Hengzongshu/ArticleAgent huggingface dataset:
In 2001, Michael Berry4 published the paper ”Knotted Zeros in the Quantum States of Hydrogen” in Foundations of Physics. In this paper we show how to place Berry’s discovery in the context of general knot theory and in the context of our formulations for quantum knots. Berry gave a time independent wave function for hydrogen, as a map from three space R3 to the complex plane and such that the inverse image of 0 in the complex plane contains a knotted curve in R3. We show that for knots in R3 this is a generic situation in that every smooth knot K in R3 has a smooth classifying map f : R3 −→ C (the complex plane) such that f−1(0) = K. This leaves open the question of characterizing just when such f are wave-functions for quantum systems. One can compare this result with the work of Mark Dennis and his collaborators and with the work of Lee Rudolph. Our approach provides great generality to the structure of knotted zeros of a wavefunction and opens up many new avenues for research in the relationships of quantum theory and knot theory. We show how this classifying construction can be related our previous work on two dimensional and three dimensional mosaic and lattice quantum knots.
Nonstationary kinetic approach has been used to study the influence of the high beta on the dispersion of slow magnetic sound wave. It is shown that in plasma with sloshing ions the oscillating unstable mode could exist even in limit of cold electrons if beta is high enough. The threshold of the instability depends strongly on the distribution of ions near injection energy. The unstable wave is maintained by the perturbation of magnetic field and become aperiodic mirror mode far beyond the instability threshold.
We refer to the set of the orders of elements of a finite group as its spectrum and say that finite groups are isospectral if their spectra coincide. In this paper, we determine all finite groups isospectral to the simple groups [Formula: see text], [Formula: see text], and [Formula: see text]. In particular, we prove that with just four exceptions, every such finite group is an extension of the initial simple group by a (possibly trivial) field automorphism.
This work is devoted to the study of one of the largest caldera eruptions of the Kurile-Kamchatka island-arc system that occurred on the island of Iturup. The object of investigation of this work are phenocrysts of quartz and plagioclase from dacite pumice of the Isthmus of the Isthmus, which is located on the island of Iturup. The purpose of this work is to determine the water content in the melts that participated in the caldera eruption of the Vetrovoy Isthmus and the patterns of their changes during the crystallization of magma. In the course of the work, the following were carried out: 1) adaptation and calibration of the Raman spectroscopy method for determining water in rhyolite melt's inclusions glasses in quartz and plagioclase from pumice stone; 2) determination of composition and estimation of water content in melt inclusions in quartz and plagioclase according to x-ray spectral analysis; 3) establishment of the regularities of the change in the water content during the evolution of the magmatic melt; 4) evaluation of fluid pressure by comparison with experimental data
Whole genome and whole exome sequencing technologies play a very important role in the studies of the genetic aspects of the pathogenesis of various diseases. The ample use of genome-wide and exome-wide association study methodology (GWAS and EWAS) made it possible to identify a large number of genetic variants associated with diseases. This information is accumulated in the databases like GWAS central, GWAS catalog, OMIM, ClinVar, etc. Most of the variants identified by the GWAS technique are located in the noncoding regions of the human genome. According to the ENCODE project, the fraction of regions in the human genome potentially involved in transcriptional control is many times greater than the fraction of coding regions. Thus, genetic variation in noncoding regions of the genome can increase the susceptibility to diseases by disrupting various regulatory elements (promoters, enhancers, silencers, insulator regions, etc.). However, identification of the mechanisms of influence of pathogenic genetic variants on the diseases risk is difficult due to a wide variety of regulatory elements.

The present review focuses on the molecular genetic mechanisms by which pathogenic genetic variants affect gene expression. At the same time, attention is concentrated on the transcriptional level of regulation as an initial step in the expression of any gene. A triggering event mediating the effect of a pathogenic genetic variant on the level of gene expression can be, for example, a change in the functional activity of transcription factor binding sites (TFBSs) or DNA methylation change, which, in turn, affects the functional activity of promoters or enhancers. Dissecting the regulatory roles of polymorphic loci have been impossible without close integration of modern experimental approaches with computer analysis of a growing wealth of genetic and biological data obtained using omics technologies.

The review provides a brief description of a number of the most well-known public genomic information resources containing data obtained using omics technologies, including (1) resources that accumulate data on the chromatin states and the regions of transcription factor binding derived from ChIP-seq experiments; (2) resources containing data on genomic loci, for which allele-specific transcription factor binding was revealed based on ChIP-seq technology; (3) resources containing in silico predicted data on the potential impact of genetic variants on the transcription factor binding sites.
We propose a model kinetic system of the hydrogen atom (two levels plus continuum) under the conditions typical for atmospheres of Type IIP supernovae in the plateau stage.

Despite the simplicity of this system, it describes realistically the basic properties of the complete system. Analysis shows that the ionization 'freeze-out' effect is always manifest at large times. We give a simple criterion for checking the statistical equilibrium of a system under the given conditions at any time.

It is shown that if the system is in non-equilibrium at early times, the time-dependent effect of ionization necessarily exists. We also generalize this criterion to the case of arbitrary multilevel systems. We discuss various factors that affect the strength of the time-dependent effect in the kinetics during the photospheric phase of a supernova explosion.
The nonlinear Schr"odinger equation is one of the fundamental models in nonlinear physics, and it has a broad range of applications, including fiber optical communications---the backbone of the internet.

Using the path-integral technique we examine the mutual information for the communication channel modeled by the nonlinear Schr"odinger equation with additive Gaussian noise. At large signal-to-noise ratio we present the mutual information through the path-integral, which is convenient for the perturbative expansion in nonlinearity.

In the limit of small noise and small nonlinearity we derive analytically the first nonzero nonlinear correction to the mutual information for the channel.
Background: Hepatocellular carcinoma (HCC) is one of the most malignant cancers worldwide. The role of autophagy in the НСС development and progression is controversial and are still not well known. It has been shown that lithium induces autophagy and apoptosis, affects on proliferation and survival of various human malignancies.

In this study we estimated lithium`s effects on autophagy in HCC in vivo.Materials and methods: Subcellular components and autophagic vacuoles were analyzed by transmission electron microscopy. The number of cells with LC3 and LAMP1 punctate was analyzed by double-immunofluorescence staining. Data are presented as mean ± standard deviation (SD). Mann–Whitney nonparametric tests were used to assess statistically significant differences at P < 0.05.

Results: Lithium carbonate increased the numerical and volume density of autophagic vacuoles and autophagy marker LC3 beta. Therefore, lithium carbonate promotes enlarged autophagic vacuoles formation in HCC cells in vivo.Conclusion: Extended and unresolved autophagy induces cancer cell death by stimulating autophagic cell death. Thus, lithium-mediated autophagy can be an attractive approach in HCC chemotherapy.
Objective: This study aims to evaluate peculiarities of composition and level of fatty acids (FAs) in erythrocyte membranes (EM) of patients with resistant arterial hypertension (RAH) which could be applied in diagnosis of pathogenic aspects of the disease, development of new therapeutic targets. Design and method: 24 males with controlled arterial hypertension (CAH) (stage 1–2), 20 subjects with RAH (53 ± 5.7years), 22 healthy males were included into the study. The Agilent 7000B (USA) GC system was applied to study FAs composition. Results: The patients with CAH demonstrated increase in ratio of saturated, monoenoic FAs as well as decrease of polyenoic ones. Significant increase was registered in levels of C14:0, C17:0, C18:0, C20:0, C18:1 n9 (p = 0.01–0.05). We registered decrease in ratio of n6 unsaturated FAs: (C18:2, C20:4, C22:4) n6, (p = 0.01–0.05). Patients with RAH displayed increase in levels of C15:0, 16:0 FAs, oleic, midic ones (p = 0.03–0.05). The registered increased level of C20:3n9 would compensate synthesis which would take place in cases of deficit of n6, n3 polyunsaturated FAs (PUFA). Increase in ratio (C20:3/C18:1) n9 tends to evoke active synthesis of substrates for formation of prostacyclins, thromboxanes which are known to possess vasoconstrictive properties. Changes in PUFA tended to be most highly pronounced, especially in cases of n3 (C22:5, C22:6; p < 0.01). Patients with RAH demonstrated 2.1-time decrease of total n3 PUFA as compared to subjects with CAH. Increase of arachidonic acid level by up to 37.8% served as an outstanding finding in patients with RAH. That was the sign of deficit of n-3 PUFA. Disbalance in structure of n3, n6 was seen in decreased n3/n6 ratio (p < 0.01). Patients with RAH demonstrated accumulation of saturated, polyunsaturated n6 FA with deficit of n3 PUFA in EM. This speaks in favor of decrease in fluidity of cellular lipid bilayer, inhibition of binding ligands with the receptor, activity of enzymes bound with membrane, including PIEZO1,2 proteins (responsible for sensitivity to pressure). Conclusions: Increase in disorganization of lipid components of cellular membrane causes progression of hypertension with further development of resistant forms, what should be considered an important link in pathogenesis and target for therapy.
1,3-Oxazines, six-membered heterocyclic compounds containing one nitrogen and one oxygen atom, have been of great interest to medicinal chemists in recent decades, due to the wide range of biological activity they exhibit, including anticancer, antibacterial, antifungal and etc. Development of new analgesic agents with high activity and low toxicity is very important task. It is known that the heterocyclic compounds synthesized from (–)-isopulegol exhibit analgesic activity.

We found that the Ritter reaction between monoterpenoid (–)-isopulegol and a number of aliphatic and aromatic nitriles in the presence of concentrated sulfuric acid led to a series of chiral 1,3-oxazine derivatives with 35–80 % yields. Carrying out the reaction of (–)-isopulegol with benzyl cyanide in the presence of CF3SO3H made it possible to increase the yield of the product from 40 %, achieved in the presence of H2SO4, to 60 %.

When studying the analgesic activity of the synthesized compounds in vivo, it was found that 1,3-oxazine at a dose of 10 mg/kg exhibited high analgesic activity reliably increasing the latent time of animals being on the hot plate and not inferior in efficiency to the reference drug sodium diclofenac administered at a similar dose.
The Chadobets alkaline ultramafic carbonatite complex is located on the Siberian craton within the southern boundary of the Permian-Triassic plume activity. The dating of xenogenic zircons from the weathering crust of carbonatites of the Chuktukon complex yielded four clusters with ages of 1870–1820, 495–385, 290–210 and 215–162 Ma. The first two clusters correspond to the dates of activity of Paleoproterozoic granitoid magmatism and Paleozoic alkaline-mafic tectono-magmatic activity, widely occurred in the Siberian craton and its southern framing. The age of crystallization of alkaline rocks of the Chadobets complex falls within the interval of 255–240 Ma. Ar-Ar dating of damtjernite and carbonatite minerals of the Chuktukon complex falls within the intervals of 250.5±3.7 and 247.1±5.7 Ma, respectively. The crystallization ages of the mela-aillikites and damtjernites of the Terina complex, according to the Ar-Ar dating, correspond to the intervals of 257.4±3.9, 241.1±3.7, and 240±3.6 Ma. The age interval of 215–162 Ma based on zircons from the carbonatite weathering crust of the Chuktukon complex reflects the geochronology of superimposed processes and indicates the different stages of alteration of igneous rocks of the Chadobets complex. The data obtained on the age of crystallization of alkaline rocks of the Chadobets complex are consistent with the age interval of Siberian plume activity within a large igneous province (LIP).
The root apical meristem (RAM) is the plant stem cell niche which provides for the formation and continuous development of the root. Auxin is the main regulator of RAM functioning, and auxin maxima coincide with the sites of RAM initiation and maintenance. Auxin gradients are formed due to local auxin biosynthesis and polar auxin transport. The PIN family of auxin transporters plays a critical role in polar auxin transport, and two mechanisms of auxin maximum formation in the RAM based on PIN-mediated auxin transport have been proposed to date: the reverse fountain and the reflected flow mechanisms.

The two mechanisms are combined here in in silico studies of auxin distribution in intact roots and roots cut into two pieces in the proximal meristem region. In parallel, corresponding experiments were performed in vivo using DR5::GFP Arabidopsis plants.

The reverse fountain and the reflected flow mechanism naturally cooperate for RAM patterning and maintenance in intact root. Regeneration of the RAM in decapitated roots is provided by the reflected flow mechanism. In the excised root tips local auxin biosynthesis either alone or in cooperation with the reverse fountain enables RAM maintenance. The efficiency of a dual-mechanism model in guiding biological experiments on RAM regeneration and maintenance is demonstrated. The model also allows estimation of the concentrations of auxin and PINs in root cells during development and under various treatments. The dual-mechanism model proposed here can be a powerful tool for the study of several different aspects of auxin function in root.
The desolvated (3,24)-connected metal–organic framework (MOF) material, MFM-160a, [Cu3(L)(H2O)3] [H6L = 1,3,5-triazine-2,4,6-tris(aminophenyl-4-isophthalic acid)], exhibits excellent high-pressure uptake of CO2 (110 wt% at 20 bar, 298 K) and highly selective separation of C2 hydrocarbons from CH4 at 1 bar pressure. Henry's law selectivities of 79:1 for C2H2:CH4 and 70:1 for C2H4:CH4 at 298 K are observed, consistent with ideal adsorption solution theory (IAST) predictions.

Solid-state 2H NMR spectroscopic studies on partially deuterated MFM-160-d12 confirm an ultra-low barrier (∼2 kJ mol–1) to rotation of the phenyl group in the activated MOF and a rotation rate 5 orders of magnitude slower than usually observed for solid-state materials (1.4 × 106 Hz cf. 1011–1013 Hz). Upon introduction of CO2 or C2H2 into desolvated MFM-160a, this rate of rotation was found to increase with increasing gas pressure.

A phenomenon attributed to the weakening of an intramolecular hydrogen bond in the triazine-containing linker upon gas binding. DFT calculations of binding energies and interactions of CO2 and C2H2 around the triazine core are entirely consistent with the 2H NMR spectroscopic observations.
Domestication has been consistently accompanied by a suite of traits called the domestication syndrome. These include increased docility, changes in coat coloration, prolonged juvenile behaviors, modified function of adrenal glands and reduced craniofacial dimensions. Wilkins et al recently proposed that the mechanistic factor underlying traits that encompass the domestication syndrome was altered neural crest cell (NCC) development. NCC form the precursors to a large number of tissue types including pigment cells, adrenal glands, teeth and the bones of the face. The hypothesis that deficits in NCC development can account for the domestication syndrome was partly based on the outcomes of Dmitri Belyaev’s domestication experiments initially conducted on silver foxes. After generations of selecting for tameness, the foxes displayed phenotypes observed in domesticated species. Belyaev also had a colony of rats selected over 64 generations for either tameness or defensive aggression towards humans.

Here we focus on the facial morphology of Belyaev’s tame, ‘domesticated’ rats to test whether: 1) tameness in rats causes craniofacial changes similar to those observed in the foxes; 2) facial shape, i.e. NCC-derived region, is distinct in the tame and aggressive rats. We used computed-tomography scans of rat skulls and landmark-based geometric morphometrics to quantify and analyze the facial skeleton.

We found facial shape differences between the tame and aggressive rats that were independent of size and which mirrored changes seen in domesticated animals compared to their wild counterparts. However, there was no evidence of reduced sexual dimorphism in the face of the tame rats. This indicates that not all morphological changes in NCC-derived regions in the rats follow the pattern of shape change reported in domesticated animals or the silver foxes. Thus, certain phenotypic trends that are part of the domestication syndrome might not be consistently present in all experimental animal models.
The article is devoted to the element composition study of 5 kidney stones types.

Calculi consisting of calcium oxalate, uric acid, hydroxyapatite, brushite and struvite were analysed by optical emission spectrometry with inductively coupled plasma (ICP-OES). The elements Ba, Ca, Cu, Fe, K, Li, Mg, Mn, Na, P, Sr and Zn were determined in each stone types. Also, correlation analysis for stones consisting of uric acid (n=100) was performed and Spearman’s rank correlation coefficient was calculated.

Average and high positive correlations were found between K/Mg, Mg/Na, Mg/P, Mg/Sr, Na/P ( r =0.41 ÷ 0.50) and Ca/Sr ( r =0.71) respectively.
We have previously shown that immunization of C57BL/6 mice, prone to spontaneous development of experimental autoimmune encephalomyelitis (EAE), with three antigens (MOG 35‐55 , DNA‐histone complex or DNA‐methylated BSA complex), alters the differentiation profiles of bone marrow haematopoietic stem cells (HSCs). These are associated with the production of autoantibodies (auto‐Abs) against these antigens and the formation of abzymes hydrolysing DNA, MOG, myelin basic protein (MBP) and histones. Immunization of mice with antigens accelerates the development of EAE.

This work is the first to analyse the ratio of auto‐Abs without and with catalytic activities at different stages of EAE development (onset, acute and remission phases) after immunization of mice with the three specific antigens. Prior to immunization and during spontaneous in‐time development of EAE, the concentration of auto‐Abs against MBP, MOG, histones and DNA and activities of IgG antibodies in the hydrolysis of substrates increased in parallel; correlation coefficients = +0.69‐0.94. After immunization with MOG, DNA‐histone complex or DNA‐met‐BSA complex, both positive (from +0.13 to +0.98) and negative correlations (from −0.09 to −0.69) were found between these values.

Our study is the first showing that depending on the antigen, the relative amount of harmful auto‐Abs without and abzymes with low or high catalytic activities may be produced only at onset and in acute or remission phases of EAE. The antigen governs the EAE development rate, whereby the ratio of auto‐Abs without catalytic activity and with enzymatic activities of harmful abzymes hydrolysing MBP, MOG, histones and DNA varies strongly between different disease phases.
We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities.

This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database.

HOCOMOCO v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. An interactive interface and bulk downloads are available on the web: http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco11. In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences.
The article describes characteristics of popular science sphere of communication: aim and content of communication, communicative environment of the author and the reader, worldviews, circumstances of the communication. Comparison with adjacent spheres of communication is made. It is demonstrated that the content of the popular science sphere is derived from science sphere and placed into the reader’s non-professional environment; and all that determines existence of two views on the subject matter of the text. The first view is based on scientific knowledge, the second sight – on common sense. The author’s aim is to reconstruct the “naïve” worldview of the reader, to dispose it and to convince the addressee that the scientific view is real life. The more complete expression of these actions of the author is a framework which sets two semantic structures. Each of them consists of reference to the channel of information, predicate of “feeling-thinking-speaking”, and thesis. The first (left-hand) structure belongs to the reader’s “naïve” worldview, the second (right-hand) – to the author’s scientific sight. Language expression of the elements of this construction can be text fragments or zero. The latter is available due to standard meanings of qualificative categories of the modality of sentence – authorization and epistemic modality
For the Routing Open Shop problem with unit execution times

the first algorithm with parameterized complexity is designed for constructing an optimal schedule

Its running time is bounded by a function (P ol(|V |) + f (m, g)) • |I|, where P ol(|V |) is a polynomial of the number of network nodes, f (m, g) is a function of the number of machines and the number of job locations, and |I| is the input length in its compact encoding