Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5′- and 3′-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.     

Studies of oxygen uptake on O2 scavengers ­prepared from different iron‐containing ­parent substances

Temperature‐programmed reduction (TPR) measurements were performed for iron oxalates, iron(III) hydroxide (both pure and with additives) and iron(II, III) oxide. On the ground of TPR curves, reduction temperatures of the iron‐containing parent substances were chosen followed by oxygen uptake determination. Comparison of oxygen uptakes points to the use of Fe(OH)₃ and Fe₃O₄ as more advantageous than that of iron oxalates. Co‐precipitation from a mixed solution of iron and manganese salts results in a product which is more resistant to particle agglomeration at elevated temperatures than that obtained by­precipitation from solution of iron salt alone. Copyright © 2002 John­Wiley & Sons, Ltd.     

X-ray scattering investigations of acrylonitrileethylene oxide block copolymers

Wide angle (WAXS) and small angle (SAXS) X-ray scattering studies are reported on block copolymers of acrylonitrile with ethylene oxide. A distinct structural similarity between the copolymers and acrylonitrile homopolymer has been found. Considerable porosity of the copolymers has been shown. The porosity very largely governs the scattering power. It was found that the pores are three dimensional “particles” (scattering exponent α = 4), probably with smooth surfaces (surface fractal dimension d_s = 2).     

Variations of internal friction in YBa2Cu3Ox superconductors

The internal friction (Q ^–1) spectrum of YBa₂Cu₃O_x superconducting ceramic exhibits several peaks. It has been confirmed that the high-temperature peak (around 240 K) depends on structural changes and varies during subsequent cycles of cooling and heating.Q ^–1 conductivity, X-ray spectra and the shielding effect have been measured on several samples having different superconducting properties obtained by various thermal treatments. Splitting is a characteristic feature of the high-temperature internal friction peak of the sample which exhibits good superconducting properties. In the case of the specimen exhibiting the worst properties the peaks decrease and overlap. In both cases an increase can be observed of this peak with the number of thermal cycles. After ageing at 470 K, the high-temperature peak disappears. Subsequent thermal cycles slightly recover it. Hysteresis of the Young modulus is also observed. The results are interpreted as transition of the 04 oxygen atom between two energy minima in the O4-Cu-O4 chain.     

The effect of cobalt on the activation of fused iron catalyst for ammonia synthesis

BET, scanning electron microscopy, X-ray diffraction, Mössbauer spectroscopy, X-ray fluorescence spectroscopy and McBain thermobalance were used to investigate the effect of cobalt on the reduction behavior and activity of used iron catalyst for ammonia synthesis. Activity tests were carried out under 10 MPa in the 350–450°C temperature rang. Studies were performed on the traditional multipromoted iron catalyst and on the series of catalysts prepared with addition of cobalt. Addition of cobalt promoted the iron catalyst for ammonia synthesis. The most active sample was that containing approx. 5.5% wt Co. Cobalt changed the reduction behavior of the catalyst. The rate of the surface change during reduction was higher for the case of the ‘cobalt catalyst’; however the rate of mass change was higher for a typical iron catalyst. The process of reduction was probably followed by the formation of an Fe₃Co compound and by the surface faceting, with the exposure of an Fe(111) plane.     

Uniqueness in Shape from Shading Revisited

We analyse the problem of representing solutions of first-orderpartial differential equations in terms of complete integrals and envelopes. In this context, we revisit the uniqueness results alreadyexisting in the shape-from-shading literature that concern eikonalequations corresponding to the images of a Lambertian hemi-sphere and aLambertian plane. We show that the approach adopted by Brooks in [2, 3] isincomplete and subsequently re-establish its uniqueness claims.     

Fehlordnung von Wüstit

Erörterung der Zusammenhänge zwischen physikalisch-chemischen Eigenschaften und der Fehlordnung kristalliner Stoffe. Übersicht über die bisherigen Ergebnisse von Untersuchungen zur Fehlordnung von Wüstit und über die daraus abgeleiteten Modelle. Erläuterung eigener Röntgenbeugungsmessungen und thermogravimetrischer Untersuchungen. Beschreibung eines Modells für die Fehlordnung des Wüstits im Temperaturbereich von rd. 970 bis 1370 K. Ermittlung der Temperaturabhängigkeit der Gleichgewichtskonstante für die Bildung von ?Komplexdefekten?.     

Polymerization of chlorophenyl glycidyl ethers. VI

Summary Polymerization of p-chlorophenyl glycidyl ether initiated by potassium glycolates (ethylene, propylene and 2-methyl propylene glycolatea) in DMSO containing some 18-crown-6 ether or glycol was investigated. For the reaction system containing the propylene glycolate asymmetrically substituted with a methyl group, relatively high polymerization rates were obtained as compared with those found for the other systems studied, the resultant polymers also having higher molecular weights and comparatively low polydispersities. Aliphatic double bonds were found to be absent in the polymers synthesized, which would suggest that in the anionic polymerization process studied the growing chain is not transferred to the monomer.Dedicated to Prof. C.I. Simionescu on the occasion of the 60th anniversary of his birthday