Biomedical subjects

Yi-Ju Chen

Publications and source records attributed to Yi-Ju Chen.

5 recordsLinked to original sources

PubMed2003

Effect of caloric restriction on Hprt lymphocyte mutation in aging rats.

Caloric restriction (CR) reduces tumor incidence and retards aging in laboratory animals, including non-human primates. Because of the relationships among mutation, disease susceptibility, and aging, we investigated whether or not CR affects the accumulation of somatic cell mutations in aging animals. Starting at approximately 2 months of age, male CD rats (Harlan Sprague-Dawley-derived) were placed on different levels of dietary intake: ad libitum (AL) feeding, and 90% (10% CR), 75% (25% CR) and 60% (40% CR) of the total calories consumed by AL animals. At 3, 6, 12, and 24 months after the beginning of CR, Hprt mutant frequencies (MFs) were determined. The MFs measured in spleen lymphocytes from AL and CR rats sacrificed at 3 months of dietary restriction were similar for all dietary groups. However, the MFs at 6, 12, and 24 months of CR were significantly higher in AL-fed rats compared with animals on 40% CR: (4.5+/-0.4)x10(-6) versus (3.3+/-0.3)x10(-6) (P=0.032) in 6 months CR rats; (10.3+/-2.3)x10(-6) versus (7.3+/-1.2)x10(-6) in 12 months CR rats (P=0.04), and (18.3+/-3.2)x10(-6) versus (7.8+/-1.0)x10(-6) (P=0.001) in 24 months CR rats. In addition, rats receiving 25% CR for 24 months had a MF, (10.7+/-2.0)x10(-6), between the 40% CR and AL rats. Multiplex PCR of the Hprt gene in mutant clones from 12 and 24 months 40% CR rats and the corresponding AL rats detected deletions in 42% of CR mutants and 19% of AL mutants. Because of the difference in Hprt MF in the two groups, the estimated MF associated with deletions in CR rats was similar to the deletion MF in AL rats. This observation implies that the lower MF in CR rats is due to a reduction in smaller Hprt mutations (i.e. base substitutions and frameshifts). The pattern of smaller Hprt mutations from AL rats suggests that many were produced by reactive oxygen species (ROS). The results indicate that CR reduces the accumulation of spontaneous somatic cell mutation in aging rats, especially those caused by base substitutions and frameshifts.

Aging↗

PubMed2003

Testing for differentially expressed genes with microarray data.

This paper compares the type I error and power of the one- and two-sample t-tests, and the one- and two-sample permutation tests for detecting differences in gene expression between two microarray samples with replicates using Monte Carlo simulations. When data are generated from a normal distribution, type I errors and powers of the one-sample parametric t-test and one-sample permutation test are very close, as are the two-sample t-test and two-sample permutation test, provided that the number of replicates is adequate. When data are generated from a t-distribution, the permutation tests outperform the corresponding parametric tests if the number of replicates is at least five. For data from a two-color dye swap experiment, the one-sample test appears to perform better than the two-sample test since expression measurements for control and treatment samples from the same spot are correlated. For data from independent samples, such as the one-channel array or two-channel array experiment using reference design, the two-sample t-tests appear more powerful than the one-sample t-tests.

DNA, Complementary↗

PubMed2003

Normalization methods for analysis of microarray gene-expression data.

This paper investigates subset normalization to adjust for location biases (e.g., splotches) combined with global normalization for intensity biases (e.g., saturation). A data set from a toxicogenomic experiment using the same control and the same treated sample hybridized to six different microarrays is used to contrast the different normalization methods. Simple t-tests were used to compare two samples for dye effects and for treatment effects. The numbers of genes that reproducibly showed significant p-values for the unnormalized data and normalized data from different methods were evaluated for assessment of different normalization methods. The one-sample t-statistic of the ratio of red to green samples was used to test for dye effects using only control data. For treatment effects, in addition to the one-sample t-test of the ratio of the treated to control samples, the two-sample t-test for testing the difference between treated and control samples was also used to compare the two approaches. The method that combines a subset approach (median or lowess fit) for location adjustment with a global lowess fit for intensity adjustment appears to perform well.

Bias↗

PubMed2002

Molecular characterization of angiogenic properties of human oral squamous cell carcinoma cells.

Little is known about the specificity of angiogenic properties of oral cancer cells and the possible mechanisms. Stimulatory effects on proliferation and migration of human umbilical vein endothelial cells (HUVEC) characterized the angiogenic properties of oral cancer cells but not normal oral keratinocytes (NOK). ELISA found the presence of vascular endothelial growth factors (VEGF) both in the tested oral cancer cells and NOK. Attenuation of the proangiogenic effects by neutralizing VEGF antibodies suggests VEGF play a key role in the acquisition of the angiogenic phenotype in oral cancer cells. Western blotting of p53 and murine double mutant 2 (Mdm2) together with p53 DNA sequencing analysis indicate that p53 function loss by mutation or overexpression of Mdm2 occurred in all tested oral cancer cells regardless of their etiology. In summary, the angiogenic property of oral cancer cells is mediated by many factors in addition to VEGF and the functional status of p53.

Carcinoma, Squamous Cell↗

PubMed1999

Contacting and forming singularities: Distinguishing examples.

A thin film bridge breaks in a way that starts at one equilibrium state and ends at another equilibrium state. The dynamical trajectory that carries it from connected to disconnected provides rare evidence regarding the singularity of passage through topological change. This nonequilibrium trajectory, called a "forming" flow, is discussed in an attempt to frame it within the larger class of singularities for which bounding surfaces do not remain material surfaces. As a contrast, the weaker "contacting" singularity is illustrated by a stagnation flow where material points reach the stagnation point in finite time. A classification scheme based on pathology of the nonunique Lagrangian motions is suggested. New results for the disconnection example include healing of surgery in post-disconnection simulations, different dynamical scalings of the just-disconnected components and a comparison of post-disconnection simulation to experiment. (c) 1999 American Institute of Physics.

Journal Article↗