Biomedical subjects

Jian-Hui Jiang

Publications and source records attributed to Jian-Hui Jiang.

At least 19 recordsLinked to original sources

PubMed2007

Support vector machine based training of multilayer feedforward neural networks as optimized by particle swarm algorithm: application in QSAR studies of bioactivity of organic compounds.

Multilayer feedforward neural networks (MLFNNs) are important modeling techniques widely used in QSAR studies for their ability to represent nonlinear relationships between descriptors and activity. However, the problems of overfitting and premature convergence to local optima still pose great challenges in the practice of MLFNNs. To circumvent these problems, a support vector machine (SVM) based training algorithm for MLFNNs has been developed with the incorporation of particle swarm optimization (PSO). The introduction of the SVM based training mechanism imparts the developed algorithm with inherent capacity for combating the overfitting problem. Moreover, with the implementation of PSO for searching the optimal network weights, the SVM based learning algorithm shows relatively high efficiency in converging to the optima. The proposed algorithm has been evaluated using the Hansch data set. Application to QSAR studies of the activity of COX-2 inhibitors is also demonstrated. The results reveal that this technique provides superior performance to backpropagation (BP) and PSO training neural networks.

Algorithms↗

PubMed2006

Ag/SiO2 core-shell nanoparticle-based surface-enhanced Raman probes for immunoassay of cancer marker using silica-coated magnetic nanoparticles as separation tools.

A simple, sensitive and highly specific immunoassay has been developed based on surface-enhanced Raman scattering for human alpha-fetoprotein (AFP), a tumor marker for the diagnosis of hepatocellular carcinoma. This strategy combines the Ag/SiO2 core-shell nanoparticles embedded with rhodamine B isothiocyanate dye molecules as Raman tags and the amino group modified silica-coated magnetic nanoparticle as immobilization matrix and separation tool. In the proposed system, a sandwich-type immunoassay was performed between polyclonal antibody functionalized Ag/SiO2 nanoparticle-based Raman tags and monoclonal antibody modified silica-coated magnetic nanoparticles. The presence of the analyte and the reaction between the antigen and antibody can be monitored by the Raman spectra of the Ag/SiO2 tags. Compared to the previous surface-enhanced Raman immunoassays, the main advantage of this strategy lies in two aspects. One is the high stability of Raman tags derived from the silica shell-coated silver core-shell nanostructure. The other is the use of silica-coated magnetic nanoparticles as immobilization matrix and separation tool, thus avoiding complicated pretreatment and washing steps. We have studied in detail the experimental parameters such as the effects of the antibody concentration modified on the Raman tags and on the magnetic particles, and the immunoreaction time. Using this strategy, concentration of human AFP up to 0.12 microg/ml was detected with a detection limit of 11.5 pg/ml.

Biomarkers, Tumor↗

PubMed2006

QCM detection of DNA targets with single-base mutation based on DNA ligase reaction and biocatalyzed deposition amplification.

A novel biosensing technique for highly specific identification of gene with single-base mutation is proposed based on the implementation of the DNA ligase reaction and the biocatalyzed deposition of an insoluble product. The target gene mediated deposition of an insoluble precipitate is then transduced by quartz crystal microbalance (QCM) measurements. In this method, the DNA target hybridizes with a capture DNA probe tethered onto the gold electrode and then with a biotinylated allele-specific detection DNA. A ligase reaction is performed to generate the ligation between the capture and the detection probes, provided there is perfect match between the DNA target and the detection probe. Otherwise even when there is an allele mismatch between them, no ligation would take place. After thermal treatment at an elevated temperature, the formed duplex melts apart that merely allows the detection probe perfectly matched with the target to remain on the electrode surface. The presence of the biotinylated allele-matched probe is then detected by the QCM via the binding to streptavidin-peroxide horseradish (SA-HRP), which catalyzes the oxidative precipitation of 3,3-diaminobenzidine (DAB) by H2O2 on the electrode and provides an amplified frequency response. The proposed approach has been successfully implemented for the identification of single-base mutation in -28 site of the beta-thalassemia gene with a detection limit of 0.1 nM, demonstrating that this method provides a highly specific and cost-efficient approach for point mutation detection.

Biosensing Techniques↗

PubMed2006

Characterization of chloramphenicol palmitate drug polymorphs by Raman mapping with multivariate image segmentation using a spatial directed agglomeration clustering method.

Chemical imaging analysis holds great potential in probing the chemical heterogeneity of samples with high spatial resolution and molecular specificity. This paper demonstrates the implementation of Raman mapping for microscopic characterization of tablets containing chloramphenicol palmitate polymorphs with the aid of a new multivariate image segmentation approach based on spatial directed agglomeration clustering. This approach performs the agglomeration clustering by stepwise merging the pixels possessing both spatial closeness and spectral similarity into clusters that define the image segmentation. The incorporation of spatial closeness into the clustering process enables the approach to improve the robustness and avoid poorly defined image segmentation arising from clusters with highly separated pixels. Additionally, the stepwise merging of clusters offers an F-statistic-based procedure to automatically ascertain the number of image segments. Raman mapping analysis of tablets containing two polymorphs of chloramphenicol palmitate followed by multivariate image segmentation reveals that the proposed technique offers the identification of each polymorph and a quantitative visualization of the spatial distribution of the polymorphs identified. This technique holds promise in rapid, noninvasive, and quantitative polymorph analysis for pharmaceutical production processes.

Chloramphenicol↗

PubMed2006

A novel piezoelectric immunoagglutination assay technique with antibody-modified liposome.

A simple rapid piezoelectric immunoagglutination assay (PEIA) technique with antibody-modified liposome has been developed for direct quantitative detection of human immunoglobulin G (hIgG). This technique is based on specific agglutination of antibody-coated liposome particles in the presence of the corresponding antigen, which can be monitored by the frequency shift of a piezoelectric device. Compared with conventional piezoelectric assays, this liposome-based PEIA does not require the immobilization of antigen or antibody on the quartz crystal surface, making the developed technique especially useful for rapid and renewable immunochemical determination. To alleviate non-specific adsorption of serum proteins, modification of the quartz crystal surface by different protocols and the composition of the assay medium have been investigated. The results indicate that the background interference can be substantially minimized through modifying the quartz crystal surface with a bovine serum albumin (BSA) layer and introducing an appropriate amount of BSA in the assay medium. The effects of the liposome composition, the liposome concentration and the concentration of poly(ethylene glycol) (PEG) in the assay medium, have also been investigated. The frequency responses of the liposome-based PEIA are linearly correlated to hIgG concentration in the range of 0.05-6 microg mL(-1) with a detection limit of 50 ng mL(-1).

Agglutination Tests↗

PubMed2006

Boosting support vector regression in QSAR studies of bioactivities of chemical compounds.

In this paper, boosting has been coupled with SVR to develop a new method, boosting support vector regression (BSVR). BSVR is implemented by firstly constructing a series of SVR models on the various weighted versions of the original training set and then combining the predictions from the constructed SVR models to obtain integrative results by weighted median. The proposed BSVR algorithm has been used to predict toxicities of nitrobenzenes and inhibitory potency of 1-phenyl[2H]-tetrahydro-triazine-3-one analogues as inhibitors of 5-lipoxygenase. As comparisons to this method, the multiple linear regression (MLR) and conventional support vector regression (SVR) have also been investigated. Experimental results have shown that the introduction of boosting drastically enhances the generalization performance of individual SVR model and BSVR is a well-performing technique in QSAR studies superior to multiple linear regression.

Algorithms↗

PubMed2006

Synthesis and characterization of surface-enhanced Raman scattering tags with Ag/SiO2 core-shell nanostructures using reverse micelle technology.

A novel simplified method for synthesis of surface-enhanced Raman scattering tags has been reported. This synthesis method is based on reverse micelle technique using Igepal CO-520 as a surfactant and the mixed solution of silver nitrate and rhodamine dyes with isothiocyanate group as water pool followed by hydrazine hydrate reduction and TEOS polymerization leading to the formation of silica layer surrounding the silver core. Compared to the method reported in literature, the proposed methodology eliminates the necessity of vitrophilic pretreatment and makes it possible to complete all different processes including the preparation of silver nanoparticles, the conjugation of dye molecules and the formation of silica shell in the microreactor. The nanoparticle-based surface-enhanced Raman tags obtained are composed of silver core conjugated with rhodamine dyes and an encasing silica shell. Both the dyes themselves and the Ag/SiO2 core-shell nanoparticles without the encapsulation of dyes exhibit no Raman signals. However, the Ag/SiO2 core-shell nanoparticles exhibit strong Raman signals when encapsulated with these dyes. This is due to the appearance of fluorescence quenching and surface-enhanced Raman scattering effect resulting from the conjugation of dyes and silver core. The Raman tags were characterized using transmission electron microscopy (TEM), UV-visible absorption spectrometry, and Raman spectrometry.

Metal Nanoparticles↗

PubMed2006

Optical detection of DNA hybridization based on fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles.

A novel system for the detection of DNA hybridization in a homogeneous format is developed. This method is based on fluorescence quenching by gold nanoparticles used as both nanoscaffolds for the immobilization of capture sequences and nanoquenchers of fluorophores attached to detection sequences. The oligonucleotide-functionalized gold nanoparticles are synthesized by derivatizing the colloidal gold solution with 5'-thiolated 12-base oligonucleotides. Introduction of sequence-specific target DNAs (24 bases) into the mixture containing dye-tagged detection sequences and oligonucleotide-functionalized gold nanoparticles results in the quenching of carboxytetramethylrhodamine-labeled DNA fluorescence because DNA hybridization occurs and brings fluorophores into close proximity with oligonucleotide-functionalized gold nanoparticles. The quenching efficiency of fluorescence increases with the target DNA concentration and provides a quantitative measurement of sequence-specific DNA in sample. A linearity is obtained within the range from 1.4 to 92 nM. The target sequence is detected down to 2 nM. This new system not only overcomes many of the drawbacks inherent in radioisotopic measurement or enzyme-linked assay but also avoids the requirement for the stem-loop structure compared with conventional molecular beacons. Furthermore, the background signal that is defined as fluorescence quenching arising from electrostatic attraction between positively charged fluorophores and negatively charged gold nanoparticles is comparatively low due to electrostatic repulsion between negatively charged oligonucleotides. In addition, this is a homogeneous assay that can offer the potential to be monitored in real time, be amenable to automation, eliminate washing steps, and reduce the risk of contamination.

Biosensing Techniques↗

PubMed2006

Chemometric classification of traditional Chinese medicines by their geographical origins using near-infrared reflectance spectra.

Some raw materials that have different places of production for the plant sources of the drugs Astragalus membranaceus and ginseng have been studied, based on their near-infrared reflectance spectra. The experimentally recorded spectra represent heavily ill-posed and highly correlative data sets. Three related methods, i.e. the Fisher linear discriminant analysis (FLDA), the ridge-type linear discriminant analysis (RLDA) and a newly proposed penalized ridge-type linear discriminant analysis (PRLDA), have been investigated. FLDA over-fits for the training objects of the two data sets to a high extent and is unstable for the predictive objects of the two data sets. RLDA shows obvious improvement in terms of over-fitting and unstability, but the stability for the predictive objects of the two data sets is too sensitive to their ridge-type penalized weights, tending to produce erroneous discrimination results. The proposed PRLDA can circumvent the two aforementioned problems with a large domain of penalized weights for correct discriminant analysis of the two data sets studied. The combination of the PRLDA method and near infrared reflectance spectroscopy can be adapted for the discrimination of the production places of plant sources of these drugs.

Algorithms↗

PubMed2005

A colorimetric method for point mutation detection using high-fidelity DNA ligase.

The present study reported proof-of-principle for a genotyping assay approach that can detect single nucleotide polymorphisms (SNPs) through the gold nanoparticle assembly and the ligase reaction. By incorporating the high-fidelity DNA ligase (Tth DNA ligase) into the allele-specific ligation-based gold nanoparticle assembly, this assay provided a convenient yet powerful colorimetric detection that enabled a straightforward single-base discrimination without the need of precise temperature control. Additionally, the ligase reaction can be performed at a relatively high temperature, which offers the benefit for mitigating the non-specific assembly of gold nanoparticles induced by interfering DNA strands. The assay could be implemented via three steps: a hybridization reaction that allowed two gold nanoparticle-tagged probes to hybrid with the target DNA strand, a ligase reaction that generates the ligation between perfectly matched probes while no ligation occurred between mismatched ones and a thermal treatment at a relatively high temperature that discriminate the ligation of probes. When the reaction mixture was heated to denature the formed duplex, the purple color of the perfect-match solution would not revert to red, while the mismatch gave a red color as the assembled gold nanoparticles disparted. The present approach has been demonstrated with the identification of a single-base mutation in codon 12 of a K-ras oncogene that is of significant value for colorectal cancers diagnosis, and the wild-type and mutant type were successfully scored. To our knowledge, this was the first report concerning SNP detection based on the ligase reaction and the gold nanoparticle assembly. Owing to its ease of operation and high specificity, it was expected that the proposed procedure might hold great promise in practical clinical diagnosis of gene-mutant diseases.

Cell Line↗

PubMed2005

QSAR analysis of substituted bis[(acridine-4-carboxamide)propyl]methylamines using optimized block-wise variable combination by particle swarm optimization for partial least squares modeling.

In the current work, we employed optimized block-wise variable combination (OBVC) by particle swarm optimization (PSO) based on partial least squares (PLS) modeling for variable combination and compared it to the traditional methods. It has been demonstrated that the modified PSO is a useful tool for searching optimized variable combination. Quantitative structure-activity relationship (QSAR) model has been formulated for a set of DNA binding topoisomerase (topo) (substituted bis[(acridine-4-carboxamide)propyl]methylamines) on murine Lewis lung carcinoma (LL(c)) cells. The spatial descriptors especially Jurs descriptors play important roles in predicting the compound's inhibitory activity to murine LL(c) cells, and polar interactions are the principal binding strength between compounds and murine LL(c) cells. In addition, rotatable bonds in molecules and molar refractivity of the compounds will markedly affect the compounds' inhibitory activity.

Acridines↗

PubMed2005

Optochemical sensor for an ornidazole assay using 1-amino-4-allyloxyanthraquinone as a fluorescent indicator.

To improve the stability of optochemical sensors (optodes), the fluorescence indicator 1-amino-4-allyloxyanthraquinone (AAA), which was synthesized by reacting allyl bromide with 1-amino-4-hydroxyanthraquinone, was covalently immobilized on surface-modified glass slides. The resulting sensor was used to determine the content of ornidazole based on fluorescence quenching. It showed a linear response toward ornidazole in the concentration range of 9.0 x 10(-6) to 1.0 x 10(-3) mol L(-1) with a detection limit of 8 x 10(-6) mol L(-1) at pH 7.5. This AAA-immobilized sensor has a rapid response, high stability and good selectivity to ornidazole.

Anthraquinones↗

PubMed2005

Oral immunization of mice with vaccine of attenuated Salmonella typhimurium expressing Helicobacter pylori urease B subunit.

OBJECTIVE: To prepare the live recombinant vaccine of attenuated Salmonella typhimurium SL3261 expressing Helicobacter pylori (H. pylori) B subunit (UreB) and to determine whether it could be used as an oral vaccine against H. pylori infection. METHODS: Using genomic DNA of H. pylori Sydney strain (SSI) as template, the H. pylori UreB gene fragment was amplified by PCR and subcloned into the expression vector pTC01. The recombinant plasmid pTC01-UreB was then transferred into LB5000 to obtain modified forms, and further conversed into the attenuated Salmonella typhimurium SL3261 to obtain recombinant SL3261/pCT01-UreB as an oral immunization reagent, which was then used to orally immunize Balb/c mice twice at a three-week interval. Twelve weeks later, anti-UreB IgA antibodies in intestinal fluid and IgG antibodies in sera were determined by ELISA. The relating data in control groups (including body weight, gastric inflammation, etc.) were also collected. RESULTS: The sequencing analysis showed that the UreB gene fragment amplified by PCR was consistent with the sequence of the H. pylori UreB gene. The restriction enzyme digestion revealed that the correct pTC01-UreB was obtained. SDS-PAGE and Western blot showed that a 61KD protein was expressed in SL3261/pTC01-UreB, which could be recognized by anti-H. pylori UreB antiserum and was absent in the control containing only Salmonella typhimurium SL3261 strain. The multiple oral immunization with SL3261/pTC01-UreB could significantly induce H. pylori specific mucosal IgA response as well as serum IgG responses. IFN-gamma and IL-10 levels were significantly increased in SL3261/pTC01-UreB group, and no obvious side effect and change in gastric inflammation were observed. CONCLUSION: The attenuated vaccine of Salmonella typhimurium expressing H. pylori UreB can be used as an oral vaccine against H. pylori infection.

Animals↗

PubMed2004

Hybridized particle swarm algorithm for adaptive structure training of multilayer feed-forward neural network: QSAR studies of bioactivity of organic compounds.

The multilayer feed-forward ANN is an important modeling technique used in QSAR studying. The training of ANN is usually carried out only to optimize the weights of the neural network and without paying attention to the network topology. Some other strategies used to train ANN are, first, to discover an optimum structure of the network, and then to find weights for an already defined structure. These methods tend to converge to local optima, and may also lead to overfitting. In this article, a hybridized particle swarm optimization (PSO) approach was applied to the neural network structure training (HPSONN). The continuous version of PSO was used for the weight training of ANN, and the modified discrete PSO was applied to find appropriate the network architecture. The network structure and connectivity are trained simultaneously. The two versions of PSO can jointly search the global optimal ANN architecture and weights. A new objective function is formulated to determine the appropriate network architecture and optimum value of the weights. The proposed HPSONN algorithm was used to predict carcinogenic potency of aromatic amines and biological activity of a series of distamycin and distamycin-like derivatives. The results were compared to those obtained by PSO and GA training in which the network architecture was kept fixed. The comparison demonstrated that the HPSONN is a useful tool for training ANN, which converges quickly towards the optimal position, and can avoid overfitting in some extent.

Journal Article↗

PubMed2004

QSAR analysis of cyclooxygenase inhibitor using particle swarm optimization and multiple linear regression.

Quantitative structure-activity relationship (QSAR) models of inhibiting action of some diarylimidazole derivatives on cylcooxygenase (COX) enzyme were constructed using modified particle swarm optimization (PSO) method. As a comparison to this method, the genetic algorithm (GA) was also tested. It has been demonstrated that the modified PSO is a useful tool for variable selection comparable to GA and even superior to GA. QSAR models are constructed separately for COX-2 inhibitory activity and selectivity of COX-2 inhibition over COX-1. The spatial descriptors play a key role in the compounds' activity and selectivity to COX-2, especially Jurs descriptors. Polar interactions are the principal binding strength between compounds and COX-2 enzyme. In addition, the aqueous desolvation free energy (FH2O) value of substituent will affect the COX-2 inhibitory activity, while the charge distribution can affect the selectivity to COX-2.

Cyclooxygenase Inhibitors↗

PubMed2004

Chinese literature associated with diagnosis of Helicobacter pylori.

AIM: To synthetically analyze and probe into the diagnosis of H pylori infection, we followed the principles of evidence-based medicine. METHODS: A total of 22 papers of prevalence survey and case-control studies were selected for studying about diadynamic methods. Using meta-analysis, we analyzed the different diadynamic methods of H pylori in China. RESULTS: Through meta-analysis, among the five diadynamic methods, the accuracy of polymerase chain reaction (PCR) was the highest (98.47%) and PCR was the most sensitive method (Sp: 99.03%). CONCLUSION: Among the five diadynamic methods, the accuracy of PCR is the highest and PCR is the most sensitive method to diagnose the infection of H pylori.

Asian People↗

PubMed2004

Modified particle swarm optimization algorithm for variable selection in MLR and PLS modeling: QSAR studies of antagonism of angiotensin II antagonists.

A version of modified particle swarm optimization (PSO) algorithm has been proposed. The PSO algorithm has been modified to adopt to the discrete combinatorial optimization problem and reduce the probability of sinking into local optima. In the modified PSO algorithm, the velocity represents the probability of element in each particle taking value 1 or 0. The modified discrete PSO algorithm is proposed to select variables in MLR and PLS modeling and to predict antagonism of angiotensin II antagonists. The modified C(p) is employed as fitness function. The results were compared to those obtained by GAs. Experimental results have demonstrated that the modified PSO is a useful tool for variable selection which converges quickly towards the optimal position.

Algorithms↗

PubMed2003

Competitive interactions of adriamycin and ethidium bromide with DNA as studied by full rank parallel factor analysis of fluorescence three-way array data.

The competitive interactions of adriamycin (AMC) and a fluorescence probe of ethidium bromide (EB) with DNA have been studied by full rank parallel factor analysis (FRA-PARAFAC) of fluorescence excitation-emission three-way data array. The excitation and emission spectra as well as the equilibrium concentrations of co-existing species in different reaction mixtures can be directly obtained by the FRA-PARAFAC treatment. The concordance of the resolved excitation and emission spectra of AMC, EB and EB-DNA with the standard spectra of these species confirmed the reliability of the equilibrium concentrations of these components in the reaction mixtures studied. The results obtained are valuable for providing a deeper insight into the competitive interaction mechanism of AMC and EB with DNA. The conclusion was directly given out that the interaction of AMC with DNA is the intercalating model. The FRA-PARAFAC method as exemplified by the present study provides an useful approach for studying the interaction of clinical drugs with DNA in the presence of disturbance of drug assistants.

Algorithms↗