[Comparative analysis of the taxonomic classification criteria for a number of groups of pathogenic DNA and RNA viruses based on genomic data].

The basis for criteria of the taxonomic classification of DNA and RNA viruses based on data of the genomic sequencing are viewed in this review. The genomic sequences of viruses, which have genome represented by double-stranded DNA (orthopoxviruses as example), positive-sense single-stranded RNA (alphaviruses and flaviviruses as example), non-segmented negative-sense single-stranded RNA (filoviruses as example), segmented negative-sense single-stranded RNA (arenaviruses and phleboviruses as example) are analyzed. The levels of genetic variability that determine the assignment of compared viruses to taxa of various orders are established for each group of viruses.

[The use of immunoglobulins and monoclonal antibodies against COVID-19].

INTRODUCTION: When a new disease occurs, one of the most affordable remedies is drugs containing specific antibodies to this infectious agent. The use of such drugs is aimed at reducing the amount of the pathogen in the macroorganism and the associated reduction in the severity of the symptoms of the disease or recovery. The purpose of this review is to analyze the experience of using immunoglobulins and monoclonal antibodies in the treatment of COVID-19 patients during the pandemic. RESULTS AND CONCLUSION: The two main groups of medical protective agents that block the penetration of the SARS-CoV-2 virus into permissive cells are drugs obtained from blood plasma of convalescents (immunoglobulin) and human monoclonal antibodies. The first group of drugs in the treatment of COVID-19 includes blood plasma of convalescents, which can be successfully used for emergency prevention. The main disadvantage of using blood plasma convalescents is the difficulty of standardization due to the different content of specific antibodies in donors. Another disadvantage is the undesirable side effects in recipients that occur after plasma administration. An alternative approach to COVID-19 therapy is the use of humanized and genetically engineered human monoclonal antibodies against certain epitopes of the SARS-CoV-2 virus. For example, monoclonal antibodies against receptor-binding domain of the S-protein, which prevents the virus from entering permissive cells and interrupts the development of infection. The advantages of these drugs are their safety, high specific activity, and the possibility of standardization. However, the complexity of their production and high cost make them inaccessible for mass use in practical medicine.

Correlations in a weakly interacting two-dimensional random flow.

We analytically examine fluctuations of vorticity excited by an external random force in two-dimensional fluid. We develop the perturbation theory enabling one to calculate nonlinear corrections to correlation functions of the flow fluctuations found in the linear approximation. We calculate the correction to the pair correlation function and the triple correlation function. It enables us to establish the criterion of validity of the perturbation theory for different ratios of viscosity and bottom friction. We find that the corrections to the second moment are anomalously weak in the cases of small bottom friction and small viscosity and relate the weakness to the energy and enstrophy balances. We demonstrate that at small bottom friction the triple correlation function is characterized by universal scaling behavior in some region of lengths. The developed perturbation method was verified and confirmed by direct numerical simulations.

Orientational effects in the polarized absorption spectra of molecular aggregates.

We present a detailed theoretical analysis of polarized absorption spectra and linear dichroism of cyanine dye aggregates whose unit cells contain two molecules. The studied threadlike ordered system with a molecular exciton delocalized along its axis can be treated as two chains of conventional molecular aggregates, rotated relative to each other at a certain angle around the aggregate axis. Our approach is based on the general formulas for the effective cross section of light absorption by a molecular aggregate and key points of the molecular exciton theory. We have developed a self-consistent theory for describing the orientational effects in the absorption and dichroic spectra of such supramolecular structures with nonplanar unit cell. It is shown that the spectral behavior of such systems exhibits considerable distinctions from that of conventional cyanine dye aggregates. They consist in the strong dependence of the relative intensities of the J- and H-type spectral bands of the aggregate with a nonplanar unit cell on the angles determining the mutual orientations of the transition dipole moments of constituting molecules and the aggregate axis as well as on the polarization direction of incident light. The derived formulas are reduced to the well-known analytical expressions in the particular case of aggregates with one molecule in the unit cell. The calculations performed within the framework of our excitonic theory combined with available vibronic theory allow us to quite reasonably explain the experimental data for the pseudoisocyanine bromide dye aggregate.

[Vaccines to prevent Ebola virus disease: current challenges and perspectives].

RELEVANCE: Ebola virus disease (EVD) is an acute infectious disease with an extremely high case fatality rate reaching up to 90%. EVD has become widely known since 2014-2016, when outbreak in West Africa occurred and led to epidemic, which caused travel-related cases on the territory of other continents. There are two vaccines against EVD, prequalified by WHO for emergency use, as well as a number of vaccines, approved by local regulators in certain countries. However, even with the availability of effective vaccines, the lack of data on immune correlates of protection and duration of protective immune response in humans and primates is limiting factor for effectively preventing the spread of EVD outbreaks. AIMS: This review highlights experience of use of EVD vaccines during outbreaks in endemic areas, summarizes data on vaccine immunogenicity in clinical trials, and discusses perspectives for further development and use of effective EVD vaccines.

Multilocus Analysis of Phylogenetic Relationships in the Crocidura suaveolens Sensu Lato Species Complex: A Comparison with Mitochondrial Data.

Multilocus analysis was for the first time used to study the phylogeny of the Crocidura suaveolens s. l. species complex. Sequencing data for 16 nuclear genes indicated that several distinct forms exist within the species complex. The structure of the complex did generally not contradict its mitochondrial phylogeny. Siberian shrew showed certain specificity of the nuclear genome, but the degree of its genetic differentiation did not correspond to the species level. Relationships of Crocidura aff. suaveolens from South Gansu and Sichuan with other forms of the species complex were clarified. Shrews from Buryatia and Khentei also belong to this form, but their mtDNA apparently introgressed from C. shantungensis in the past. Hybridization of C. suaveolens s. str. with C. aff. suaveolens and C. güeldenstaedtii occurred recently. Due to multiple introgression events in the history of C. suaveolens s. l., a far larger set of loci is necessary for the analysis of the phylogenetic relationships between its forms.

Phylogeny of the Dipus sagitta Species Complex by Nuclear Gene Sequences.

The northern three-toed jerboa Dipus sagitta had long been considered to be a single polytypic species. High genetic diversity of D. sagitta was earlier revealed on the basis of several mitochondrial and nuclear genes, and several separate species were hypothesized to occur within the taxon. However, the relationships between phylogenetic lineages have not been established because of the small sample size of nuclear genes. In the present work, a far larger set of nuclear DNA loci was used, and thus, a higher resolution of the phylogenetic tree was achieved for ten D. sagitta forms. The structure revealed for the species mainly confirmed the topology and relationships of the mtDNA lineages. Yet the mitochondrial and nuclear phylogenies were not completely consistent. Some of the D. sagitta genetic lineages were therefore assumed to be a product of reticular evolutionary processes. The taxon was concluded to be the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

[Revision surgery after previous spinal decompression and fusion for lumbar spinal stenosis]. / Revizionnye khirurgicheskie vmeshatel'stva posle dekompressivno-stabiliziruyushchikh operatsii po povodu poyasnichnogo stenoza.

Nowadays, vertebral stenosis is the most common indication for surgical treatment in patients over 65 years old in spine surgery. According to the literature, there are conflicting data on the incidence and indications for revision surgery after previous spinal decompression and fusion for lumbar spinal stenosis. OBJECTIVE: To evaluate the incidence and indications for revision surgery after previous spinal decompression and fusion for lumbar spinal stenosis. MATERIAL AND METHODS: A retrospective single-center study enrolled 1233 patients with lumbar spine stenosis who underwent spinal decompression and fusion surgery between 2014 and 2018. The number and causes of readmission were evaluated. RESULTS: There were 164 readmissions. Revision surgery at the same level was performed in 63 patients (38.4%), at the higher level - 72 (43.9%), at the lower level - in 29 (17.7%) patients. The most common indication for readmission was spondyloarthrosis with facet joint syndrome (94 (57.3%) patients). The second common complication was pseudoarthrosis (26 (15.9%) patients). These ones comprised 2.1% of all patients with lumbar spine stenosis. CONCLUSION: The most common indication for readmission was adjacent segment degeneration. The most severe complications requiring complex and even multiple stage revision surgery were pseudoarthrosis and postoperative spondylodiscitis. Causes of readmission are significantly changing at different periods after surgery.

Continuous absorption and emission of light by the heteronuclear rare gas (ArXe)+ and (KrXe)+ ions.

Studies of radiative transitions between ground and charge transfer excited terms of heteronuclear rare-gas (ArXe)+ and (KrXe)+ ions with small and moderate dissociation energies (D0 ArXe+ =179 and D0 KrXe+ =389 meV) are reported. Potential energy curves and dipole transition matrix elements are evaluated using ab initio calculations based on the CASSCF method followed by the NEVPT2 treatment and perturbative description of relativistic effects as implemented in the ORCA suite. We develop an efficient approach for the calculations of Boltzmann-averaged cross sections, rate constants, and absorption and emission coefficients associated with the integral contributions of bound-bound and bound-free transitions from a manifold of rovibrational states of the (RgXe)+ ion. A similar approach is used for the description of the free-free and free-bound transitions between different electronic terms of a quasimolecular (RgXe)+ ion temporarily formed during a collision of Ar or Kr atoms with Xe+ ions. Our method is based on the quantal version of the theory of non-adiabatic transitions in molecular and quasimolecular systems combined with the approximation of a quasicontinuum for rovibrational energy levels. This allowed us to obtain a semianalytic expression for the integral absorption properties particularly relevant at elevated temperatures. We perform a comprehensive analysis of the identified radiative processes in local thermodynamic equilibrium plasmas of rare gas Rg/Xe mixtures containing both atomic, Xe+, and molecular, RgXe+, ions and determine their role in the formation of the absorption and emission spectra in a wide range of wavelengths and gas temperatures. The results obtained are in good agreement with the available experimental data.

The Omicron Variant of the Sars-Cov-2 Virus As the Dominant Agent of a New Risk of Disease amid the COVID-19 Pandemic.

Over the two years that have passed since the WHO announced on March 11, 2020, a pandemic of the new coronavirus disease COVID-19, more than 460 million cases of the disease have been detected in the world, of which more than five million have been fatal. During the natural evolution of the COVID-19 pathogen, dominant variants emerge that account for most new infections. The WHO constantly monitors coronavirus mutations that potentially pose an epidemiological danger. Currently, the WHO divides modified variants of the SARS-CoV-2 virus into variants of concern (VOC) and variants of interest (VOI). The WHO-designated group of variants of concern includes potentially the most dangerous lines, which are characterized by a complex of new properties. This group also includes the Omicron variant, which has become the dominant agent of the new wave of the COVID-19 pandemic. The aim of this work is to analyze the characteristics of the SARS-CoV-2 Omicron strain, the dominant agent of the new wave of the COVID-19 pandemic. The proposed mechanism of origin of the Omicron variant, its geographical distribution, the features of the disease caused by it, and the distinguishing features from diseases caused by the Delta variant and the original Wuhan strain of the SARS-CoV-2 virus, mutations of the Omicron variant compared to the parent strain of the SARS-CoV-2 virus, the genetic variability of the Omicron variant, and the epidemiological characteristics of the disease it causes are considered. Particular attention is paid to evaluation of the preventive and therapeutic effectiveness of the existing medical means of protection against COVID-19 in relation to the Omicron strain.

Fractal Structure of Brain Electrical Activity of Patients With Mental Disorders.

This work was aimed at a comparative analysis of the degree of multifractality of electroencephalographic time series obtained from a group of healthy subjects and from patients with mental disorders. We analyzed long-term records of patients with paranoid schizophrenia and patients with depression. To evaluate the properties of multifractal scaling of various electroencephalographic time series, the method of maximum modulus of the wavelet transform and multifractal analysis of fluctuations without a trend were used. The stability of the width and position of the singularity spectrum for each of the test groups was revealed, and a relationship was established between the correlation and anticorrelation dynamics of successive values of the electroencephalographic time series and the type of mental disorders. It was shown that the main differences between the multifractal properties of brain activity in normal and pathological conditions lie in the different width of the multifractality spectrum and its location associated with the correlated or anticorrelated dynamics of the values of successive time series. It was found that the schizophrenia group is characterized by a greater degree of multifractality compared to the depression group. Thus, the degree of multifractality can be included in a set of tests for differential diagnosis and research of mental disorders.

Experimental demonstration of optical stochastic cooling.

Particle accelerators and storage rings have been transformative instruments of discovery, and, for many applications, innovations in particle-beam cooling have been a principal driver of that success1. Stochastic cooling (SC), one of the most important conceptual and technological advances in this area2-6, cools a beam through granular sampling and correction of its phase-space structure, thus bearing resemblance to a 'Maxwell's demon'. The extension of SC from the microwave regime up to optical frequencies and bandwidths has long been pursued, as it could increase the achievable cooling rates by three to four orders of magnitude and provide a powerful tool for future accelerators. First proposed nearly 30 years ago, optical stochastic cooling (OSC) replaces the conventional microwave elements of SC with optical-frequency analogues and is, in principle, compatible with any species of charged-particle beam7,8. Here we describe a demonstration of OSC in a proof-of-principle experiment at the Fermi National Accelerator Laboratory's Integrable Optics Test Accelerator9,10. The experiment used 100-MeV electrons and a non-amplified configuration of OSC with a radiation wavelength of 950 nm, and achieved strong, simultaneous cooling of the beam in all degrees of freedom. This realization of SC at optical frequencies serves as a foundation for more advanced experiments with high-gain optical amplification, and advances opportunities for future operational OSC systems with potential benefit to a broad user community in the accelerator-based sciences.

Manifestation of the anisotropic properties of the molecular J-aggregate shell in the optical spectra of plexcitonic nanoparticles.

The theoretical studies of light absorption and scattering spectra of the plexcitonic two-layer triangular nanoprisms and three-layer nanospheres are reported. The optical properties of such metal-organic core-shell and core-double-shell nanostructures were previously explained within the framework of pure isotropic models for describing their outer excitonic shell. In this work, we show that the anisotropy of the excitonic shell permittivity can drastically affect the optical spectra of such hybrid nanostructures. This fact is confirmed by directly comparing our theory with some available experimental data, which cannot be treated using conventional isotropic shell models. We have analyzed the influence of the shell anisotropy on the optical spectra and proposed a type of hybrid nanostructure that seems the most convenient for experimental observation of the effects associated with the anisotropy of the excitonic shell. A strong dependence of the anisotropic properties of the J-aggregate shell on the material of the intermediate spacer layer is demonstrated. This allows proposing a new way to effectively control the optical properties of metal-organic nanostructures by selecting the spacer material. Our results extend the understanding of physical effects in optics of plexcitonic nanostructures to more complex systems with the anisotropic and multi-excitonic properties of their molecular aggregate shell.

Amorphization and nanocrystal formation in a Pd-Ni-Cu-P alloy after cooling under different conditions.

Structure formation during solidification of a Pd-Ni-Cu-P melt is studied. It is demonstrated that changes in the heat transfer conditions lead to a nonlinear change in the characteristics of the structure. The article presents the regimes of cooling the samples and the results of their structure and composition studies. It is found that a decrease in the cooling rate of the alloy leads to an increase in the size, proportion and composition of nanoinclusions in an amorphous matrix. X-ray diffraction method, electron probe microanalysis, transmission microscopy and scanning calorimetry are used for samples characterization. This article is part of the theme issue 'Transport phenomena in complex systems (part 2)'.

[The molecular evolution of Dabie bandavirus (Phenuiviridae: Bandavirus: Dabie bandavirus), the agent of severe fever with thrombocytopenia syndrome].

Since the Dabie bandavirus (DBV; former SFTS virus, SFTSV) was identified, the epidemics of severe fever with thrombocytopenic syndrome (SFTS) caused by this virus have occurred in several countries in East Asia. The rapid increase in incidence indicates that this infectious agent has a pandemic potential and poses an imminent global public health threat.The analysis of molecular evolution of SFTS agent that includes its variants isolated in China, Japan and South Korea was performed in this review. The evolution rate of DBV and the estimated dates of existence of the common ancestor were ascertained, and the possibility of reassortation was demonstrated.The evolutionary rates of DBV genome segments were estimated to be 2.28 × 10-4 nucleotides/site/year for S-segment, 2.42 × 10-4 for M-segment, and 1.19 × 10-4 for L-segment. The positions of positive selection were detected in the viral genome.Phylogenetic analyses showed that virus may be divided into two clades, containing six different genotypes. The structures of phylogenetic trees for S-, M- and L-segments showed that all genotypes originate from the common ancestor.Data of sequence analysis suggest that DBV use several mechanisms to maintain the high level of its genetic diversity. Understanding the phylogenetic factors that determine the virus transmission is important for assessing the epidemiological characteristics of the disease and predicting its possible outbreaks.

[Flow cytometry evaluation of the rhesus monkey cellular immunity following the Zaire ebolavirus (Filoviridae; Ebolavirus: Zaire ebolavirus) experimental infection].

INTRODUCTION: The outbreaks of the Zaire ebolavirus (ZE) disease (ZED) that have arisen in the last decade determine the need to study the infection pathogenesis, the formation of specific immunity forming as well as the development of effective preventive and therapeutic means. All stages of fight against the ZED spread require the experimental infection in sensitive laboratory animals, which are rhesus monkeys in case of this disease .The aim of the study is to evaluate the rhesus monkey cellular immunity following the ZE experimental infection by the means of flow cytometry (cytofluorimetry). MATERIAL AND METHODS: Male rhesus monkeys were intramuscularly infected by the dose of 15 LD50 (dose of the pathogen that causes 50% mortality of infected animals) of the ZE, the Zaire strain (ZEBOV). Levels of 18 peripheral blood lymphocyte populations of the animals before the ZE experimental infection and at the terminal stage of the disease were assessed using flow cytometry. RESULTS AND DISCUSSION: The certain changes in the levels of the lymphocyte populations were observed following infection, indicating simultaneous activation and suppression of the immune system during ZED. The increase in content was observed for T-lymphocytes, T-helper and cytotoxic T-lymphocytes expressing the corresponding markers of early activation. The decrease was recorded for T-lymphocytes and double-positive T-lymphocytes expressing corresponding markers of late activation, as well as natural killer cells expressing CD8 (p < 0.05). CONCLUSION: For the first time in the Russian Federation, the rhesus monkey cellular immunity before and after the ZE experimental infection was assessed using flow cytometry.

Entropic characterization of the coil-stretch transition of polymers in random flows.

Polymer molecules in a flow undergo a coil-stretch phase transition on an increase of the velocity gradients. Model-independent identification and characterization of the transition in a random flow has been lacking so far. Here we suggest to use the entropy of the extension statistics as a proper measure due to strong fluctuations around the transition. We measure experimentally the entropy as a function of the local Weisenberg number and show that it has a maximum, which identifies and quantifies the transition. We compare the new approach with the traditional one based on the theory using either linear Oldroyd-B or nonlinear finite extensible nonlinear elastic polymer models.

Single-pass Cr:ZnSe amplifier for broadband infrared undulator radiation.

An amplifier based on a highly-doped chromium zinc-selenide (Cr:ZnSe) crystal is proposed to increase the pulse energy emitted by an electron bunch after it passes through an undulator magnet. The primary motivation is a possible use of the amplified undulator radiation emitted by a beam circulating in a particle accelerator storage ring to increase the particle beam's phase-space density-a technique dubbed optical stochastic cooling (OSC). This paper uses a simple four energy level model to estimate the single-pass gain of Cr:ZnSe and presents numerical calculations combined with wave-optics simulations of undulator radiation to estimate the expected properties of the amplified undulator wave-packet.

Coherent vortex in two-dimensional turbulence: Interplay of viscosity and bottom friction.

We examine coherent vortices appearing as a result of the inverse cascade of two-dimensional turbulence in a finite box in the case of pumping with arbitrary correlation time in the quasilinear regime. We demonstrate that the existence of the vortices depends on the ratio between the values of the bottom friction coefficient α and the viscous damping of the flow fluctuations at the pumping scale νk_{f}^{2} (ν is the kinematic viscosity coefficient and k_{f} is the characteristic wave vector at the pumping scale). The coherent vortices appear if νk_{f}^{2}≫α and cannot exist if νk_{f}^{2}≪α. Therefore there is a border value α∼νk_{f}^{2} separating the regions. In numerical simulations, νk_{f}^{2}/α can be arbitrary, whereas in a laboratory experiment νk_{f}^{2}/α≲1 and the coherent vortices can be observed solely near the border value of νk_{f}^{2}/α.

[The use of transgenic mosquitoes for prevention of spread of arboviral diseases.]

The mosquitoes of Aedes genus are the most important vector such arboviral diseases as dengue, yellow, Chikungunya, West Nile and Zika fevers. Work is currently in progress to control the transmission of agents of these diseases by forming of transgenic mosquitoes in order to altering the capacity of wild mosquitoes to support of virus replication. There are two main strategies of genetic control of mosquitoes population. Sterile Insect Technique (SIT), that mainly uses population suppression methods for making self-sustaining genetic systems and Release of insects carrying of a Dominant Lethal (RIDL) that uses mainly gene transfer methods for making of self-limiting genetic systems. The RIDL is more expensive, but it has some significant preferences, according compares with SIT. The field trials of genetic control methods are conducted in several countries from 2009 to present time. Genetic control, transgenic technologies to induce sterility, genetic elimination and stable transformation of Aedes mosquitoes are viewed in this review.