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Kidney is a major target for adverse effects associated with corticosteroids. A microarray dataset was generated to examine changes in gene expression in rat kidney in response to methylprednisolone. Four control and 48 drug-treated animals were killed at 16 times after drug administration. Kidney RNA was used to query 52 individual Affymetrix chips,(More)
Part I (Mak et al., 1987, J. Biomechanics 20, 703-714) presented the theoretical solutions for the biphasic indentation of articular cartilage under creep and stress-relaxation conditions. In this study, using the creep solution, we developed an efficient numerical algorithm to compute all three material coefficients of cartilage in situ on the joint(More)
We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, ∼152 bp, in fission yeast and that transcriptional start sites(More)
The main objective of this study is to determine the nature of electric fields inside articular cartilage while accounting for the effects of both streaming potential and diffusion potential. Specifically, we solve two tissue mechano-electrochemical problems using the triphasic theories developed by Lai et al. (1991, ASME J. Biomech Eng., 113, pp. 245-258)(More)
An important step toward understanding signal transduction mechanisms modulating cellular activities is the accurate predictions of the mechanical and electro-chemical environment of the cells in well-defined experimental configurations. Although electro-kinetic phenomena in cartilage are well known, few studies have focused on the electric field inside the(More)
MOTIVATION The extension of mapped sequence tags is a common step in the analysis of single-end next-generation sequencing (NGS) data from protein localization and chromatin studies. The optimal extension can vary depending on experimental and technical conditions. Improper extension of sequence tags can obscure or mislead the interpretation of NGS results.(More)
SUMMARY The rapid advancement of genomic technology has revealed the enormous complexity and combinatorial nature of chromatin modifications. To facilitate interpretation of the combinatorial nature of chromatin, we have developed a novel method to integrate all chromatin datasets into distinct nucleosome types (nucleosome alphabet). We have applied this(More)
Previous studies have described a transcriptional "memory effect," whereby transcript levels of many Abf1-regulated genes in the budding yeast Saccharomyces cerevisiae are undiminished even after Abf1 has dissociated from its regulatory sites. Here we provide additional support for this effect and investigate its molecular basis. We show that the effect is(More)
Rheological flow properties of link-stable and link-free proteoglycan (PG) aggregates in concentrated solutions were measured using a cone-on-plate viscometer. A second-order constitutive model, based upon the statistical-network theories of Lodge, [Rheol. Acta 7, 379-392 (1968)] and De Kee and Carreau [J. Non-Newtonian Fluid Mech. 6, 127-143 (1979)], was(More)
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