Bit-parallel approximate string matching algorithms with transposition

Using bit-parallelism has resulted in fast and practical algorithms for approximate string matching under Levenshtein edit distance, which permits a single edit operation to insert, delete or substitute a character. Depending on the parameters of the search, currently the fastest non-filtering algorithms in practice are the O(km/wn) algorithm of Wu and Manber, the O((k+2)(m−k)/wn) algorithm of Baeza-Yates and Navarro, and the O(m/wn) algorithm of Myers, where m is the pattern length, n is the text length, k is the error threshold and w is the computer word size. In this paper we discuss a uniform way of modifying each of these algorithms to permit also a fourth type of edit operation: transposing two adjacent characters in the pattern. This type of edit distance is also known as Damerau edit distance. In the end we also present an experimental comparison of the resulting algorithms.     

Reflection of Long Game Formulas

We study game formulas the truth of which is determined by a semantical game of uncountable length. The main theme is the study of principles stating reflection of these formulas in various admissible sets. This investigation leads to two weak forms of strict-II¹₁ reflection (or ∑₁-compactness). We show that admissible sets such as H(ω₂) and L_ω2 which fail to have strict-II¹₁ reflection, may or may not, depending on set-theoretic hypotheses satisfy one or both of these weaker forms. Mathematics Subject Classification : 03C70, 03C75.     

Spectral pattern recognition of improved voice quality

The self-organizing map (a neural network) was applied to the spectral pattern recognition of voice quality in 34 subjects: 15 patients operated on because of insufficient glottal closure and 19 subjects not treated for voice disorders. The voice samples, segments of sustained /a/, were perceptually rated by six experts. A self-organized acoustic feature map was first computed from tokens of /a/ and then used for the analysis of the samples. The locations of the samples on the map were determined and the distances from a normal reference were compared with the perceptual ratings. The map locations corresponded to the degree of audible disorder: the samples judged as normal were overlapping or close to the normal reference, whereas the samples judged as dysphonie were located further away from it. The comparison of pre- and postoperative samples of the patients showed that the perceived improvement of voice quality was also detected by the map.     

Cationic poly(methacryl oxyethyl trimethylammonium) and its poly(ethylene glycol)‐grafted analogue as capillary coating materials in electrophoresis

Cationic polyelectrolytes were synthesized and used as semipermanent coating materials for capillaries in electrophoresis. The polyelectrolytes used were a homopolymer of poly(methacryl oxyethyl trimethylammonium chloride) (PMOTAC) and its poly(ethylene glycol) (PEG)‐grafted analogue. Two PMOTAC polyelectrolytes, with molar masses of 85,000 and 300,000 g/mol, and PEG‐grafted PMOTAC with a molar mass of 280,000 g/mol were synthesized and then characterized by size exclusion chromatography (SEC) and nuclear magnetic resonance (NMR) spectroscopy. Attachment of the polyelectrolytes to the wall of the fused silica capillary for electrophoresis caused the electroosmotic flow (EOF) to reverse. The polyelectrolyte coatings were tested over the pH range 2–11 at different buffer ionic strengths, and the most stable and strongest anodic EOFs were obtained at acidic pH values with low ionic strength buffers. Between runs the capillary is merely rinsed for 2 or 3 min with the background electrolyte solution. With the PMOTAC coatings at pH values ≤5, the RSDs of the EOFs were less than 2.9% after 60 injections. The effects of the molar mass of the polycation and of PEGylation of PMOTAC on the interactions between the polycations and basic proteins were studied at acidic pH values. The differences in the effective electrophoretic mobilities, resolution values, and plate numbers of the proteins with the different coatings were due to the EOF, as demonstrated through calculations of reduced mobilities, relative resolution values, and relative plate numbers. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2655–2663, 2007     

Radiation degradation of copolymers of methyl methacrylate and 3-oximino-2-butanone methacrylate

Copolymers of methyl methacrylate and 3-oximino-2-butanone methacrylate (OM) were investigated as deep-UV and e-beam resists. Their increased sensitivity relative to PMMA (up to 50 times) was correlated with the radiation chemical yields of the volatile products and main chain scissions. The degradation of these copolymers, activated by the 3-oximino-2-butanone entity, is discussed in terms of energy absorption mechanisms and the subsequent scission reactions.     

Ein Beitrag zur Bestimmung der niederen Fetts?uren nach der Halbdestillationsmethode

Zusammenfassung Die Verschiebung der Halbdestillationswerte derverdünnten Lösungen der niederen Fettsäuren je nach der Konzentration wurde auf Grund der Untersuchungen vonKonowalow und vonWiegner nachgeprüft.Wie aus den Analysenergebnissen hervorgeht, steigt sowohl der Wert von k als auch der Halbdestillationswert bei Ameisensäure und Essigsäure, deren Halbdestillationswert kleiner als 50% ist, in verdünnten Lösungenfortgesetzt mit zunehmender Konzentration der Lösungen. Bei der Propionsäure und der Buttersäure dagegen, bei denen der Halbdestillationswert schon über 50% beträgt,wächst der Wert von k nur bis zu einer bestimmten, verhältnismäig niedrigen Konzentration — bei der Propionsäure 0,2 n und bei der Buttersäure 0,04 n —an, um von da fortan zu sinken.Beim Analysieren von Zweisäurengemischen, in denen das Aufeinanderwirken der Säuren infolge ihrer verschiedenen Dissoziationskonstanten die Verhältnisse kompliziert, sind die erhaltenen Ergebnisse nicht direkt zu verwerten.Diese Arbeit schließt sich an die Erklärung der Methodik an, die bei dem auf Anregung des Herrn Professor Dr.Unto Vartiovaara durchgeführten Untersuchungen über die bakterielle Cellulosezersetzung gegeben wurde.     

Gel permeation chromatography of branched polyethylene

The effect of long-chain branching must be considered in gel permeation chromatography to evaluate the molecular weight polydispersity of branched polyethylenes. Osmotic molecular weights of fractions of branched polyethylene were correlated with elution volumes; weight-average and number-average molecular weights of a branched polyethylene were determined. Molecular weight changes on crosslinking polyethylene by ionizing radiation are accompanied by branching and cannot be simply interpreted by gel permeation chromatography.     

Chemically-assisted fragmentation combined with multi-dimensional liquid chromatography and matrix-assisted laser desorption/ionization post source decay, matrix-assisted laser desorption/ionization tandem time-of flight or matrix-assisted laser desorption/ionization tandem mass spectrometry for improved sequencing of tryptic peptides

Derivatization of tryptic peptides using an Ettan CAF matrix-assisted laser desorption/ionization (MALDI) sequencing kit in combination with MALDI-post source decay (PSD) is a fast, accurate and convenient way to obtain de novo or confirmative peptide sequencing data. CAF (chemically assisted fragmentation) is based on solid-phase derivatization using a new class of water stable sulfonation agents, which strongly improves PSD analysis and simplifies the interpretation of acquired spectra. The derivatization is performed on solid supports, ZipTip(microC18, limiting the maximum peptide amount to 5 microg. By performing the derivatization in solution enabled the labeling of tryptic peptides derived from 100 microg of protein. To increase the number of peptides that could be sequenced, derivatized peptides were purified using multidimensional liquid chromatography (MDLC) prior to MALDI sequencing. Following the first dimension strong cation exchange (SCX) chromatography step, modified peptides were separated using reversed-phase chromatography (RPC). During the SCX clean up step, positively charged peptides are retained on the column while properly CAF-derivatized peptides (uncharged) are not. A moderately complex tryptic digest, prepared from six different proteins of equimolar amounts, was CAF-derivatized and purified by MDLC. Fractions from the second dimension nano RPC step were automatically sampled and on-line dispensed to MALDI sample plates and analyzed using MALDI mass spectrometry fragmentation techniques. All proteins in the derivatized protein mixture digest were readily identified using MALDI-PSD or MALDI tandem mass spectrometry (MS/MS). More than 40 peptides were unambiguously sequenced, representing a seven-fold increase in the number of sequenced peptides in comparison to when the CAF-derivatized protein mix digest was analyzed directly (no MDLC-separation) using MALDI-PSD. In conclusion, MDLC purification of CAF-derivatized peptides significantly increases the success rate for de novo and confirmative sequencing using various MALDI fragmentation techniques. This new approach is not only applicable to single protein digests but also to more complex digests and could, thus, be an alternative to electrospray ionization MS/MS for peptide sequencing.