Hengzongshu/ArticleAgent huggingface dataset:
We study intensity distribution of transmission resonances under the conditions of electromagnetically induced transparency (EIT) with lin||lin configuration in 87Rb vapor. We demonstrate that for various orientations of the external magnetic field all seven resolved EIT resonances exhibit maxima or minima at certain directions of the linear polarization of the laser field. This effect can be used for development of a high-precision vector EIT magnetometer.
In the course of evolution, viruses have developed various molecular mechanisms to evade the defense reactions of the host organism. When understanding the mechanisms used by viruses to overcome manifold defense systems of the animal organism, represented by molecular factors and cells of the immune system, we would not only comprehend better but also discover new patterns of organization and function of these most important reactions directed against infectious agents. Here, study of the orthopoxviruses pathogenic for humans, such as variola (smallpox), monkeypox, cowpox, and vaccinia viruses, may be most important. Analysis of the experimental data, presented in this paper, allows to infer that variola virus and other orthopoxviruses possess an unexampled set of genes whose protein products efficiently modulate the manifold defense mechanisms of the host organisms compared with the viruses from other families.
Magnetic field dependence of long-lived spin states (LLSs) of the β-CH2 protons of aromatic amino acids was studied. LLSs are spin states, which are immune to dipolar relaxation, thus having lifetimes far exceeding the longitudinal relaxation times; the simplest example of an LLS is given by the singlet state of two coupled spins. LLSs were created by means of the photo-chemically induced dynamic nuclear polarization technique. The systems studied were amino acids, histidine and tyrosine, with different isotopomers. For labeled amino acids with the α-CH and aromatic protons substituted by deuterium at low fields the LLS lifetime, TLLS, for the β-CH2 protons was more than 40 times longer than the T1-relaxation time. Upon increasing the number of protons the ratio TLLS/T1 was reduced; however, even in the fully protonated amino acids it was about 10; that is, the long-lived mode was still preserved in the system. In addition, the effect of paramagnetic impurities on spin relaxation was studied; field dependencies of T1 and TLLS were measured. LLSs were also formed in tyrosine-containing dyads; a TLLS/T1 ratio of ∼7 was found, usable for extending the spin polarization lifetime in such systems.
The processes of Van der Waals clusters formation in supersonic gas flows expanding into a rarefied medium are discussed in this report. The necessary conditions for cluster formation, methods for measuring the average size and size distribution of clusters in a rarefied gas flow are considered. The problems associated with electron-beam ionization of clusters during mass spectrometry of clustered flows are analyzed. The process of intracluster energy exchange in mixtures, that leads to the possibility of inverse pumping of electronic levels of atoms, is illustrated. The problems arising during optical measurements of density in cluster flows are demonstrated. The effect of large clusters formation on the shape and structure of supersonic flows is shown.
We study the stationary Navier--Stokes equations in the whole plane with a compactly supported force term and with a prescribed constant spatial limit. Prior to this work, existence of solutions to this problem was only known under special symmetry and smallness assumptions. In the paper we solve the key difficulties in applying Leray's {\it invading domains method} and, as a consequence, prove the existence of $D$-solutions in the whole plane for arbitrary compactly supported force. The boundary condition at infinity are verified in two different scenarios: (I) the~limiting velocity is sufficient large with respect to the external force, (II) both the total integral of force and the~limiting velocity vanish. Hence, our method produces large class of new solutions with prescribed spatial limits. Moreover, we show the uniqueness of $D$-solutions to this problem in a perturbative regime. The main tools here are two new estimates for general Navier-Stokes solutions, which have rather simple forms. They control the difference between mean values of the velocity over two concentric circles in terms of the Dirichlet integral in the annulus between them.
Till yet there is no data concerning mechanisms of autoimmune diseases development.

Experimental autoimmune encephalomyelitis (EAE) prone C57BL/6 (T- and B-lymphocyte response), non-autoimmune CBA, and Th mice with T cell response were immunized with myelin oligodendrocyte glycoprotein (MOG35–55) to compare different characteristics of autoimmune reaction development. Bone marrow differentiation profiles of hematopoietic stem cells (HSCs), lymphocyte proliferation in various organs associated with the production of antibodies against DNA, myelin basic protein (MBP), and MOG, as well as abzymes hydrolyzing these antigens, were analyzed before and after immunization. Profiles of HSC differentiation [BFU-E (erythroid burst-forming unit (early erythroid colonies), CFU-E (erythroid burst-forming unit (late erythroid colonies), CFU-GM (granulocytic-macrophagic colony-forming unit), and CFU-GEMM granulocytic-erythroid-megakaryocytic-macrophagic colony-forming unit] and patterns of lymphocyte proliferation in different organs (brain, spleen, thymus, and lymph nodes) were very different for C57BL/6, CBA, and Th mice.

We conclude that only C57BL/6 mice were predisposed to spontaneous and MOG-induced acceleration of EAE development. CBA mice are not prone to the development of autoimmune reactions. After immunization, Th mice demonstrate changes in several parameters similar to C57BL/6 and other to CBA mice; Th mice are more prone to developing autoimmune reactions than CBA mice. Our data may be important for understanding the combined presence in mice lymphocytes with T and B cell responses for spontaneous and induced autoimmune diseases.
The ability of the nervous system to detect a wide range of noxious stimuli is crucial to avoid life-threatening injury and to trigger protective behavioral and physiological responses. Pain represents a complex phenomenon, including nociception associated with cognitive and emotional processing. Animal experimental models have been developed to understand the mechanisms involved in pain response, as well as to discover novel pharmacological and non-pharmacological anti-pain therapies.

Due to the genetic tractability, similar physiology, low cost, and rich behavioral repertoire, the zebrafish (Danio rerio) is a powerful aquatic model for modeling pain responses. Here, we summarize the molecular machinery of zebrafish responses to painful stimuli, as well as emphasize how zebrafish-based pain models have been successfully used to understand specific molecular, physiological, and behavioral changes following different algogens and/or noxious stimuli (e.g., acetic acid, formalin, histamine, Complete Freund's Adjuvant, cinnamaldehyde, allyl isothiocyanate, and fin clipping).

We also discuss recent advances in zebrafish-based studies and outline the potential advantages and limitations of the existing models to examine the mechanisms underlying pain responses from evolutionary and translational perspectives. Finally, we outline how zebrafish models can represent emergent tools to explore pain behaviors and pain-related mood disorders, as well as to facilitate analgesic therapy screening in translational pain research.
Technology of reprogramming of somatic cells to a pluripotent state allows generating induced pluripotent stem cells (iPSCs) and carrying out a broad range of studies. iPSCs can be obtained from patients suffering from inherited diseases to model the diseases and to study their pathological mechanisms at the molecular level after iPSC differentiation in relevant cell types. Another approach to model and study inherited diseases is using iPSCs from healthy donors and genome editing tools. The approach allows generating a panel of isogenic lines, which gives new opportunities in drug screening and toxicological testing. Moreover, iPSCs and their derivatives can be further used for substitutive cell therapy and transplantology. In this study, we generated iPSCs from human embryonic fibroblasts using episomal vectors. The lines obtained expressed pluripotency markers, had a stable karyotype – 46:XY, and did not contain episome integrations into genome. The cell lines gave rise to derivatives of three germ layers during spontaneous differentiation in vitro and in vivo .
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology.

Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle.

We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.
We consider the evolution of the ground state in the two Higgs doublet model during cooling down of the Universe after the big bang. Different regions in the space of free parameters of this model correspond to different sequences of thermal phase transitions. We discuss different paths of thermal evolution and corresponding evolution of physical properties of the system for different modern values of the parameters.
Rationale: The development of eukaryote genome engineering tools based on CRISPR-Cas programmable bacterial nucleases systems opens wide horizons for gene therapies, human disease cell modeling, as well as investigation into manifestation of disease phenotypes and visualization of cellular processes. The safety and approximation of experiments both at the cellular and organismal levels depend on the accuracy of introducing double-stranded breaks into the target DNA regions. The search for new variants of more accurate CRISPR-Cas nucleases and evaluation of their ability to hydrolyze nucleosome DNA in vivo is considered a critical task for the development of the genome engineering technologies. Aim: To analyze the activity of the programmable nuclease AsCpf1 (Cas12a), with low level of off-target activity, in the human genome loci that are safe for the introduction of transgenic constructs (“safe harbor”) and to compare its efficiency with that of the widely used SpCas9 nuclease in HEK293 cells. Materials and methods: We performed the bioinformatics analysis of the association between target regions with nucleosomes and other proteins in the safe harbor loci AAVS1 and GSH-Ch1 and the transcriptionally inactive gene MYBPC3 (cardiac myosin binding protein 3) based on ATAC-seq data for the HEK293FT cells obtained from the NCBI SRA database. Plasmids encoding SpCas9 and AsCpf1 nucleases and guide RNA to the target regions were constructed and transfected into the HEK293FT cells. Events in the target regions of the HEK293FT cell genome were studied in the sequenograms with the TIDE algorithm. Results: The results of the ATAC-seq experiments for HEK293FT cells have shown that the AAVS1 locus can be referred as open chromatin with a low nucleosome density, while the GSH-Ch1 locus can be attributed to closed chromatin. In HEK293FT cells, the cardiac MYBPC3 gene has intermediate chromatin density. Assessment of the efficiency of introducing breaks into the studied HEK293FT cell chromatin loci by nucleases has shown that SpCas9 is able to cope with chromatin of any nucleosome density, while AsCpf1 can effectively introduce DNA breaks only at loci with open chromatin, such as AAVS1 and MYBPC3 . Editing events occur at a very low rate at the GSH-Ch1 locus with a high nucleosome density. Conclusion: We have found low efficiency of the AsCpf1 nuclease in the genomic safe harbor locus GSH-Ch1, which is characterized by a high nucleosome density. When planning an experiment on AsCpf1 nuclease genome editing, the epigenetic chromatin landscape and the nucleosome density should be considered, as well as chromatin opening substances should be used.
Members of the family Filoviridae produce variously shaped, often filamentous, enveloped virions containing linear non-segmented, negative-sense RNA genomes of 15-19 kb. Several filoviruses (e.g., Ebola virus) are pathogenic for humans and are highly virulent. Several filoviruses infect bats (e.g., Marburg virus), whereas the hosts of most other filoviruses are unknown.

This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on Filoviridae, which is available at www.ictv.global/report/filoviridae.
The use of nuclear polarized fuel, i.e. polarized D, T or $^3$He, for coming fusion reactors promises to increase their energy output and to optimize the complete fusion process in various ways. But before these advantages can be utilized, several questions must be answered and technical issues must be overcome. Among others, the members of the PREFER collaboration started to investigate the different challenges of 'polarized fusion'.
We derive a dispersive model of shear shallow water flows which takes into account a non-uniform horizontal velocity. This model generalizes the Green–Naghdi model to the case of shear flows. Besides the classical dispersion term in the Green–Naghdi model related to the acceleration of the free surface, it also contains a new dispersion parameter related to the flow structure. This parameter is related to the second moment of the velocity fluctuation with respect to the vertical coordinate. The distinction between shearing and turbulence based on the scale of variation of the velocity fluctuation is proposed. In particular, an equation for the turbulence generation is derived. Solitary waves for this model are obtained in explicit form. Comparison of solitary wave profiles with experimental ones is also performed. The agreement is very good apart from the small region near the top of the wave.
The etiologic factor of idiopathic scoliosis (IS) is a subject of discussions for scientists of different disciplines. The great number of theories testifies to an absence of a uniform sight on etiology and pathogenesis of this pathology.

101 probands with II–IV grade IS and 703 family members of I–III degree of relationship were examined by clinical-genetic, radiological and optical-topographical methods. The pedigrees were processed by a method of segregation analysis. G3 exon of agrecan gene was studied from isolated family DNA by method of PCR reaction.

Segregation analysis of pedigrees, in which proband had II–IV grade IS has shown, that IS is inherited according to autosomal-dominant type with incomplete genotype penetrance depending on sex and age. It is revealed that idiopathic scoliosis is controlled by a major gene. Study of connection of agrecan gene to determination of IS development on a small sample of pedigrees has not revealed a reliable association of IC with polymorphism of G3 exon. Investigation of another exons of agrecan gene on expanded pedigrees is continued.
Recent theoretical predictions of ``unprecedented proximity'' of the electronic ground state of iridium fluorides to the SU(2) symmetric ${j}_{\mathrm{eff}}=1/2$ limit, relevant for superconductivity in iridates, motivated us to investigate their crystal and electronic structure.

To this aim, we performed high-resolution x-ray powder diffraction, Ir ${\mathrm{L}}_{3}$-edge resonant inelastic x-ray scattering, and quantum chemical calculations on ${\mathrm{Rb}}_{2}[{\mathrm{IrF}}_{6}]$ and other iridium fluorides.

Our results are consistent with the Mott insulating scenario predicted by Birol and Haule [Phys. Rev. Lett. 114, 096403 (2015)], but we observe a sizable deviation of the ${j}_{\mathrm{eff}}=1/2$ state from the SU(2) symmetric limit. Interactions beyond the first coordination shell of iridium are negligible, hence the iridium fluorides do not show any magnetic ordering down to at least 20 K. A larger spin-orbit coupling in iridium fluorides compared to oxides is ascribed to a reduction of the degree of covalency, with consequences on the possibility to realize spin-orbit-induced strongly correlated physics in iridium fluorides.
A trend in the global technological progress in the last few decades is the development of microsystem technology, microelectromechanical systems and corresponding technologies. Fluid mixing is an extremely important process widely used in various microfluidic devices (chemical microreactors, chemical and biological analyzers, drug delivery systems, etc.). To increase the mixing rate, it is necessary to use special devices: micromixers. This paper presents the results of a hydrodynamic simulation of Y-shaped micromixers. Flows are analyzed for both low and moderate Reynolds numbers. The passive and active mixers are considered. The dependence of the mixing efficiency on the Reynolds and Péclet numbers, as well as the possibility of using the hydrophobic and ultra-hydrophobic coatings is analyzed. Five different flow regimes were identified: (1) stationary vortex-free flow (Re < 5); (2) stationary symmetric vortex flow with two horseshoe vortices (5 < Re < 150); (3) stationary asymmetric vortex flow (150 < Re < 240); (4) non-stationary periodic flow (240 < Re < 400); and (5) stochastic flow (Re > 400). The maximum mixing efficiency was obtained for stationary asymmetric vortex flow.
Parahydrogen can be used in catalytic hydrogenations to achieve substantial enhancement of NMR signals of the reaction products and in some cases of the reaction reagents as well. The corresponding nuclear spin hyperpolarization technique, known as parahydrogen-induced polarization (PHIP), has been applied to boost the sensitivity of NMR spectroscopy and magnetic resonance imaging by several orders of magnitude. The catalyst properties are of paramount importance for PHIP because the addition of parahydrogen to a substrate must be pairwise. This requirement significantly narrows down the range of the applicable catalysts.

Herein, we study an efficient silica-supported vanadium oxo organometallic complex (VCAT) in hydrogenation and dehydrogenation reactions in terms of efficient PHIP production. This is the first example of group 5 catalyst used to produce PHIP. Hydrogenations of propene and propyne with parahydrogen over VCAT demonstrated production of hyperpolarized propane and propene, respectively. The achieved NMR signal enhancements were 200–300-fold in the case of propane and 1300-fold in the case of propene. Propane dehydrogenation in the presence of parahydrogen produced no hyperpolarized propane, but instead the hyperpolarized side-product 1-butene was detected. Test experiments of other group 5 (Ta) and group 4 (Zr) catalysts showed a much lower efficiency in PHIP as compared to that of VCAT.

The results prove the general conclusion that vanadium-based catalysts and other group 4 and group 5 catalysts can be used to produce PHIP. The hydrogenation/dehydrogenation processes, however, are accompanied by side reactions leading, for example, to C4, C2, and C1 side products. Some of the side products like 1-butene and 2-butene were shown to appear hyperpolarized, demonstrating that the reaction mechanism includes pairwise parahydrogen addition in these cases as well.
This paper discusses the numerical simulation of the 69-Degree Delta Wing Body for computing the sonic boom signature in the near field.

For flow field calculation, the commercial CFD flow solver ANSYS Fluent is employed. The computational mesh in the perturbed flow regions was refined two times using the automatic gradient adaptation.

The results are in agreement with the results obtained by other researchers.
We report a study of the infrared response by localized surface plasmon resonance (LSPR) modes in gold micro- and nanoantenna arrays with various morphologies and surface-enhanced infrared absorption (SEIRA) by optical phonons of semiconductor nanocrystals (NCs) deposited on the arrays. The arrays of nano- and microantennas fabricated with nano- and photolithography reveal infrared-active LSPR modes of energy ranging from the mid to far-infrared that allow the IR response from very low concentrations of organic and inorganic materials deposited onto the arrays to be analyzed. The Langmuir–Blodgett technology was used for homogeneous deposition of CdSe, CdS, and PbS NC monolayers on the antenna arrays. The structural parameters of the arrays were confirmed by scanning electron microscopy. 3D full-wave electromagnetic simulations of the electromagnetic field distribution around the micro- and nanoantennas were employed to realize the maximal SEIRA enhancement for structural parameters of the arrays whereby the LSPR and the NC optical phonon energies coincide. The SEIRA experiments quantitatively confirmed the computational results. The maximum SEIRA enhancement was observed for linear nanoantennas with optimized structural parameters determined from the electromagnetic simulations. The frequency position of the feature’s absorption seen in the SEIRA response evidences that the NC surface and transverse optical phonons are activated in the infrared spectra.
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.
Nitrogen-rich porous materials have outstanding gas sorption and separation capacity. Using cage amines in the synthesis of metal–organic frameworks is a simple approach for generating the free nitrogen donor centers within the channels of porous materials without the post-synthetic modification. 1,4-Diazabicyclo[2.2.2]octane has a linear arrangement of nitrogen centers and can be used as a linear linker for the design of porous MOF materials. Urotropine has four nitrogen atoms and can act as a tetrahedral four-connected, pyramidal three-connected or bent two-connected linker. Such a diversity of coordination possibilities enriches the structural chemistry of MOFs and allows obtaining the frameworks with unique secondary building units and topology. The presence of cage amines in the structure affects the sorption characteristics of the materials. They demonstrate high selectivity to CO 2 and can participate as a heterogeneous base catalyst in the organic reactions. Besides that the cage-amine based metal–organic frameworks demonstrate photoluminescent properties and can be used as nanoreactors for photochemical transformations. These compounds are also an important object of thermodynamic studies helping us better understand the nature of host–guest interaction in the supramolecular systems.