6 research outputs found
UNIVERSAL SPACES FOR ZERO-DIMENSIONAL CLOSED IMAGES OF METRIC SPACES : dedicate to my mother on her 77th birthday
Get PDFapplication/pdfUsing an iterative method due to Stephen Watson, we shall construct universal spaces for O-dimensional Lasnev spaces. We can show that Watson method can be applied not only for all classes of large cardinalities, but also to make their universal spaces homogeneous for certain classes. We also study relationship between universal spaces made from complete metric spaces and those made from ＄￥sigma＄-discrete metric spaces.departmental bulletin pape
Ligand-based Activity Cliff Prediction Models with Applicability Domain
Get PDFActivity cliffs (ACs) are formed by pairs of structurally similar compounds with large differences in potency. Predicting ACs is of high interest in lead optimization for drug discovery. Previous AC prediction models that focused on matched molecular pair (MMP) cliffs produced adequate performances. However, the extrapolation ability of these models is unclear because the main scaffold for MMPs, the core structure, could exist in both training and test data sets. Also, representation of MMPs did not consider the attachment points where the core and R-group substituents are connected. In this study, we aimed to improve a ligand-based AC prediction method using molecular fingerprints. We incorporated applicability domain, which was defined using R-path fingerprints to consider the local environment around an attachment point. Rigorous evaluation of the extrapolation ability of AC prediction models showed that MMP-cliffs were accurately predicted for nine biological targets. Furthermore, incorporation of training MMPs with cores distinct from those of test MMPs improved the predictability compared with using training MMPs with only similar cores.journal articl
Effect of 6S RNA on the transcription from σ and σ-specific promoters on linear DNA fragments
No full text<p><b>Copyright information:</b></p><p>Taken from "Studies on the function of the riboregulator 6S RNA from : RNA polymerase binding, inhibition of transcription and synthesis of RNA-directed transcripts"</p><p></p><p>Nucleic Acids Research 2007;35(6):1885-1896.</p><p>Published online 1 Mar 2007</p><p>PMCID:PMC1874619.</p><p>© 2007 The Author(s)</p> Products from transcription reactions were separated on denaturing polyacrylamide gels and visualized by autoradiography. Reactions with the or P1 promoters are shown on the left or right side, respectively. The different holoenzymes employed (E70, E38) are indicated above the lanes. For each system the amount of 6S RNA present in the reaction was varied (lanes 1, 6, 11, 16: 0 nM, lane 2, 7, 12, 17: 10 nM, lane 3, 8, 13, 18: 50 nM, lane 4, 9, 14, 19: 100 nM, lane 5, 10, 15, 20: 250 nM). A 260 bp radiolabelled DNA fragment, indicated at the margin, was included as internal standard for quantification. The positions of the run-off transcripts for the (∼124 nt) and P1 (64 nt) promoters are marked. An arrow denotes a product that consistently arises when 6S RNA is incubated with RNA polymerase, even in the absence of any template DNA
