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     

Parameter Uncertainty and Policy Intensity: Some Extensions and Suggestions for Further Work

The effects of parameter uncertainty on optimal policy have been a matter of interest for academics, and even for some policymakers, for a long time. Two lines of literature have developed analytical results on this matter. The first line uses static models and the second dynamic models. In this dynamic line most of the results are confined to models with a single state and a single control variable. In this paper we want to encourage the analysis of more general dynamic cases. To do so, the results in the dynamic line are extended from one-state and one-control finite horizon models to models with a pair of control variables. We then discuss some of the hurdles which must be surmounted for the results to be made more general and suggests some lines for further research. JEL classification: C61; E61     

Dealumination–aging pattern of REUSY zeolites contained in fluid cracking catalysts

The evolution of the properties of a REUSY zeolite contained in a fluid cracking catalyst was investigated under laboratory steam deactivation procedures and in age fractions of the corresponding equilibrium catalyst (Ecat). The aging pattern, defined by the evolution of the zeolite surface area (ZSA) related to the decrease of the unit cell size (UCS), was similar between lab-steamed zeolites and Ecat fractions. A sharp drop in ZSA occurred at ca. 2.430 nm UCS. A study done by FT-IR spectroscopy suggested that zeolite dealumination initially took place more extensively on the sodalite cages and double six-member rings (D6R) of the structure and that the final collapse of the zeolite framework occurred through destruction of the 12-member rings (12M). This can be explained by a crystal fracture and break down process and disassembling of the sodalite cages in the faujasite structure. NH₃ microcalorimetry showed that strong acid sites in faujasites are destroyed by steam aging, but this effect does not lead to a reduction in the cracking activity of the Ecat form. The microactivity test (MAT) showed that the specific activity declined sharply at 2.430 nm UCS. Differences in product selectivity were related to the extent of damage of the zeolite, extra-framework alumina and mesoporosity. While further aging canceled the effect attributed to extra-framework alumina differences attributed to mesoporosity increased.     

A comprehensive study of hazelnut oil composition with comparisons to other vegetable oils,particularly olive oil.

Crude and refined hazelnut oils from different countries were characterised by major and minor compounds. Fatty acids, triacylglycerides, waxes, sterols, methyl-sterols, terpenic and aliphatic alcohols, tocopherols, tocotrienols and hydrocarbons were identified and quantified by gas chromatography and high-performance liquid chromatography. The levels of these chemical compounds in hazelnut oils together with the equivalent carbon numbers and triacylglyceride carbon numbers, were compared with the results of analyses of samples of other vegetable oils. The statistical procedure of cluster analysis was used to characterise hazelnut oils versus other edible oils.     

The effects of nonlocal impact ionization on the speed of avalanche photodiodes

The nonlocal enhancement in the velocities of charge carriers to ionization is shown to outweigh the opposing effects of dead space, increasing the avalanche speed of short avalanche photodiodes (APDs) over the predictions of a conventional local model which ignores both of these effects. The trends in the measured gain-bandwidth product of two short InAlAs APDs reported in the literature support this result. Relatively large speed benefits are predicted to result from further small reductions in the lengths of short multiplication regions.     

Collection Conduits Including Subsurface Drains

Numerous types of pipes and channels with spatially increasing flows in environmental engineering applications are identified by type and function and referred to as collection conduits. An overview of methods for designing and analyzing collection conduits is provided. Full conduits with nonuniform and uniform inflow are first considered. Dimensional analysis is then employed to demonstrate the relationship between variables for open channels; that leads to the identification of possibilities for generalized numerical solutions. Prior collection conduit applications are discussed within the framework of the dimensional analysis (which also pertains to some constant-flow applications). A previously unpublished generalized numerical solution for rectangular collection conduits is presented. Subsurface drains are addressed with particular emphasis, including the use of numerical methods to develop a new generalized chart and relation to other design methods. Among the important conclusions for subsurface drains is that the somewhat common practice of using Manning’s equation alone for such problems is not generally adequate. Examples and practical design suggestions are included, and the use of computer-based numerical methods is discussed more generally.     

Retrograde Amnesia Induced by Drugs Acting on Different Molecular Systems.

The gamma aminobutyric acid-A (GABAA) agonist, muscimol, the glutamate N-methyl-D-aspartate (NMDA) receptor antagonist, D-2-amino-5-phosphonopentanoic acid (AP5), and the inhibitor of the extracellularly regulated kinases (ERKs), UO 126, cause retrograde amnesia when administered to the hippocampus. In the present study, the authors found that they all cause retrograde amnesia for 1-trial inhibitory avoidance, not only when infused into the dorsal CA1 region of the hippocampus, but also when infused into the basolateral amygdala or the entorhinal, parietal, and posterior cingulate cortices. The posttraining time course of the effect of each drug was, however, quite different across brain structures. Thus, in all of them, NMDA receptors and the ERK pathway are indispensable for memory consolidation, and GABAA receptor activation inhibits memory consolidation: but in each case, their influence is interwoven differently. (PsycINFO Database Record (c) 2010 APA, all rights reserved)