Hengzongshu/ArticleAgent huggingface dataset:
The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are a lot of web services which are currently available for de novo motif discovery in datasets containing information about DNA/protein binding. An enormous motif diversity makes their finding challenging. In order to avoid the difficulties, researchers use different stochastic approaches. Unfortunately, the efficiency of the motif discovery programs dramatically declines with the query set size increase. This leads to the fact that only a fraction of top “peak” ChIP-Seq segments can be analyzed or the area of analysis should be narrowed. Thus, the motif discovery in massive datasets remains a challenging issue. Argo_Compute Unified Device Architecture (CUDA) web service is designed to process the massive DNA data. It is a program for the detection of degenerate oligonucleotide motifs of fixed length written in 15-letter IUPAC code. Argo_CUDA is a full-exhaustive approach based on the high-performance GPU technologies. Compared with the existing motif discovery web services, Argo_CUDA shows good prediction quality on simulated sets. The analysis of ChIP-Seq sequences revealed the motifs which correspond to known transcription factor binding sites.
Hematopoiesis is a convenient model to study how chromatin dynamics plays a decisive role in regulation of cell fate. During erythropoiesis a population of stem and progenitor cells becomes increasingly lineage restricted, giving rise to terminally differentiated progeny. The concerted action of transcription factors and epigenetic modifiers leads to a silencing of the multipotent transcriptome and activation of the transcriptional program that controls terminal differentiation. This article reviews some aspects of the biology of red blood cells production with the focus on the extensive chromatin reorganization during differentiation.
The special and temporal distribution of several posttranslational histone modifications (H3K4me2, H3K4me3, H3K9me2, H3K27me2, H3K9ac, H3K14ac, H3K18ac, H3K27ac, H3S10ph, H3S28ph, H3T3ph, H3K4me1-H3T3ph, H3K4me3/H3T3ph H3T11ph, H2AT121ph, and H2A.XS139ph) has been analysed during microsporogenesis of tobacco. Homogeneous distribution of the euchromatin marks H3K4me2 and H3K4me3 throughout the entire chromatin of amphidiploid Nicotiana tabacum suggests that both subgenomes were transcriptionally active. Localization of hyperacetylated clusters of H3K18 and H3K27 close to nucleoli suggests that both modifications were possibly involved in transcription of the 45S rDNA. A subset of chromosomes showed clusters of hypermethylated H3K9me2 and H3K27me2 regions. The cell-cycle dependent phosphorylation of histone H3 during meiosis revealed a high conservation compared to other plant species. In addition to meiotic prophase I, we observed phospho-H2A.X signals during the second stage of meiosis in N. tabacum.
This paper extends frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. (i) Create lifespan Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross-spectral tensors were shared. After visual and automatic quality control, developmental equations for the mean and standard deviation of qEEG traditional and Riemannian DPs were calculated using additive mixed-effects models. We demonstrate qEEG "batch effects" and provide methods to calculate harmonized z-scores. (ii) We also show that harmonized Riemannian norms produce z-scores with increased diagnostic accuracy predicting brain dysfunction produced by malnutrition in the first year of life and detecting COVID induced brain dysfunction. (iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.
Salivary gland polytene chromosomes demonstrate banding pattern, genetic meaning of which is an enigma for decades.Till now it is not known how to mark the band/interband borders on physical map of DNA and structures of polytene chromosomes are not characterized in molecular and genetic terms.It is not known either similar banding pattern exists in chromosomes of regular diploid mitotically dividing nonpolytene cells.Using the newly developed approach permitting to identify the interband material and localization data of interband-specific proteins from modENCODE and other genomewide projects, we identify physical limits of bands and interbands in small cytological region 9F13-10B3 of the X chromosome in D. melanogaster, as well as characterize their general molecular features.Our results suggests that the polytene and interphase cell line chromosomes have practically the same patterns of bands and interbands reflecting, probably, the basic principle of interphase chromosome organization.Two types of bands have been described in chromosomes, early and late-replicating, which differ in many aspects of their protein and genetic content.As appeared, origin recognition complexes are located almost totally in the interbands of chromosomes.
The semiconductor tracker (SCT) is one of the tracking systems for charged particles in the ATLAS detector. It consists of 4088 silicon strip sensor modules. During Run 2 (2015–2018) the Large Hadron Collider delivered an integrated luminosity of 156 fb -1 to the ATLAS experiment at a centre-of-mass proton-proton collision energy of 13 TeV. The instantaneous luminosity and pile-up conditions were far in excess of those assumed in the original design of the SCT detector. Due to improvements to the data acquisition system, the SCT operated stably throughout Run 2. It was available for 99.9% of the integrated luminosity and achieved a data-quality efficiency of 99.85%. Detailed studies have been made of the leakage current in SCT modules and the evolution of the full depletion voltage, which are used to study the impact of radiation damage to the modules.
Liver fluke causes severe liver damage in an infected human. However, the infection often remains neglected due to the lack of pathognomonic signs. Nanoparticle-enhanced magnetic resonance imaging (MRI) offers a promising technique for detecting liver lesions induced by parasites.

Surface modification of iron oxide nanoparticles produced by coprecipitation from a solution of Fe3+ and Fe2+ salts using 3-aminopropylsilane (APS) was carried out. The APS-modified nanoparticles were characterized by transmission electron microscopy, fourier transform infrared spectroscopy, and thermogravimetric analysis. Magnetic resonance properties of MNPs were investigated in vitro and in vivo.The amount of APS grafted on the surface of nanoparticles (0.60±0.06 mmol g-1) was calculated based on elemental analysis and infrared spectroscopy data. According to transmission electron microscopy data, there were no essential changes in the structure of nanoparticles during the modification. The APS-modified nanoparticles exhibit high magnetic properties; the calculated relaxivity r2 was 271 mmol-1 s-1. To obtain suspension with optimal hydrodynamic characteristics, amino groups on the surface of nanoparticles were converted into an ionic form with HCl. Cellular uptake of modified nanoparticles by rat hepatoma cells and human monocytes in vitro was 74.1±4.5 and 10.0±3.7 pg [Fe] per cell, respectively. Low cytotoxicity of the nanoparticles was confirmed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and Annexin V/7-aminoactinomycin D flow cytometry assays.

For the first time, magnetic nanoparticles were applied for contrast-enhanced MRI of liver lesions induced by Opisthorchis felineus.The synthesized APS-modified iron oxide nanoparticles showed high efficiency as an MRI contrast agent for the evaluation of opisthorchiasis-related liver damage.
We present recent results on measurements of intensity spatio-temporal dynamics in passively mode-locked fibre laser. We experimentally uncover distinct, dynamic and stable spatio-temporal generation regimes of various stochasticity and periodicity properties in though-to-be unstable laser. We present a method to distinguish various types of generated coherent structures, including rogue and shock waves, within the radiation by means of introducing of intensity ACF evolution map. We also discuss how the spectral dynamics could be measured in fiber lasers generating irregular train of pulses of quasi-CW generation via combination of heterodyning and intensity spatio-temporal measurement concept.
The problem of thermocapillary deformation and film breakdown in a thin horizontal layer of viscous incompressible liquid with a free surface is considered. The deformable liquid layer is locally heated.

The problem of thermocapillary deformation of the locally heated horizontal liquid layer has been solved numerically for two-dimensional unsteady case. The lubrication approximation theory is used. Capillary pressure, viscosity and gravity are taken into account. Evaporating rate is supposed to be proportional to the temperature difference between the liquid and ambient. Heat transfer in the substrate is also simulated. The numerical algorithm for the joint solution of the energy equation and the evolution equation for the thickness of liquid layer has been developed.

The model predicts the thermocapillary deformation of the liquid surface and the formation of dry spots. The dynamics of liquid surface, the dry spots formation and the velocity of the contact line have been calculated. The deformation of the free surface has been calculated for different values of the heating power and thickness of the liquid layer. The effect of surface tension coefficient and wetting contact angle on the velocity of the contact line motion has been analyzed. It has been obtained that the velocity of the contact line increases with the increase of the wetting contact angle value and of the surface tension coefficient.
A model of a hypersonic air intake based on the principle of compression along the directions of the captured jet converging in space is studied. Such an air intake allows a high compression ratio and a compact section of the internal channel, which simplifies the heat protection of the air intake and the combustion chamber.

Experimental studies were carried out in a pulsed wind tunnel IT-302M for Mach number M = 6 - 8 in the range of angles of attack from 0° to 8°. Numerical simulation has been performed based on solving the full averaged Navier-Stokes equations, supplemented k-w turbulence model.

The pressure distributions on the compression surfaces and in the air intake channel are obtained, the coefficients of the total pressure recovery and flow rate, the Mach number in the throat of the air intake are determined. The features of the flow structure for three variants of the air intake in the area of external compression are established: with side walls, side walls with slots and without side walls. The influence of the boundary layer bleed and lateral spreading on the launch and integral characteristics of a hypersonic air intake with a compact cross-section of the inner channel is determined. Satisfactory agreement between the calculated and experimental data is shown.
The review presents the results of investigations of gene polymorphism of enzymes involved in estrogen metabolism: CYP1A1, CYP1A2, CYP19 and SULT1A1

in the buccal epithelium samples from 703 women by RFLP (Restriction Fragment Length Polymorphism)

The significant association of the presence of allele C and genotype T / C and C / C gene CYP1A1, allele A and genotype C / A and A / A CYP1A2 gene and the T allele and genotype C / T and C / C gene SYP19 with the risk of adenomyosis
Recently, when studying folding of a SH3 domain, we discovered that the flows of transitions between protein states can be surprisingly similar to turbulent fluid flows. This similarity was not restricted by a vortex pattern of the flow fields but extended to a spatial correlation of flow fluctuations, resulting, in particular, in the structure functions such as in the Kolmogorov theory of homogeneous and isotropic turbulence.

Here, we undertake a detailed analysis of spatial distribution of folding flows and their similarity to turbulent fluid flows. Using molecular dynamics simulations, we study folding of another benchmark system—Trp-cage miniprotein, which has different content of secondary structure elements and mechanism of folding. Calculating the probability fluxes of transitions in a three-dimensional space of collective variables, we have found that similar to the SH3 domain, the structure functions of the second and third orders correspond to the Kolmogorov functions.

The spatial distributions of the probability fluxes are self-similar with a fractal dimension, and the fractal index decreases toward the native state, indicating that the flow becomes more turbulent as the native state is approached. We also show that the process of folding can be viewed as Brownian diffusion in the space of probability fluxes. The diffusion coefficient plays a role of the key parameter that defines the structures functions, similar to the rate of dissipation of kinetic energy in hydrodynamic turbulence. The obtained results, first, show that the very complex dynamics of protein folding allows a simple characterization in terms of scaling and diffusion of probability fluxes, and, secondly, they suggest that the turbulence phenomena similar to hydrodynamic turbulence are not specific of folding of a particular protein but are common to protein folding.
Possible signatures which may indicate an existence of antimatter in the Galaxy and in the early universe are reviewed. A model which could give rise to abundant antimatter in the Galaxy is considered.
The aim of the study was to identify new anatomical landmarks of the aortic root and the relationship between the sizes of anatomical structures using the method of computed tomography angiography to improve models of heart valves and the methods for their selection in clinical practice.Materials and Methods.The dataset of computed tomography angiography prior to aortic valve replacement in 262 patients was analyzed.The mean age was 75.0±5.9years.99 (37.8±3.0%)men and 163 (62.2±3.0%)women took part in the study.The annulus fibrosus, sinotubular junction, and height of the sinuses of Valsalva were measured.Results.In the tricuspid aortic valve group (n=251), in more than 50% of the cases, the diameter of the annulus fibrosus ranged from 23 to 26 mm.No significant association between the diameter of the annulus fibrosus and patient height (r=0.35;p=0.01) or body surface area (r=0.25;p=0.01) and the height of the sinuses of Valsalva (r=0.34;p=0.01) were revealed.Based on the ratio of the height of the sinuses of Valsalva and the diameter of the annulus fibrosus, three variants of the structure of the aortic root were identified: type A -K>1.05; type B -0.95≤K≤1.05;type C -K<0.95.Type C of the aortic root was found to predominate in most cases, namely, in 98.0±0.9%(n=246).In the bicuspid aortic valve group (n=11), 2 patients had a type A of the aortic root, 1 patient had a type B, and 8 patients had a type C. Conclusion.A classification of variants of the aortic root structure has been proposed, which will be useful not only for practitioners when choosing a treatment method, but also for researchers to understand the structural characteristics of the aortic root in patients with its pathology.
The system of the equations which in long-wave approach describes a non-stationary 3D non-isothermal film flow in the presence of thermocapillarity is derived. The used model, unlike lubrication theory, is applicable not only for small, but also for a moderate Reynolds number in a wide range of hydrodynamic and thermal parameters of a flow and does not assume a priori set a temperature profile in a film. Based on the derived equations the numerical simulation of stationary 3D thermocapillary rivulets in a liquid film flowing over a "semi-infinite" heater is executed.
Quasi-solutions are obtained with the help of the vanishing anisotropic temporal diffusion method.

In the present paper we have proved the existence of quasi-solutions of genuinely nonlinear forward-backward ultra-parabolic equations. Moreover, at the present stage of our research we assume that various choices of temporal artificial diffusion coefficients lead to entropy solutions or to quasi-solutions. The latter assumption is the subject of our further scientific research.
The use of a Teflon implant for Jannetta surgery in patients with trigeminal neuralgia is complicated in rare cases by the development of a Teflon granuloma and can cause recurrent facial pain.

The article presents a clinical case of a Teflon granuloma developed after microvascular decompression of the trigeminal nerve root, describes the surgical findings and histological picture, and analyzes the literature, causes of granuloma development, and recommendations for treatment of these patients.
Wild potato germplasm serves as a natural pool of agronomically valuable traits for potato breeding, such as resistance to pathogens and abiotic stresses, quality, and consumer-oriented traits. The introgression of these traits into cultivated potato is hampered by the different kinds of incompatibility and linkages between desirable and undesirable features in hybrid progeny. The trait donor improvement via correction of negative characteristics prior to hybridization to domestic potato can be a solution to the linkage drag problem.

The de novo domestication concept for developing new crops using gene editing technologies was previously proposed and performed for tomato and physalis. In this review, we collected information about donor properties of different wild potato species and developed a strategy for potato germplasm enhancement using the de novo domestication approach. The possible modifications of several candidate genes responsible for undesirable traits in wild potato, including high steroidal glycoalkaloid content, self-incompatibility, tuberization under short day conditions, and long stolons are proposed.

The current challenges and future prospects of implementing the de novo domestication strategy for potato are discussed.
The purpose of the study was to analyze the antitumor effects of the extract of mycelium from Duddingtonia flagrans (strain F-882) on xenografts of human C33a cervical cancer cells. Material and Methods. To evaluate the antitumor effect, we used the absolute values of xenograft volumes and calculated the tumor growth inhibition and the index of tumor growth. Results . At the first stage of the experiment, a 4-week subcutaneous injection of the water extract of F-882 resulted in an almost twofold slowdown in xenograft growth, with the tumor growth inhibition value of 50.6 %. In the second stage of the experiment, a 2.5-week subcutaneous injection followed by a 1.5-week intratumoral injection of F-882 also caused the tumor growth inhibition. After completing F-882 injections, the effect of tumor growth inhibition continued for 2.5 weeks and the tumor growth inhibition value was 58.7 %. Conclusion. The mycelium extract F-882 was shown to have an antitumor effect on subcutaneous xenografts of human C33a cervical carcinoma cells.
The motivation of this joint complex studies is related to the actual necessity of analyzing the strong wind impact in the coastline of the 'sea-land' typical for Taiwan Island, as well as due to the long-established creative collaboration between partners from the Khristianovich Institute of Theoretical and Applied Mechanics SB RAS and National Cheng Kung University in Taiwan.

Experimental studies were carried out in wind tunnels in Novosibirsk and Taiwan, in particular, in November this year, planned further experiments in wind tunnels in Taiwan. Numerical studies were carried out mainly in St. Petersburg, where for more than twenty years the package VP2/3 (velocity-pressure, 2D/3D) has been developing. Design and manufacturing of circular and semicircular cylinders having the structured surface has been performed, for which some preliminary physical experiments in the test section of T-325M wind tunnel of ITAM SB RAS within the Reynolds and Mach numbers range citied above were carried out.

Interest to the flow past a semicircular cylinder is high due to its phenomenal characteristics: ultra-low negative lift at zero angle of attack. In this paper, this effect is explained numerically, and this body is recommended for testing methods, models and packages. The influence of the Mach number on the flow past a semicircular cylinder at zero angle of attack is illustrated in the Mach number range M = 0 - 0.5. Turbulent regime with a throttling effect gave an exceptional result - the stabilization of the flow in the wake behind the circular cylinder when air is gone through the outlet channel from the zone of increased pressure in front of the body with the release of the jet inside the near wake. There is made a comparison of the experimental behavior of the resistance of a circular cylinder with an increase in the Reynolds number and the calculated dependence for a cylinder in a casing with holes. A three-fold decrease in drag on high Re numbers was detected. Completion of the test section of the T-325M wind tunnel of ITAM SB RAS allowed to increase (in several times) the Reynolds number of an incompressible flow.
We assume that current state of the Universe can be described by the Inert Doublet Model, containing two scalar doublets, one of which is responsible for EWSB and masses of particles and the second one having no couplings to fermions and being responsible for dark matter.

We consider possible evolutions of the Universe to this state during cooling down of the Universe after inflation.

We found that in the past Universe could pass through phase states having no DM candidate. In the evolution via such states in addition to a possible EWSB phase transition (2-nd order) the Universe sustained one 1-st order phase transition or two phase transitions of the 2-nd order.