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.

High-Strength Composite Fibers: Realizing True Potential of Carbon Nanotubes in Polymer Matrix through Continuous Reticulate Architecture and Molecular Level Couplings

Carbon nanotubes have unprecedented mechanical properties as defect-free nanoscale building blocks, but their potential has not been fully realized in composite materials due to weakness at the interfaces. Here we demonstrate that through load-transfer-favored three-dimensional architecture and molecular level couplings with polymer chains, true potential of CNTs can be realized in composites as Initially envisioned. Composite fibers with reticulate nanotube architectures show order of magnitude improvement in strength compared to randomly dispersed short CNT reinforced composites reported before. The molecular level couplings between nanotubes and polymer chains results in drastic differences in the properties of thermoset and thermoplastic composite fibers, which indicate that conventional macroscopic composite theory falls to explain the overall hybrid behavior at nanoscale.

Constrained high-order statistical blind deconvolution of spectral data

A constrained high-order statistical algorithm is proposed to blindly deconvolute the measured spectral data and estimate the response function of the instruments simultaneously. In this algorithm, no prior-knowledge is necessary except a proper length of the unit-impulse response. This length can be easily set to be the width of the narrowest spectral line by observing the measured data. The feasibility of this method has been demonstrated experimentally by the measured Raman and absorption spectral data.

The spectroscopic properties of Er3(+)-doped TeO2-Nb2O5 glasses with high mechanical strength performance

(100 - x)TeO2 - xNb(2)O(5) (x=5-20) mobic tellurite glasses doped with 0.5 mol.% Er2O3 were synthesized, and their thermal, mechanical, and spectroscopic properties were measured and compared to the properties of the typical 75TeO(2)-20ZnO-5Na(2)O (TZN) tellurite glass. The refractive index (n(d)), density (p), and glass transition temperature (T-g) of bulk glasses increase with the Nb2O5 content. The Vickers microhardness (H-v) of bulk glass in niobic tellurite glasses also increases with the Nb2O5 content. The values (2.5-3.2 GPa) of H, in the niobic tellurite glasses are 47-88% larger than that (1.7 GPa) in TZN glass. The effect of Nb2O5 content on absorption spectra, the Judd-Ofelt parameters Omega(t) (t = 2, 4, 6), fluorescence spectra and the lifetimes of Er3+ :I-13/2 level were also investigated, and the stimulated emission crosssection was calculated from McCumber theory. With increasing Nb2O5 content in the glass composition, the Omega(t) (t = 2, 4, 6) parameters, fluorescence full width at half maximum (FWHM) Of I-13/2 of Er3+ increase, while the I-4(13/2) lifetimes of Er3+ decreases. Compared with TZN glass, the gain bandwidth properties of Er3+-doped TeO2-Nb2O5 glass is much larger than in tellurite glass based TeO2-ZnO-Na2O system, bismush-based glass, germanate, and silicate glasses, which indicates that TeO2-Nb2O5 glasses are better choice as a practical available host material for broadband Er3+-doped amplifier. (c) 2005 Elsevier B.V. All rights reserved.

Is there a close relationship between synonymous codon bias and codon-anticodon binding strength in human genes?

Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon bin

Statistical analysis of sequence features of introns with positive transcriptional regulation in yeast genes

A great deal of experimental studies have shown that many introns of eukaryotic genes function as regulators of transcription. However, comprehensive studies of this problem have not yet been conducted. After checking the transcription frequencies of some Saccharomyces cerevisiae (yeast), genes and their introns, a remarkable phenomenon was discovered that generally the introns of the genes with higher transcription frequencies are longer, and the introns of the genes with lower transcription frequencies are shorter. This suggests that the longer introns of genes with higher transcription frequencies may contain some characteristic sequence structures, which could enhance the transcription of genes. Therefore, two sets of introns of yeast genes were chosen for further study. The transcription frequencies of the first set of genes are higher (>30), and those of the second set of genes are lower (less than or equal to10). Some oligonucleotides are detected by statistically comparative analyses of the occurrence frequencies of oligonucleotides (mainly tetranucleotides and pentanucleotides), whose occurrence frequencies in the first set of introns; are significantly higher than those in the second set of introns, and are also significantly higher than those in the exons flanking the introns of the first set. Some of these extracted oligonucleotides are the same as the regulatory elements of transcription revealed by experimental analyses. Besides, the distributions of these extracted oligonucleotides in the two sets of introns and the exons show that the sequence structures of the first set of introns are favorable for transcription of genes.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

Relationships between the biomass of algal crusts in fields and their compressive strength

In the desert areas of China investigated by the authors, various biological crusts were predominately associated with three blue-green algal (cyano bacterial) species, Microcoleus vaginatus Gom., Phormidium tenue (Menegh.) Gom. and Seytonema javanicum (Mitz.) Born et Flah. Their biomass and their compressive strength were measured simultaneously in the field in this study. It was also found that the compressive strength of algal crusts was enhanced with the increasing of algal biomass from an undetectable level to a value as high as 9.6mg g(-1) dry soil. However, when the algal biomass decreased, the compressive strength did not descend immediately, but remained relatively steady. The higher the algal biomass became, the thicker were the algal crusts formed. Given the same biomass, the highest compressive strength of man-made algal crusts in fields was found at an algal ratio of 62.5% M. vaginatus, 31.25% P. tenue and 6.25% S. javanicum, and it reached 0.89kgcm(-2). When the biomass of the crusts increased above the value of 8.16 mg chl ag(-1) dry soil, the compressive strength would not ascend easily. It indicated that the compressive strength of man-made algal crusts appeared temporarily saturated in the field. (c) 2006 Elsevier Ltd. All rights reserved.

Direct detection of the relative strength of Rashba and Dresselhaus spin-orbit interaction: Utilizing the SU(2) symmetry

We propose a simple method to detect the relative strength of Rashba and Dresselhaus spin-orbit interactions in quantum wells (QWs) without relying on the directional-dependent physical quantities. This method utilizes the two different critical gate voltages that leading to the remarkable signals of SU(2) symmetry, which happens to reflect the intrinsic-structure-inversion asymmetry of the QW. We support our proposal by the numerical calculation of in-plane relaxation times based on the self-consistent eight-band Kane model. We find that the two different critical gate voltages leading to the maximum spin-relaxation times [one effect of the SU(2) symmetry] can simply determine the ratio of the coefficients of Rashba and Dresselhaus terms. Our proposal can also be generalized to extract the relative strengths of the spin-orbit interactions in quantum-wire and quantum-dot structures.

Electromagnetic-field-induced cohesive force enhancement in a metallic nanowire

We theoretically study the conducting electronic contribution to the cohesive force in a metallic nanowire irradiated under a transversely polarized external electromagnetic field at low temperatures and in the ballistic regime. In the framework of the free-electron model, we have obtained a time-dependent two-level electronic wavefunction by means of a unitary transformation. Using a thermodynamic statistical approach with this wavefunction, we have calculated the cohesive force in the nanowire. We show that the cohesive force can be divided into two components, one of which is independent of the electromagnetic field (static component), which is consistent with the existing results in the literature. The magnitude of the other component is proportional to the electromagnetic field strength. This extra component of the cohesive force is originally from the coherent coupling between the two lateral energy levels of the wire and the electromagnetic field.

Statistical investigation on morphology development of gallium nitride in initial growth stage

Morphology of Gallium Nitride (GaN) in initial growth stage was observed with atomic force microscopy (AFM) and scanning electron microscopy (SEM), It was found that the epilayer developed from islands to coalesced film. Statistics based on AFM observation was carried out to investigate the morphology characteristics. It was found that the evolution of height distribution could be used to describe morphology development. Statistics also clearly revealed variation of top-face growth rate among islands. Indium-doping effect on morphology development was also statistically studied. The roughening and smoothing behavior in morphology development was explained. (C) 2002 Elsevier Science B.V. All rights reserved.