We present a novel algorithm named FAST for aligning protein three-dimensional structures. FAST uses a directionality-based scoring scheme to compare the intra-molecular residueresidue relationships in two structures. It employs an elimination heuristic to promote sparseness in the residue-pair graph and facilitate the detection of the global optimum. In order to test the overall accuracy of FAST, we determined its sensitivity and specificity with the SCOP classification (version 1.61) as the gold standard. FAST achieved higher sensitivities than several existing methods (DaliLite, CE, and K2) at all specificity levels. We also tested FAST against 1033 manually curated alignments in the HOMSTRAD database. The overall agreement was 96%. Close inspection of examples from broad structural classes indicated the high quality of FAST alignments. Moreover, FAST is an order of magnitude faster than other algorithms that attempt to establish residue-residue correspondence. Typical pairwise alignments take FAST less than a second with a Pentium III 1.2GHz CPU. FAST software and a web server are available at http:// biowulf.bu.edu/FAST/. Proteins 2005;58:618 -627.
We present an analysis of physical chemical constraints on the accuracy of DNA micro-arrays under equilibrium and nonequilibrium conditions. At the beginning of the article we describe an algorithm for choosing a probe set with high specificity for targeted genes under equilibrium conditions. The algorithm as well as existing methods is used to select probes from the full Saccharomyces cerevisiae genome, and these probe sets, along with a randomly selected set, are used to simulate array experiments and identify sources of error. Inasmuch as specificity and sensitivity are maximum at thermodynamic equilibrium, we are particularly interested in the factors that affect the approach to equilibrium. These are analyzed later in the article, where we develop and apply a rapidly executable method to simulate the kinetics of hybridization on a solid phase support. Although the difference between solution phase and solid phase hybridization is of little consequence for specificity and sensitivity when equilibrium is achieved, the kinetics of hybridization has a pronounced effect on both. We first use the model to estimate the effects of diffusion, crosshybridization, relaxation time, and target concentration on the hybridization kinetics, and then investigate the effects of the most important kinetic parameters on specificity. We find even when using probe sets that have high specificity at equilibrium that substantial crosshybridization is present under nonequilibrium conditions. Although those complexes that differ from perfect complementarity by more than a single base do not contribute to sources of error at equilibrium, they slow the approach to equilibrium dramatically and confound interpretation of the data when they dissociate on a time scale comparable to the time of the experiment. For the best probe set, our simulation shows that steady-state behavior is obtained in a relaxation time of approximately 12-15 h for experimental target concentrations approximately (10(-13) - 10(-14))M, but the time is greater for lower target concentrations in the range (10(-15)-10(-16))M. The result points to an asymmetry in the accuracy with which up- and downregulated genes are identified.
The growing application of composite materials in aerospace leads to the urgent need of non-destructive testing and evaluation (NDT&E) techniques capable of detecting defects such as impact damage and delamination possibly existing in those materials. Eddy current pulsed thermography is an emerging non-destructive testing (NDT) technique capable of detecting such defects. However, the characterization of delamination within composite materials is difficult to be achieved by a single pulse excitation especially in carbon fiber reinforced plastic materials as the extraction of thermal diffusion in such multi-layered structures is challenging. To cope with this problem, this paper proposes the eddy current pulsecompression thermography (ECPuCT) combining the Barker code modulated eddy current excitation and pulse-compression technique to enhance the capability of characterizing delamination on carbon fiber reinforced plastic materials. Additionally, a thermal pattern enhanced method based on kernel principal component analysis technique is used to locate the delaminated areas. Two features, including a newly proposed crossing point of impulse responses related to defective and non-defective areas and skewness of impulse responses are investigated for delamination depth evaluation. Results show that delamination can be detected within depths ranging from 0.46 mm to 2.30 mm and both the proposed features have a monotonic relationship with delamination depths.
Hyperhomocysteinemia (HH) is a factor that predisposes individuals to thrombosis
Variational mode decomposition (VMD) method has been widely used in the field of signal processing with significant advantages over other decomposition methods in eliminating modal aliasing and noise robustness. The number (usually denoted by K) of intrinsic mode function (IMF) has a great influence on decomposition results. When dealing with signals including complex components, it is usually impossible for the existing methods to obtain correct results and also effective methods for determining K value are lacking. A method called center frequency statistical analysis (CFSA) is proposed in this paper to determine K value. CFSA method can obtain K value accurately based on center frequency histogram. To shed further light on its performance, we analyze the behavior of CFSA method with simulation signal in the presence of variable components amplitude, components frequency, and components number as well as noise amplitude. The normal and fault vibration signals obtained from a bearing experimental setup are used to verify the method. Compared with maximum center frequency observation (MCFO), correlation coefficient (CC), and normalized mutual information (NMI) methods, CFSA is more robust and accurate, and the center frequencies results are consistent with the main frequencies in FFT spectrum.
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