A framework for mutational signature analysis based on DNA shape parameters

The mutation risk of a DNA locus depends on its oligonucleotide context. In turn, mutability of oligonucleotides varies across individuals, due to exposure to mutagenic agents or due to variable efficiency and/or accuracy of DNA repair. Such variability is captured by mutational signatures, a mathematical construct obtained by a deconvolution of mutation frequency spectra across individuals. There is a need to enhance methods for inferring mutational signatures to make better use of sparse mutation data (e.g., resulting from exome sequencing of cancers), to facilitate insight into underlying biological mechanisms, and to provide more accurate mutation rate baselines for inferring positive and negative selection. We propose a conceptualization of mutational signatures that represents oligonucleotides via descriptors of DNA conformation: base pair, base pair step, and minor groove width parameters. We demonstrate how such DNA structural parameters can accurately predict mutation occurrence due to DNA repair failures or due to exposure to diverse mutagens such as radiation, chemical exposure, and the APOBEC cytosine deaminase enzymes. Furthermore, the mutation frequency of DNA oligomers classed by structural features can accurately capture systematic variability in mutagenesis of >1,000 tumors originating from diverse human tissues. A nonnegative matrix factorization was applied to mutation spectra stratified by DNA structural features, thereby extracting novel mutational signatures. Moreover, many of the known trinucleotide signatures were associated with an additional spectrum in the DNA structural descriptor space, which may aid interpretation and provide mechanistic insight. Overall, we suggest that the power of DNA sequence motif-based mutational signature analysis can be enhanced by drawing on DNA shape features.

One-Pot Preparation of Metal–Polymer Nanocomposites in Irradiated Aqueous Solutions of 1-Vinyl-1,2,4-triazole and Silver Ions

Metal–polymer nanocomposite polyvinyltriazole–silver nanoparticles were obtained using one-pot synthesis in irradiated aqueous solutions of 1-vinyl-1,2,4-triazole (VT) and silver ions. Gel permeation chromatography data show that upon radiation initiation, the molecular weight of poly(1-vinyl-1,2,4-triazole) increases with increasing monomer concentration. To study the kinetics of polymerization and the features of the radiation–chemical formation of nanoparticles, UV-Vis spectroscopy was used. TEM images show a relatively small average size of the forming nanoparticles (2–3 nm) and a narrow size distribution, which shows the effective stabilization of nanoparticles by triazole substituents at a molar ratio of VT and silver ions of 25/1. The addition of ethyl alcohol was used to increase the efficiency of synthesis and suppress the crosslinking of macromolecules in solution. The results of the work show that aqueous–alcoholic solutions of 1 wt.% VT can be used to obtain soluble nanocomposite materials. 10 wt.% monomer solutions have prospects for use in the preparation of polymer gels filled with nanoparticles.

INFLUENCE OF RADIATION CONDITIONS ON CRACKING OF COMPOSITE SCINTILLATORS

The article analyzes two main hypotheses describing the cracking of a composite scintillator in the irradiation zone. This is the "temperature" and "radiation-chemical" hypothesis of cracking. The analysis is based on experi-mental data that we obtained by irradiating scintillators and the results of model chemical experiments.

INFLUENCE OF RADIATION CONDITIONS ON CRACKING OF COMPOSITE SCINTILLATORS

The article analyzes two main hypotheses describing the cracking of a composite scintillator in the irradiation zone. This is the "temperature" and "radiation-chemical" hypothesis of cracking. The analysis is based on experi-mental data that we obtained by irradiating scintillators and the results of model chemical experiments.

Unsteady MHD Plane Couette-Poiseuille Flow of Fourth-Grade Fluid with Thermal Radiation, Chemical Reaction and Suction Effects

This study investigates the unsteady MHD flow of a fourth-grade fluid in a horizontal parallel plates channel. The upper plate is oscillating and moving while the bottom plate is stationary. Solutions for momentum, energy and concentration equations are obtained by the He-Laplace scheme. This method was also used by Idowu and Sani [12] and there is agreement with our results. The effect of various flow parameters controlling the physical situation is discussed with the aid of graphs. Significant results from this study show that velocity and temperature fields increase with the increase in the thermal radiation parameter, while velocity and concentric fields decrease with an increase in the chemical reaction parameter. Furthermore, velocity, temperature and concentric fields decrease with an increase in the suction parameter. It is also interesting to note that when S4 = 0, our results will be in complete agreement with Idowu and Sani [12] results. The results of this work are applicable to industrial processes such as polymer extrusion of dye, draining of plastic films etc.

Investigation of mixed convection magnetized Casson nanomaterial flow with activation energy and gyrotactic microorganisms

Present article addresses mixed convection magnetohydrodynamic Casson nanomaterial flow by stretchable cylinder. The effects of thermal, solutal and motile density stratifications at the boundary of the surface are accounted. Flow governing expressions are acquired considering aspects of permeability, thermal radiation, chemical reaction, viscous dissipation and activation energy. The obtained flow model is made dimensionless through transformations and then tackled by NDsolve code in Mathematica. Physical impacts of sundry variables on nanomaterial velocity, temperature distribution, volume fraction of microorganisms and mass concentration is investigated through plots. Furthermore, quantities of engineering interest like surface drag force, heat transfer rate, density number and Sherwood number are computed and analyzed. We observed that fluid velocity diminishes for higher curvature variable, Casson fluid material variable, Hartmann number and permeability parameter. Fluid temperature has a direct relation with Eckert number, thermophoresis variable, Brownian dispersal parameter, Prandtl number and Hartmann number. Volume fraction of gyrotactic microorganisms is decreasing function of bioconvection Lewis number, stratification parameter and bioconvection Peclet number. Detailed observations are itemized at the end.

Preparation of iron oxide nanopowders by the radiation-chemical method

Various magnetic nanopowders of iron oxide were obtained using the radiation-chemical method when irradiated with a nanosecond electron beam. The main physical and chemical characteristics of the prepared nanopowders were studied, such as structure, porosity, thermal resistance and magnetic properties. It was found that, by selecting precursors and the composition of the solution, it is possible to control not only the textural properties and yield of the obtained nanopowders (by changing the dose and dose rate intensity of the electron beam), but also to obtain crystalline or amorphous nanopowders, on which their magnetic properties depend.

ENERGY SAVING OF WOOD DUE TO ITS MODIFICATION

Modified wood is wood that is improved with special modifiers in order to increase its strength, durability and water-, bio-, fire- and corrosion resistance, which, unlike natural wood, makes it more resistant to various environmental factors. This wood is good to use in construction, and it will be effective for further development, as the buildings will be used longer, and less likely to be subject to repair and reconstruction, which will reduce deforestation. The most popular methods of modification are thermomechanical modification with preliminary steaming of wood, its heating, or with preliminary impregnation with mineral oils; thermochemical modification; chemical modification; radiation-chemical modification. Each type of the above modifications differs in its properties, and also have their own impact on a particular type of wood. The most common and most effective method of modification is achieved by thermomechanical processing. Since it is when the wood is heated, after the introduction of the necessary modifiers into it, the polymers begin to heat up, due to which the vessels of the wood harden, which affects its density. To avoid the destruction of wood, it is very important to monitor the temperature and prevent it from reaching high heating levels.

Using Non-Fourier’s Heat Flux and Non-Fick’s Mass Flux Theory in the Radiative and Chemically Reactive Flow of Powell–Eyring Fluid

The behavior of convective boundary conditions is studied to delineate their role in heat and mass relegation in the presence of radiation, chemical reaction, and hydro-magnetic forces in three-dimensional Powell–Eyring nanofluids. Implications concerning non-Fourier’s heat flux and non-Fick’s mass flux with respect to temperature nanoparticle concentration were examined to discuss the graphical attributes of the principal parameters. An efficient optimal homotopy analysis method is used to solve the transformed partial differential equations. Tables and graphs are physically interpreted for significant parameters.

Mathematical modeling of loading of heavy-class robotic complexes on a tracked chassis into transport aircraft of EMERCOM of Russia

Рассмотрен один из возможных подходов к математическому моделированию загрузки робототехнического комплекса (РТК) тяжелого класса на гусеничном шасси с независимой торсионной подвеской в транспортный самолет. Данный подход представляет собой часть обоснованной оценки авиатранспортабельности специальных РТК. Он базируется на построении и решении системы линейных уравнений, в результате чего определяются параметры, по которым оценивается факт «вписывания» конструкции образца РТК в размеры грузовой кабины самолета. Актуальность статьи обусловливается, во-первых, потребностью в создании специальных РТК тяжелого класса для применения при тушении пожаров на особо опасных объектах, во-вторых, значительным вкладом оценки возможностей по загрузке в самолеты РТК в априорную аналитическую оценку авиатранспортабельности специальных РТК как до создания опытных образцов, так и в ходе оперативной подготовки к перебазированию в районы чрезвычайных ситуаций и, в третьих, определенной сложностью графоаналитического моделирования рассматриваемой загрузки. The threat of man-made danger with such sources as accidents at radiation, chemical and explosive objects exists at present time. That’s why it is advisable to create heavy-class fire robotic complexes on a tracked chassis, as the most effective means of extinguishing fires in these conditions. The consequences of emergencies depend on a quick and timely response. Therefore, when creating the new promising fire equipment, one of the most important issues to be addressed is to ensure its air transportability. At the stage of development of advanced heavy-class fire-fighting robotic systems on a tracked chassis with the planned possibility of their air transportability, it is very important to perform an a priori assessment of this property before creating a prototype. Modeling of loading involves solving a variety of problems, the main and most complex of which is the calculation of the spatial position of the structure of a particular robotic complex model with a tracked chassis relative to the internal contours of the cargo cabin of the aircraft. There are several types of structures for springing support rollers of tracked chassis. This article discusses tracked chassis with independent torsion bar suspension widely used in modern military equipment. It is advisable to focus the development of heavy-class fire robotics on the use of torsion bar suspension. The calculation of parameters that form the basis of mathematical modeling consists in solving a system of nonlinear equations (including algebraic and trigonometric operations). One of the equations describes the condition of the equilibrium of forces, the second - the equilibrium of moments, the rest (according to the number of support rollers minus one) describe the conditions for the location of the torsion axes on a given construction axis. The proposed calculation method provides for the transformation of this system into a system of linear algebraic equations which ensure an approximate solution, and the organization of an iterative process that ensures the convergence of a sequence of approximate solutions to the solution of the original system of nonlinear equations. The approach presented in the article can be used as the basis for modeling the loading of a special robotic complex on a tracked chassis with an independent torsion suspension into the cargo cabin of a transport aircraft. In turn, this modeling allows us to perform the reasonable a priori assessment of the air transportability of the robotic complex, carried out both at the stage of layout of the sample during its creation and during operation.