Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences

The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution.     

Interior-architectured ZnO nanostructure for enhanced electrical conductivity via stepwise fabrication process

Fabrication of ZnO nanostructure via direct patterning based on sol-gel process has advantages of low-cost, vacuum-free, and rapid process and producibility on flexible or non-uniform substrates. Recently, it has been applied in light-emitting devices and advanced nanopatterning. However, application as an electrically conducting layer processed at low temperature has been limited by its high resistivity due to interior structure. In this paper, we report interior-architecturing of sol-gel-based ZnO nanostructure for the enhanced electrical conductivity. Stepwise fabrication process combining the nanoimprint lithography (NIL) process with an additional growth process was newly applied. Changes in morphology, interior structure, and electrical characteristics of the fabricated ZnO nanolines were analyzed. It was shown that filling structural voids in ZnO nanolines with nanocrystalline ZnO contributed to reducing electrical resistivity. Both rigid and flexible substrates were adopted for the device implementation, and the robustness of ZnO nanostructure on flexible substrate was verified. Interior-architecturing of ZnO nanostructure lends itself well to the tunability of morphological, electrical, and optical characteristics of nanopatterned inorganic materials with the large-area, low-cost, and low-temperature producibility.     

Synthesis of single-walled carbon nanotubes using hemoglobin-based iron catalyst

Hemoglobin (Hb) was used as a catalyst for the growth of single-walled carbon nanotubes (SWCNTs). Hb was deposited onto a hydrophilic treated substrate by spin coating method. After oxidation at 800 °C, protein chains were decomposed and iron oxide nanoparticles remained with an average diameter of 2.29 nm. High quality SWCNTs were synthesized with an average diameter of 1.22 nm. The protein chains prevent iron atoms aggregation and so the size of the nanoparticles is smaller than that from ferritin-like proteins.     

Liquid salt cooled flexible conversion ratio fast reactor: Neutronic design

This paper presents the neutronic design of a liquid salt cooled fast reactor with flexible conversion ratio. The main objective of the design is to accommodate interchangeably within the same reactor core alternative transuranic actinides management strategies ranging from pure burning to self-sustainable breeding. Two, the most limiting, core design options with unity and zero conversion ratios are described. Ternary, NaCl-KCl-MgCl₂ salt was chosen as a coolant after a rigorous screening process, due to a combination of favourable neutronic and heat transport properties. Large positive coolant temperature reactivity coefficient was identified as the most significant design challenge. A wide range of strategies aiming at the reduction of the coolant temperature coefficient to assure self-controllability of the core in the most limiting unprotected accidents were explored. However, none of the strategies resulted in sufficient reduction of the coolant temperature coefficient without significantly compromising the core performance characteristics such as power density or cycle length. Therefore, reactivity control devices known as lithium thermal expansion modules were employed instead. This allowed achieving all the design goals for both zero and unity conversion ratio cores. The neutronic feasibility of both designs was demonstrated through calculation of reactivity control and fuel loading requirements, fluence limits, power peaking factors, and reactivity feedback coefficients.     

Infinite-horizon Scheduling Algorithms for Optimal Search for Hidden Objects

This paper considers discrete search problems in which a decision-maker has to find objects lost or hidden in a given set of locations so as to minimize the expected losses incurred. Given a chance to look for a hidden object in the same location infinitely many times, this type of problem, in contrast to standard scheduling problems, has an infinite sequence as its solution. Thus we are concerned to find an algorithm that yields an optimal solution, rather than the optimal sequence itself. Using combinatorial techniques, fast optimal algorithms for solving the problems are obtained, and optimality conditions are presented for search criteria, under which the local-search algorithms yield the global optimum.     

Interferon-β Activity Is Affected by S100B Protein

Interferon-β (IFN-β) is a pleiotropic cytokine secreted in response to various pathological conditions and is clinically used for therapy of multiple sclerosis. Its application for treatment of cancer, infections and pulmonary diseases is limited by incomplete understanding of regulatory mechanisms of its functioning. Recently, we reported that IFN-β activity is affected by interactions with S100A1, S100A4, S100A6, and S100P proteins, which are members of the S100 protein family of multifunctional Ca²⁺-binding proteins possessing cytokine-like activities (Int J Mol Sci. 2020;21(24):9473). Here we show that IFN-β interacts with one more representative of the S100 protein family, the S100B protein, involved in numerous oncological and neurological diseases. The use of chemical crosslinking, intrinsic fluorescence, and surface plasmon resonance spectroscopy revealed IFN-β binding to Ca²⁺-loaded dimeric and monomeric forms of the S100B protein. Calcium depletion blocks the S100B–IFN-β interaction. S100B monomerization increases its affinity to IFN-β by 2.7 orders of magnitude (equilibrium dissociation constant of the complex reaches 47 pM). Crystal violet assay demonstrated that combined application of IFN-β and S100B (5–25 nM) eliminates their inhibitory effects on MCF-7 cell viability. Bioinformatics analysis showed that the direct modulation of IFN-β activity by the S100B protein described here could be relevant to progression of multiple oncological and neurological diseases.     

Novel acylflavones from Sideritis syriaca ssp. syriaca

In the framework of the detailed phytochemical analysis of the aerial parts of Sideritis syriaca, two novel acylflavones were isolated together with three acetylated flavone glycosides and acylated flavone glycosides. The novel acylflavones were identified as isoscutellarein 7-trans-p-coumarate and apigenin 7-,4′-bis(trans-p-coumarate). Their structures were elucidated by means of UV, 1D and 2D NMR, LC–DAD–MS and confirmed by HR-MS spectroscopy.     

Rank normalization of impact factors will resolve Vanclay’s dilemma with TRIF

The ThomsonReuters impact factor is a viable, widely used and informative measure of journal visibility and frequency of use. It is accurate, transparent and easy to use. It is a live and evolving system, that can broaden its scope and implement new features and methods. Some of Vanclay’s suggestions, like wider use of order statistics, or our suggestion of rank normalization might be implemented by JCR in the future.     

Cluster Monte Carlo and numerical mean field analysis for the water liquid-liquid phase transition

Using Wolff's cluster Monte Carlo simulations and numerical minimization within a mean field approach, we study the low temperature phase diagram of water, adopting a cell model that reproduces the known properties of water in its fluid phases. Both methods allow us to study the thermodynamic behavior of water at temperatures, where other numerical approaches - both Monte Carlo and molecular dynamics - are seriously hampered by the large increase of the correlation times. The cluster algorithm also allows us to emphasize that the liquid-liquid phase transition corresponds to the percolation transition of tetrahedrally ordered water molecules.     

Promoting quality improvement research

The authors show how an internal grant program can stimulate quality improvement research by providing technical and financial support to clinicians and employees.