Nucleosides and Nucleotides. Part 18. p-nitrobenzenesulfonyl nitroimidazole as a new condensing agent in the triester synthesis of oligonucleotides

p-Nitrobenzenesulfonyl nitroimidazole (p-NBSNI) ( 5 ) has been shown to be an efficient and convenient condensing agent in the coupling of protected nucleotide fragments. Its utility has been demonstrated by a direct comparison with previously-described condensing agents in the synthesis of various di- and tetradeoxy-nucleotides.     

Characterization of partially transesterified poly(beta-hydroxyalkanoate)s using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was used for the characterization of a partially transesterified poly(beta-hydroxyalkanoate), PHA, polymer produced by the bacterial strain Alcaligenes eutrophus using saponified vegetable oils as the sole carbon sources. The transesterification was carried out separately under acidic and basic conditions to obtain PHA oligomers weighing less than 10 kDa. The intact oligomers were detected in their cationized [M + Na](+) and [M + K](+) forms by MALDI-TOFMS. A composition analysis, using the MALDI-TOF spectra, indicate that the oligomers obtained via acid catalysis were terminated with a methyl 3-hydroxybutyrate end group, and those obtained by base catalysis had a methyl crotonate (olefinic) termination. In addition to HB (hydroxy butyrate), the oligomers were found to contain a small percentage of HV (hydroxy valerate). This was independently confirmed using gas chromatography/mass spectrometry (GC/MS). In comparison, the analysis of a commercial PHA polymer, transesterified under identical conditions, only showed the presence of HB, i.e. a pure PHB homopolymer. Copyright 1999 John Wiley & Sons, Ltd.     

PEPCAT—A new tool for conformational analysis of peptides

We report a new technique for the efficient analysis and visualization of peptide and protein conformations and conformational relationships, which we have implemented in a computer program called PEPCAT. PEPCAT (an abbreviation for Peptide Conformational Analysis Tool) provides a simple, graphical, and flexible framework that allows the user to define a specific structural feature or juxtaposition of amino acids and to follow the fate of the motif during a molecular dynamics simulation. Here we describe the PEPCAT analysis of the effects of environmental and chemical modifications on conformational preferences of a regulator of hemopoiesis, namely the pentapeptide pyro‐EEDCK, and of a conformational transition in the immunosuppressant drug cyclosporin A. PEPCAT, however, can be applied to the conformational analysis of peptides and proteins in general. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 446–461, 2000     

Nonlinear shear‐free radiative collapse

We study realistic models of relativistic radiating stars undergoing gravitational collapse which have vanishing Weyl tensor components. Previous investigations are generalized by retaining the inherent nonlinearity at the boundary. We transform the boundary condition to an Abel equation of the first kind. A variety of nonlinear solutions is generated all of which can be written explicitly. Several classes of infinite solutions exist. Copyright © 2007 John Wiley & Sons, Ltd.     

Zero‐coupon bond prices in the Vasicek and CIR models: Their computation as group‐invariant solutions

We compute prices of zero‐coupon bonds in the Vasicek and Cox–Ingersoll–Ross interest rate models as group‐invariant solutions. Firstly, we determine the symmetries of the valuation partial differential equation that are compatible with the terminal condition and then seek the desired solution among the invariant solutions arising from these symmetries. We also point to other possible studies on these models using the symmetries admitted by the valuation partial differential equations. Copyright © 2007 John Wiley & Sons, Ltd.     

Interferometric methods to measure orbital and spin, or the total angular momentum of a single photon

We propose interferometric methods capable of measuring either the total angular momentum, or simultaneously measuring the spin and orbital angular momentum of single photons. This development enables the measurement of any angular momentum eigenstate of a single photon. The work allows the investigation of single-photon two-qubit entangled states and has implications for high density information transfer.     

Where are the GaPs? A rational approach to monomer acquisition and selection

Gridding and partitioning (GaP) is a computational method for the classification and selection of monomers for combinatorial libraries. The molecules are described in terms of the pharmacophoric groups they contain and where those pharmacophoric groups can be located in three-dimensional space. The approach involves a detailed conformational analysis of each molecule. This conformational analysis is done within a common coordinate frame, thus enabling the monomers to be compared. The use of a partitioned space is central to this particular application as it facilitates the identification of regions of space which are not well represented by existing compounds. Several ways to extend the use of partitioned pharmacophore spaces are described. Applications of the approach in monomer acquisition and in library design are outlined.     

PLUMS: a program for the rapid optimization of focused libraries

PLUMS is a new method to perform rational monomer selection for combinatorial chemistry libraries. The algorithm has been developed to optimize focused libraries with specific two-dimensional and/or three-dimensional properties. A preliminary step is the identification of those molecules in the initial virtual library which satisfy the imposed property constraints; we define these molecules as the virtual hits. From the virtual hits, PLUMS generates a starting library, which is the true combinatorial library that includes all the virtual hits. Monomers are then removed in an iterative fashion, thus reducing the size of the library. At each iteration, the worst monomer is removed. Each sublibrary is selected using a global scoring function, which balances effectiveness and efficiency. The iterative process continues until one is left with a library that consists entirely of virtual hits. The optimal library, which is the best compromise between effectiveness and efficiency, can then be selected according to the score. During the iterative process, equivalent solutions may well occur and are taken into account by the algorithm, according to a user-defined parameter. The number of monomers for each substitution site and the size of the library are parameters that can be either optimized or used to constrain the selection. The results obtained on two test libraries are presented. PLUMS was compared with genetic algorithms (GA) and monomer frequency analysis (MFA), which are widely used for monomer selection. For the two test libraries, PLUMS and GA gave equivalent results. MFA is the fastest method, but it can give misleading solutions. Possible advantages and disadvantages of the different methods are discussed.     

High-resolution segmented EPI in a motor task fMRI study

A high-resolution gradient echo, multi-slice segmented echo planar imaging method was used for functional MRI (fMRI) using a motor task at 1.5 Tesla. Functional images with an in-plane resolution of 1 mm and slice thickness of 4 mm were obtained with good white-gray matter contrast. The multi-shot approach, combined with a short total readout period of 82 ms, limits blurring effects for short T(2)(*) tissues (such as gray matter), assuring truly high-resolution images. In all subjects, motor functions were clearly depicted in the contralateral central sulcus over several slices and sometimes activation was detected in the supplementary motor area and/or ipsilateral central sulcus. The average signal change of 11+/-3% was much higher than in standard low-resolution fMRI EPI experiments, as a result of larger relative blood fractions.     

Improving image quality and T(1) measurements using saturation recovery turboFLASH with an approximate K-space normalisation filter

We present a method for reducing the image point-spread function and measuring T(1) using saturation recovery turboFLASH (SRTF) with centric-ordered k-space and a k-space correction filter designed to compensate for longitudinal magnetisation evolution during image acquisition. The method provides a two point T(1) measurement that reduces inaccuracies and image artefacts caused by longitudinal magnetisation evolution in conventional turboFLASH methods. The method is designed for use in rapid, quantitative measurements of contrast agent uptake in vivo.