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1.  VHH Phage-Based Competitive Real-Time Immuno-Polymerase Chain Reaction for Ultrasensitive Detection of Ochratoxin A in Cereal 
Analytical Chemistry  2014;86(15):7471-7477.
Phage display-mediated immuno-polymerase chain reaction (PD-IPCR) is an ultrasensitive detection technology that combines the advantages of immuno-PCR and phage display. The phage particle, which displayed antibody fragments including single-chain fragment variable (scFv), variable domain of heavy-chain antibodies (VHH), and antigen-binding fragment (Fab) on the surface can be directly used in IPCR, supplying both the detection antibody and deoxyribonucleic acid (DNA) template. In this work, we used ochratoxin A (OTA) as a model system to study the capacity of PD-IPCR in the detection of toxic small molecular weight compounds, especially mycotoxins. An alpaca-derived VHH library was constructed and subjected to four cycles of panning. In total, 16 clones with four unique sequences were selected by competitive binding with OTA. The clone VHH-28 resulted in the lowest 50% inhibitory concentration of 0.31 ng/mL in the phage enzyme-linked immunosorbent assay (ELISA) and was selected to develop the VHH phage-based real-time immuno-PCR (RT-IPCR). The detection limit of the VHH phage-based RT-IPCR was 3.7 pg/L, with a linear range of 0.01–1000 pg/mL. This method was compared with conventional ELISA, and validation results indicated the reliability of VHH phage-based RT-IPCR in the detection of OTA in cereal samples. This study provides a new idea for the ultrasensitive detection of mycotoxins and other toxic small molecular weight compounds.
PMCID: PMC4306448  PMID: 24992514
2.  Levo-tetrahydropalmatine attenuates oxaliplatin-induced mechanical hyperalgesia in mice 
Scientific Reports  2014;4:3905.
Common chemotherapeutic agents such as oxaliplatin often cause neuropathic pain during cancer treatment in patients. Such neuropathic pain is difficult to treat and responds poorly to common analgesics, which represents a challenging clinical issue. Corydalis yanhusuo is an old traditional Chinese medicine with demonstrated analgesic efficacy in humans. However, the potential analgesic effect of its active component, levo-tetrahydropalmatine (l-THP), has not been reported in conditions of neuropathic pain. This study found that l-THP (1–4 mg/kg, i.p.) produced a dose-dependent anti-hyperalgesic effect in a mouse model of chemotherapeutic agent oxaliplatin-induced neuropathic pain. In addition, we found that the anti-hyperalgesic effect of l-THP was significantly blocked by a dopamine D1 receptor antagonist SCH23390 (0.02 mg/kg), suggesting a dopamine D1 receptor mechanism. In contrast, l-THP did not significantly alter the general locomotor activity in mice at the dose that produced significant anti-hyperalgesic action. In summary, this study reported that l-THP possesses robust analgesic efficacy in mice with neuropathic pain and may be a useful analgesic in the management of neuropathic pain.
PMCID: PMC3904142  PMID: 24469566
3.  Rehabilitation training improves exercise tolerance after percutaneous coronary intervention 
Journal of Biomedical Research  2012;26(4):248-252.
The aim of this present study was to investigate the effects of training on exercise tolerance of patients with coronary heart disease after percutaneous coronary intervention. Fifty-seven cases of coronary heart disease after percutaneous coronary intervention were divided randomly into the rehabilitation training group (26 cases) and control group (31 cases). Patients in the rehabilitation training group received rehabilitation training at different stages and exercise intensities 3 d after percutaneous coronary intervention for 3 months. The heart rate, blood pressure, ECG changes in treadmill exercise test, and the frequency of anginal episodes were observed. The results showed that NST and ΣST of ECG and the frequency of anginal episodes were significantly reduced in the rehabilitation training group. In addition, exercise tolerance was improved and the total exercise time was lengthened in these patients. Moreover, ST segment depression time and emergence time of angina with exercise were also lengthened compared with controls (P < 0.05, or 0.01). However, the heart rate and blood pressure before and after exercise of the two groups were similar. The study indicated that rehabilitation training could significantly relieve angina, amend ischemic features of ECG, and improve exercise tolerance of coronary heart disease patients after percutaneous coronary intervention.
PMCID: PMC3596740  PMID: 23554756
coronary heart disease; percutaneous coronary intervention; rehabilitation training; exercise tolerance; treadmill exercise test
4.  Propofol pharmacokinetics in China: A multicentric study 
Indian Journal of Pharmacology  2012;44(3):393-397.
A multicenter population pharmacokinetics study of propofol was performed to establish a new population model.
Materials and Methods:
Three thousand two hundred and fifty-nine blood samples of 220 participants were measured by HPLC-UV or HPLC-FLU or GC-MS. Target-controlled infusion after single bolus or continuous infusion was applied for propofol anesthesia. The samples were taken from 2 to 1500 min. The concentration-time profiles were analyzed by nonlinear mixed effect model (NONMEM) with first order estimation method. The inter-individual variability and the residual variability were described by exponential model and constant coefficient variation model. The stepwise modeling strategy using PsN was applied for covariate modeling. The criteria of forward addition and backward elimination were (α = 0.01 and α = 0.005, χ2, df = 1). The final model was evaluated by bootstrap using PDx and visual predictive check using PsN. 500 bootstraps and 1000 simulation were run.
The propofol population model was described by 3-compartment model with inter-individual variability of CL, V1, Q2, and Q3 describing by exponential model. The inter-individual variability of V2, V3 were not included because it is reported that the parameter was near its boundary. The typical value of CL, V1, Q2, V2, Q3 and V3 were 1.28 L · min-1, 10.1 × (age/44)-0.465 × (1 + 0.352 × sex) L, 0.819 L · min-1, 36.0 L, 0.405 × (bodyweight/60)1.58 L · min-1 and 272 L, respectively. Coefficients of inter-individual variability of CL, V1, Q2 and Q3 were 30.5%, 35.6%, 43.7% and 66.9%, respectively, and the coefficients of variation of HPLC-UV, GC-MS and HPLC-FLU were 13.3%, 16.9% and 24.2%, respectively. The bootstrap evaluation showed that the final model parameter estimates were within ± 3.39% compared with bootstrap median. The curves of observations percentiles were distributed within the corresponding 95 prediction percentiles by the visual predictive check.
The three-compartment model with first-order elimination could describe the pharmacokinetics of propofol fairly well. The involved fixed effects are age, body weight and sex. The population model was evaluated to be stable by bootstrap and visual predictive check.
PMCID: PMC3371467  PMID: 22701254
Propofol; multicenter; nonlinear mixed effect model
5.  GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes 
Bioinformatics (Oxford, England)  2004;20(18):3710-3715.
GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script.
The full source code and documentation for GO::TermFinder are freely available from
PMCID: PMC3037731  PMID: 15297299
6.  Implementation of GenePattern within the Stanford Microarray Database 
Nucleic Acids Research  2008;37(Database issue):D898-D901.
Hundreds of researchers across the world use the Stanford Microarray Database (SMD; to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.
PMCID: PMC2686537  PMID: 18953035
7.  TB database: an integrated platform for tuberculosis research 
Nucleic Acids Research  2008;37(Database issue):D499-D508.
The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. The promise of the genomics era for TB control is substantial, but has been hindered by the lack of a central repository that collects and integrates genomic and experimental data about this organism in a way that can be readily accessed and analyzed. The Tuberculosis Database (TBDB) is an integrated database providing access to TB genomic data and resources, relevant to the discovery and development of TB drugs, vaccines and biomarkers. The current release of TBDB houses genome sequence data and annotations for 28 different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces. In addition, TBDB provides access to a suite of comparative genomics and microarray analysis software. By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB ( provides a unique discovery platform for TB research.
PMCID: PMC2686437  PMID: 18835847
8.  OntologyWidget – a reusable, embeddable widget for easily locating ontology terms 
BMC Bioinformatics  2007;8:338.
Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form.
We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website [1]. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat [2] on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format.
We have developed OntologyWidget, an easy-to-use ontology search and display tool that can be used on any web page by creating a simple html description. OntologyWidget provides a rapid auto-complete search function paired with an interactive tree display. We have developed a web service layer that communicates between the web page interface and a database of ontology terms. We currently store 40 of the ontologies from the OBO website [1], as well as a several others. These ontologies are automatically updated on a weekly basis. OntologyWidget can be used in any web-based application to take advantage of the ontologies we provide via web services or any other ontology that is provided elsewhere in the correct format. The full source code for the JavaScript and description of the OntologyWidget is available from .
PMCID: PMC2080642  PMID: 17854506
9.  The Stanford Microarray Database: implementation of new analysis tools and open source release of software 
Nucleic Acids Research  2006;35(Database issue):D766-D770.
The Stanford Microarray Database (SMD; ) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release.
PMCID: PMC1781111  PMID: 17182626
10.  The Stanford Microarray Database: data access and quality assessment tools 
Nucleic Acids Research  2003;31(1):94-96.
The Stanford Microarray Database (SMD; serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 3500 microarrays, including data from 85 publications, and this total is increasing rapidly. In this article, we describe some of SMD's newer tools for accessing public data, assessing data quality and for data analysis.
PMCID: PMC165525  PMID: 12519956
11.  SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data 
Nucleic Acids Research  2003;31(1):219-223.
The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. SOURCE's GeneReports include aliases, chromosomal location, functional descriptions, GeneOntology annotations, gene expression data, and links to external databases. We curate published microarray gene expression datasets and allow users to rapidly identify sets of co-regulated genes across a variety of tissues and a large number of conditions using a simple and intuitive interface. SOURCE provides content both in gene and cDNA clone-centric pages, and thus simplifies analysis of datasets generated using cDNA microarrays. SOURCE is continuously updated and contains the most recent and accurate information available for human, mouse, and rat genes. By allowing dynamic linking to individual gene or clone reports, SOURCE facilitates browsing of large genomic datasets. Finally, SOURCEs batch interface allows rapid extraction of data for thousands of genes or clones at once and thus facilitates statistical analyses such as assessing the enrichment of functional attributes within clusters of genes. SOURCE is available at
PMCID: PMC165461  PMID: 12519986
12.  The Stanford Microarray Database 
Nucleic Acids Research  2001;29(1):152-155.
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.). SMD makes use of many public resources to connect expression information to the relevant biology, including SGD [Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H. et al. (2000) Nucleic Acids Res., 28, 77–80], YPD and WormPD [Costanzo,M.C., Hogan,J.D., Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E., Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et al. (2000) Nucleic Acids Res., 28, 73–76], Unigene [Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Nucleic Acids Res., 28, 10–14], dbEST [Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332–333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45–48] and can be accessed at
PMCID: PMC29818  PMID: 11125075
13.  Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data 
Nucleic Acids Research  2001;29(1):80-81.
Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the Saccharomyces Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at
PMCID: PMC29796  PMID: 11125055
14.  Integrating functional genomic information into the Saccharomyces Genome Database 
Nucleic Acids Research  2000;28(1):77-80.
The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the ‘locus page’ and directs users to the detailed information they seek. SGD is endeavoring to integrate the existing information about yeast genes with the large volume of data generated by functional analyses that are beginning to appear in the literature and on web sites. New features will include searches of systematic analyses and Gene Summary Paragraphs that succinctly review the literature for each gene. In addition to current information, such as gene product and phenotype descriptions, the new locus page will also describe a gene product’s cellular process, function and localization using a controlled vocabulary developed in collaboration with two other model organism databases. We describe these developments in SGD through the newly reorganized locus page. The SGD is accessible via the WWW at http://genome-www. stanford. edu/Saccharomyces/
PMCID: PMC102447  PMID: 10592186

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