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     

Evolution and structure of drying material bridges of pharmaceutical excipients: studies on a microscope slide

An experimental procedure was developed to study directly the process by which liquid bridges between small particles in a granule form and solidify. The evolution of saturated solutions of such pharmaceutical excipients as lactose and mannitol in a liquid bridge was studied on a system situated on a microscope slide. Solidification and crystallization kinetics and phase composition during and immediately following bridge formation were observed directly. It was shown that bridges on the microscope slide and in the granule behave very much the same regardless of the different length and diffusion-scales of the two systems.We found that solid bridge formation takes place in several consecutive but distinct steps. In the case of lactose, considerable shrinkage of the initial liquid bridge takes place prior to the onset of crystallization. Further bridge solidification at ambient conditions occurs via simultaneous crystallization and vitrification within minutes. As a result, a “solid” bridge usually contains both a crystalline and a non-crystalline phase, the crystalline phase being predominately α-lactose monohydrate. Most of the non-crystalline phase eventually converts to crystalline β-lactose but the process may take many hours or even days. Results for this process are compared for samples obtained from different manufacturers of commercially available lactose. In the case of mannitol, different polymorphic forms crystallize as the drying/crystallization process progresses. A formed “solid” bridge usually contains several polymorphs of mannitol. The relevance of the behavior of the two model systems (pure lactose and pure mannitol) to a real granulation and tabletting process is discussed.     

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.     

The Person Reference Process in Spontaneous Trait Inferences.

Five studies examined whether spontaneous trait inferences uniquely reference the person who performed a trait-implying behavior. On each study trial in 5 studies, participants saw 2 faces and a behavioral sentence referring to one of them. Later, participants saw face-trait pairs and indicated whether they had seen the trait word in the sentence presented with the face. Participants falsely recognized implied traits more when these traits were paired with actors' faces than with control faces. This effect was replicated for a large set effaces (120), after a week delay between study and recognition test, when equal attention was paid to each face, and when the orientation of the face at recognition was different from the orientation at encoding. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Reconfigurable hardware implementation of a phase-correlation stereoalgorithm

This paper describes the implementation of a stereo-vision system using Field Programmable Gate Arrays (FPGAs). Reconfigurable hardware, including FPGAs, is an attractive platform for implementing vision algorithms due to its ability to exploit parallelism often found in these algorithms, and due to the speed with which applications can be developed as compared to hardware. The system outputs 8-bit, subpixel disparity estimates for 256× 360 pixel images at 30,fps. A local-weighted phase correlation algorithm for stereo disparity [Fleet, D. J.: {Int. Conf. Syst. Man Cybernetics 1:48–54 (1994)] is implemented. Despite the complexity of performing correlations on multiscale, multiorientation phase data, the system runs as much as 300 times faster in hardware than its software implementation. This paper describes the hardware platform used, the algorithm, and the issues encountered during its hardware implementation. Of particular interest is the implementation of multiscale, steerable filters, which are widely used in computer vision algorithms. Several trade-offs (reducing the number of filter orientations from three to two, using fixed-point computation, changing the location of one localized low-pass filter, and using L1 instead of L2 norms) were required to both fit the design into the available hardware and to achieve video-rate processing. Finally, results from the system are given both for synthetic data sets as well as several standard stereo-pair test images.     

Role of Perceived Importance in Intergroup Contact.

Furthering G. W. Allport's (1954) contentions for optimal contact, the authors introduce a new construct: the perceived importance of contact. They propose that perceived importance is the best proximal predictor of contact's reduction of prejudice. If individuals have opportunities for contact at work or in the neighborhood, their chances to have intergroup acquaintances and friends increase. Intergroup contact among acquaintances and friends can be perceived as more or less important, which in turn determines intergroup evaluations. A 1st study shows that the new measure of perceived importance is indeed distinct from established quantity and quality indicators. The results are cross-validated in a 2nd study that also sheds light on the meaning of importance. In 3rd and 4th studies, structural equation analyses and a meta-analysis support the hypotheses. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

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.