Hengzongshu/ArticleAgent huggingface dataset:
The system of averaged equations of motion, continuity, and transport equations for normal Reynolds stresses and dissipation rate of turbulent kinetic energy is employed in the thin shear layer approximation to describe a flow in swirling turbulent jets. The turbulent shear stresses are determined from the non-equilibrium algebraic relations of Rodi.

The numerical realization of the model is based on the application of a finite-difference algorithm on moving grids, preserving the laws of momentum and angular momentum conservation. As an example to model a swirling turbulent jet, numerical simulation of swirling turbulent wake flows with varied total momentum and angular momentum is performed. A modification of diffusion terms in the transport equations is considered, based on the improved algebraic Ilyushin approximations of third-order moments that take into account the flow swirl.

The computation results are in satisfactory agreement with the known experimental data of Lavrentyev Institute of Hydrodynamics of the Siberian Branch of the Russian Academy of Sciences (LIH SB RAS). A numerical analysis of the self-similarity of decay for the far turbulent wake with zero excess momentum and nonzero angular momentum is made. The computation results for swirling turbulent wake behind a towed sphere are presented.
The mineral composition and melt inclusions of ultramafic lamprophyres of the Terina complex were investigated. The rocks identified were aillikites, mela-aillikites, and damtjernites, and they were originally composed of olivine macrocrysts and phenocrysts, as well as phlogopite phenocrysts in carbonate groundmass, containing phlogopite, clinopyroxene and feldspars. Minor and accessory minerals were fluorapatite, ilmenite, rutile, titanite, and sulphides. Secondary minerals identified were quartz, calcite, dolomite, serpentine, chlorite, rutile, barite, synchysite-(Ce), and monazite-(Ce). Phlogopite, calcite, clinopyroxene, Ca-amphibole, fluorapatite, magnetite, and ilmenite occurred as daughter-phases in melt inclusions. The melt inclusions also contained Fe–Ni sulphides, synchysite-(Ce) and, probably, anhydrite. The olivine macrocrysts included orthopyroxene and ilmenite, and the olivine phenocrysts included Cr-spinel and Ti-magnetite inclusions. Crystal-fluid inclusions in fluorapatite from damtjernites contain calcite, clinopyroxene, dolomite, and barite. The data that were obtained confirm that the ultramafic lamprophyres of the Terina complex crystallized from peridotite mantle-derived carbonated melts and they have not undergone significant fractional crystallization. The investigated rocks are considered to be representative of melts that are derived from carbonate-rich mantle beneath the Siberian craton.
Gonadal atrophy is the most typical and dramatic manifestation of intraspecific hybrid dysgenesis syndrome leading to sterility of Drosophila melanogaster dysgenic progeny. The P-M system of hybrid dysgenesis is primarily associated with germ cell degeneration during the early stages of Drosophila development at elevated temperatures.

In the present study, we have defined the phase of germ cell death as beginning at the end of embryogenesis immediately following gonad formation. The early stages of germ cell formation in dysgenic flies showed sensitivity to developmental temperature increases at any stage of the Drosophila life cycle including the imago. Analysis of germ cell reactions to hybrid dysgenesis induction revealed significant changes in subcellular structure, especially mitochondria, prior to germ cell breakdown.

The mitochondrial pathology can be the reason for the activation of cell death pathways in dysgenic germ cells and lead to gonadal atrophy. Summary We investigated the hybrid dysgenesis in the context of germ cell development and observed the dysgenic effect is associated with dramatic pathological changes in structure of germ cell mitochondria and lead to massive and quick cell death. The temperature-dependent screening of germ cells developmental pattern in dysgenic background showed that these cells are susceptible to the hybrid dysgenesis at any drosophila life-cycle stage, including in the imago.
In this paper the flow structure in a four-vortex furnace of a pulverized coal boiler has been studied.

The results of an experimental study of inner aerodynamics carried out on a laboratory isothermal model of a combustion device are presented. Using the particle image velocimetry method, flow velocity distributions have been obtained in a number of sections.

A spatial flow structure consisting of four stable conjugate vortices with vertical flow rotation axes has been visualized.
The paper study are the conditions of formation of metal-ceramic tracks regarding the parameters of the laser action. Optimization of laser action on the powder mixture was carried out. The mechanical properties of laser tracks have been studied. It is demonstrated that both the ceramic particle size and concentration vary at different focusing modes. It is found that the clad metal-ceramic structure has 4 – 5 times higher microhardness – 854 HV0.1 as compared to the substrate 178 HV0.1.
Thermal decomposition of complex salts [M(NH3)4]A (M = Pt, Pd; A = CrO4, Cr2O7) in oxygen atmosphere goes through the stage of formation of the phase MCrO2 with delafossite structure and it's further decomposition and formation of the chromium oxide(III) and monometallic platinum or palladium.Thermal decomposition of complex salts [M(NH3)4]A (M = Pt, Pd; A = CrO4, Cr2O7) in hydrogen atmosphere proceeds with partial reduction of chromium to an metallic state and the formation of a metal solid solution MxCr1-x (M = Pt, Pd) with a chromium content up to 22 at.% and a chromium oxide(III).Catalytic properties of bimetallic Pt-Cr2O3 and Pd-Cr2O3 composites obtained by thermal decomposition in hydrogen atmosphere at the temperature 500 °C differs a lot from monometallic Pt and Pd in CO TOX and PROX processes.Addition of Cr2O3 boosted oxidative activity of metals probably due to appearance of metal-oxide interface, which is of crucial importance in catalysis.
In this work we studied transition mechanics of a dynamic hydrogen bond network of water into a stable hydrogen bond network during gas clathrate hydrate formation process.

For this purpose, we used Molecular Dynamic simulation methods and a bunch of home-made programs for determining structural properties during transition process.

We have found that at certain conditions the network transformation process involves the whole system from the very beginning and could be considered as a collective effect, that results in high speed of hydrate formation.
The paper reports on the investigation of the flow and flame front dynamics in a premixed conical methane/air flame perturbed by an acoustic field.

The investigation is carried out by using stereoscopic particle image velocimetry and planar laser-induced fluorescence of HCHO to measure simultaneously the instantaneous velocity field and flame front location in the axial plane. The optical techniques provided information about local velocity and velocity gradients, stretching and curvature of the flame front. Flow conditions when the flame is covered from the top by a cooled metallic flat plate are also considered.

It is found that the flow and flame front lose axial symmetry when the obstacle is present because of disruption of the global instability mechanism of the combustion products plume driven by bouncy force.
We apply the differential equation method to the calculation of the total Born cross section of the process Z1Z2→Z1Z2e+e−.

We obtain explicit expression for the cross section exact in the relative velocity of the nuclei.
Natural gas (methane, CH4) is widely considered as a promising energy carrier for mobile applications. Maximizing the storage capacity is the primary goal for the design of future storage media. Here we report the CH4 storage properties in a family of isostructural (3,24)-connected porous materials, MFM-112a, MFM-115a, and MFM-132a, with different linker backbone functionalization. Both MFM-112a and MFM-115a show excellent CH4 uptakes of 236 and 256 cm3 (STP) cm–3 (v/v) at 80 bar and room temperature, respectively. Significantly, MFM-115a displays an exceptionally high deliverable CH4 capacity of 208 v/v between 5 and 80 bar at room temperature, making it among the best performing metal–organic frameworks for CH4 storage. We also synthesized the partially deuterated versions of the above materials and applied solid-state 2H NMR spectroscopy to show that these three frameworks contain molecular rotors that exhibit motion in fast, medium, and slow regimes, respectively. In situ neutron powder diffraction studies on the binding sites for CD4 within MFM-132a and MFM-115a reveal that the primary binding site is located within the small pocket enclosed by the [(Cu2)3(isophthalate)3] window and three anthracene/phenyl panels. The open Cu(II) sites are the secondary/tertiary adsorption sites in these structures. Thus, we obtained direct experimental evidence showing that a tight cavity can generate a stronger binding affinity to gas molecules than open metal sites. Solid-state 2H NMR spectroscopy and neutron diffraction studies reveal that it is the combination of optimal molecular dynamics, pore geometry and size, and favorable binding sites that leads to the exceptional and different methane uptakes in these materials.
Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1' of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg-DNA complexes have been solved, yet no structure with A opposite the lesion is available.

Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation. The catalytic dyad, Pro1-Glu2, was modeled in all four possible protonation states. Only one transition was observed in the experimental reaction rate pH dependence plots, and Glu2 kept the same set of interactions regardless of its protonation state, suggesting that it does not limit the reaction rate. The adenine base opposite oxoG was highly distorting for the adjacent nucleotides: in the more stable syn models it formed non-canonical bonds with out-of-register nucleotides in both the damaged and the complementary strand, whereas in the anti models the adenine either formed non-canonical bonds or was expelled into the major groove. The side chains of Arg109 and Phe111 that Fpg inserts into DNA to maintain its kinked conformation tended to withdraw from their positions if A was opposite to the lesion. The region showing the largest differences in the dynamics between oxoG:C and oxoG:A substrates was unexpectedly remote from the active site, located near the linker joining the two domains of Fpg. This region was also highly conserved among 124 analyzed Fpg sequences. Three sites trapping water molecules through multiple bonds were identified on the protein-DNA interface, apparently helping to maintain enzyme-induced DNA distortion and participating in oxoG recognition.

Overall, the discrimination against A opposite to the lesion seems to be due to incorrect DNA distortion around the lesion-containing base pair and, possibly, to gross movement of protein domains connected by the linker.
In this work, the method of lattice Boltzmann equations was applied to simulate the systems of two and three parallel laminar plane jets. Simulation was carried out for different Reynolds numbers (Re = 20-200).

For the case of two jets, the character of jet interaction has been determined to be, in general, non-stationary, but for small Re values, the process becomes stable due to the action of viscosity forces. For the case of three jets, the character of jets interaction is found to differ significantly from the case of two jets and is non-stationary even for small Re numbers.
Currently, indicators are used for comparison such as mean, median and mode. And the choice of three options is carried out not on formal criteria, but on the basis of general reasoning. They are already beginning to be used when comparing regions by biologists. These measures have not yet been applied in economic analysis.

The article proposes new methods of measurement of differences between of RF regions economic development level. The authors propose to build a system of comparisons on the basis of Bregman divergences. The divergence of Kulback-Leibler (KL-divergence) is investigated, primarily, the variant of the Bregman divergence. Pairwise comparisons of the level of immigration to the regions as a criterion of quality of measurement of differences are proposed. The main calculations are made on the example of the level of wages in the regions of the South of Western Siberia.

The conclusion is made about the prospects of using the existing variants of Bregman divergence, as well as about the possibility of developing new divergence options that best match the comparative attractiveness of the regions for immigrants.
Helical vortices whose parameters have a strong influence on the efficiency of the apparatus is often occur in technical devices using swirling flow (cyclones, separators, etc.). To date the internal structure of such vortices is poorly understood. In [1] a model of helical vortex with uniform vorticity distribution in the core is proposed. Vortices arising in real flow always have a smooth vorticity distribution due to the viscosity action. The problem on steady moving helical vortices with the vortex core of small size in an inviscid fluid was solved in [2]. The non-orthogonal ‘helical’ coordinate system was introduced that allowed author to reduce the problem to two dimensional one. However, the velocity of the vortex motion was written only in the form of a quadratures computation of which is difficult.

This paper presents first attempt for research on the diffusion and dynamics of a viscous helical vortex.
Population structure is an important factor driving genetic changes.Comparing social (termites) and nonsocial (cockroaches) insects we found the difference in their mitochondrial mutational spectrum: transition transversion ratio (ts/tv) is higher in termites compared to cockroaches suggesting potential influence of population structure on mutational patterns.
The lethal yellow mutation in agouti loci (Ay mutation) reduces the activity of melanocortin (MC) receptors and causes hyperphagia, obesity and type two diabetes mellitus in aging mice (Ay mice). It is unknown if changes in distinct elements of the metabolic system such as white adipose tissue (WAT) and brown adipose tissue (BAT), and skeletal muscle will manifest before the development of obesity.

The aim of this work was to measure the relative gene expression of key proteins that regulate carbohydrate-lipid metabolism in WAT, BAT and skeletal muscle in Ay mice before the development of obesity. C57Bl/6J mice bearing a dominant autosomal mutation Ay (Ay /a mice) and mice of the standard genotype (a/a mice, control) have been studied in three age groups: 10, 15 and 30 weeks. The relative mRNA level of genes was measured by real-time PCR in skeletal muscles (uncoupling protein 3 (Ucp3) and carnitine palmitoyl transferase 1b (Cpt1b) (free fatty acids oxidation), solute carrier family 2 (facilitated glucose transporter), member 4 (Slc2a4) (glucose uptake)), in WAT lipoprotein lipase (Lpl) (triglyceride deposition), hormone-sensitive lipase (Lipe) (lipid mobilization), and Slc2a4 (glucose uptake)), and in BAT: uncoupling protein 1 (Ucp1) (energy expenditure).

The expression of Cpt1b was reduced in young Ay mice (10 weeks), there was no transient peak of transcription of Cpt1b, Ucp3 in skeletal muscle tissue and Lipe, Slc2a4 in WAT in early adult Ay mice (15 weeks), which was noted in а/а mice. Reduction of the transcriptional activity of the studied genes in skeletal muscle and white adipose tissue can initiate the development of melanocortin obesity in Ay mice.
In the majority of colorectal cancer (CRC) cases, the genetic basis of predisposition remains unexplained.

The goal of the study was to assess the regulatory SNPs (rSNPs) in the human genome and to reveal СRC drivers based on the available chromatin immunoprecipitation sequencing (ChIP-Seq, ChIA-PET) and transcriptional profiling (RNA-Seq) data. We combined positional (locations within genome regulatory elements) and functional (associated with allele-specific binding and expression) criteria followed by an analysis using genome-wide association studies (GWAS) and minor allele frequency (MAF) datasets. DeSeq2 analysis through 70 CRC patients reinforced the regulatory potential.

rSNPs (1,476) that were associated with significant (P < 0.01) allele-specific events resulting in thirty that exhibited a link with CRC according to the MAF and 27, with a risk of malignancy in general according to GWAS. Selected rSNPs may modify the expression of genes for tumor suppressors and the regulators of signaling pathways, including noncoding RNAs. However, the rSNPs from the most represented group affect the expression of genes related to splicing. Our findings strongly suggest that the identified variants might contribute to CRC susceptibility, which indicates that aberrant splicing is one of the key mechanisms for unraveling disease etiopathogenesis and provides useful inputs for interpreting how genotypic variation corresponds to phenotypic outcome.
Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incorporate negative Nanog autoregulation and might not include positive feedbacks from Nanog to Oct4 and Sox2.

Thorough parametric analysis of the mathematical model based on this revisited core regulatory circuit identified that there are substantial changes in model dynamics occurred depending on the strength of Oct4 and Sox2 activation and molecular complexity of Nanog autorepression.

The analysis showed the existence of four dynamical domains with different numbers of stable and unstable steady states. We hypothesize that these domains can constitute the checkpoints in a developmental progression from naïve to primed pluripotency and vice versa. During this transition, parametric conditions exist, which generate an oscillatory behavior of the system explaining heterogeneity in expression of pluripotent and differentiation factors in serum ESC cultures. Eventually, simulations showed that addition of positive feedbacks from Nanog to Oct4 and Sox2 leads mainly to increase of the parametric space for the naïve ESC state, in which pluripotency factors are strongly expressed while differentiation ones are repressed.
Poly-Si crystallization mechanism is examined by conducting numerical simulations, combining the thermal diffusion equation with a rigorous coupled wave analysis method. The ripples at the boundary of poly-Si grains are modeled as a grating surface structure.

Under laser beam irradiation, the melting front profiles are accurately analyzed by including surface diffraction, polarization of the laser, and laser energy density. For two different lasers, XeCl excimer laser (λ = 308 nm) and Yb:YAG solid state laser (λ= 343 nm), the energy density range at which poly-Si grains are gradually ordered was determined.

Furthermore, the energy density window of the Yb:YAG laser is found to be four times larger than that of XeCl laser. On the other hand, the Yb:YAG laser may produce amorphous-Si phase after completing the crystallization process. It is suggested that this amorphous-Si phase could be avoided, if a double pulse laser is used.
Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.

Here we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. All calculations were implemented by in-house PERL scripts.

Authors using algorithms for predicting effects of mutations should be aware of the bias described here. Supplementary data are available at Bioinformatics online. The article 10.1093/bioinformatics/bty348, published alongside this paper, also addresses the problem of biases in protein stability change predictions.
The potential scattering of electrons carrying non--zero quanta of the orbital angular momentum (OAM) is studied in a framework of the generalized Born approximation, developed in our recent paper by Karlovets \textit{et al.}, Phys. Rev. A. {\textbf 92}, 052703 (2015).

We treat these so--called \textit{twisted} electrons as spatially localized wave--packets. The simple and convenient expressions are derived for a number of scattering events in collision of such a vortex electron with a single potential, located at a given impact parameter with respect to the wave-packet's axis. The more realistic scenarios are also considered with either localized (mesoscopic) targets or infinitely wide (macroscopic) ones that consist of the randomly distributed atoms. Dependence of the electron scattering pattern on a size and on a relative position of the target is studied in detail for all three scenarios of the single--potential--, mesoscopic-- and the macroscopic targets made of hydrogen in the ground $1s$ state.

The results demonstrate that the angular distribution of the outgoing electrons can be very sensitive to the OAM and to kinematic parameters of the focused twisted beams, as well as to composition of the target. Scattering of vortex electrons by atoms can, therefore, serve as a valuable tool for diagnostic of such beams.