vaccines against cervical cancer have been proven difficult. One of the major causes of the failure is due to the use of the wrong mouse models based on transplantable tumours in testing the efficacy of vaccines. Now that a transgenic epithelial mouse model has been developed to closely mimic cervical cancer, the mechanisms needed to eliminate this type of cancer could be studied. The E7 oncoprotein of Human Papillomavirus (HPV) is the most expressed HPV protein in cervical cancers and its continuous production is essential to maintain the cancerous state and therefore the obvious target in the development of vaccines. Skin grafts expressing the HPV 16 E7 protein (E7 autografts) are not spontaneously rejected from an MHC matched immunocompetent host. Interestingly, simultaneous placement of an MHC mismatched skin (allograft) next to an E7 autograft results in the E7 autograft rejection. However when the allograft also expresses E7, the E7 autograft is rejected more slowly. Autograft rejection requires CD8+ T cells, and is accelerated by removal of CD4+ T cells after placement of the E7 expressing allograft, suggesting induction of an E7 specific CD4+ regulatory T cell population by the E7 expressing allograft. This observation may have implications in designing effective vaccines and immunotherapy against cervical cancers in women

Progressive image transmission over OFDM systems using multiple antennas

A Joint source-channel coding (JSCC) scheme for SPIHT coded image transmission over OFDM systems with spatial diversity is proposed where no feedback channel is available. By using diversity techniques, the fading effects can be dramatically decreased and we show that subchannels in OFDM systems are indeed flat Rayleigh fading channels and approach Gaussian noisy channels when the diversity gain gets large, as a result, the system performance can be improved. The simulation results are presented with different number of antennas and different multipath delay and Doppler spread

Modeling the Influence of Antifreeze Proteins on Three-Dimensional Ice Crystal Melt Shapes using a Geometric Approach

The melting of pure axisymmetric ice crystals has been described previously by us within the framework of so-called geometric crystal growth. Nonequilibrium ice crystal shapes evolving in the presence of hyperactive antifreeze proteins (hypAFPs) are experimentally observed to assume ellipsoidal geometries ("lemon" or "rice" shapes). To analyze such shapes we harness the underlying symmetry of hexagonal ice Ih and extend two-dimensional geometric models to three-dimensions to reproduce the experimental dissolution process. The geometrical model developed will be useful as a quantitative test of the mechanisms of interaction between hypAFPs and ice.Comment: 15 pages, 5 figures; Proc. R. Soc. A, Published online before print June 27, 201

Quantum resonance and anti-resonance for a periodically kicked Bose-Einstein Condensate in a one dimensional Box

We investigate the quantum dynamics of a periodically kicked Bose-Einstein Condensate confined in a one dimensional (1D) Box both numerically and theoretically, emphasizing on the phenomena of quantum resonance and anti-resonance. The quantum resonant behavior of BEC is different from the single particle case but the anti-resonance condition ($T = 2\pi$ and $\alpha = 0$) is not affected by the atomic interaction. For the anti-resonance case, the nonlinearity (atom interaction) causes the transition between oscillation and quantum beating. For the quantum resonance case, because of the coherence of BEC, the energy increase is oscillating and the rate is dramatically affected by the many-body interaction. We also discuss the relation between the quantum resonant behavior and the KAM or non-KAM property of the corresponding classical system.Comment: 7 pages, 7 figure

Zero Modes of Matter Fields on Scalar Flat Thick Branes

Zero modes of various matters with spin 0, 1 and 1/2 on a class of scalar flat thick branes are discussed in this paper. We show that scalar field with spin 0 is localized on all thick branes without additional condition, while spin 1 vector field is not localized. In addition, for spin 1/2 fermionic field, the zero mode is localized on the branes under certain conditions.Comment: 11 pages,no figure