Hengzongshu/ArticleAgent huggingface dataset:
In this paper we describe the properties of the crystal of guanylurea hydrogen phosphate (NH[Formula: see text])[Formula: see text]CNHCO(NH[Formula: see text])H[Formula: see text]PO[Formula: see text] (GUHP) and propose its application in terahertz photonics and optoelectronics. GUHP crystal has a wide window of transparency and a high optical threshold in the visible and NIR spectral regions and narrow absorption bands in the terahertz frequency range.

The spectral characteristics of absorption and refraction in the THz range were found to be strongly dependent on crystal temperature and orientation. Computer simulations made it possible to link the nature of the resonant response of the medium at THz frequencies with the molecular structure of the crystal, in particular, with intermolecular hydrogen bonds and the layered structure of the lattice.

The possibility of application of the crystal under study for the conversion of femtosecond laser radiation from visible an NIR to terahertz range was demonstrated. It was shown that dispersion properties of the crystal allow the generation of narrow band terahertz radiation, whose spectral properties are determined by conditions close to phase matching. The properties of the generated terahertz radiation under various temperatures suggest the possibility of phonon mechanism of enhancement for nonlinear susceptibility of the second order.
Age-related macular degeneration (AMD) is a complex, multifactorial neurodegenerative disease that constitutes the most common cause of irreversible blindness in the elderly in developed countries. Incomplete knowledge about its pathogenesis prevents the search for effective methods of prevention and treatment of AMD, primarily its &ldquo;dry&rdquo; type, which is by far the most common (90% of all AMD cases). In recent years, AMD became younger: late stages of the disease are now detected in relatively young people. It is known that AMD pathogenesis&mdash;according to the age-related structural and functional changes in the retina&mdash;is linked with inflammation, hypoxia, oxidative stress, mitochondrial dysfunction, and an impairment of neurotrophic support, but the mechanisms that trigger the conversion of normal age-related changes to the pathological process as well as the reason for early AMD development remain unclear. In the adult mammalian retina, de novo neurogenesis is very limited. Therefore, the structural and functional features that arise during its maturation and formation can exert long-term effects on further ontogenesis of this tissue. The aim of this review is to discuss possible contributions of the changes/disturbances in retinal neurogenesis to the early development of AMD.
Background Anopheles coluzzii and An. arabiensis belong to the An. gambiae complex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. Findings In this study, we produced de novo chromosome-level genome assemblies for An. coluzzii and An. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 Mbp and 256.8 Mbp of the total assemblies for An. coluzzii and An. arabiensis , respectively. Each assembly consists of three chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomiccoordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in An. coluzzii and An. arabiensis . Conclusion The new chromosome-level assemblies will facilitate functional and population genomic studies in An. coluzzii and An. arabiensis . The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.
Inflorescences of wheat species, spikes, are characteristically unbranched and bear one sessile spikelet at a spike rachis node. Development of supernumerary spikelets (SSs) at rachis nodes or on the extended rachillas is abnormal. Various wheat morphotypes with altered spike morphology, associated with the development of SSs, present an important genetic resource for studies on genetic regulation of wheat inflorescence development. Here we characterized diploid and tetraploid wheat lines of various non-standard spike morphotypes, which allowed for identification of a new mutant allele of the WHEAT FRIZZY PANICLE (WFZP) gene that determines spike branching in diploid wheat Ttiticum monococcum L. Moreover, we found that the development of SSs and spike branching in wheat T. durum Desf. was a result of a wfzp-A/TtBH-A1 mutation that originated from spontaneous hybridization with T. turgidum convar. сompositum (L.f.) Filat. Detailed characterization of the false-true ramification phenotype controlled by the recessive sham ramification 2 (shr2) gene in tetraploid wheat T. turgidum L. allowed us to suggest putative functions of the SHR2 gene that may be involved in the regulation of spikelet meristem fate and in specification of floret meristems. The results of a gene interaction test suggested that genes WFZP and SHR2 function independently in different processes during spikelet development, whereas another spike ramification gene(s) interact(s) with SHR2 and share(s) common functions. SS mutants represent an important genetic tool for research on the development of the wheat spikelet and for identification of genes that control meristem activities. Further studies on different non-standard SS morphotypes and wheat lines with altered spike morphology will allow researchers to identify new genes that control meristem identity and determinacy, to elucidate the interaction between the genes, and to understand how these genes, acting in concert, regulate the development of the wheat spike.
Combustion of solid fuels in general includes a number of stages: heating, drying, devolatilization, ignition, and burn-out of coke. The stage of coke residue burn-out is the leading one.

In this paper, analytical solutions for the burn-out of the coke part of an anthracite particle were developed using the asymptotic procedures, and combustion of anthracite particles with the size of 100 µm and less (presented size for the flare process) and 12 mm or more (characteristic size for burning in a fluidized bed) was calculated. The models of the 'hard' ash frame, as well as the model 'with segregating' ash, have been implemented.

In the first case, combustion occurs in the kinetic regime, and in the second, it occurs in the diffusion regime.
Accumulation of complete genome sequences of diverse organisms creates new possibilities for evolutionary inferences from whole-genome comparisons. In the present study, we analyze the distributions of substitution rates among proteins encoded in 19 complete genomes (the interprotein rate distribution). To estimate these rates, it is necessary to employ another fundamental distribution, that of the substitution rates among sites in proteins (the intraprotein distribution). Using two independent approaches, we show that intraprotein substitution rate variability appears to be significantly greater than generally accepted. This yields more realistic estimates of evolutionary distances from amino-acid sequences, which is critical for evolutionary-tree construction. We demonstrate that the interprotein rate distributions inferred from the genome-to-genome comparisons are similar to each other and can be approximated by a single distribution with a long exponential shoulder. This suggests that a generalized version of the molecular clock hypothesis may be valid on genome scale. We also use the scaling parameter of the obtained interprotein rate distribution to construct a rooted whole-genome phylogeny. The topology of the resulting tree is largely compatible with those of global rRNA-based trees and trees produced by other approaches to genome-wide comparison.
A distinct platform appearance of the Neoproterozoic-Paleozoic sediments, the synchronous occurrence of ancient and Mesozoic sedimentary complexes in the axial most submerged part of the Yenisei–Khatanga linear depression.

A comprehensive analysis of geophysical data was carried out and a model of the deep structure of the Yenisei–Khatanga regional trough was constructed. A wide territorial distribution of trap magmatism was revealed, which is not localized in the linear structure of the trough.

It is concluded that the formation of the Yenisei-Khatanga regional trough is not associated with the Late Permian–Early Triassic rifting.
Cardiovascular diseases (CVDs), the leading cause of death worldwide, generally refer to a range of pathological conditions with the involvement of the heart and the blood vessels. A sizable fraction of the susceptibility loci is known, but the underlying mechanisms have been established only for a small proportion. Therefore, there is an increasing need to explore the functional relevance of trait-associated variants and, moreover, to search for novel risk genetic variation.

We have reported the bioinformatic approach allowing effective identification of functional non-coding variants by integrated analysis of genome-wide data. Here, the analysis of 1361 previously identified regulatory SNPs (rSNPs) was performed to provide new insights into cardiovascular risk. We found 773,471 coding co-segregating markers for input rSNPs using the 1000 Genomes Project. The intersection of GWAS-derived SNPs with a relevance to cardiovascular traits with these markers was analyzed within a window of 10 Kbp. The effects on the transcription factor (TF) binding sites were explored by DeFine models. Functional pathway enrichment and protein-protein interaction (PPI) network analyses were performed on the targets and the extended genes by STRING and DAVID.

Eighteen rSNPs were functionally linked to cardiovascular risk. A significant impact on binding sites of thirteen TFs including those involved in blood cells formation, hematopoiesis, macrophage function, inflammation, and vasoconstriction was found in K562 cells. 21 rSNP gene targets and 5 partners predicted by PPI were enriched for spliceosome and endocytosis KEGG pathways, endosome sorting complex and mRNA splicing REACTOME pathways. Related Gene Ontology terms included mRNA splicing and processing, endosome transport and protein catabolic processes. Together, the findings provide further insight into the biological basis of CVDs and highlight the importance of the precise regulation of splicing and alternative splicing.
H3K4me3 is typically found in the promoter region of genes and is a mark associated with an open chromatin state and active gene transcription. Nonetheless, the role of H3K4me3 in the regulation of transcription is still debated.

To improve the understanding of the connection between H3K4me3 density in promoters and gene expression, we assessed the correlation between these two parameters. We utilized genome-wide high-throughput RNA sequencing (RNA-seq) data and H3K4me3-based chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq), carried out on the same samples of the prefrontal cortex from 10 male C57Bl6 mice with different stress experience. In addition, we assessed the correlation between H3K4me3 density and gene expression in datasets of cell-specific genes.

Altogether, the results are useful for the elucidation of H3K4me3 involvement in the regulation of transcription in the murine prefrontal cortex.
The Novosibirsk Free Electron Laser (NovoFEL) is based on a four-turn microtron-recuperator. To ensure its stable operation and radiation generation, it is necessary to provide a stable mode of electron beam recirculation and minimize beam losses on the vacuum chamber wall on all the beam way in the accelerator beamline. To this end it is necessary to know the longitudinal distribution of these losses along the beamline. A system for registration of beam losses was created. The system applies optical fibers placed along the vacuum chamber and nearby it. If local electron beam losses occur somewhere in the vacuum chamber, electrons falling to the vacuum chamber wall cause generation of X- and gamma rays. This radiation in turn originates optical emission in an optical fiber nearby the region of electron "precipitation" on the chamber wall. Then, executing some transformation and processing of the time dependencies of signals from these optical fibers, one can obtain the longitudinal distribution of electron beam losses along the accelerator line in all its four turns.
At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. Synergistic action of multiple pathways greatly complicates the experimental study of the molecular genetic mechanisms of the organism's reactions. As a result, a significant part of the regulatory ensemble in such complex reactions remains unidentified.

We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism's response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes.

Here we showed metaRE performance for identification of cold stress-responsive cis-regulatory code in Arabidopsis thaliana. MetaRE identified potential binding sites for known as well as unknown cold response regulators. Software with source files, documentation, and example data files are freely available online at the repository (https://github.com/cheburechko/MetaRE).
Molybdenum disulfide (MoS2) was grown on a laser-processed periodic-hole sapphire substrate through chemical vapor deposition. The main purpose was to investigate the mechanism of MoS2 growth in substrate with a periodic structure. By controlling the amount and position of the precursor, adjusting the growth temperature and time, and setting the flow rate of argon gas, MoS2 grew in the region of the periodic holes. A series of various growth layer analyses of MoS2 were then confirmed by Raman spectroscopy, photoluminescence spectroscopy, and atomic force microscopy. Finally, the growth mechanism was studied by transmission electron microscopy (TEM). The experimental results show that in the appropriate environment, MoS2 can be successfully grown on substrate with periodic holes, and the number of growth layers can be determined through measurements. By observing the growth mechanism, composition analysis, and selected area electron diffraction diagram by TEM, we comprehensively understand the growth phenomenon. The results of this research can serve as a reference for the large-scale periodic growth of MoS2. The production of periodic structures by laser drilling is advantageous, as it is relatively simpler than other methods.
The influence of aluminum on the detonation and electrical characteristics of an explosive has been studied experimentally. Comparison of the data obtained by different methods allowed us to formulate conclusions about the course of the chemical reaction of the emulsion explosive with aluminum.
Finding novel biomarkers for human pathologies and predicting clinical outcomes for patients is rather challenging. This stems from the heterogenous response of individuals to disease which is also reflected in the inter-individual variability of gene expression responses. This in turn obscures differential gene expression analysis (DGE). In the midst of the COVID-19 pandemic, we wondered whether an alternative to DGE approaches could be applied to dissect the molecular nature of a host-response to infection exemplified here by an analysis of H1N1 influenza, community/hospital acquired pneumonia (CAP) and sepsis. To this end, we turned to the analysis of ensemble gene noise. Ensemble gene noise, as we defined it here, represents a variance within an individual for a collection of genes encoding for either members of known biological pathways or subunits of annotated protein complexes. From the law of total variance, ensemble gene noise depends on the stoichiometry of the ensemble genes’ expression and on their average noise (variance). Thus, rather than focusing on specific genes, ensemble gene noise allows for the holistic identification and interpretation of gene expression disbalance on the level of gene networks and systems. Comparing H1N1, CAP and sepsis patients we spotted common disturbances in a number of pathways/protein complexes relevant to the sepsis pathology which lead to an increase in the ensemble gene noise. Among others, these include mitochondrial respiratory chain complex I and peroxisomes which could be readily targeted for adjuvant treatment by methylene blue and 4-phenylbutyrate respectively. Finally, we showed that ensemble gene noise could be successfully applied for the prediction of clinical outcome, namely mortality, of CAP and sepsis patients. Thus, we conclude that ensemble gene noise represents a promising approach for the investigation of molecular mechanisms of a pathology through a prism of alterations in coherent expression of gene circuits.
The Geobacillus icigianus G1w1(T) strain was isolated from sludge samples of unnamed vaporing hydrothermal (97°С) outlets situated in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russian Federation; 54°25'51.40″N, 160°7'41.40″E). The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes.
Using conjugate gradient and lattice dynamics methods the theoretical study of thermodynamics properties of methane sI and propane sII hydrates doped with small amount of potassium hydroxide was conducted. Potassium hydroxide was partially embedded in the host framework lattice of hydrate. The vibration densities of states were found and the stability of the doped hydrate was confirmed. For a wide range of temperatures the free energy curves were built and compared to results for non-doped hydrate structures. Based on this data the thermal expansion coefficient dependence on the temperature was calculated and the possibility of methane and propane hydrate self-preservation was studied.
We conjecture that the random walk and the corresponding diffusion in the relativistic velocity space is an adequate method for describing the acceleration process in relativistic jets. Considering a simple toy model, the main features of diffusion in the velocity space are demonstrated in both non-relativistic and relativistic regimes.
The Eurasian malaria vector Anopheles messeae is a widely spread and genetically diverse species. Five widespread polymorphic chromosomal inversions were found in natural populations of this mosquito. A cryptic species, Anopheles daciae, was differentiated from An. messeae by the presence of several nucleotide substitutions in the Internal Transcribed Spacer 2 (ITS2) region of ribosomal DNA. However, because of the absence of a high-quality reference cytogenetic map, the inversion polymorphisms in An. daciae and An. messeae remain poorly understood. Moreover, a recently determined heterogeneity in ITS2 in An. daciae questioned the accuracy of the previously used Restriction Fragment Length Polymorphism (RFLP) assay for species diagnostics. In this study, a standard-universal cytogenetic map was constructed based on orcein stained images of chromosomes from salivary glands for population studies of the chromosomal inversions that can be used for both An. messeae and An. daciae. In addition, a new ITS2-RFLP approach for species diagnostics was developed. Both methods were applied to characterize inversion polymorphism in populations of An. messeae and An. daciae from a single location in Western Siberia in Russia. The analysis demonstrates that cryptic species are remarkably different in their frequencies of chromosomal inversion variants. Our study supports previous observations that An. messeae has higher inversion polymorphism in all autosomes than the cryptic species An. daciae.
Generally, conditions for deep sub-Doppler laser cooling do not match conditions for strong atomic localization, that takes place in a deeper optical potential and leads to higher temperature. Moreover, for a given detuning in a deep optical potential the secular approximation, which is frequently used for a quantum description of laser cooling, fails. Here we investigate the atomic localization in optical potential, using a full quantum approach for atomic density matrix beyond the secular approximation. It is shown that laser cooling in a deep optical potential, created by a light field with polarization gradients, can be used as an alternative method for the formation of high contrast spatially localized structures of atoms for the purposes of atom lithography and atomic nanofabrication. Finally, we analyze possible limits for the width and contrast of localized atomic structures that can be reached in this type of light mask.
Gliomas are the most common type of malignant brain tumors. Standard treatment of gliomas consists of surgical excision of the tumor with subsequent chemotherapy and radiotherapy. Tumor cells are characterized by rapid division with an increased uptake of glucose and its catabolism during glycolysis. To maintain rapid division, the level of glycolysis of the tumor cell is significantly increased, compared with normal cells. It is known that some nanoparticles (NP) have the property of accumulating in tumors. In particular, NPs of manganese oxide can penetrate into the brain and, with considerable accumulation, cause toxic effects. These facts served as a prerequisite for studying the effects of manganese oxide NPs on the viability of glioma cells. The purpose of this work was to study the effects of manganese oxide NPs, as well as their combination with gamma irradiation on the glycolysis of glioma cells. The cells were irradiated using the research radiobiological gamma-installation IGUR-1 based on 137Cs. The level of cell glycolysis was determined using the standard glycolytic stress test on a Seahorse XFp platform. Cell viability was determined using the ViaCount reagent staining of living and dead cells. Their count was performed using flow cytometry. We showed that the glycolysis of U-87 MG glioma cells was significantly reduced when incubated for 48 hours with manganese oxide NPs. Irradiation in combination with NPs or alone did not have significant effects on glycolysis of gliomas. Glioma incubation with manganese oxide NPs for 72 hours led to a significant reduction in cell viability. This study may be useful for the development of new therapies and diagnosis of gliomas.
Efficiency of collective beam-plasma interaction strongly depends on the growth rates of dominant instabilities excited in the system. Nevertheless, exact calculations of the full unstable spectrum in the framework of relativistic kinetic theory for arbitrary magnetic fields and particle distributions were unknown until now.

In this paper, we give an example of such a calculation answering the question whether the finite thermal spreads of plasma electrons are able to suppress the fastest growing modes in the beam-plasma system.

It is shown that nonrelativistic temperatures of Maxwellian plasmas can stabilize only the oblique instabilities of relativistic beam. On the contrary, non-Maxwellian tails typically found in laboratory beam-plasma experiments are able to substantially reduce the growth rate of the dominant longitudinal modes affecting the efficiency of turbulent plasma heating.