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     

Scattering and absorption by thin metal wires in rectangularwaveguide-FDTD simulation and physical experiments

The high-frequency internal impedance model of a round ohmic conductor is incorporated into the subcell thin-wire formulation of the finite-difference time-domain method to model the microwave properties of metal wires. For magnetic metals, such as steel, an effective conductivity is introduced to account for the increase in ohmic loss due to the high-frequency permeability. Physical experiments with half-wave resonant copper- and steel-wire inclusions, supported by a dielectric slab in a standard S-band rectangular waveguide, support the formulation     

Predicting postlaryngectomy voice outcome in an era of primary tracheoesophageal fistulization: a retrospective evaluation

The aim of this study was to investigate the effect of the absence of elongate spermatids (ES) from the rat seminiferous epithelium on the quantitative secretion and synthesis of the three major Sertoli cell secretory proteins--SGP-1, SGP-2 and CP-2. Seminiferous tubules (ST) were isolated (a) from normal 28-day-old rats, in which the most mature germ cell type is the round spermatid, (b) from normal adult rats at stages IX-XIV of the spermatogenic cycle, i.e. after spermiation, or at stages I-V and VI-VIII, when ES are still attached to the Sertoli cell, and (c) at stages VI-VIII from normal adult rats and from rats treated with methoxyacetic acid (MAA) in order to specifically deplete ES at these stages. Two-dimensional SDS PAGE combined with computerized image analysis was used to analyse 35S-methionine-labelled intracellular and secreted proteins. In the case of SGP-1 and SGP-2, almost all of the protein synthesized by ST was secreted. The total amount of both SGP-1 and CP-2 secreted by unstaged ST from immature rats was significantly lower than that secreted by unstaged ST from adult rats. The total amount of SGP-1 and CP-2 secreted by adult ST at stages IX-XIV of the spermatogenic cycle also declined dramatically compared to ST at earlier stages. The proportion of the total CP-2 synthesized by ST which was secreted also declined in all situations in which ES were absent from the seminiferous epithelium. The synthesis of only SGP-2 was changed by ES depletion from ST at stages VI-VIII, which was almost doubled compared to synthesis of this protein by ST from control rats. Our results suggest strongly that the secretion of SGP-1 and SGP-2 is via the constitutive pathway, and that regulation of these two proteins by ES is at the level of protein synthesis. In contrast, the regulation of CP-2 by ES is predominantly at the level of secretion, suggesting that this protein is secreted via a regulated pathway. Our findings add to the evidence showing that ES play a major role in the regulation of Sertoli cell function.     

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.     

ATMOSPHERIC DEPOSITION OF CHEMICAL SPECIES TO POLAR SNOW

Particles and gases can deposit from the atmosphere to polar snow by several mechanisms. Dry deposition can be considered to consist of three steps: aerodynamic transport from the free atmosphere to the viscous sublayer near the surface, boundary layer transport across the sublayer, and interactions with the surface. The particle dry deposition mass flux is dominated by the largest particles present in a size distribution. Wet deposition includes in-cloud and below-cloud scavenging, where the former refers to uptake of particles during nucleation of cloudwater as well as scavenging of particles and gases by existing droplets and ice crystals. Of all the wet deposition mechanisms, nucleation scavenging is often the most important mechanism for particles in the polar regions. Finally, incorporation of particles and gases into fog droplets and subsequent settling of the fog to the snow surface can be an important removal process in regions of frequent fog. For Summit, Greenland, the total deposition of MSA, SO₄^2-, Na⁺, K⁺, and Ca²⁺ during May 24-July 13, 1993 was dominated by wet deposition: this mechanism accounted for an average of 62% of the total deposition for these species. Fog and dry deposition accounted for 21% and 17% of the total, respectively. These results suggest that all three mechanisms may need to be considered when estimating total deposition of certain chemical species to polar snow.     

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     

Integrated carbon nanotube field emission differential amplifier: Modeling and measurement of the common-mode rejection ratio

A novel integrated vacuum field emission (VFE) differential amplifier (diff-amp) utilizing carbon nanotube (CNT) emitters has been developed. A dual-mask microfabrication process was employed to achieve a VFE diff-amp by integrating identical CNT VFE transistors with built-in split gates and integrated anodes. The identical pair of triode amplifiers was well-matched in their device characteristics. The measured ac small-signal characteristics of the diff-amp showed a common-mode-rejection ratio (CMRR) of ~ 320 (~ 50 dB). The proposed analytical model of the CMRR was verified to be in good agreement with the experimental data. The successful implementation of the CNT diff-amp demonstrates a new way to achieve temperature and radiation tolerant VFE integrated microelectronics.     

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.     

Rat hepatocyte plasma membrane acyl:CoA synthetase activity

The presence of long chain acyl:CoA synthetases in mammalian microsomes and mitochondria has been established previously by Aas (Biochim. Biophys. Acta 231, 32–47 [1971]). The presence of a plasma membrane-associated enzyme was investigated in rat hepatocyte plasma membranes, where an enzyme exhibiting high activity and with a preferred substrate of 18-carbon chain length was discovered. The results are consistent with the presence of a single enzyme. The effect of the degree of unsaturation of the fatty acid substrates was not as pronounced as that arising from the length of the carbon chain. The pattern of substrate preference of the enzyme was ω3 polyenoic fatty acids >ω6 polyenoic acids >ω9 monoenoic acids > saturated acids. This may relate to the similar substrate preference pattern exhibited by the fatty acyl desaturase enzymes. The role played by long chain acyl:CoA synthetase in hepatocyte metabolism is uncertain, but it may relate to the incorporation of polyenoic fatty acids from the circulation into cell membranes and the trapping of other fatty acids within the cell for further metabolism.