Practical algorithms for transposition-invariant string-matching

We consider the problems of (1) longest common subsequence (LCS) of two given strings in the case where the first may be shifted by some constant (that is, transposed) to match the second, and (2) transposition-invariant text searching using indel distance. These problems have applications in music comparison and retrieval. We introduce two novel techniques to solve these problems efficiently. The first is based on the branch and bound method, the second on bit-parallelism. Our branch and bound algorithm computes the longest common transposition-invariant subsequence (LCTS) in time O((m²+loglogσ)logσ) in the best case and O((m²+logσ)σ) in the worst case, where m and σ, respectively, are the length of the strings and the size of the alphabet. On the other hand, we show that the same problem can be solved by using bit-parallelism and thus obtain a speedup of O(w/logm) over the classical algorithms, where the computer word has w bits. The advantage of this latter algorithm over the present bit-parallel ones is that it allows the use of more complex distances, including general integer weights. Since our branch and bound method is very flexible, it can be further improved by combining it with other efficient algorithms such as our novel bit-parallel algorithm. We experiment on several combination possibilities and discuss which are the best settings for each of those combinations. Our algorithms are easily extended to other musically relevant cases, such as δ-matching and polyphony (where there are several parallel texts to be considered). We also show how our bit-parallel algorithm is adapted to text searching and illustrate its effectiveness in complex cases where the only known competing method is the use of brute force.     

Acousto-optic mode coupling of partially coherent light in two-mode optical fibers

An acoustic pulse propagating on a two-mode fiber can act as a beam splitter in a scanning interferometer. When this device is employed in white-light interferometry, the effects of distributed coupling and dispersive interferometer arms need to be considered. A theory suitable for treating acousto-optic interaction of partially coherent light in a moving interaction region was developed. It was found that differential optical dispersion should be negligible and the acoustic pulse length short. Also the coherence time should be short but long compared to the intermodal group delay difference over a pulse length. Experiments with long acoustic pulses were performed, and fairly good agreement with theory was obtained.     

α-Halo sulfides in the alkylation of 2-pyrimidinones

When α-halo sulfides are reacted with ambident 2-pyrimidinones, the major product is due to N-alkylation, the minor product to O-alkylation. N-Alkylation is favoured by the presence of a tertiary amine in a solvent of low dielectric constant and also by a change of the α-halo sulfide substituent from chlorine to iodine. Complete selectivity can be achieved. The course of the reaction is rationalized in terms of the HSAB-principle.     

BRCA1 mutation screening using restriction endonuclease fingerprinting-single-strand conformation polymorphism in an automated capillary electrophoresis system

Efficient mutation scanning techniques are needed for the rapid detection of novel disease-associated mutations and rare-sequence variants of putative importance. The large size of the breast cancer 1 gene (BRCA1) and the many mutations found throughout its entire coding sequence make screening for mutations in this gene particularly challenging. We have developed a method for screening exon 11 of the BRCA1 gene based on restriction enzyme digestion of fluorescence-labeled polymerase chain reaction (PCR) products followed by single-strand conformation polymorphism (SSCP) using an automated capillary electrophoresis system, denoted capillary restriction endonuclease fingerprinting (REF)-SSCP electrophoresis. Using this strategy on a control set of samples, we were able to detect 17 of 18 known sequence alterations. The method was then applied to screen 73 Norwegian females with family histories of breast and/or ovarian cancer. A total of 172 sequence alterations were detected, including substitutions, insertions, and deletions. One novel substitution of unknown function was identified. Sequencing of all samples negative in the capillary REF-SSCP system gave no additional mutations confirming the high sensitivity of the described methodology. Capillary REF-SSCP electrophoresis appeared as a technically convenient technique, requiring amplification of fewer PCR fragments than traditional SSCP. The novel strategy allows high-throughput mutation scanning without radioactive labeling and polyacrylamide gel electrophoresis (PAGE).     

Detection of trace amounts of Ni by laser-induced fluorescence in graphite furnace with intensified charge coupled device

A laser-induced fluorescence in graphite furnace (LIF-GF) set-up has been equipped with an intensified CCD detector (ICCD) that enables simultaneous multichannel detection of large wavelength regions. The main advantages of such a system in comparison with conventional photomultiplier detection are: simultaneous detection of several fluorescence wavelengths for easy characterization of excitation and fluorescence spectra and for an increase of the absolute sensitivity and spectral selectivity; simultaneous monitoring of background signals, such as those due to matrix interferences, blackbody radiation and scattered laser light; decrease of the susceptibility to radio-frequency pick-ups emitted from the pump laser due to the delayed read-out procedure; time-resolved studies of fluorescence spectra for improved elemental selectivity or for studies of atomization processes, and a possibility to perform two-dimensional imaging of height distributions of atomization and, in combination with an imaging spectrometer, diffusion processes in the furnace. The first work on LIF-GF with ICCD detection has been performed on Ni. The most sensitive and versatile excitation and detection wavelengths have been identified. Detection limits in water solutions by the LIF-GF technique have been improved by two orders of magnitude and are found to be 0.015 pg with ICCD and 0.01 pg using a photomultiplier at the most sensitive excitation and detection wavelengths. Nickel in concentrations has been detected in aqueous standard reference samples with sodium concentrations ranging from to % (riverine water and estuarine water) with good accuracy and precision. The Ni contents of standard riverine and estuarine water were determined to 1.00 ± 0.11 and 0.75 ± 0.07 ng/ml, respectively. The certified concentrations are 1.03 ± 0.10 and 0.743 ± 0.078 .     

Mass spectrometry of onium compounds—XI: Ionization potentials of hydroxy and mercapto pyridines

Ionization potential measurements of the volatile species from the three isomers of the tautomeric hydroxyl and mercapto pyridines show that these are in the hydroxy and mercapto forms rather than appearing as lactams and betaines. The corresponding N-methyl lactams and S- and O-methyl ethers were also studied for comparative purposes.     

Monte Carlo simulation of RRKM unimolecular decomposition in molecular beam experiments. I. Basic considerations and calculational procedure

A simulation method is described for the comparison of a molecular decomposition theory, based on the fundamental RRKM theory, with crossed molecular beam experiments. In the present formulation, the method is applied to the case with long-lived collision complexes surrounded by a centrifugal barrier. The procedure uses Monte Carlo techniques to simulate the formation and decomposition of the complexes, thus effectively solving the high-dimensional integrals resulting but seldom solved in the analytical treatments. Several computational problems, like singularities in the c.m. angular distributions, have been circumvented in this procedure. Angular momentum conservation, the simultaneous interaction of several decomposition channels and strict flux conservation are included in the procedure. Dynamical features can be introduced, as will be shown in forthcoming papers.     

Animal models for treatment of unresectable liver tumours: a histopathologic and ultra-structural study of cellular toxic changes after electrochemical treatment in rat and dog liver

INTRODUCTION: Electrochemical treatment (EChT) has been taken under serious consideration as being one of several techniques for local treatment of malignancies. The advantage of EChT is the minimal invasive approach and the absence of serious side effects. Macroscopic, histopathological and ultra-structural findings in liver following a four-electrode configuration (dog) and a two-electrode EChT design (dog and rat) were studied. MATERIALS AND METHODS: 30 female Sprague-Dawley rats and four female beagle dogs were studied with EChT using Platinum:Iridium electrodes and the delivered dose was 5, 10 or 90 C (As). After EChT, the animals were euthanized. RESULTS: The distribution of the lesions was predictable, irrespective of dose and electrode configuration. Destruction volumes were found to fit into a logarithmic curve (dose-response). Histopathological examination confirmed a spherical (rat) and cylindrical/ellipsoidal (dog) lesion. The type of necrosis differed due to electrode polarity. Ultra-structural analysis showed distinct features of cell damage depending on the distance from the electrode. Histopathological and ultra-structural examination demonstrated that the liver tissue close to the border of the lesion displayed a normal morphology. CONCLUSIONS: The in vivo dose-planning model is reliable, even in species with larger tissue mass such as dogs. A multi-electrode EChT-design could obtain predictable lesions. The cellular toxicity following EChT is clearly identified and varies with the distance from the electrode and polarity. The distinct border between the lesion and normal tissue suggests that EChT in a clinical setting for the treatment of liver tumours can give a reliable destruction margin.     

Muffin-tin orbital Wannier-like functions for insulators and metals.

Herein, we outline a method that is able to generate truly minimal basis sets that accurately describe either a group of bands, a band, or even just the occupied part of a band. These basis sets are the so-called NMTOs, muffin-tin orbitals of order N. For an isolated set of bands, symmetrical orthonormalization of the NMTOs yields a set of Wannier functions that are atom-centered and localized by construction. They are not necessarily maximally localized, but may be transformed into those Wannier functions. For bands that overlap others, Wannier-like functions can be generated. It is shown that NMTOs give a chemical understanding of an extended system. In particular, orbitals for the pi and sigma bands in an insulator, boron nitride, and a semimetal, graphite, will be considered. In addition, we illustrate that it is possible to obtain Wannier-like functions for only the occupied states in a metallic system by generating NMTOs for cesium. Finally, we visualize the pressure-induced s-->d transition.