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Biomedical subjects

Wei Pan

Publications and source records attributed to Wei Pan.

At least 37 records · Page 2Linked to original sources
PubMed2006

[Comparative proteome analysis of hepatoma cells at subcellular level].

The subcellular proteome strategy can complement the separation power of two-dimensional electrophoresis, a step for subcellular fractionation is introduced before electrophoresis is conducted, and more proteins will be displayed in two-dimensional gels. A comparative analysis of proteomic profiling of mitochondria and nuclei was conducted between hepatoma cell and hepatocyte, in order to find more information involved in cancer development. The cultured hepatoma cell line QGY-7703 and hepatocyte line LO2 were used as research models in this work. Subcellular fractionation for mitochondrion and nucleus were done by ultracentrifugation, then two-dimensional electrophoresis was applied to the separation of mitochondrial and nuclear proteins, imaging analysis for the selection of differentially-expressed protein spots, and MALDI-TOF-MS for the identification of proteins. 54 spots from electrophoresis gels were selected as differentially-expressed protein for MS analysis which resulted in identification for 22 proteins. Among the 22 differentially-expressed proteins, 17 show a up-regulated expression and 5 show a down-regulated expression. These differentially-expressed proteins found in this work have a wide coverage of functions which are related to energy metabolism, cytosheleton, protein biosynthesis, pre-mRNA splicing and processing, apoptosis regulation. These results imply that cancer cell has experienced a fundamental change in structure and metabolism pattern.

Carcinoma, Hepatocellular↗
PubMed2006

[Proteomic approach to the effect of epirubicin on hepatoma cells at subcellular level].

Epirubicin is an antineoplastic agent known as an anthracycline. It acts directly on DNA by blocking its replication and transcription, so apoptosis can be induced for cancer cells. The protein expression of cancer cells will be altered due to the induction of pharmacological action of epirubicin, so it is important to pay attention to the altered profiling of proteins. Here proteomic strategy was applied to the hepatoma cells at subcellular level, comparative proteome analysis of mitochondria and nucleus were conducted between the hepatoma cells administered with epirubicin and the not-administered. Centrifugation was used for the subcellular fractionation, then 2-DE for the separation of proteins, imaging analysis for the diction of expression-altered spots, and MALDI-TOF-MS for the identification of proteins. In total, 15 proteins were found to have altered their expression after the induction of epirubicin, among them, 5 proteins showed up-regulated expression and 10 showed down-regulated expression. These altered proteins are involved in life processes of cells such as energy metabolism, protein biosynthesis, structure of cell skeleton, processing and maturation of mRNA, heat shock of cells and apoptosis.

Carcinoma, Hepatocellular↗
PubMed2005

Small-sample performance of the robust score test and its modifications in generalized estimating equations.

The sandwich variance estimator of generalized estimating equations (GEE) may not perform well when the number of independent clusters is small. This could jeopardize the validity of the robust Wald test by causing inflated type I error and lower coverage probability of the corresponding confidence interval than the nominal level. Here, we investigate the small-sample performance of the robust score test for correlated data and propose several modifications to improve the performance. In a simulation study, we compare the robust score test to the robust Wald test for correlated Bernoulli and Poisson data, respectively. It is confirmed that the robust Wald test is too liberal whereas the robust score test is too conservative for small samples. To explain this puzzling operating difference between the two tests, we consider their applications to two special cases, one-sample and two-sample comparisons, thus motivating some modifications to the robust score test. A modification based on a simple adjustment to the usual robust score statistic by a factor of J/(J - 1) (where J is the number of clusters) reduces the conservativeness of the generalized score test. Simulation studies mimicking group-randomized clinical trials with binary and count responses indicated that it may improve the small-sample performance over that of the generalized score and Wald tests with test size closer to the nominal level. Finally, we demonstrate the utility of our proposal by applying it to a group-randomized clinical trial, trying alternative cafeteria options in schools (TACOS).

Adolescent↗
PubMed2005

Electrochemical synthesis of gold nanocrystals and their 1D and 2D organization.

Size-controlled gold nanocrystals were conveniently synthesized through direct electroreduction of bulk AuCl(4)(-) ions in the presence of poly(N-vinylpyrrolidone) (PVP). PVP greatly enhanced the gold particle formation process and also significantly retarded the gold electrodeposition process, allowing the electrochemical synthesis of gold nanocrystals to be carried out in the form of simple electroreduction. This novel electrochemical method may be extended to synthesis of other noble metal nanoparticles with controllable size on a large scale. The PVPK90-protected gold nanocrystals spontaneously self-assembled into nearly ordered 2D close-packed arrays and interesting 1D nanostructures. The aggregation of unstable PVPK17-protected gold nanocrystals resulted in the formation of ultrathin single-crystalline films. PVP plays multifunctional roles in controlling the size and shape of gold nanocrystals and in inducing individual gold nanocrystals to construct 1D nanostructures. The nanoparticle self-assembling technique based on PVP offers a simple, but effective, path to organize individual gold nanoparticles into various 1D and 2D nanostructured materials.

Crystallization↗
PubMed2005

A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data.

MOTIVATION: False discovery rate (FDR) is defined as the expected percentage of false positives among all the claimed positives. In practice, with the true FDR unknown, an estimated FDR can serve as a criterion to evaluate the performance of various statistical methods under the condition that the estimated FDR approximates the true FDR well, or at least, it does not improperly favor or disfavor any particular method. Permutation methods have become popular to estimate FDR in genomic studies. The purpose of this paper is 2-fold. First, we investigate theoretically and empirically whether the standard permutation-based FDR estimator is biased, and if so, whether the bias inappropriately favors or disfavors any method. Second, we propose a simple modification of the standard permutation to yield a better FDR estimator, which can in turn serve as a more fair criterion to evaluate various statistical methods. RESULTS: Both simulated and real data examples are used for illustration and comparison. Three commonly used test statistics, the sample mean, SAM statistic and Student's t-statistic, are considered. The results show that the standard permutation method overestimates FDR. The overestimation is the most severe for the sample mean statistic while the least for the t-statistic with the SAM-statistic lying between the two extremes, suggesting that one has to be cautious when using the standard permutation-based FDR estimates to evaluate various statistical methods. In addition, our proposed FDR estimation method is simple and outperforms the standard method.

Algorithms↗
PubMed2005

A comparative study of discriminating human heart failure etiology using gene expression profiles.

BACKGROUND: Human heart failure is a complex disease that manifests from multiple genetic and environmental factors. Although ischemic and non-ischemic heart disease present clinically with many similar decreases in ventricular function, emerging work suggests that they are distinct diseases with different responses to therapy. The ability to distinguish between ischemic and non-ischemic heart failure may be essential to guide appropriate therapy and determine prognosis for successful treatment. In this paper we consider discriminating the etiologies of heart failure using gene expression libraries from two separate institutions. RESULTS: We apply five new statistical methods, including partial least squares, penalized partial least squares, LASSO, nearest shrunken centroids and random forest, to two real datasets and compare their performance for multiclass classification. It is found that the five statistical methods perform similarly on each of the two datasets: it is difficult to correctly distinguish the etiologies of heart failure in one dataset whereas it is easy for the other one. In a simulation study, it is confirmed that the five methods tend to have close performance, though the random forest seems to have a slight edge. CONCLUSIONS: For some gene expression data, several recently developed discriminant methods may perform similarly. More importantly, one must remain cautious when assessing the discriminating performance using gene expression profiles based on a small dataset; our analysis suggests the importance of utilizing multiple or larger datasets.

Data Interpretation, Statistical↗
PubMed2005

Does it always help to adjust for misclassification of a binary outcome in logistic regression?

It is well known that in logistic regression, where the outcome is measured with error, a biased estimate of the association between the outcome and a risk factor may result if no proper adjustment is made. Hence, it seems tempting to always adjust for possible misclassification of the outcome. Here we show that it is not always beneficial to do so because, though the adjustment reduces the bias, it also inflates the variance, leading to a possibly larger mean squared error of the estimate. In the context of a data set on agricultural injuries, numerical evidence is provided through simulation studies.

Accidents, Occupational↗
PubMed2005

Genome-wide localization of mobile elements: experimental, statistical and biological considerations.

BACKGROUND: The distribution and location of insertion elements in a genome is an excellent tool to track the evolution of bacterial strains and a useful molecular marker to distinguish between closely related bacterial isolates. The information about the genomic locations of IS elements is available in public sequence databases. However, the locations of mobile elements may vary from strain to strain and within the population of an individual strain. Tools that allow de novo localization of IS elements and are independent of existing sequence information are essential to map insertion elements and advance our knowledge of the role that such elements play in gene regulation and genome plasticity in bacteria. RESULTS: In this study, we present an efficient and reliable method for linear mapping of mobile elements using whole-genome DNA microarrays. In addition, we describe an algorithm for analysis of microarray data that can be applied to find DNA sequences physically juxtaposed with a target sequence of interest. This approach was used to map the locations of the IS5 elements in the genome of Escherichia coli K12. All IS5 elements present in the E. coli genome known from GenBank sequence data were identified. Furthermore, previously unknown insertion sites were predicted with high sensitivity and specificity. Two variants of E. coli K-12 MG1655 within a population of this strain were predicted by our analysis. The only significant difference between these two isolates was the presence of an IS5 element upstream of the main flagella regulator, flhDC. Additional experiments confirmed this prediction and showed that these isolates were phenotypically distinct. The effect of IS5 on the transcriptional activity of motility and chemotaxis genes in the genome of E. coli strain MG1655 was examined. Comparative analysis of expression profiles revealed that the presence of IS5 results in a mild enhancement of transcription of the flagellar genes that translates into a slight increase in motility. CONCLUSION: In summary, this work presents a case study of an experimental and analytical application of DNA microarrays to map insertion elements in bacteria and gains an insight into biological processes that might otherwise be overlooked by relying solely on the available genome sequence data.

DNA Transposable Elements↗
PubMed2005

Incorporating biological information as a prior in an empirical bayes approach to analyzing microarray data.

Currently the practice of using existing biological knowledge in analyzing high throughput genomic and proteomic data is mainly for the purpose of validations. Here we take a different approach of incorporating biological knowledge into statistical analysis to improve statistical power and efficiency. Specifically, we consider how to fuse biological information into a mixture model to analyze microarray data. In contrast to a standard mixture model where it is assumed that all the genes come from the same (marginal) distribution, including an equal prior probability of having an event, such as having differential expression or being bound by a transcription factor (TF), our proposed mixture model allows the genes in different groups to have different distributions while the grouping of the genes reflects biological information. Using a list of about 800 putative cell cycle-regulated genes as prior biological knowledge, we analyze a genome-wide location data to detect binding sites of TF Fkh1. We find that our proposal improves over the standard approach, resulting in reduced false discovery rates (FDR), and hence it is a useful alternative to the current practice.

Journal Article↗
PubMed2005

Small interfering RNA inhibits SARS-CoV nucleocapsid gene expression in cultured cells and mouse muscles.

SARS-CoV is a newly identified coronavirus that causes severe acute respiratory syndrome (SARS). Currently, there is no effective method available for prophylaxis and treatment of SARS-CoV infections. In the present study, the influence of small interfering RNA (siRNA) on SARS-CoV nucleocapsid (N) protein expression was detected in cultured cells and mouse muscles. Four siRNA expression cassettes driven by mouse U6 promoter targeting SARS-CoV N gene were prepared, and their inhibitory effects on expression of N and enhanced green fluorescence protein (EGFP) fusion protein were observed. A candidate siRNA was proved to down-regulate N and EGFP expression actively in a sequence-specific manner. The expression vector of this siRNA was constructed and confirmed to reduce N and EGFP expression efficiently in both cultured cells and adult mouse muscles. Our findings suggest that the siRNA should provide the basis for prophylaxis and therapy of SARS-CoV infection in human.

Animals↗
PubMed2005

Consecutive rotation of crystallographic orientation in lateral growth.

A consecutive rotation of crystallographic orientation has been observed in lateral crystallization of NH4Cl on a glass substrate, which induces a periodic distribution of faceted and roughened regions on the surface of a crystallite aggregate. Experimental observation indicates that this phenomenon derives from the asymmetric surface energies at the growth front, which deform the nascent nucleus and tilt the crystallographic orientation in the nucleation-mediated layered growth. We suggest that this effect is significant for a class of lateral growth where nucleation plays a dominate role.

Journal Article↗
PubMed2005

Genistein stimulates the osteoblastic differentiation via NO/cGMP in bone marrow culture.

The soybean phytoestrogen, genistein (Gen), has anabolic effects on bone through mechanisms that remain to be elucidated. We examined the role of nitric oxide (NO) and its downstream effector guanylyl cyclase (GC) in mediating the effects of Gen on the proliferation and osteoblastic maturation of primary mouse bone marrow-derived mesenchymal stem cells (BMSCs). Gen (10(-8) approximately 10(-6) M) resulted in a dose-dependent increase in cell proliferation as measured by increased [3H]thymidine incorporation, and stimulated osteoblastic maturation as assessed by culture duration-dependent increments in alkaline phosphatase (ALP) activity, calcium deposition into extracellular matrix and Runx2/Cbfa1 gene expression in BMSCs cultures. Gen also resulted in a dose-dependent increase in NO synthase (NOS) activity, NO formation, and cGMP production in BMSCs cultures. The effects of Gen were mimicked by 17beta-estradiol (E2, 10(-8) M). Concurrent treatment with the estrogen receptor (ER) antagonist ICI182,780 (10(-7) M) or the NOS inhibitor L-NAME (3 x 10(-3) M) diminished the Gen (10(-6) M)-mediated increase in NOS activity, NO production, and cGMP content. In contrast, a soluble GC inhibitor 1H-[1,2,4]oxadiazolo [4,3,-a]quinoxalin-1-one (ODQ, 10(-6) M) selectively blocked the Gen (10(-6) M)-mediated increase in cGMP content but not in NO production and NOS activity. Moreover, inhibition of ER, NOS activity or cGMP blocked Gen-induced proliferation and osteoblastic differentiation of BMSCs and Runx2/Cbfa1 gene expression in culture. Gen has estrogen-like activity and stimulates the proliferation and osteoblastic differentiation of mouse BMSCs at least in part through NO/cGMP pathway.

Alkaline Phosphatase↗
PubMed2005

Immune responses against SARS-coronavirus nucleocapsid protein induced by DNA vaccine.

The nucleocapsid (N) protein of SARS-coronavirus (SARS-CoV) is the key protein for the formation of the helical nucleocapsid during virion assembly. This protein is believed to be more conserved than other proteins of the virus, such as spike and membrane glycoprotein. In this study, the N protein of SARS-CoV was expressed in Escherichia coli DH5alpha and identified with pooled sera from patients in the convalescence phase of SARS. A plasmid pCI-N, encoding the full-length N gene of SARS-CoV, was constructed. Expression of the N protein was observed in COS1 cells following transfection with pCI-N. The immune responses induced by intramuscular immunization with pCI-N were evaluated in a murine model. Serum anti-N immunoglobulins and splenocytes proliferative responses against N protein were observed in immunized BALB/c mice. The major immunoglobulin G subclass recognizing N protein was immunoglobulin G2a, and stimulated splenocytes secreted high levels of gamma interferon and IL-2 in response to N protein. More importantly, the immunized mice produced strong delayed-type hypersensitivity (DTH) and CD8(+) CTL responses to N protein. The study shows that N protein of SARS-CoV not only is an important B cell immunogen, but also can elicit broad-based cellular immune responses. The results indicate that the N protein may be of potential value in vaccine development for specific prophylaxis and treatment against SARS.

Animals↗
PubMed2005

Machine safety evaluation in small metal working facilities: an evaluation of inter-rater reliability in the quantification of machine-related hazards.

BACKGROUND: Each year there are an estimated 4.2-6.7 amputations per 10,000 workers in the metal fabrication trades in the United States. The Minnesota Machine Guarding Study evaluates the effectiveness of a peer-based technical and educational intervention designed to reduce exposure to amputation hazards among workers in small machining/metal working shops. The study reported here involved the development and evaluation of methods for measuring machine safety, which will be used in the intervention study. METHODS: Using OSHA regulations, ANSI standards, and industry best practices, we developed 23 machine-safety scorecards. The safety scores were dependent on the presence or absence of guards, other safety devices and implements, and the presence or absence of acceptable administrative programs. Inter-rater reliability was assessed for the evaluation of eight types of commonly used metal fabrication machines. RESULTS: Of the 23 most common types of machines, there were a sufficient number of machines to evaluate inter-rater reliability for eight types. Three raters in four shops assessed fifty-nine machines. Overall, the kappa statistic ranged from 0.57 to 0.84, indicating good to very good concordance between raters. In general, machines did not fare well with regard to compliance with current standards. DISCUSSION: The ability to assess machine-related hazards is important in industries where it is difficult to identify and count injuries in a timely fashion. Machinists and safety professionals may use this scoring system as a means of reproducible assessment of machine safety.

Accidents, Occupational↗
PubMed2005

Family protection and prevention of alcohol use among Hispanic youth at high risk.

Research regarding prevention strategies for Hispanic youth stress the importance of family interventions because of the particular importance of family as a protective factor within the Hispanic community. Starting in 1995, the Center for Substance Abuse Prevention conducted the National Cross-Site Evaluation of High Risk Youth Programs, a 5-year drug and alcohol prevention study with a sample of approximately 10,500 youth, including nearly 3,000 Hispanic youth. Youth were surveyed regarding their alcohol use patterns and risk and protective factors, with several measures of family relationships, including family connectedness, family supervision, and parental attitudes toward their child's alcohol use. Analyses indicate that family factors are highly linked to alcohol use among Hispanics, particularly among Hispanic females. Longitudinal growth curve analyses indicate that improving the connections that young Hispanic females have to their parents can have positive long-term effects on delaying or reducing their alcohol use.

Adolescent↗
PubMed2005

Borrowing information from relevant microarray studies for sample classification using weighted partial least squares.

With an increasing number of publicly available microarray datasets, it becomes attractive to borrow information from other relevant studies to have more reliable and powerful analysis of a given dataset. We do not assume that subjects in the current study and other relevant studies are drawn from the same population as assumed by meta-analysis. In particular, the set of parameters in the current study may be different from that of the other studies. We consider sample classification based on gene expression profiles in this context. We propose two new methods, a weighted partial least squares (WPLS) method and a weighted penalized partial least squares (WPPLS) method, to build a classifier by a combined use of multiple datasets. The methods can weight the individual datasets depending on their relevance to the current study. A more standard approach is first to build a classifier using each of the individual datasets, then to combine the outputs of the multiple classifiers using a weighted voting. Using two quite different datasets on human heart failure, we show first that WPLS/WPPLS, by borrowing information from the other dataset, can improve the performance of PLS/PPLS built on only a single dataset. Second, WPLS/WPPLS performs better than the standard approach of combining multiple classifiers. Third, WPPLS can improve over WPLS, just as PPLS does over PLS for a single dataset.

Gene Expression Profiling↗