Biomedical subjects

Xueguang Shao

Publications and source records attributed to Xueguang Shao.

At least 19 recordsLinked to original sources

PubMed2006

An adaptive strategy for selecting representative calibration samples in the continuous wavelet domain for near-infrared spectral analysis.

Sample selection is often used to improve the cost-effectiveness of near-infrared (NIR) spectral analysis. When raw NIR spectra are used, however, it is not easy to select appropriate samples, because of background interference and noise. In this paper, a novel adaptive strategy based on selection of representative NIR spectra in the continuous wavelet transform (CWT) domain is described. After pretreatment with the CWT, an extension of the Kennard-Stone (EKS) algorithm was used to adaptively select the most representative NIR spectra, which were then submitted to expensive chemical measurement and multivariate calibration. With the samples selected, a PLS model was finally built for prediction. It is of great interest to find that selection of representative samples in the CWT domain, rather than raw spectra, not only effectively eliminates background interference and noise but also further reduces the number of samples required for a good calibration, resulting in a high-quality regression model that is similar to the model obtained by use of all the samples. The results indicate that the proposed method can effectively enhance the cost-effectiveness of NIR spectral analysis. The strategy proposed here can also be applied to different analytical data for multivariate calibration.

Journal Article↗

PubMed2006

Prediction of low-energy isomers of large fullerenes from C132 to C160.

To predict energetically favored isomers, we used a topological scheme as a prescreening tool to select candidate isomers for each fullerene from C(106) to C(160). Comparison with the PM3 and tight-binding (TB) potential calculated results and few published data for the low-energy isomers of C(106) to C(130) indicates that the prescreening approach is feasible. For each fullerene from C(132) up to C(160), the selected 1000 candidate isomers were further optimized by PM3 and TB potential. The analysis of the semiempirical PM3 and TB results of C(106) to C(160) provides some qualitative features of the large fullerenes. Furthermore, calculations at the B3LYP/6-31G*//B3LYP/3-21G level of theory were carried out on the top ten PM3 and TB low-energy isomers of C(132) to C(160) to accurately predict the stable isomers, and the HOMO-LUMO gap, the ionization energy, and electron affinity of the lowest-energy isomers were also investigated at the same level.

Journal Article↗

PubMed2006

A fast surface-matching procedure for protein-ligand docking.

A very simple, fast, and efficient scheme is proposed for performing preliminary protein-ligand docking as the first step of intensive high-throughput virtual screening. The procedure acts as a surface-complementarity filter that first calculates the 2D-contour maps of both the protein cavity and of the ligands using a spherical harmonics description of the associated molecular surfaces. Next, the obtained 2D-fingerprint images are compared to detect their complementarity. This scheme was tested on three typical cases of protein cavities, namely, a well-closed pocket, a small open pocket, and a large open one. For that purpose, for each case, a sample of 101 ligand conformers was generated (the X-ray one and 100 different conformers generated using simulated annealing), and these conformational samples were ranked according to the complementarity with the protein cavity surface. Compared to traditional docking procedures such as FRED (considered as typical of a very fast rigid body docking algorithms) and GOLD (considered as typical of the more accurate flexible docking algorithms), our procedure was much faster and more successful in detecting the right X-ray conformation. We did, however, identify a certain weakness in the case of the very large pocket where results were not as expected. In general, our method could be used for incorporating indirectly flexibility in protein-ligand docking calculations as such a scheme can easily handle several conformational states of both the protein and the ligand.

Binding Sites↗

PubMed2006

Molecular dynamics study of the inclusion of cholesterol into cyclodextrins.

The interaction of three cyclodextrins (CDs), viz. beta-CD, heptakis (2,6-di-O-methyl)-beta-CD (DM-beta-CD), and 2-hydroxypropyl-beta-CD (HP-beta-CD), with cholesterol was investigated using molecular dynamics (MD) simulations. The free energy along the reaction pathway delineating the inclusion of cholesterol into each CD was computed using the adaptive biasing force method. The association constant and the corresponding association free energy were derived by integrating the potential of mean force (PMF) over a representative ordering parameter. The results show that the free energy profiles possess two local minima corresponding to roughly equally probable binding modes. Among the three CDs, DM-beta-CD exhibits the highest propensity to associate with cholesterol. Ranking for binding cholesterol, viz. DM-beta-CD > HP-beta-CD > beta-CD, agrees nicely with experiment. Partitioning of the PMF into free energy components illuminates that entering of cholesterol into the CD cavity is driven mainly by electrostatic interactions, whereas deeper inclusion results from van der Waals forces and solvation effects. Additional MD simulations were performed to investigate the structural stability of the host-guest complexes near the free energy minima. The present results demonstrate that association of cholesterol and CDs follows two possible binding modes. Although the latter are thermodynamically favorable for all CDs, one of the two inclusion complexes appears to be preferred kinetically in the case of DM-beta-CD.

Cholesterol↗

PubMed2006

Determination and characterization of the pyrolysis products of isoprocarb by GC-MS.

The pyrolysis behavior of isoprocarb (an insecticide with contact and stomach action) is investigated using pyrolysis-gas chromatography-mass spectrometry. The pyrolysis products are separated using an HP-5 column under temperature program with helium as the carrier gas. The total of 80 separated pyrolysis components at 600 degrees C, 750 degrees C, and 900 degrees C under helium atmosphere are identified using a probability-based matching search procedure, combined with the correlation of boiling point (BP) and Lee retention index (RI). Some of the BP values of the tentative components are estimated using the group contributions method because experimental values are not available. The levels of the identified components are estimated by the peak area normalization method from the chromatogram. It is found that isoprocarb decomposes more with the increase of temperature, and a large number of mono aromatics and polycyclic aromatic hydrocarbons and their derivatives are produced when the pyrolysis temperature is higher than 750 degrees C. The content of the decomposition products in the pyrolysate varies from 0.04% to 22.20%.

Carbamates↗

PubMed2006

Determination of pyrethroid residues in tobacco by means of solid phase microextraction and GC/MS with the aid of ultrasonic assisted extraction using water as extracting solvent.

A rapid and simple sampling approach using solid phase microextraction (SPME) for pyrethroid residues analysis in flue-cured tobacco was studied. The fibers coated with poly-dimethylsiloxane (PDMS) at 100 microm thickness were chosen. Extraction time of 180 s, desorption time of 120 s and desorption temperature of 280 degrees C were selected. The whole sampling process, only including an ultrasonic assisted extraction step and a solid phase microextraction step, can be completed within 15 min. The associated SPME and ultrasonic assisted extraction using water as extracting solvent shows good results for tobacco pyrethroid residues determination. Results indicated that four pyrethroids can be determined simultaneously, and the limits of detection are below 35 ng g(-1) using GC/MS in selected ion monitoring (SIM) mode. The reproducibility of the technique is found to be better than 11.8% RSD.

Animals↗

PubMed2005

A comparison of accelerated solvent extraction, Soxhlet extraction, and ultrasonic-assisted extraction for analysis of terpenoids and sterols in tobacco.

The performance of accelerated solvent extraction in the analysis of terpenoids and sterols in tobacco samples was investigated and compared with those of Soxhlet extraction and ultrasonically assisted extraction with respect to yield, extraction time, reproducibility and solvent consumption. The results indicate that although the highest yield was achieved by Soxhlet extraction, ASE appears to be a promising alternative to classical methods since it is faster and uses less solvent, especially when applied to the investigation of large batch tobacco samples. However, Soxhlet extraction is still the preferred method for analyzing sterols since it gives a higher extraction efficiency than other methods.

Alkanes↗

PubMed2005

Structural transition from icosahedra to decahedra of large Lennard-Jones clusters.

The lowest icosahedral and decahedral energies of LJ1001-1610 clusters are obtained using a greedy search method (GSM) based on lattice construction. By comparing the lowest energies of icosahedral and decahedral clusters with the same atoms, the structural transition of LJ clusters is studied. Results show that the critical size from icosahedra to decahedra is located at N = 1034. When the cluster size is larger than 1034, the optimal structures are decahedra except the LJ1367-1422 clusters near the magic number, 1402, of icosahedra. However, the energies of icosahedra near the next magic number, 2044, are higher than that of decahedra, which implies that decahedra will be the optimal structure when the cluster size is larger than 1422, even for those clusters near the magic numbers of icosahedra.

Journal Article↗

PubMed2005

Chiral recognition of aromatic compounds by beta-cyclodextrin based on bimodal complexation.

The chiral recognition of the selected aromatic chiral compounds by native beta-cyclodextrin (beta-CD) based on bimodal complexation was studied using a flexible docking algorithm FDOCK. A quantitative empirical free energy relationship model was employed to predict the complex stability constants and the preferred binding modes. The results showed that the calculated complex stability constants are in good agreement with the experimental data. Furthermore, the main force responsible for host-guest complexation is the van der Waals force and the chiral molecules are completely included into the beta-CD cavity. The chiral recognition for the selected aromatic chiral compounds is the result of the van der Waals force counterbalancing with the other effects, such as the electrostatic interaction and the hydrophobic effect.

Algorithms↗

PubMed2005

An efficient approach for theoretical study on the low-energy isomers of large fullerenes C90-C140.

An approach that consists of a molecular mechanics method based on the second generation reactive empirical bond order (REBO) potential and the more accurate semiempirical method PM3 (Parametric Method No. 3) was proposed to predict the energetically favored isomers of the fullerenes from C90 to C140 at the semiempirical level. All the 578,701 isolated-pentagon-rule isomers of fullerenes from C90 to C140 were enumerated from topological structures and systematically searched using an energy minimization method to select the best 100 low-energy isomers based on the REBO potential for each fullerene. Then these candidate isomers were further optimized by PM3 and ranked again to determine the top low-energy isomers. This approach was applied to calculate the energetically favored isomers of C90-C140. The results of C90-C120 are in good agreement with the published results by quantum-chemical methods. Furthermore, the top five low-energy isomers of C90-C120, as well as C122-C140 which have scarcely been systematically studied before, are also predicted with the approach. The analysis of the structures showed that the hexagon-neighbor rule is an important factor to the stability of C90-C140. The time cost for the systematical search based on the REBO potential was also discussed. It indicates that the approach proposed is efficient for predicting the energetically favored isomers of large fullerenes at the semiempirical level.

Journal Article↗

PubMed2005

Geometry optimization and conformational analysis of (C60)N clusters using a dynamic lattice-searching method.

A newly developed unbiased global optimization method, named dynamic lattice searching (DLS), is used to locate putative global minima for all (C6O)N clusters with Girifalco potential up to N=150. A simple greedy strategy is adopted for the basic frame, so DLS has a very high convergence speed and may converge at various configurations. As most structures are packed by basic tetrahedra, some sequences are defined by both configurations and the size of the basic tetrahedra. A sequence-based conformational analysis is carried out with the defined sequences by counting the hit number over 10,000 independent DLS runs for all the cases up to N = 5. It was found that the hit rate of a sequence is related to the size of the basic tetrahedra. U.e of this method proved that the Leary tetrahedral sequence is dominant in a certain range of cluster sizes, although the sequence has no potential energy advantage. The calculation results are also consistent with those of annealing experiments at high temperature, both in magic numbers and height of the peaks in the mass spectrum.

Journal Article↗

PubMed2005

Simultaneous wavelength selection and outlier detection in multivariate regression of near-infrared spectra.

Near-infrared (NIR) spectrometry will present a more promising tool for quantitative measurement if the robustness and predictive ability of the partial least square (PLS) model are improved. In order to achieve the purpose, we present a new algorithm for simultaneous wavelength selection and outlier detection; at the same time, the problems of background and noise in multivariate calibration are also solved. The strategy is a combination of continuous wavelet transform (CWT) and modified iterative predictors and objects weighting PLS (mIPOW-PLS). CWT is performed as a pretreatment tool for eliminating background and noise synchronously; then, mIPOW-PLS is proposed to remove both the useless wavelengths and the multiple outliers in CWT domain. After pretreatment with CWT-mIPOW-PLS, a PLS model is built finally for prediction. The results indicate that the combination of CWT and mIPOW-PLS produces robust and parsimonious regression models with very few wavelengths.

Journal Article↗

PubMed2004

A new hybrid strategy for constructing a robust calibration model for near-infrared spectral analysis.

A new hybrid algorithm is proposed for construction of a high-quality calibration model for near-infrared (NIR) spectra that is robust against both spectral interference (including background and noise) and multiple outliers. The algorithm is a combination of continuous wavelet transform (CWT) and a modified iterative reweighted PLS (mIRPLS) procedure. In the proposed algorithm the spectral interference is filtered by CWT at the first stage then mIRPLS is proposed to detect the multiple outliers in the CWT domain. Compared with the original IRPLS method, mIRPLS does not need to adjust variable parameters to achieve optimum calibration results, which makes it very convenient to perform in practice. The final PLS model is constructed robustly because both the spectral interference and multiple outliers are eliminated. In order to validate the effectiveness and universality of the algorithm, it was applied to two different sets of NIR spectra. The results indicate that the proposed strategy can greatly enhance the robustness and predictive ability of NIR spectral analysis.

Journal Article↗

PubMed2004

A dynamic lattice searching method for fast optimization of Lennard-Jones clusters.

A highly efficient unbiased global optimization method called dynamic lattice searching (DLS) was proposed. The method starts with a randomly generated local minimum, and finds better solution by a circulation of construction and searching of the dynamic lattice (DL) until the better solution approaches the best solution. The DL is constructed adaptively based on the starting local minimum by searching the possible location sites for an added atom, and the DL searching is implemented by iteratively moving the atom located at the occupied lattice site with the highest energy to the vacant lattice site with the lowest energy. Because the DL can greatly reduce the searching space and the number of the time-consuming local minimization procedures, the proposed DLS method runs at a very high efficiency, especially for the clusters of larger size. The performance of the DLS is investigated in the optimization of Lennard-Jones (LJ) clusters up to 309 atoms, and the structure of the LJ(500) is also predicted. Furthermore, the idea of dynamic lattice can be easily adopted in the optimization of other molecular or atomic clusters. It may be a promising approach to be universally used for structural optimizations in the chemistry field.

Journal Article↗

PubMed2004

Extraction of mass spectra and chromatographic profiles from overlapping GC/MS signal with background.

An adaptive immune algorithm (AIA) was proposed for resolution of the overlapping GC/MS signal with background. By using AIA, the chromatographic profiles corresponding to the independent components (ICs) in the overlapping signal are calculated with the mass spectra extracted by means of independent component analysis (ICA). The number of the ICs in the overlapping signal is determined by the difference between the reconstructed and the original data. Both simulated and experimental data are investigated with the proposed AIA approach. It was found that the mass spectra and chromatographic profiles of the components in an overlapping multicomponent GC/MS signal can be accurately resolved with the existence of background, and the results are better than that by using an interactive self-modeling mixture analysis (SIMPLISMA) method. The AIA approach may be a promising tool for the resolution of overlapping GC/MS signal.

Journal Article↗

PubMed2004

An adaptive immune optimization algorithm for energy minimization problems.

Based on the immune theory of biology, a novel evolutionary algorithm, adaptive immune optimization algorithm (AIOA), is proposed. In AIOA, density regulation and immune selection is adopted to control the individual diversity and the convergence adaptively. By an application of the algorithm to the optimization of test functions, it is shown that the algorithm is a highly efficient optimization method compared with other stochastic optimization methods. The algorithm was also applied to the optimization of Lennard-Jones clusters, and the results show that the method can find the optimal structure of N</=80 with a very high efficiency. The proposed algorithm may be a good tool for fast global optimization in chemical or biological molecular simulations.

Journal Article↗

PubMed2004

Variable selection by modified IPW (iterative predictor weighting)-PLS (partial least squares) in continuous wavelet regression models.

Variable selection is often used to produce more robust and parsimonious regression models. But when they are applied directly to the raw near-infrared spectra, it is not easy to select appropriate variables because background and noise will often overshadow or overlap the absorption bands of analyte. In this work, a new hybrid algorithm based on the selection of the most informative variables in the continuous wavelet transform (CWT) domain is described. The strategy is a combination of CWT and a procedure of modified iterative predictor weighting-partial least square (mIPW-PLS). After elimination of the background and noise in NIR spectra by CWT, the mIPW-PLS approach is used to select the most informative CWT coefficients. With the selected CWT coefficients, a PLS model is built finally for prediction. It is indicated that the extraction of most important variables in the CWT domain can effectively avoid the interference of background and noise, and result in a high quality of regression model with a very small number of variables and fewer PLS components.

Journal Article↗

PubMed2004

An improved transmutation method for quantitative determination of the components in multicomponent overlapping chromatograms.

An improved method is proposed for the quantitative determination of multicomponent overlapping chromatograms based on a known transmutation method. To overcome the main limitation of the transmutation method caused by the oscillation generated in the transmutation process, two techniques--wavelet transform smoothing and the cubic spline interpolation for reducing data points--were adopted, and a new criterion was also developed. By using the proposed algorithm, the oscillation can be suppressed effectively, and quantitative determination of the components in both the simulated and experimental overlapping chromatograms is successfully obtained.

Journal Article↗