Retrieving definitional content for ontology development

Ontology construction requires an understanding of the meaning and usage of its encoded concepts. While definitions found in dictionaries or glossaries may be adequate for many concepts, the actual usage in expert writing could be a better source of information for many others. The goal of this paper is to describe an automated procedure for finding definitional content in expert writing. The approach uses machine learning on phrasal features to learn when sentences in a book contain definitional content, as determined by their similarity to glossary definitions provided in the same book. The end result is not a concise definition of a given concept, but for each sentence, a predicted probability that it contains information relevant to a definition. The approach is evaluated automatically for terms with explicit definitions, and manually for terms with no available definition.     

Asymmetric epoxidation using a singly-bound supported Katsuki-type (salen)Mn complex

We have successfully prepared an unsymmetrical analogue of a Katsuki-type salen ligand having a single hydroxyalkyl group at its 6-position, and also its Mn(III) complex; attachment of the complex to a polymer gives a highly enantioselective and recoverable catalyst for epoxidation of 1,2-dihydronaphthalene.     

Nonaqueous capillary electrophoretic separation of basic enantiomers using octakis(2,3-O-dimethyl-6-O-sulfo)-gamma-cyclodextrin, a new, single-isomer chiral resolving agent

The enantiomers of 34 pharmaceutical weak-base analytes were separated by nonaqueous capillary electrophoresis in acidic methanol background electrolytes using the sodium salt of the new, single-isomer chiral resolving agent, octakis(2,3-O-dimethyl-6-O-sulfo)-gamma-cyclodextrin (ODMS). The effective mobilities, separation selectivities and peak resolution values of the weak-base analytes were determined as a function of the ODMS concentration in the 0-40 mM range and were found to follow the theoretical predictions of the charged resolving agent migration model (CHARM model) modified for ionic strength effects. Fast, efficient separations were achieved for both comparatively small and large enantiomers.     

Evaluation of enzymatic digestion and liquid chromatography-mass spectrometry peptide mapping of the integral membrane protein bacteriorhodopsin

A method for the complete peptide mapping of the model integral membrane protein bacteri-orhodopsin is demonstrated. Utilizing more effective enzymatic digestion, procedures with capillary liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) and tandem mass spectrometry (MS/MS), all predicted tryptic digestion products were detected, as well as peptides from all previously reported post-translational modifications of bacteriorhodopsin. A significant contribution of chymotryptic-like digestion products was also observed. A characterization of the behavior of hydrophobic integral membrane peptides in a reversed-phase liquid chromatographic separation is also provided. The method reported here offers improved compatibility of the solubilizing reagents with both the chromatography and mass spectrometry, rendering it suitable for high-throughput proteomic applications.     

The transfer between instruments of a reflectance near-infrared assay for paracetamol in intact tablets

This study compares several correction methods to facilitate the transfer of a validated near-infrared (NIR) assay for paracetamol in intact tablets between two reflectance NIR instruments of the same type. Transfer was defined as the ability to accurately predict the true assay value of a sample measured on a NIR system using an assay developed on a different system, and was assessed using a comprehensive set of statistical tests. Direct electronic transfer of the calibration models, representing the NIR assay, was not possible as a result of a definite residual spectrum between instruments. The use of a correction method based on the standardisation of the material used to record the reference spectrum also proved ineffective. Two methods investigated did succeed, the first employed a response surface calculated between the reflectance values of a set of six certified photometric standards measured on both instruments, with all full range partial least square (PLS) regression models subsequently transferred. The next was correction of the spectra from the second instrument utilising the residual spectrum between the mean sample of the validation set measured on both instruments. Through this approach all PLS regression models and also a single multiple linear regression (MLR) model were transferred. As an outcome of this study guidelines are suggested for the transfer of NIR assays along with the criteria deemed necessary to conclusively prove transfer and justify any correction method utilised. The significant criteria were determined to be the paired t-test with both the UV reference assay data and the original NIR assay data, and comparison of the coefficient of multiple determinations.     

Quantum dot nanocrystals for in vivo molecular and cellular imaging

Semiconductor quantum dots (QD) are nanometer-sized crystals with unique photochemical and photophysical properties that are not available from either isolated molecules or bulk solids. In comparison with organic dyes and fluorescent proteins, QD are emerging as a new class of fluorescent labels with improved brightness, resistance against photobleaching and multicolor fluorescence emission. These properties could improve the sensitivity of biological detection and imaging by at least 10- to 100-fold. Further development in high-quality near-infrared-emitting QD should allow ultrasensitive and multicolor imaging of molecular targets in deep tissue and living animals. Here, we discuss recent developments in QD synthesis and bioconjugation, applications in molecular and cellular imaging as well as promising directions for future research.     

Detection of VX contamination in soil through solid-phase microextraction sampling and gas chromatography/mass spectrometry of the VX degradation product bis(diisopropylaminoethyl)disulfide

A solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS) sampling and analysis method was developed for bis(diisopropylaminoethyl)disulfide (a degradation product of the nerve agent VX) in soil. A 30-min sampling time with a polydimethylsiloxane-coated fiber and high temperature alkaline hydrolysis allowed detection with 1.0 microg of VX spiked per g of agricultural soil. The method was successfully used in the field with portable GC-MS instrumentation. This method is relatively rapid (less than 1 h), avoids the use of complex preparation steps, and enhances analyst safety through limited use of solvents and decontamination of the soil before sampling.     

Lithiation of 2-Alkyl-3-amino- and 2-Alkyl-3-(methylamino)-4(3H)-quinazolinones(1)

3-Amino-2-methyl-4(3H)-quinazolinone has been doubly lithiated, on nitrogen and in the 2-methyl group, with n-butyllithium. The lithium reagent thus obtained reacts with a variety of electrophiles (D(2)O, benzophenone, cyclohexanone, cyclopentanone, acetophenone, benzaldehyde, tetraisopropylthiuram disulfide (TITD)) to give the corresponding 2-substituted derivatives in very good yields. Reactions of the dilithio reagent with 2 molar equiv of methyl iodide or phenyl isocyanate give disubstituted derivatives. Double lithiation of the 2-ethyl and 2-propyl analogues have been achieved using LDA, and subsequent reactions with most electophiles are then similar. In the reaction of the dianion of the 2-ethyl compound with TITD, deamination from position 3 takes place with the formation of the 2-substituted derivative. In reactions with prochiral ketones, the dianion of the 2-ethyl compound gives very high diastereoselectivity. Lithiation and subsequent reactions of 3-(methylamino) analogues take place in a similar manner, thus providing access to a range of substituted 3-(methylamino)-2-alkyl-4(3H)-quinazolinones by a general procedure. Lithiation of 3-(dimethylamino)-2-ethyl-4(3H)-quinazolinone did not take place under similar conditions. Lithiation of 3-amino-2-unsubstituted-4(3H)-quinazolinone was also unsuccessful.     

Electrostatic water models

The possiblity of creating a useful model for the electrostatic potential around the water molecule is examined from two different starting points. It is suggested that the simplest and most accurate model will have three point charges on the nuclei together with a diffuse Gaussian charge centered near the nuclear center of the charge. This will represent the lone-pair cloud, include the penetration effects, and improve the representation of the electron density. The alternative use of atomic dipoles is explored but seen to be less effective.