Hengzongshu/ArticleAgent huggingface dataset:
The three-dimensional organization of the genome is tightly connected to its biological function. The Hi-C approach was recently introduced as a method that can be used to identify higher-order chromatin interactions genome-wide. The aim of this study was to determine genome-wide chromatin interaction frequencies using the Hi-C approach in mouse sperm cells and embryonic fibroblasts. The obtained data demonstrate that the three-dimensional genome organizations of sperm and fibroblast cells show a high degree of similarity both with each other and with the previously described mouse embryonic stem cells. Both A- and B-compartments and topologically associated domains are present in spermatozoa and fibroblasts. Nevertheless, sperm cells and fibroblasts exhibit statistically significant differences between each other in the contact probabilities of defined loci. Tight packaging of the sperm genome results in an enrichment of long-range contacts compared with the fibroblasts. However, only 30% of the differences in the number of contacts are based on differences in the densities of their genome packages; the main source of the differences is the gain or loss of contacts that are specific for defined genome regions. We find that the dependence of the contact probability on genomic distance for sperm is close to the dependence predicted for the fractal globular folding of chromatin. Overall, we can conclude that the three-dimensional structure of the genome is passed through generations without being dramatically changed in sperm cells.
Proportional electroluminescence (EL) in gaseous Ar has for the first time been systematically studied in the two-phase mode, at 87 K and 1.00 atm. Liquid argon had a minor (56 ppm) admixture of nitrogen, which allowed to understand, inter alia, the effect of N2 doping on the EL mechanism in rare-event experiments using two-phase Ar detectors.

The measurements were performed in a two-phase Cryogenic Avalanche Detector (CRAD) with EL gap located directly above the liquid-gas interface. The EL gap was optically read out in the Vacuum Ultraviolet (VUV), near 128 nm (Ar excimer emission), and in the near Ultraviolet (UV), at 300-450 nm (N2 Second Positive System emission), via cryogenic PMTs and a Geiger-mode APD (GAPD).

Proportional electroluminescence was measured to have an amplification parameter of 109+-10 photons per drifting electron per kV overall in the VUV and UV, of which 51+-6% were emitted in the UV. The measured EL threshold, at an electric field of 3.7+-0.2 kV/cm, was in accordance with that predicted by the theory. The latter result is particularly relevant to DarkSide and SCENE dark matter search-related experiments, where the operation electric field was thereby on the verge of appearance of the S2 (ionization-induced) signal. The results obtained pave the way to the development of N2-doped two-phase Ar detectors with enhanced sensitivity to the S2 signal.
One of the major effects of domestication is change of animal coat colour to up to complete white colour of the whole body. It is possible that white colour of livestock animals had aesthetic significance for humans as well. The first step towards detection of genes and mutations controlling white colouring in animals is the genome-wide association studies. These studies, however, have not been done for the cattle breeds native to the Russian Federation.

The aim of this study was therefore to identify genomic intervals and candidate genes that could be responsible for white face colouring in eight Russian cattle breeds. The data on genome-wide genotyping of 131,709 high-quality single nucleotide polymorphisms (SNPs) on 148 animas have been used in the program EMMAX. Association analysis has been performed using two related phenotypes: a) the white face with the rest of the body of any colour and b) white face with the rest of the body of different (non-white) colour.

In the first case, the only statistically significant marker found was the SNP BovineHD0500019319 located on cattle chromosome (BTA) 5. The same SNP was the most significant within the cluster of three SNPs on BTA5: 68,803,879–69,365,854 associated also with the second phenotype. Five genes were found within this interval in the cattle genome, out of which the most likely functional candidate was SLC41A2, with the SNP BovineHD0500019319 found within its intronic sequence. SLC41A2 encodes a magnesium transporter protein. However, the function of this gene is not well established. Other members of this gene family are the key genes controlling differences in human skin and animal coat colour. Additional significant association signals with the second phenotype have been detected in BTA 1–4, 6–15, 18, 19, 24, 27, and 29. Overall, 37 genomic intervals have been detected associated with white face colouring in eight Russian native cattle breeds.
In contrast to previous publications, we assumed that an intrinsic surface impedance due to a finite electric conductivity of the metal can be of the same order as the roughness-induced impedance.

We derived a dispersion relation of a surface wave at a rough metal-air interface.

We then applied our results to the analysis of a long-standing problem of the discrepancy between the experimental data on the propagation of surface waves in the terahertz range of frequencies and the classical Drude theory.
The paper discusses the results of measurement for three components of tensor analyzing power for the reaction of incoherent [Formula: see text]-meson photoproduction on a deuteron within the proton energy range of 15–200[Formula: see text]MeV and the neutron energy range of 15–150[Formula: see text]MeV. The experiment was performed on the deuterium internal gas target of VEPP-3 electron accelerator using the protons and neutrons coincidence counting technique. The results of measurements of the tensor analyzing power’s components are compared with the results of statistical modeling performed within the frameworks of a theoretical model.
We demonstrate mode-locking and single-pulse generation in fibre laser with record-setting cavity length of 25 km. Substantial increase in the pulse round trip duration leads to ultra-low repetition rate of 8.097 kHz and pulse energy of 3.7 μJ.
One of the ways of ensuring information security are intrusion detection systems (IDS). IDS are used to detect malicious activity on the network. The standard approach to the detection of attacks it is looking for specific patterns, such as byte sequences in network traffic, or known malicious instruction sequences used by malware. This approach is highly efficient, but it does not able to detect the attacks without patterns. Modern approaches to detection of attacks use deep learning. The purpose of this work was to explore the possibility of building a universal classifier of network traffic based on a deep neural network. For this, a recurrent autoencoder was trained on TCP packets from the CICIDS2017 dataset. During training the neural network was a model in which the expected vector was set the same as the original one. And learning was on normal traffic. The main idea was that a recurrent autoencoder trained in this way should recover anomalous traffic with a high loss. The TCP package is considered malicious if the recovery loss is above the threshold. However, the accuracy of recovering normal TCP packets was low due to the insufficient model capacity and the lack of the suitable representation learning method. After the results analyzing, we proposed an approach that can improve accuracy of detection for some attacks. Based on this approach, the VAEGAN network was trained on normal network flows from CICIDS2017. The VAEGAN was used to detect malicious network flows: to calculate the anomaly score for flow; if score is above the threshold – the flow is malicious. The VAEGAN network showed a high percentage of attacks detection and the F-score value – 0.933.
Eigenvalue-type equations for Löwdin-Amos-Hall spin-paired (corresponding) orbitals are developed to provide an alternative to the standard spin-polarized Hartree-Fock or Kohn-Sham equations in dealing with broken-symmetry (BS) states. To derive paired orbitals for different spins (PODS) equations there has been applied Adams-Gilbert "localizing" operator approach. The PODS equations contain different operators for different spins the eigenvectors of which are paired orbitals associated with the same eigenvalue for each pair. Preliminary applications to simple systems show viability of this approach. Although the spectrum of possible applications of the PODS equations seems to be quite wide, they would be especially useful for obtaining and analyzing the S(z) = 0 BS solutions for the systems with antiferromagnetic structure.
One of the main difficulties in the formation and increase of revenues from hydrocarbon resources is the deterioration of the quality of the mineral resource base and changes in the geography of production. One can observe an increase in the depletion and water content of the fields, an increase in the proportion of highly viscous and high-sulfur oil; the share of stocks in hard-to-reach and infrastructural underdeveloped regions is growing. One of the tools for encouraging subsoil users to develop such resources is to ensure lower rates of deductions to state bodies. The study presents an improved methodological approach to estimating and forecasting state budget revenues from hydrocarbon resources. The main stages of development are investigated and the main trends of the system of tax deductions from oil production are revealed. Explained the use of an approach focused on the forecast of production indicators of production, taking into account the structure of the mineral resource base. The calculations showed the need to reform the system of formation of government revenues from hydrocarbon resources. In the structure of government revenues from hydrocarbon resources, there is a tendency to increase the role of the mineral extraction tax in comparison with the export duty.
Replication of chromosomes is central to heredity. To become available for replication machinery, DNA invariably needs to dissociate from chromatin proteins. Yet, chromatin landscape must be promptly re-established during or soon after replication. Although this process underlies the epigenetic inheritance, little is known about its molecular mechanisms.

This mini-review is focused on Drosophila melanogaster SUppressor of UnderReplication (SUUR) protein, which is involved both in replication and chromatin maintenance in polytene tissues. Existing data suggest that it is involved in the regulation of chromatin renewal during replication. According to this model, SUUR protein moves along the chromosomes together with the replication complex. When the replication fork enters the repressed, H3K27me3- or H3K9me3-enriched, chromatin, SUUR-containing complex slows down the replisome until these histone modifications are properly placed on the newly-synthesized DNA strands.

Suggested model provides an insight into the mechanism of epigenetic information inheritance. This hypothesis could be tested by further analysis of the interplay between local enrichment of repressive histone modifications and the replication fork progression rate.
simple models of lambda phage DNA tertiary structure

The fluorescence polarization of acridine orange-stained, oriented lambda phages was measured. The parameters of DNA packing within the phage head cos2 theta and cos4 theta were calculated (theta, angle between the direction of a small segment of DNA and the phage axis).

It is shown that simple models of lambda phage DNA tertiary structure are not consistent with calculated values. A new model is proposed.
Currently, molecular parasitologists are searching for new agents against trematodiases. Redox metabolism is important for parasites as far as long-lived adult parasites inside a mammalian host are exposed to redox challenges. Antioxidants have been poorly studied as anthelmintic agents, in particular against the foodborne trematodes. Study of in vitro anthelmintic activity of nonenzymatic natural and synthetic antioxidants of various chemical structures was performed using standard motility and mortality assays against juvenile and adult Opisthorchis felineus worms. Promising agents have been found among both natural and synthetic compounds. The mitochondria-targeted antioxidant SkQ1 [10-(6′-plastoquinonyl)decyltriphenylphosphonium] in motility assays was as effective (half-maximal inhibitory concentration [IC50] 0.6–1.4 μM) as praziquantel (IC50 0.47–1.4 μM), and SkQ1 was significantly more effective than praziquantel in mortality assays. Moreover, extensive tegument damage of the adult fluke was revealed after SkQ1 treatment. Flavonoids manifested potency too, with IC50 values in a micromolar range (5.1–17.4 μM). Other natural and synthetic compounds tested against helminths were significantly less effective than praziquantel. Results of our study indicate that SkQ1 and flavonoids have high anthelmintic activities against the liver flukes. We propose that structure–activity relationship research might be worthwhile based on the structures of the most effective substances.
Mutation frequencies vary along a nucleotide sequence, and nucleotide positions with an exceptionally high mutation frequency are called hotspots. Mutation hotspots in DNA often reflect intrinsic properties of the mutation process, such as the specificity with which mutagens interact with nucleic acids and the sequence-specificity of DNA repair/replication enzymes. They might also reflect structural and functional features of target protein or RNA sequences in which they occur. The determinants of mutation frequency and specificity are complex and there are many analytical methods for their study. This paper discusses computational approaches to analysing mutation spectra (distribution of mutations along the target genes) that include many detectable (mutable) positions. The following methods are reviewed: mutation hotspot prediction; pairwise and multiple comparisons of mutation spectra; derivation of a consensus sequence; and analysis of correlation between nucleotide sequence features and mutation spectra. Spectra of spontaneous and induced mutations are used for illustration of the complexities and pitfalls of such analyses. In general, the DNA sequence context of mutation hotspots is a fingerprint of interactions between DNA and DNA repair/replication/modification enzymes, and the analysis of hotspot context provides evidence of such interactions.
The information has been analytically concentrated for an aggravation mode by reduction of modelled relations to dominant positive feedback loops

the doomsday of capitalist reproduction because of neglect of the scientific foundations of environmental management is determined by initial magnitudes of only two variables - the resource intensity of net output and the ratio of net output to proved reserves in the model economy

The magnitudes of remaining parameters (relating, first, to technical progress, distribution shares of labour compensation, rent, and profit in the net product, second, to the rate of growth of labor force and the rate of investment in fixed capital) affect only the nuances of a transition regime to a collapse
A study of hadron production at the nucleon-antinucleon threshold has been performed with the CMD-3 detector at the VEPP-2000 e + e − collider. A very fast rise with an about 1 MeV width has been observed in the e + e − → pp ̅ cross section. A sharp drop in the e + e − → 3(π + π − ) cross section has been con?rmed and found to have a width of less than 2 MeV, in agreement with the observed fast rise of the e + e − → pp ̅ cross section. For the ?rst time a similar sharp drop is demonstrated in the e + e − → K + K − π + π − cross section. The behavior of the e + e − → 3(π + π − ), K + K − π + π − cross sections cannot be explained by an interference of any resonance amplitude with continuum, therefore this phenomenon cannot be due to a narrow near-threshold resonance. No such structure has been observed in the e + e − → 2(π + π − ) cross section.
The paper puts forward a methodological approach to the evaluation of the effectiveness of venture capital investments in innovative projects in pharmaceutical industry using real options method. The proposed approach is tested on the real innovative project with venture financing in the pharmaceutical industry. The paper concludes that the value of the compound real option increases the overall value of the innovative project due to the factor of staged investment and a possibility to stop financing. The efficiency of using real options method when applied to the evaluation of the effectiveness of innovative projects by a venture investor is shown
СОДЕРЖАТЕЛЬНЫЕ УСЛОВИЯ ПРАВОМЕРНОГО ОГРАНИЧЕНИЯ ПРАВ И СВОБОД
Aim. To study the relation between the consumption of the main macronutrients and food groups with the risk of fatal outcomes from cardiovascular diseases (CVD) in people with newly diagnosed diabetes and those who are informed about type 2 diabetes mellitus (T2DM). Material and methods. This prospective analysis included 681 people (284 men and 397 women) with T2DM at baseline HAPIEE (Health, Alcohol and Psychosocial factors In Eastern Europe) 2003 (05) – December 31, 2018 and averaged 14.7 ± 0.7 years. There were 207 incident CV mortality during follow-up period (107 men, 100 women). The questionnaire on the presence of T2DM included information on the awareness of individuals about the presence of T2DM (“Did the doctor tell you that you have T2DM?”). The actual nutrition data included information on the consumption of 147 foods. The hazard ratio was estimated using Cox regression. Results and discussion. In men who aware of T2DM, the risk of developing a fatal CV event decreases with an increase in the consumption of “all-season” fruits (HR 0.413; 95 % confidence interval (CI) 0.234-0.786) and increases with an increase in the consumption of chicken eggs (HR 1.907 95 % CI 1.051-3.437), and alcohol (HR 1.031; 95 % CI 1.001- 1.061). In men who are unaware of T2DM, with an increase in nut consumption, the risk of developing fatal CV events decreases (HR 0.821; 95 % CI 0.679-0.992) and increases with increasing consumption of dairy products (HR 1.105; 95 % CI 1.000-1.221). In women aware of T2DM, consumption of white bread increases the risk (HR 1.489; 95 % CI 1.105-2.004), on the contrary, consumption of black bread reduces the risk of an undesirable outcome (HR 0.575; 95 % CI 0.424-0.818). Conclusions. In men who aware of T2DM, the most significant risk factors were the poor all-season fruits intake and excessive chicken eggs consumption. In women with type 2 diabetes, an increase in white bread consumption is of importance to increasing the risk of an undesirable CV outcome, and an increase in black bread consumption counts for reducing the risk.
Here we explore the effect of the nature of organic ligands in rhenium cluster complexes [Re 6 Q 8 L 6 ] 4− (where Q=S or Se, and L=benzotriazole, 1,2,3‐triazole or 1,2,4‐triazole) on the biological properties of the complexes, in particular on the cellular toxicity, cellular internalization and localization. Specifically, the study describes the synthesis and detailed characterization of the structure, luminescence and electrochemical properties of the four new Re 6 clusters with 1,2,3‐ and 1,2,4‐triazoles. Biological assays of these complexes are also discussed in addition to those with benzotriazole using cervical cancer (HeLa) and immortalized human fibroblasts (CRL‐4025) as model cell lines. Our study demonstrates that the presence of hydrophobic and π‐bonding rich units such as the benzene ring in benzotriazole significantly enhances cellular internalization of rhenium clusters. These ligands facilitate binding of the clusters to DNA, which results in increased cytotoxicity of the complexes.
Fiber-like Maxwell body is frequently used to model the mechanical behaviour of advanced composite materials, which appear in engineering and bio-mechanical applications.

Here we consider a material model of the fiber-like Maxwell body based on the Sidoroff decomposition of the deformation gradient. In our case this decomposition yields a multiplicative split of the fiber stretch into inelastic and elastic parts. One of the advantages of the model is that various hyperelastic potentials can be employed for a greater accuracy. Three different potentials are analyzed in this paper: the classical Holzapfel potential and its modifications. The first modification accounts for a fiber slackness and the second one is intended for applications with a local fiber buckling. In terms of these three potentials, we analyze the performance of a universal iteration-free time-stepping scheme. Robustness and accuracy of this algorithm are tested.

The iteration-free method is shown to compare favourably to the classical Euler-backward which includes the Newton iteration process.
We consider several versions of incomplete nested factorization methods for solving the large systems of linear algebraic equations (SLAEs) with sparse matrices which arise in grid approximations of the multi-dimensional boundary value problems. Our approach is based on the two-level iterative process in the Krylov subspaces in 3D case. Corresponding hierarchical incomplete factorization is applied to the block tridiagonal matrix structure. At the upper level, the diagonal blocks correspond to 2D grid subproblems which are factorized in the line-by-line framework. Instead of the low and upper triangular matrix factors, the alternating triangular matrices are used, which allows to apply the parallel counter sweeping approaches. The improvement of preconditioners is made by means of generalized compensation principles. To solve SLAE iterative conjugate direction methods in Krylov subspaces are applied. The efficiency of the proposed methods are demonstrated on the set of representative test problems.
The a-SiO x :H thin films were deposited by the gas-jet electron beam plasma chemical vapor deposition method with different stoichiometry (x=0.15-1.0) for different SiH 4 flow rates. The concentration of hydrogen in the films increases with the growth rate in ranges from 1.5 to 4.8 at.%. Further annealing leads to the effusion of hydrogen from the structure of the material and the compression of the structure, which leads to a reduction in the thickness for all films. X-ray diffraction measurements showed that the as-deposited films crystallized to form nc-Si about 4-8 nm in size after annealing at 1000°C.
Currently, several long non-coding RNAs (lncRNAs) (TUG1, MALAT1, MEG3 and others) have been discovered to regulate normal visual function and may potentially contribute to dysfunction of the retina.

We decided to extend these analyses of lncRNA genes to the retinal pigment epithelium (RPE) to determine whether there is conservation of RPE-expressed lncRNA between human and bovine genomes. We reconstructed bovine RPE lncRNAs based on genome-guided assembly. Next, we predicted homologous human transcripts based on whole genome alignment.

We found a small set of conserved lncRNAs that could be involved in signature RPE functions that are conserved across mammals. However, the fraction of conserved lncRNAs in the overall pool of lncRNA found in RPE appeared to be very small (less than 5%), perhaps reflecting a fast and flexible adaptation of the mammalian eye to various environmental conditions.
Wilson's disease is a rare autosomal recessive disorder of copper metabolism. The copper accumulation in the viscera appears due to the functional impairment of copper-transporting ATPase, which is encoded by the ATP7B gene.

In this study, PBMCs of a patient with two ATP7B mutations were reprogrammed. The first mutation is a missense mutation p.H1069Q, which is the most frequent mutation in the human population. At the same time, the second one is a frameshift mutation p.Lys1013fs.

The generated iPSC line had a normal karyotype, maintained the original genotype, expressed pluripotency markers, and demonstrated the ability to differentiate into derivatives of the three germ layers.