Feature based fuzzy matching of 2D gel electrophoresis images

Automatic alignment (matching) of two-dimensional gel electrophoresis images is of primary interest in the evolving field of proteomics. In the present study, feature-based matching techniques, in their classical and robust versions, are described, and an automatic method of fuzzy alignment (FA) is introduced. This method allows automatic matching of two gel images with different numbers of features with unknown correspondence. Performance of FA is tested on simulated and real data sets.     

Phase equilibria in the V2O5-FeVMoO7 system

The progress of the reactions of water with brownmillerite (C₄AF⁺) and its mixtures with gypsum (C¯SH₂) and calcium sulphoaluminate (C₄A₃¯S) was investigated by means of calorimetric measurements in situ and X-ray diffractometry to determine the reaction heat and the conversion of the solid reactants as functions of time up to 50 h. The rapid reaction of C₄AF with water and the modifying effect of sulphates on the composition of the hydrated phases were confirmed. The presence of sulphates causes the induction period during the reactions of aluminium and iron-containing clinker phases with water. These phenomena are important technologically too, especially in cements with increased contents of C₄AF and of sulphate-yielding phases (C¯SH₂ and C₄A₃¯S).

---

Zusammenfassung Der Verlauf der Hydratation von Brownmillerit Ca₄AF^* bzw. seinen Mischungen mit Gips (C¯SH₂) und Calcium-sulfat-aluminat (C₄A₃¯S) wurde durch kalorimetrische Messungen in situ und Röntgendiffraktometrie verfolgt, um die Abhängigkeit der Reaktionswärme und des Umsatzes der festen Reaktanden von der Zeit (bis 50 h) zu bestimmen. Die schnelle Reaktion von C₄AF mit Wasser und der modifizierende Effekt der Sulfate auf die Zusammensetzung der hydratisierten Phase wird bestätigt. Die Anwesenheit von Sulfat bewirkt eine Induktionsperiode bei der Reaktion von alumimum- und eisenhaltigen Klinkerphasen mit Wasser. Diese Erscheinungen sind von technischer Bedeutung, insbesondere für Zemente mit erhöhtem Gehalt an C₄AF und sulfatbildenden Phasen wie C¯SH₂ und C₄A₃¯S.

---

(4 · l23 · Fe2O3) (4 · 3l23 · SO3) ( 50 ). . - . , , - .

---

Dedicated to F. Hanic, D. Sc. on the occasion of his 60th birthday     

Chromatographic and spectroscopic investigation of the associative changes with the selected higher fatty alcohols

An attempt was made to compare usefulness of the ir spectroscopic technique with paper chromatography in the investigations concerning self-association of higher fatty alcohols. A conclusion was drawn that only the complementary application of both analytical methods better enabled to trace the establishing of association equilibria in the given experimental conditions.     

On the optimal partitioning of data with K-means,growing K-means,neural gas,and growing neural gas

In this paper, the performance of new clustering methods such as Neural Gas (NG) and Growing Neural Gas (GNG) is compared with the K-means method for real and simulated data sets. Moreover, a new algorithm called growing K-means, GK, is introduced as the alternative to Neural Gas and Growing Neural Gas. It has small input requirements and is conceptually very simple. The GK leads to nearly optimal values of the cost function, and, contrary to K-means, it is independent of the initial data set partition. The incremental property of GK additionally helps to estimate the number of "natural" clusters in data, i.e., the well-separated groups of objects in the data space.     

Synthesis of Acyclic Nitroazole Nucleosides and Their Incorporation into Oligonucleotides,and Their Duplex and Triplex Formation

Acyclic nucleosides of 4‐nitro‐1H‐imidazole and 4‐nitropyrazole have been synthesized by nucleophilic addition of the appropriate 4‐nitroazole to (?)‐(S)‐(hydroxymethyl)oxirane in the presence of a catalytic amount of potassium carbonate. (+)‐(R)‐3‐(4‐nitro‐1H‐imidazol‐1‐yl)propane‐1,2‐diol and (+)‐(R)‐3‐(2‐methyl‐4‐nitro‐1H‐imidazol‐1‐yl)propane‐1,2‐diol were also obtained in an independent reaction starting from appropriate 1,4‐dinitro‐1H‐imidazole and (+)‐(R)‐3‐aminopropane‐1,2‐diol. (+)‐(R)‐3‐(4‐Nitropyrazol‐1‐yl)propane‐1,2‐diol was also obtained by direct noncatalyzed addition of 4‐nitropyrazole to (?)‐(S)‐(hydroxymethyl)oxirane, whereas the (S)‐enantiomer was obtained by reaction of 4‐nitropyrazole with (+)‐(S)‐1,2‐O‐isopropylideneglycerol under Mitsunobu reaction conditions, followed by a cleavage of the isopropylidene group with 80% AcOH. Racemization during any of these syntheses has not been observed. 3‐(4‐Nitroazol‐1‐yl)propane‐1,2‐diols were incorporated into a 26‐mer oligonucleotide. UV Thermal melting studies of duplexes of the oligonucleotides with 4‐nitropyrazole or 4‐nitro‐1H‐imidazole paired with four natural bases showed moderately decreased stabilities of the duplexes. A narrow range of melting temperatures, typically being within 2° for each acyclic nucleoside, fulfill one of the requirements of using acyclic 4‐nitroazoles as general bases. Single incorporation of 4‐nitroazoles into a 14‐mer triplex forming oligonucleotide resulted in considerably decreased triplex stabilities.     

Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

Computational design of protein catalysts with enhanced stabilities for use in research and enzyme technologies is a challenging task. Using force-field calculations and phylogenetic analysis, we previously designed the haloalkane dehalogenase DhaA115 which contains 11 mutations that confer upon it outstanding thermostability (T_m = 73.5 °C; ΔT_m > 23 °C). An understanding of the structural basis of this hyperstabilization is required in order to develop computer algorithms and predictive tools. Here, we report X-ray structures of DhaA115 at 1.55 Å and 1.6 Å resolutions and their molecular dynamics trajectories, which unravel the intricate network of interactions that reinforce the αβα-sandwich architecture. Unexpectedly, mutations toward bulky aromatic amino acids at the protein surface triggered long-distance (∼27 Å) backbone changes due to cooperative effects. These cooperative interactions produced an unprecedented double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates to the active site, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site. Despite these spatial restrictions, experimental tracing of the access tunnels using krypton derivative crystals demonstrates that transport of ligands is still effective. Our findings highlight key thermostabilization effects and provide a structural basis for designing new thermostable protein catalysts.

Illustration of cooperative thermostabilization effects of the double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site.     

Studies of the reaction mechanism between copper(II) sulphate and excess copper(I) sulphide

The reaction process between CuSO₄ and excess Cu₂S in the temperature range 650–750 K was investigated by methods of thermal analysis and by studying the phase contentss of the products as a function of the fractional conversion. The reaction proceeds in three steps, with Cu₂S and a new phase described by the formula Cu₂SO₂ as intermediates. This new phase is liquid under the conditions of the reaction. The final product of the reaction is a defective crystalline Cu₂O.

---

Zusammenfassung Der Verlauf der Reaktion zwischen CuSO₄ und überschüssigem Cu₂S im Temperaturbereich von 650–750 K wurde mittels thermoanalytischer Methoden und durch Ermittlung der Phasenzusammensetzung in AbhÄngigkeit von der Konversion untersucht. Die Reaktion verlÄuft in drei Schritten mit Cu₂S und einer neuen Phase der Zusammensetzung Cu₂SO₂ als Zwischenproduke. Die neue Phase ist unter den Reaktionsbedingungen eine Flüssigkeit. Endprodukt der Reaktion ist nicht völlig kristallines Cu₂O.

---

CuSO₄ Cu₂S 650–750 K . Cu₂S , Cu₂SO₂ . Cu₂O .

     

The role of quantum interference in determining transport properties of molecular bridges

An analytical approach to the electron transport phenomena in molecular devices is presented. The analyzed devices are composed of various molecular bridges attached to two semi-infinite electrodes. Molecular system is described within the tight-binding model, while the coupling to the electrodes is analyzed through the use of Newns-Anderson chemisorption theory. The current-voltage (I-V) characteristics are calculated through the integration of transmission function in the standard Landauer formulation. The essential question of quantum interference effect of electron waves is diseussed in three aspects: (i) the geometry of a molecular bridge, (ii) the presence of an external magnetic field and (iii) the location of chemical substituent.     

A comparison of two algorithms for warping of analytical signals

The alignment of analytical signals is an important preprocessing step when further analysis (e.g. PCA) requires the same lengths of all of them. Two techniques for alignment of profiles, namely dynamic time warping (DTW) and correlation optimized warping (COW) were tested and compared. The attention was focused on chromatographic and spectroscopic profiles. Simulated and two sets of real data were studied in this study.