A combined statistical model for multiple motifs search

Transcription factor binding sites (TFBS) play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with de¯nite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite di®erent from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for ¯nding over- represented short sequence segments in di®erent kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from di®erent species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite di®erent, the results show that this model is rather general and sensible.

Experimental Study on the Combined Evaporation Effect and Thermocapillary Convection in a Thin Liquid Layer

The coupling mechanisms and flow characteristics of thermocapillary convection in a thin liquid layer with evaporating interface were studied. The planar liquid layer, with the upper surface open to air, was imposed externally horizontal temperature differences. The measured average evaporating rates and interfacial temperature profiles indicated the relative importance of evaporation effect and thermocapillary convection under different temperature gradients. A temperature jump was found at the interface, which was thought to be related to the influence of evaporation effect. All above mentioned results were repeated in a rarely evaporating liquid to compare the influence of evaporation effect.

Single attosecond pulse generation in He+ by controlling the instant ionization rate using attosecond pulse trains combined with an intense laser pulse

High-order harmonics and single attosecond pulse generation by using an infrared laser pulse combined with attosecond pulse trains (APT) interacting with He+ have been investigated. We show that the ionization for different instant time intervals can be controlled by altering the time delay between the APT and the infrared pulse. Consequently, APT can be used as a tool to control the efficiency of high-order harmonics emitted at different times. By choosing appropriate APT and time delay, the driving pulse width for single attosecond pulse generation can be extended up to six optical cycles. (c) 2007 Optical Society of America.

Ridge optical waveguide in an Er3+/Yb3+ co-doped phosphate glass produced by He+ ion implantation combined with Ar+ ion beam etching

This paper reports on the fabrication and characterization of a ridge optical waveguide in an Er3+/Yb3+ co-doped phosphate glass. The He+ ion implantation (at energy of 2.8 MeV) is first applied onto the sample to produce a planar waveguide substrate, and then Ar+ ion beam etching (at energy of 500 eV) is carried out to construct rib stripes on the sample surface that has been deposited by a specially designed photoresist mask. According to a reconstructed refractive index profile of the waveguide cross section, the modal distribution of the waveguide is simulated by applying a computer code based on the beam propagation method, which shows reasonable agreement with the experimentally observed waveguide mode by using the end-face coupling method. Simulation of the incident He ions at 2.8 MeV penetrating into the Er3+/Yb3+ co-doped phosphate glass substrate is also performed to provide helpful information on waveguide formation.

Combined effects of polyfluorinated and perfluorinated compounds on primary cultured hepatocytes from rare minnow (Gobiocypris rarus) using toxicogenomic analysis

Polyfluorinated and perfluorinated compounds (PFCs) are used in numerous commercial products and have been ubiquitously detected in the environment as well as in the blood of humans and wildlife. To assess the combined effects caused by PFCs in mixtures, gene expression profiles were generated using a custom cDNA microarray to detect changes in primary cultured hepatocytes of rare minnows exposed to six individual PFCs (perfluorooctanoic acid, perfluorononanoic acid, perfluorodecanoic acid, perfluorododecanoic acid, perfluorooctane sulfonate, and 8:2 fluorotelomer alcohol) and four formulations of the PFCs mixtures. Mixtures as well as individual compounds consistently regulated a particular gene set, which suggests that these conserved genes may play a central role in the toxicity mediated by PFCs. Specifically, a number of genes regulated by the mixtures were identified in this study, which were not affected by exposure to any single component. These genes are implicated in multiple biological functions and processes, including fatty acid metabolism and transport, xenobiotic metabolism, immune responses, and oxidative stress. More than 80% of the altered genes in the PFOA- and PFOS-dominant mixture groups were of the same gene set, while the gene expression profiles from single PFOA and PFOS exposures were not as similar. This work contributes to the development of toxicogenomic approaches in combined toxicity assessment and allows for comprehensive insights into the combined action of PFCs mixtures in multiple environmental matrices. (C) 2009 Elsevier B.V. All rights reserved.