Publications by authors named "Yan-Ping Zhou"

24 Publications

  • Page 1 of 1

A cross-sectional seroepidemiology study of seven major enteroviruses causing HFMD in Guangdong, China.

J Infect 2021 07 16;83(1):119-145. Epub 2021 Apr 16.

National Institutes for Food and Drug Control, No.31, Huatuo Street, Beijing, P.R. China. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jinf.2021.04.011DOI Listing
July 2021

Efficacy of a coxsackievirus A6 vaccine candidate in an actively immunized mouse model.

Emerg Microbes Infect 2021 Dec;10(1):763-773

Wuhan Institute of Biological Products Co. Ltd., Wuhan, People's Republic of China.

Coxsackievirus A6 (CV-A6) has been emerging as a major pathogen of hand, foot and mouth disease (HFMD). Study on the pathogenesis of CV-A6 infection and development of vaccines is hindered by a lack of appropriate animal models. Here, we report an actively immunized-challenged mouse model to evaluate the efficacy of a Vero-cell-based, inactivated CV-A6 vaccine candidate. The neonatal Kunming mice were inoculated with a purified, formaldehyde-inactivated CV-A6 vaccine on days 3 and 9, followed by challenging on day 14 with a naturally selected virulent strain at a lethal dose. Within 14 days postchallenge, all mice in the immunized groups survived, while 100% of the Alum-only inoculated mice died. Neutralizing antibodies (NtAbs) were detected in the serum of immunized suckling mice, and the NtAb levels correlated with the survival rate of the challenged mice. The virus loads in organs were reduced, and pathological changes and viral protein expression were weak in the immunized mice compared with those in Alum-only inoculated control mice. Elevated levels of interleukin-4, 6, interferon γ and tumour necrosis factor α were also observed in Alum-only control mice compared with immunized mice. Importantly, the virulent CV-A6 challenge strain was selected quickly and conveniently from a RD cell virus stock characterized with the natural multi-genotypes. The virulent determinants were mapped to V124M and I242 V at VP1. Together, our results indicated that this actively immunized mouse model is invaluable for future studies to develop multivalent vaccines containing the major component of CV-A6 against HFMD.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/22221751.2021.1906755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8079124PMC
December 2021

Low toxicity and high immunogenicity of an inactivated vaccine candidate against COVID-19 in different animal models.

Emerg Microbes Infect 2020 Dec;9(1):2606-2618

National Institutes for Food and Drug Control, Beijing, People's Republic of China.

The ongoing COVID-19 pandemic is causing huge impact on health, life, and global economy, which is characterized by rapid spreading of SARS-CoV-2, high number of confirmed cases and a fatality/case rate worldwide reported by WHO. The most effective intervention measure will be to develop safe and effective vaccines to protect the population from the disease and limit the spread of the virus. An inactivated, whole virus vaccine candidate of SARS-CoV-2 has been developed by Wuhan Institute of Biological Products and Wuhan Institute of Virology. The low toxicity, immunogenicity, and immune persistence were investigated in preclinical studies using seven different species of animals. The results showed that the vaccine candidate was well tolerated and stimulated high levels of specific IgG and neutralizing antibodies. Low or no toxicity in three species of animals was also demonstrated in preclinical study of the vaccine candidate. Biochemical analysis of structural proteins and purity analysis were performed. The inactivated, whole virion vaccine was characterized with safe double-inactivation, no use of DNases and high purity. Dosages, boosting times, adjuvants, and immunization schedules were shown to be important for stimulating a strong humoral immune response in animals tested. Preliminary observation in ongoing phase I and II clinical trials of the vaccine candidate in Wuzhi County, Henan Province, showed that the vaccine is well tolerant. The results were characterized by very low proportion and low degree of side effects, high levels of neutralizing antibodies, and seroconversion. These results consistent with the results obtained from preclinical data on the safety.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/22221751.2020.1852059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7733911PMC
December 2020

Adenosine A receptor activation prevents DOCA-salt induced hypertensive cardiac remodeling via iBAT.

Biochem Biophys Res Commun 2020 Feb 19. Epub 2020 Feb 19.

State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Hypertensive cardiac remodeling is a constellation of abnormalities that includes cardiomyocyte hypertrophy and death and tissue fibrosis. Adenosine is a long-known vasodilator, through interacting with its four cell surface receptor subtypes in cardiovascular system. However, it is unclear that whether adenosine A receptor (AR) activation is involved in the cardiac remodeling in hypertension. WT mice were utilized to induce DOCA-salt sensitive hypertension and received AR agonist CGS21680 or antagonist KW6002 treatment. Cardiac functional phenotyping measurement by echocardiography showed that CGS21680 improved cardiac dysfunction in DOCA-salt mice. Moreover, CGS21680 reduced cardiomyocyte hypertrophy, cardiac inflammation and fibrosis. However, iBAT depletion surgery induces dramatic cardiac remodeling in DOCA-salt mice, and the protective function of CGS21680 was blocked without intact iBAT. Mechanistically, AR agonist CGS21680 increased iBAT-derived fibroblast growth factor 21 (FGF21). Our data suggest that activation of AR could be a potential therapeutic strategy in preventing heart damage in hypertension.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbrc.2020.02.035DOI Listing
February 2020

Decrease of Perivascular Adipose Tissue Browning Is Associated With Vascular Dysfunction in Spontaneous Hypertensive Rats During Aging.

Front Physiol 2018 18;9:400. Epub 2018 Apr 18.

State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Department of Hypertension at Ruijin Hospital and Shanghai Institute of Hypertension, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Functional perivascular adipose tissue (PVAT) is necessary to maintain vascular physiology through both mechanical support and endocrine or paracrine ways. PVAT shows a brown adipose tissue (BAT)-like feature and the browning level of PVAT is dependent on the anatomic location and species. However, it is not clear whether PVAT browning is involved in the vascular tone regulation in spontaneously hypertensive rats (SHRs). In the present study, we aimed to illustrate the effect of aging on PVAT browning and subsequent vasomotor reaction in SHRs. Herein we utilized histological staining and western blot to detect the characteristics of thoracic PVAT (tPVAT) in 8-week-old and 16-week-old SHR and Wistar-Kyoto (WKY) rats. We also detected vascular reactivity analysis to determine the effect of tPVAT on vasomotor reaction during aging. The results showed that tPVAT had a similar phenotype to BAT, including smaller adipocyte size and positive uncoupling protein-1 (UCP1) staining. Interestingly, the tPVAT of 8-week-old SHR showed increased BAT phenotypic marker expression compared to WKY, whereas the browning level of tPVAT had a more dramatic decrease from 8 to 16 weeks of age in SHR than age-matched WKY rats. The vasodilation effect of tPVAT on aortas had no significant difference in 8-week-old WKY and SHR, whereas this effect is obviously decreased in 16-week-old SHR compared to WKY. In contrast, tPVAT showed a similar vasoconstriction effect in 8- or 16-week-old WKY and SHR rats. Moreover, we identified an important vasodilator adenosine, which regulates adipocyte browning and may be a potential PVAT-derived relaxing factor. Adenosine is dramatically decreased from 8 to 16 weeks of age in the tPVAT of SHR. In summary, aging is associated with a decrease of tPVAT browning and adenosine production in SHR rats. These may result in attenuated vasodilation effect of the tPVAT in SHR during aging.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fphys.2018.00400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5915562PMC
April 2018

Triterpenoid Saponins from Anemone rivularis var. Flore-Minore and Their Anti-Proliferative Activity on HSC-T6 Cells.

Molecules 2018 Feb 23;23(2). Epub 2018 Feb 23.

Institute of Materia Medica, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.

Five previously undescribed triterpenoid saponins (-), along with eight known ones (-), were isolated from the whole plants of var. . Their structures were clarified by extensive spectroscopic data and chemical evidence. For the first time, the lupane-type saponins ( and ) were reported from the genus. The anti-proliferative activity of all isolated saponins was evaluated on hepatic stellate cells (HSC-T6). Saponins and , which possess more monosaccharides than the others, displayed potent anti-proliferative activity, with IC values of 18.21 and 15.56 μM, respectively.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/molecules23020491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6017197PMC
February 2018

Prognostic values of long non-coding RNA MIR22HG for patients with hepatocellular carcinoma after hepatectomy.

Oncotarget 2017 Dec 11;8(69):114041-114049. Epub 2017 Dec 11.

Chinese Medicine Pharmacy of Integrative Medicine Center, 302 Hospital of People's Liberation Army, Beijing, People's Republic of China.

Hepatocellular carcinoma (HCC) is the fifth most frequently diagnosed cancer worldwide and the second most frequent cause of cancer death. The aim of this study is to identify the association between the expression of long non-coding RNA (lncRNA) MIR22HG and the clinical and tumor characteristics of patients with HCC, and to explore the prognostic significance of lncRNA MIR22HG on patients with HCC. We retrospectively reviewed 127 patients with HCC(42 female, 85 male) who were managed in our hospital between May 1 2010 and June 30 2016. The expressions of lncRNA MIR22HG were detected by real-time PCR. Prognostic factors were evaluated using Kaplan-Meier curves and Cox proportional hazards models. For the entire cohort of 127 patients, the normalized real-time PCR showed that the expression of lncRNA MIR22HG was lower in HCC tissues compared with corresponding nontumorous tissues. MTT assay showed that si-MIR22HG remarkably inhibited the proliferation tumor cells in three HCC cell lines including SMMC-7721, Huh-7 and Hep3B. Moreover, under-expression of MIR22HG was closely related to tumor encapsulation, microvascular invasion (MVI), and TNM stage. Cox proportional hazards analysis demonstrated that lncRNA MIR22HG under-expression was an independent risk factor associated with the prognosis of patients with HCC. In conclusion, we found that lncRNA MIR22HG expressed significantly lower in HCC tissues compared with non-tumorous tissues. Under-expression of lncRNAMIR22HG was an independent risk factor associated with the prognosis of patients with HCC.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18632/oncotarget.23110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768384PMC
December 2017

A systematic review and meta-analysis comparing the prognosis of multicentric occurrence and vs. intrahepatic metastasis in patients with recurrent hepatocellular carcinoma after hepatectomy.

HPB (Oxford) 2017 10 19;19(10):835-842. Epub 2017 Jul 19.

Department of Traditional Chinese Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, PR China.

Background: The aim of this meta-analysis was to evaluate the prognosis of patients with different types of hepatocellular cancer (HCC) recurrence following hepatectomy. Specifically, it evaluated overall survival and disease-free survival in HCC patients with multicentric occurrence (MO) or intrahepatic metastasis (IM).

Methods: Medline, Cochrane, EMBASE, and Google Scholar were searched until August 22, 2016 using the following search terms: hepatocellular carcinoma, multicentric occurrence, intrahepatic metastasis, early recurrence, and late recurrence. Prospective, retrospective, and case control studies were included.

Results: The pooled results showed that patients in the MO group had lower risk of death than the IM group (pooled HR = 0.495, 95% CI = 0.378 to 0.648, P < 0.001). The MO group also had significantly longer disease-free survival than the IM group (pooled HR = 0.774, 95% CI = 0.663 to 0.903, P = 0.001). Sensitivity analysis indicated that no one study dominated the findings and that the data are robust. Overall the included studies were of good quality.

Conclusion: This study found that MO patients have greater survival following surgery than IM patients, indicating the prognosis of MO patients is significantly better than that for IM patients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.hpb.2017.06.002DOI Listing
October 2017

Adverse events of monoclonal antibodies used for cancer therapy.

Biomed Res Int 2015 5;2015:428169. Epub 2015 May 5.

Department of Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.

In 1997, the first monoclonal antibody (MoAb), the chimeric anti-CD20 molecule rituximab, was approved by the US Food and Drug administration for use in cancer patients. Since then, the panel of MoAbs that are approved by international regulatory agencies for the treatment of hematopoietic and solid malignancies has continued to expand, currently encompassing a stunning amount of 20 distinct molecules for 11 targets. We provide a brief scientific background on the use of MoAbs in cancer therapy, review all types of monoclonal antibodies-related adverse events (e.g., allergy, immune-related adverse events, cardiovascular adverse events, and pulmonary adverse events), and discuss the mechanism and treatment of adverse events.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1155/2015/428169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4436450PMC
March 2016

Inhibition of TRB3 Protects Photoreceptors against Endoplasmic Reticulum Stress-Induced Apoptosis after Experimental Retinal Detachment.

Curr Eye Res 2016 10;41(2):240-8. Epub 2015 Apr 10.

a Department of Ophthalmology , Shanghai First People's Hospital, School of Medicine, Shanghai JiaoTong University , Shanghai , China .

Purpose: To investigate the expression of tribbles homologue 3 (TRB3) and its regulation on endoplasmic reticulum stress (ERS)-induced photoreceptor apoptosis after retinal detachment (RD) using a rat model.

Methods: RD animal model was created in Wistar rats by subretinal injection of 1% sodium hyaluronate. At various time points after RD, expression of TRB3 was detected by quantitative real-time PCR and Western blotting. TRB3 protein distribution in retina was evaluated by immunohistochemistry. RNA interference was used to inhibit TRB3 expression and subretinal injection of lentivirus TRB3 shRNA (LV-TRB3-sh) was performed. The rats were then randomly divided into four groups: normal control group, RD group, vehicle + RD group and LV-TRB3-sh + RD group. The mRNA and protein level of TRB3 as well as Caspase-12 were detected. TdT-mediated fluorescein-16-dUTP nick-end labeling (TUNEL) assay was used to detect the apoptosis of retinal cells. Retinal outer nuclear layer (ONL) thickness was measured to assess retina damage in each group.

Results: TRB3 expression and TRB3-positive cell count were significantly increased after RD and peaked at day 3 after RD. The ratio of TUNEL-positive photoreceptors and expression of ERS-induced apoptosis marker Caspase-12 in LV-TRB3-sh + RD group were significantly reduced. The ONL thickness in LV-TRB3-sh + RD group was thicker than that both in RD group and vehicle + RD group.

Conclusion: TRB3 expression is up-regulated in retinas after RD and knockdown of TRB3 protects photoreceptors against ERS-induced apoptosis. TRB3 may be a crucial molecule in photoreceptor apoptosis induced by ERS after RD.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3109/02713683.2015.1006371DOI Listing
October 2016

The origin and development of plaques and phosphorylated tau are associated with axonopathy in Alzheimer's disease.

Neurosci Bull 2011 Oct;27(5):287-99

Wuhan Institute for Neuroscience and Neuroengineering, South-Central University for Nationalities, Wuhan 430074, China.

Objective: The production of neurotoxic β-amyloid and the formation of hyperphosphorylated tau are thought to be critical steps contributing to the neuropathological mechanisms in Alzheimer's disease (AD). However, there remains an argument as to their importance in the onset of AD. Recent studies have shown that axonopathy is considered as an early stage of AD. However, the exact relationship between axonopathy and the origin and development of classic neuropathological changes such as senile plaques (SPs) and neurofibrillary tangles (NFTs) is unclear. The present study aimed to investigate this relationship.

Methods: Postmortem tracing, combined with the immunohistochemical or immunofluorescence staining, was used to detect axonopathy and the formation of SPs and NFTs.

Results: Axonal leakage-a novel type of axonopathy, was usually accompanied with the extensive swollen axons and varicosities, and was associated with the origin and development of Aβ plaques and hyperphosphorylated tau in the brains of AD patients.

Conclusion: Axonopathy, particularly axonal leakage, might be a key event in the initiation of the neuropathological processes in AD.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12264-011-1736-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560317PMC
October 2011

A robust boosting regression tree with applications in quantitative structure-activity relationship studies of organic compounds.

J Chem Inf Model 2011 Apr 18;51(4):816-28. Epub 2011 Mar 18.

Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, P. R. China.

A regression tree (RT) was extensively utilized in quantitative structure-activity relationship studies (QSAR), due to its inherently promising attributes. The issues of instability and inclination to overfitting and suboptima, however, often occur in RT. In the present study, a robust version of boosting was invoked to simultaneously improve the stability and generalization ability of RT, forming a new method called robust boosting regression tree (RBRT). RBRT works by sequentially employing the RT method to model the robustly reweighted versions of the original training set and then aggregating these resultant predictors via weighted median. The designed RBRT was applied to predict the bioactivities of flavoniod derivatives and the anti-HIV activities of HIV-1 inhibitors, compared with boosting RT (BRT) and RT. The results of these two data sets demonstrated that the introduction of robust boosting drastically enhances the stability and generalization ability of RT, and RBRT is superior to BRT in QSAR studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci100429uDOI Listing
April 2011

Cloning, molecular characterization of a 13-kDa antigen from Schistosoma japonicum, Sj13, a putative salivary diagnosis candidate for Schistosomiasis japonica.

Parasitol Res 2009 Oct 29;105(5):1435-44. Epub 2009 Jul 29.

Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.

Saliva has been suggested as an easily accessible and a noninvasive diagnostic alternative for detection of antibodies. To identify and characterize Schistosoma japonicum (S. japonicum) antigens that are recognized by saliva of infected host, we have used a pool of saliva from infected patients to immunoscreen an egg cDNA library of S. japonicum. The open reading frame of the isolated two clones encodes same protein of 116 amino acids exhibiting 100% identity to an amino acid sequence (AY222893) of S. japonicum in NCBInr database. The protein encoded is inferred a secretory protein with a molecular mass of 13 kDa (Sj13) and shares no homology to any entries in the NCBInr database, demonstrating that Sj13 might be a schistosome-specific protein. Reverse transcriptase polymerase chain reaction, Western blotting, and immunolocalization analysis revealed Sj13 could be detected in cercaria, adult, and egg and was localized to forehead and tegument of cercaria, cell body ("cytons") of adult worm, egg shell, and epidermal plate of miracidium. Furthermore, Sj13 showed a good antigenicity when reacted with saliva or serum from schistosomiasis patients. The recombinant Sj13 (rSj13) expressed and purified from Escherichia coli was applied to detect its specific salivary antibody for schistosomiasis diagnosis by an indirect enzyme linked immunosorbent assay (ELISA). Preliminary laboratory test of 116 subjects, 40 with parasitologically proven S. japonicumm infection, 46 with other infectious diseases, and 30 negative controls exhibited 92.50% sensitivity with saliva/rSj13 and 95.00% with serum/SWAP (P > 0.05). The specificity of the ELISA using saliva/rSj13 was 92.11% versus 85.53% with serum/SWAP (P < 0.05). No direct correlations of anti-Sj13 IgG levels with egg counts in stool were observed in saliva detection. These results suggest that Sj13 specific salivary antibody detection may be useful as an antigen for the salivary diagnosis of schistosomiasis japonica and contribute to epidemiological study of schistosomiasis infection in endemic areas.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00436-009-1575-xDOI Listing
October 2009

Modified particle swarm optimization algorithm for adaptively configuring globally optimal classification and regression trees.

J Chem Inf Model 2009 May;49(5):1144-53

Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.

The configuration of classification and regression trees (CART) used to include tree-growing by greedy recursive partitioning, which selects the splitting parameters (i.e., splitting variables and values) involved in tree, and tree-pruning, which aims to obtain a final tree of right size. This method is successful for most applications; however, it presents some well-known limitations and drawbacks, such as, less comprehensibility, inclination to overfitting, and suboptima. In the present study, the modified discrete particle swarm optimization method was invoked to adaptively configure the globally optimal CART (MPSOCART) via simultaneously selecting the optimal splitting parameters in CART and the appropriate structure of CART. A new objective function was formulated to decide the appropriate CART architecture and the optimum splitting parameters. The proposed MPSOCART was applied to predict the bioactivities of flavonoid derivatives and inhibitory activities of inhibitors of epidermal growth factor receptor tyrosine kinase, compared with partial least-squares and CART induced by greedy recursive partitioning. The comparison revealed that MPSO was a useful tool for inducing a globally optimal CART, which converges fast to the optimal solution and avoid overfitting in great extent.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci800374hDOI Listing
May 2009

Expression profile, localization of an 8-kDa calcium-binding protein from Schistosoma japonicum (SjCa8), and vaccine potential of recombinant SjCa8 (rSjCa8) against infections in mice.

Parasitol Res 2009 Mar 18;104(4):733-43. Epub 2008 Nov 18.

Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd road, Guangzhou 510080, China.

Researches on genes expressed in a cercarial stage-specific manner may help us understand the molecular events and functions during schistosome invasion of skin. A genomic clone encoding 8-kDa calcium-binding protein (SjCa8) specifically expressed in cercariae and skin-stage schistosomulum (transformed within 3 h) was obtained from cercariae. Recombinant protein was expressed in vector pET32a (+) and purified using a Ni-NTA purification system. The target protein SjCa8 was determined by matrix-assisted laser desorption/ionization time-of-flight (TOF)/TOF mass spectrometer after thrombin digestion and dialysis. Reverse transcriptase polymerase chain reaction and Western blot revealed SjCa8 can be detected in cercaria and skin-stage schistosomulum but not lung-stage schistosomulum, adult, or egg and was localized to head gland, penetration gland tubes, and penetration glands where Ca(2+) was abundant, and the cercarial tegument (but not tegument of tail) and body-tail junction. Furthermore, SjCa8 was interestingly detected in cercarial secretions. The characterization of SjCa8 indicated that it may undergo structural and physiological modifications, including repair of the surface membrane, changes in permeability that account for the loss of water tolerance, activities of calcium-depending enzymes, and immune signaling, etc. Furthermore, vaccination with rSjCa8 plus adjuvant induced protective effect with 50.39% worm reduction rate and significantly high hepatic and intestine egg reduction rates (54.16%, 50.63%, respectively), which is possibly mediated through an apparent induction of Th1-type immune response for strikingly high level of IgG2a and IgG2b developed in immunized C57BL/6 mice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00436-008-1249-0DOI Listing
March 2009

Ensemble preprocessing of near-infrared (NIR) spectra for multivariate calibration.

Anal Chim Acta 2008 Jun 20;616(2):138-43. Epub 2008 Apr 20.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.

Preprocessing of raw near-infrared (NIR) spectral data is indispensable in multivariate calibration when the measured spectra are subject to significant noises, baselines and other undesirable factors. However, due to the lack of sufficient prior information and an incomplete knowledge of the raw data, NIR spectra preprocessing in multivariate calibration is still trial and error. How to select a proper method depends largely on both the nature of the data and the expertise and experience of the practitioners. This might limit the applications of multivariate calibration in many fields, where researchers are not very familiar with the characteristics of many preprocessing methods unique in chemometrics and have difficulties to select the most suitable methods. Another problem is many preprocessing methods, when used alone, might degrade the data in certain aspects or lose some useful information while improving certain qualities of the data. In order to tackle these problems, this paper proposes a new concept of data preprocessing, ensemble preprocessing method, where partial least squares (PLSs) models built on differently preprocessed data are combined by Monte Carlo cross validation (MCCV) stacked regression. Little or no prior information of the data and expertise are required. Moreover, fusion of complementary information obtained by different preprocessing methods often leads to a more stable and accurate calibration model. The investigation of two real data sets has demonstrated the advantages of the proposed method.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.aca.2008.04.031DOI Listing
June 2008

Determination of glucose in plasma by dry film-based Fourier transformed-infrared spectroscopy coupled with boosting support vector regression.

Anal Sci 2007 Jul;23(7):793-8

State Key Laboratory of Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, PR China.

In the present study, a dry film-based Fourier transformed-infrared (FT-IR) spectroscopic technique, coupled with boosting support vector regression (BSVR), was employed for a blood glucose assay. Potassium thiocyanate (KSCN) was taken in the dry-film method as an internal standard to compensate for any film thickness variation. This technique circumvents interference from water absorption, and requires only 5 microl of a sample. Moving window partial least-squares regression (MWPLSR) was used for wavenumber interval selection before multivariate modeling. By using the BSVR modeling technique, glucose in plasma could be determined over a 0.4 - 20 mmol/l concentration range with satisfactory accuracy. The performance of the BSVR methodology was compared with that of conventional support vector regression (SVR) as well as partial-least squares (PLS). The results demonstrated that BSVR is an effective multivariate calibration tool, providing better performance than conventional PLS and SVR.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2116/analsci.23.793DOI Listing
July 2007

Radial basis function network-based transform for a nonlinear support vector machine as optimized by a particle swarm optimization algorithm with application to QSAR studies.

J Chem Inf Model 2007 Jul-Aug;47(4):1438-45. Epub 2007 Jun 8.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.

The support vector machine (SVM) has been receiving increasing interest in an area of QSAR study for its ability in function approximation and remarkable generalization performance. However, selection of support vectors and intensive optimization of kernel width of a nonlinear SVM are inclined to get trapped into local optima, leading to an increased risk of underfitting or overfitting. To overcome these problems, a new nonlinear SVM algorithm is proposed using adaptive kernel transform based on a radial basis function network (RBFN) as optimized by particle swarm optimization (PSO). The new algorithm incorporates a nonlinear transform of the original variables to feature space via a RBFN with one input and one hidden layer. Such a transform intrinsically yields a kernel transform of the original variables. A synergetic optimization of all parameters including kernel centers and kernel widths as well as SVM model coefficients using PSO enables the determination of a flexible kernel transform according to the performance of the total model. The implementation of PSO demonstrates a relatively high efficiency in convergence to a desired optimum. Applications of the proposed algorithm to QSAR studies of binding affinity of HIV-1 reverse transcriptase inhibitors and activity of 1-phenylbenzimidazoles reveal that the new algorithm provides superior performance to the backpropagation neural network and a conventional nonlinear SVM, indicating that this algorithm holds great promise in nonlinear SVM learning.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci700047xDOI Listing
October 2007

QSAR study of angiotensin II antagonists using robust boosting partial least squares regression.

Anal Chim Acta 2007 Jun 24;593(1):68-74. Epub 2007 Apr 24.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.

In the current study, robust boosting partial least squares (RBPLS) regression has been proposed to model the activities of a series of 4H-1,2,4-triazoles as angiotensin II antagonists. RBPLS works by sequentially employing PLS method to the robustly reweighted versions of the training compounds, and then combing these resulting predictors through weighted median. In PLS modeling, an F-statistic has been introduced to automatically determine the number of PLS components. The results obtained by RBPLS have been compared to those by boosting partial least squares (BPLS) repression and partial least squares (PLS) regression, showing the good performance of RBPLS in improving the QSAR modeling. In addition, the interaction of angiotensin II antagonists is a complex one, including topological, spatial, thermodynamic and electronic effects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.aca.2007.04.031DOI Listing
June 2007

Artificial neural network-based transformation for nonlinear partial least-square regression with application to QSAR studies.

Talanta 2007 Feb 27;71(2):848-53. Epub 2006 Jun 27.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P R.China.

In the present study a new version of nonlinear partial least-square method based on artificial neural network transformation (ANN-NLPLS) has been proposed. This algorithm firstly transforms the training descriptors into the hidden layer outputs using the universal nonlinear mapping carried by an artificial neural network, and then utilizes PLS to relate the outputs of the hidden layer to the bioactivities. The weights between the input and hidden layers are optimized by a particle swarm optimization (PSO) method using the criterion of minimized model error via PLS modeling. An F-statistic is introduced to determine automatically the number of PLS components during the weight optimization. The performance is assessed using a simulated data set and two quantitative structure-activity relation (QSAR) data sets. Results of these three data sets demonstrate that ANN-NLPLS offers enhanced capacity in modeling nonlinearity while circumventing the overfitting frequently involved in nonlinear modeling.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.talanta.2006.05.058DOI Listing
February 2007

Optimized sample-weighted partial least squares.

Talanta 2007 Feb 12;71(2):561-6. Epub 2006 Jun 12.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.

In ordinary multivariate calibration methods, when the calibration set is determined to build the model describing the relationship between the dependent variables and the predictor variables, each sample in the calibration set makes the same contribution to the model, where the difference of representativeness between the samples is ignored. In this paper, by introducing the concept of weighted sampling into partial least squares (PLS), a new multivariate regression method, optimized sample-weighted PLS (OSWPLS) is proposed. OSWPLS differs from PLS in that it builds a new calibration set, where each sample in the original calibration set is weighted differently to account for its representativeness to improve the prediction ability of the algorithm. A recently suggested global optimization algorithm, particle swarm optimization (PSO) algorithm is used to search for the best sample weights to optimize the calibration of the original training set and the prediction of an independent validation set. The proposed method is applied to two real data sets and compared with the results of PLS, the most significant improvement is obtained for the meat data, where the root mean squared error of prediction (RMSEP) is reduced from 3.03 to 2.35. For the fuel data, OSWPLS can also perform slightly better or no worse than PLS for the prediction of the four analytes. The stability and efficiency of OSWPLS is also studied, the results demonstrate that the proposed method can obtain desirable results within moderate PSO cycles.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.talanta.2006.04.039DOI Listing
February 2007

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.

J Comput Chem 2007 Jan;28(2):519-27

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcc.20561DOI Listing
January 2007

Adaptive configuring of radial basis function network by hybrid particle swarm algorithm for QSAR studies of organic compounds.

J Chem Inf Model 2006 Nov-Dec;46(6):2494-501

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.

The configuring of a radial basis function network (RBFN) consists of selecting the network parameters (centers and widths in RBF units and weights between the hidden and output layers) and network architecture. The issues of suboptimum and overfitting, however, often occur in RBFN configuring. This paper presented a hybrid particle swarm optimization (HPSO) algorithm to simultaneously search the optimal network structure and parameters involved in the RBFN (HPSORBFN) with an ellipsoidal Gaussian function as a basis function. The continuous version of PSO was used for parameter training, while the modified discrete PSO was employed to determine the appropriate network topology. The proposed HPSORBFN algorithm was applied to modeling the inhibitory activities of substituted bis[(acridine-4-carboxamide)propyl]methylamines to murine P388 leukemia cells and the bioactivities of COX-2 inhibitors. The results were compared with those obtained from RBFNs with the parameters optimized by continuous PSO and by conventionally RBFN training the algorithm for a fixed network topology, indicating that the HPSO was competent for RBFN configuring in that it converged quickly toward the optimal solution and avoided overfitting.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci600218dDOI Listing
February 2007

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

Eur J Pharm Sci 2006 Jul 18;28(4):344-53. Epub 2006 Apr 18.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejps.2006.04.002DOI Listing
July 2006
-->