Quantitative pharmacophore models with inductive logic programming

Three-dimensional models, or pharmacophores, describing Euclidean constraints on the location on small molecules of functional groups (like hydrophobic groups, hydrogen acceptors and donors, etc.), are often used in drug design to describe the medicinal activity of potential drugs (or ‘ligands’). This medicinal activity is produced by interaction of the functional groups on the ligand with a binding site on a target protein. In identifying structure-activity relations of this kind there are three principal issues: (1) It is often difficult to “align” the ligands in order to identify common structural properties that may be responsible for activity; (2) Ligands in solution can adopt different shapes (or `conformations’) arising from torsional rotations about bonds. The 3-D molecular substructure is typically sought on one or more low-energy conformers; and (3) Pharmacophore models must, ideally, predict medicinal activity on some quantitative scale. It has been shown that the logical representation adopted by Inductive Logic Programming (ILP) naturally resolves many of the difficulties associated with the alignment and multi-conformation issues. However, the predictions of models constructed by ILP have hitherto only been nominal, predicting medicinal activity to be present or absent. In this paper, we investigate the construction of two kinds of quantitative pharmacophoric models with ILP: (a) Models that predict the probability that a ligand is “active”; and (b) Models that predict the actual medicinal activity of a ligand. Quantitative predictions are obtained by the utilising the following statistical procedures as background knowledge: logistic regression and naive Bayes, for probability prediction; linear and kernel regression, for activity prediction. The multi-conformation issue and, more generally, the relational representation used by ILP results in some special difficulties in the use of any statistical procedure. We present the principal issues and some solutions. Specifically, using data on the inhibition of the protease Thermolysin, we demonstrate that it is possible for an ILP program to construct good quantitative structure-activity models. We also comment on the relationship of this work to other recent developments in statistical relational learning. Editors: Tamás Horváth and Akihiro Yamamoto     

A DNA-binding element for a steroid receptor-binding factor is flanked by dual nuclear matrix DNA attachment sites in the c-myc gene promoter

The receptor-binding factor (RBF) for the avian oviduct progesterone (Pg) receptor (PR) has previously been shown to be a unique 10-kDa nuclear matrix protein that generates high affinity PR-binding sites on avian DNA. This paper describes the use of Southwestern blot and DNA gel shift analyses with RBF protein to identify a minimal 54-base pair RBF-binding element in the matrix-associated region (MAR) of the Pg-regulated c-myc gene promoter. This element contains a 5'-GC-rich domain and a 3'-AT-rich domain, the latter of which has a homopurine/homopyrimidine structure. The gel shift assays required the generation of an RBF-maltose fusion protein (RBF-MBP), which specifically binds this element and is supershifted when the anti-RBF polyclonal antibody is added. Computer analysis of the full-length amino acid sequence for RBF predicts a DNA-binding motif involving a beta-sheet structure at the N-terminal domain. Southern blot analyses using nuclear matrix DNA suggests that there are dual MAR sites in the c-myc promoter, which flank an intervening domain containing the RBF element. The co-transfection of this MAR sequence, containing the RBF element and cloned into a luciferase reporter vector, together with an RBF expression vector construct, into steroid treated human MCF-7 cells, results in a decrease of the c-myc promoter activity relative to control transfections containing only the parent vector of the RBF expression construct. These data suggest that a unique chromatin/nuclear matrix structure, composed of the RBF-DNA element complex which is flanked by nuclear matrix attachment sites, serves to bind the PR and repress the c-myc promoter.     

MANAGING DISTRIBUTED COMPUTING Five Practices for Success

Management of distributed environments requires corporate IS managers to shift from being operators of a central utility to facilitators who can recognize the synergy among loosely related groups of users. Success depends on the development of new ways of visualizing and measuring the service delivery process.     

Evidence for two types of spatial representations: Hemispheric specialization for categorical and coordinate relations.

Analyses of human object recognition abilities led to the hypothesis that 2 kinds of spatial relation representations are used in human vision. Evidence for the distinction between abstract categorical spatial relation representations and specific coordinate spatial relation representations was provided in 4 experiments. These results indicate that Ss make categorical judgments—on/off, left/right, and above/below—faster when stimuli are initially presented to the left cerebral hemisphere, whereas they make evaluations of distance—in relation to 2 mm, 3 mm, or 1 in. (2.54 cm)—faster when stimuli are initially presented to the right cerebral hemisphere. In addition, there was evidence that categorical representations developed with practice. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Simulation of magnetic component models in electric circuitsincluding dynamic thermal effects

It is essential in the simulation of power electronics applications to model magnetic components accurately. In addition to modeling the nonlinear hysteresis behavior, eddy currents and winding losses must be included to provide a realistic model. In practice the losses in magnetic components give rise to significant temperature increases which can lead to major changes in the component behavior. In this paper a model of magnetic components is presented which integrates a nonlinear model of hysteresis, electro-magnetic windings and thermal behavior in a single model for use in circuit simulation of power electronics systems. Measurements and simulations are presented which demonstrate the accuracy of the approach for the electrical, magnetic and thermal domains across a variety of operating conditions, including static thermal conditions and dynamic self heating     

What We Mean by Future-Proofing

Perhaps the most powerful claim that advocates of fiber can make,on top of the massive bandwidthfiber makes possible today, is that fiber is future-proof. That is, the fiber that is laid today can be upgraded so that the same strands of glass can carry massively more bandwidth in the future.     

Learning about tools in infancy.

These experiments explored the role of prior experience in 12- to 18-month-old infants' tool-directed actions. In Experiment 1, infants' use of a familiar tool (spoon) to accomplish a novel task (turning on lights inside a box) was examined. Infants tended to grasp the spoon by its handle even when doing so made solving the task impossible (the bowl did not fit through the hole in the box, but the handle did) and even though the experimenter demonstrated a bowl-grasp. In contrast, infants used a novel tool flexibly and grasped both sides equally often. In Experiment 2, infants received training using the novel tool for a particular function; 3 groups of infants were trained to use the tool differently. Later, infants' performance was facilitated on tasks that required infants to grasp the part of the tool they were trained to grasp. The results suggest that (a) infants' prior experiences with tools are important to understanding subsequent tool use, and (b) rather than learning about tool function (e.g., hammering), infants learn about which part of the tool is meant to be held, at least early in their exposure to a novel tool. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Desire and the couch: Perspectives from both sides of the analytic encounter.

This report summarizes the panel held at the 109th Annual Convention, American Psychological Association, August 26, 2001, San Francisco. The chair was William Glover and the speakers were Samuel Gerson, Karen Maroda, and Andre Patsalides. The invited symposium was directed at discussing different perspectives related to the presence of desire in the analytic process. (PsycINFO Database Record (c) 2010 APA, all rights reserved)