Hengzongshu/ArticleAgent huggingface dataset:
Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered.

To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-κB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies. To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD).

The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA. Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced false positives at least at higher stringencies. Based on this analysis, SiteGA adds substantial specificity even to optimized PWMs and may be considered for large-scale genome analysis. It adds to the range of techniques available for TFBS prediction, and EPD analysis has led to a list of genes which appear to be regulated by the above TFs.
A molecular mechanism of somaclonal variation is proposed Oxidative stress caused by altered oxygen regime, the disturbance of the normal antioxidant status and the presence of strong prooxidants in cell culturing media are suggested to be the main reasons of the variations. Primary, secondary and final products of lipid peroxidation caused by oxidative stress can be directly responsible for plant genome instability. The proposed mechanism of somaclonal variation could be the basis for development of new biotechnological approaches to this process.
Terahertz (THz) plasmonic devises based on periodical corrugated structures are promising for sensing applications in biology and medicine but have not been developed so far because spoof surface plasmons (SSPs) on such structures were studied insufficiently in the THz spectral range.

In the paper, the propagation of THz SSPs along one-dimensional subwavelength rectangular plane gratings with a dielectric substance in the grooves was studied and optimal parameters of gratings (period, aspect ratio and groove depth) for sensing of dielectric were found.

First grating samples were made and tested using the THz radiation of the Novosibirsk free electron laser.
A strictly determined number of external sensory organs, macrochaetes, acting as mechanoreceptors, are orderly located on drosophila head and body. Totally, they form the bristle pattern, which is a species-specific characteristic of drosophila. Each mechanoreceptor comprises four specialized cells derived from the single sensory organ precursor (SOP) cell. The conserved bristle pattern combined with a comparatively simple structure of each mechanosensory organ makes macrochaetes a convenient model for studying the formation spatial structures with a fixed number of elements at certain positions and the mechanism underlying cell differentiation.

The macrochaete morphogenesis consists of three stages. At the first stage, the proneural clusters segregate from the massive of ectodermal cells of the wing imaginal disc. At the second stage, the SOP cell is determined and its position in the cluster is specified. At the third stage, the SOP cell undergoes two asymmetric divisions, and the daughter cells differentiate into the components of mechanoreceptor: shaft, socket, bipolar neuron, and sheath. The critical factor determining the neural pathway of cell development is the content of proneural proteins, products of the achaete-scute (AS-C) gene complex, reaching its maximum in the SOP cell.

The experimental data on the main genes and their products involved in the control of bristle pattern formation are systematized. The roles of achaete-scute complex, EGFR and Notch signaling pathways, and selector genes in these processes are considered. An integral scheme describing the functioning of the system controlling macrochaete development in D. melanogaster is proposed based on analysis of literature data.
This decay is predicted to proceed predominantly via the $b\ensuremath{\rightarrow}s\ensuremath{\gamma}$ radiative penguin process with a high energy photon.

We search for the charmless ${B}^{0}$ decay with final state particles $p\overline{\mathrm{\ensuremath{\Lambda}}}{\ensuremath{\pi}}^{\ensuremath{-}}\ensuremath{\gamma}$ using the full data sample that contains $772\ifmmode\times\else\texttimes\fi{}1{0}^{6}B\overline{B}$ pairs collected at the $\mathrm{\ensuremath{\Upsilon}}(4S)$ resonance with the Belle detector at the KEKB asymmetric-energy ${e}^{+}{e}^{\ensuremath{-}}$ collider.

No significant signal is found. We set an upper limit of $6.5\ifmmode\times\else\texttimes\fi{}1{0}^{\ensuremath{-}7}$ for the branching fraction of ${B}^{0}\ensuremath{\rightarrow}p\overline{\mathrm{\ensuremath{\Lambda}}}{\ensuremath{\pi}}^{\ensuremath{-}}\ensuremath{\gamma}$ at the 90% confidence level.
The possibility of mechanochemical synthesis and influence of mechanical activation on thermal synthesis of borides and boron carbides of mass-low metals is investigated. Formation of compound Mg1-xAlxB2 in literature up to x = 0.4 was established on shifts of reflexes (002) and (110) pure MgB2 aside the large corners.

The opportunity of mechanochemical synthesis in the mill AGO-2 of such compounds as AlB2 and CaC2B2 is established. Influence of mechanical activation in the mill SPEX 8000 on synthesis of such compound as Mg0.5Al0.5B2 is shown. Features of synthesis in systems containing metal magnesium are considered.

Mechanical activation also influences on the process of thermal synthesis: compound Mg0.5Al0.5B2 is obtained in the conditions inaccessible to traditional thermal synthesis; in our case x = 0.5 and as it was necessary to expect shifts of these reflexes exceeds shifts measured in literature only for x ≤ 0.4. The opportunity of application of crystalline boron for mechanochemical synthesis of borides and boron carbides of mass-low metals is established, that it was not represented probable to make in its ceramic synthesis. We revealed also that thermal analysis in conditions of helium results in crystallization almost all activated samples, and the analysis of received X-ray reflexes unambiguously allows to assert that mechanical activation accelerates synthesis of reaction products in the investigated systems in comparison with the traditional methods of its synthesis.
Photoelectron scattering in a p-GaN(Cs,O) photocathode was studied by photoelectron emission spectroscopy at low temperatures.

It has been experimentally established that the transfer of photoelectrons from the bulk of a p-GaN(Cs,O) photocathode to vacuum is accompanied by the emission of a cascade of optical phonons in the bulk and at the GaN–vacuum interface.

Based on how the high-energy features of the photoelectron energy distribution shift with the photon energy, we find mhh / m0 = 2.3 ± 0.3.
The possibility of using of a pair of compression piston - cylinder with the unique performance features for the conversion of hydrocarbons are discusses. The experimental facility enables working in the pressure range that would be unattainable in diesel engines. The necessary degree of compression is managed and maintained by the computer system with a feedback.
We study, within QCD collinear factorization and including BFKL resummation at the next-to-leading order, the production of Mueller–Navelet jets at LHC with center-of-mass energy of 7 TeV. The adopted jet vertices are calculated in the approximation of a small aperture of the jet cone in the pseudorapidity-azimuthal angle plane. We consider several representations of the dijet cross section, differing only beyond the next-to-leading order, to calculate a few observables related with this process. We use various methods of optimization to fix the energy scales entering the perturbative calculation and compare our results with the experimental data from the CMS collaboration.
MicrosymposiaLiquid crystals are ordered soft materials consisting of assembled molecules.They can be used as new functional materials for electron, ion, or molecular transportation, sensory, catalytic, optical, and bio-active materials [1,2].Herein, we describe new approaches to functionalization of liquid crystals and show how the design of liquid-crystalline structures formed by supramolecular assembly and nano-segregation leads to the formation of a variety of new functional soft materials.
Проблемная научно-исследовательская лаборатория гидрогеохимии инженерной школы при-
Nitrogen abundance is one of the most uncertain among all elements in the Earth's interior. Recent data indicate an affinity between Fe‐nitrides and Fe‐carbides in the Earth's mantle and inner core.

In this work P‐V‐T equations of state of ε‐Fe 3 N 0.8 and ε‐Fe 3 N 1.26 (which is close to Fe 7 N 3 ) have been determined using a combination of multianvil and synchrotron radiation techniques at pressures up to 30 GPa and temperatures up to 1473 K. A fit of the P‐V‐T data to the Vinet‐Rydberg and Mie‐Grüneisen‐Debye equations of state yields the following thermoelastic parameters... We also determined a preliminary equation of state for γ‐Fe 4 N y and calculated y = 0.35(2) from the data at 20–30 GPa.

It is likely that all presumably paramagnetic ε‐Fe 3 N x with x = 0.75–1.5 have similar thermoelastic properties with a minor increase of the bulk modulus with increasing N content. The melting temperature of ε‐Fe 3 N x increases from approximately 1473 to 1573 K in the pressure range from 5 to 30 GPa. Combining the results with a recent experimental study on the stability of β‐Fe 7 N 3 , isostructural with Fe 7 C 3 , and a theoretical study of the magnetic transitions in ε‐Fe 3 N x , we estimate the density of Fe‐nitrides at the Earth's inner core conditions. Our results indicate that at 5000–6000 K, 2.0–3.2 wt % N can explain the density deficit in Earth's inner core.
The ever-growing genome-wide association studies (GWAS) have revealed widespread pleiotropy. To exploit this, various methods which consider variant association with multiple traits jointly have been developed. However, most effort has been put on improving discovery power: how to replicate and interpret these discovered pleiotropic loci using multivariate methods has yet to be discussed fully. Using only multiple publicly available single-trait GWAS summary statistics, we develop a fast and flexible multi-trait framework that contains modules for (i) multi-trait genetic discovery, (ii) replication of locus pleiotropic profile, and (iii) multi-trait conditional analysis. The procedure is able to handle any level of sample overlap. As an empirical example, we discovered and replicated 23 novel pleiotropic loci for human anthropometry and evaluated their pleiotropic effects on other traits. By applying conditional multivariate analysis on the 23 loci, we discovered and replicated two additional multi-trait associated SNPs. Our results provide empirical evidence that multi-trait analysis allows detection of additional, replicable, highly pleiotropic genetic associations without genotyping additional individuals. The methods are implemented in a free and open source R package MultiABEL. Author summary By analyzing large-scale genomic data, geneticists have revealed widespread pleiotropy, i.e. single genetic variation can affect a wide range of complex traits. Methods have been developed to discover such genetic variants. However, we still lack insights into the relevant genetic architecture - What more can we learn from knowing the effects of these genetic variants? Here, we develop a fast and flexible statistical analysis procedure that includes discovery, replication, and interpretation of pleiotropic effects. The whole analysis pipeline only requires established genetic association study results. We also provide the mathematical theory behind the pleiotropic genetic effects testing. Most importantly, we show how a replication study can be essential to reveal new biology rather than solely increasing sample size in current genomic studies. For instance, we show that, using our proposed replication strategy, we can detect the difference in genetic effects between studies of different geographical origins. We applied the method to the GIANT consortium anthropometric traits to discover new genetic associations, replicated in the UK Biobank, and provided important new insights into growth and obesity. Our pipeline is implemented in an open-source R package MultiABEL, sufficiently efficient that allows researchers to immediately apply on personal computers in minutes.
This paper analyzes the magnetoconductance and the manifestations of the different charge carrier species in the entire parameter space of transport channels in three dimensional topological insulators
Alzheimer's disease (AD) is the most common type of dementia and is currently incurable, and mitogen-activated protein kinase (MAPK) p38 is implicated in the pathogenesis of AD. p38 MAPK inhibition is considered a promising strategy against AD, but there are no safe inhibitors capable of penetrating the blood-brain barrier. Earlier, we have shown that mitochondria-targeted antioxidant plastoquinonyl-decyltriphenylphosphonium (SkQ1) at nanomolar concentrations can prevent, slow down, or partially alleviate AD-like pathology in accelerated-senescence OXYS rats.

Here we confirmed that dietary supplementation with SkQ1 during active progression of AD-like pathology in OXYS rats (aged 12-18 months) suppresses AD-like pathology progression, and for the first time, we showed that its effects are associated with suppression of p38 MAPK signaling pathway (MAPKsp) activity. Transcriptome analysis, western blotting, and immunofluorescent staining revealed that SkQ1 suppresses p38 MAPKsp activity in the hippocampus at the level of expression of genes involved in the p38 MAPKsp and reduces the phosphorylation of intermediate kinases (p38 MAPK and MK2) and a downstream protein (αB-crystallin).

Thus, the anti-AD effects of SkQ1 are associated with improvement in the functioning of relevant signaling pathways and intracellular processes, thus making it a promising therapeutic agent for human AD.
The GeneNet (gnw/genenet/) accumulate information on reactive oxygen species (ROS) signals and reduction/oxidation (redox) regulation of transcription factors.

Redox-regulation gene network is the adaptation to oxidative stress and integrative system of local gene networks via key transcription factors.

The cross-talk of signals and the interference of gene networks occur in the integrative gene network
Background: DNA repair is a vitally important process that protects the cell's genome from ongoing damage.Six DNA repair pathways are commonly outlined: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, recombination repair, and non-homologous end joining.Of these, base excision repair that deals with small non-bulky lesions removes the greatest number of damaged nucleotides daily.Unlike many other cellular pathways, base excision repair is not carried out by multienzyme complexes but rather involves many DNA-mediated transient protein-protein interactions that pass the damaged DNA between consecutive participants of the pathway.

Methods: Direct structural characterization of such DNA substrate channeling remains elusive, and most of what is known about it was obtained through enzyme kinetics and modeling.Results: DNA glycosylases, the enzymes that initiate base excision repair, are actively displaced from their enzyme-product complexes by abasic site (AP) endonucleases, the next enzyme in the pathway.Several accessory proteins, such as XRCC1, PCNA, and PARP1, guide the dynamic assembly and disassembly of DNA repair complexes providing regulatory modifications and scaffolding.Interestingly, eukaryotic and bacterial DNA repair proteins are often homologous but the eukaryotic proteins carry additional extended intrinsically disordered domains, which are believed either to be involved into dynamic protein-protein interactions or provide additional DNA-binding capabilities outside the welldefined DNA binding domains.

Conclusion: Overall, DNA repair, and especially base excision DNA repair, relies on extensive conformational rearrangements of the participating proteins, which is necessary both for damage recognition and for progress along the repair pathway.As such, they represent a promising target for studies with cryo-EM techniques.
Найдены асимптотические разложения математического ожидания времени пребывания траектории случайного блуждания с нулевым сносом выше растущего уровня

На распределение скачков блуждания налагается условие Крамера о существовании экспоненциального момента

Библиография: 13 наименований
The electron attachment effect on DBD characteristics in chlorine and its mixtures with xenon has been studied. Characteristics of the DBDs in pure chlorine and in xenon-chlorine mixtures with a chlorine fraction of 0.1-5% were modeled using the fluid model. It is shown that the electron attachment limits a magnitude of the DBD current, contributes to formation of multiple current spikes, appearance of a double layer near the dielectric surface and formation of XeCl* excimer molecules, and leads to a redistribution of the power deposited into the discharge: more power is deposited into ions and less power is deposited into electrons.
MicroRNAs (miRNAs) are promising biomarkers in cancer research. Quantitative PCR (qPCR), also known as real-time PCR, is the most frequently used technique for measuring miRNA expression levels. The use of this technique, however, requires that expression data be normalized against reference genes. The problem is that a universal internal control for quantitative analysis of miRNA expression by qPCR has yet to be known. The aim of this work was to find the miRNAs with stable expression in the thyroid gland, brain and bone marrow according to NanoString nCounter miRNA quantification data. As a results, the most stably expressed miRNAs were as follows: miR-361-3p, -151a-3p and -29b-3p in the thyroid gland; miR-15a-5p, -194-5p and -532-5p in the brain; miR-140-5p, -148b-3p and -362-5p in bone marrow; and miR-423-5p, -28-5p and -532-5p, no matter what tissue type. These miRNAs represent promising reference genes for miRNA quantification by qPCR.
In contrast to diradicals connected by alternant hydrocarbons, only a few studies have addressed diradicals connected by nonalternant hydrocarbons and their heteroatom derivatives.

Here, the synthesis, structure, and magnetic properties of pyrrole-2,5-diyl–linked bis(nitronyl nitroxide) and bis(iminonitroxide) diradicals are described. The diradicals show characteristic electron spin resonance spectra in dilute glassy solutions, from which conclusions about the presence of distinct conformations, their symmetry, and interspin distance were made. X-ray diffraction analysis of the diradicals revealed that paramagnetic moieties lie in the plane of the pyrrole ring, because of the formation of an intramolecular hydrogen bond, ONO…H−N, with O…H distances of 2.15–2.23 Å. The N–O groups participating in the formation of H-bonds have greater bond lengths (~1.29 Å) as compared with nonparticipating groups (~1.27 Å).

The nitronyl nitroxide and iminonitroxide diradicals showed an intramolecular antiferromagnetic interaction, with J = −77.3 and −22.2 cm−1, respectively (H = −2JS1⋅S2).
The shadow method of image analysis is the most commonly used experimental technique for investigation of evaporating droplet dynamics and wettability. So, the shadow method uncertainty and limit of its applicability for analysis of evaporating droplets are actual issues. In this paper, we experimentally study the applicability limit of the shadow image analysis and contributions of errors, connected with non-telecentricity of the optical system, as well as diffraction and numerical errors, at various stages of droplet evaporation.
Objective. To specify a morphogenetic pathogenesis of the Scheuermann’s disease. Material and Methods. Growth plates, intervertebral discs, vertebral body tissue (surgical material) from 25 patients of 12–14 years old with Scheuermann’s disease of Grade II–III were examined. In-depth morphohystochemical, biochemical, and ultrastructural analyses were used to study glycosaminoglycans, oxidation-reduction enzymes, alkaline and acid phosphatase, RNA, DNA, and qualitative and quantitative composition of glycosaminoglycans. Results. Pathogenetic mechanisms of Scheuermann’s disease development are presented basing of previously obtained data on genetic dependence of this pathology. The starter of the spine kyphotic deformity is a disturbance of proteoglycan molecule synthesis and conformation in ventral growth plates of vertebral bodies. The structural change in proteoglycans, which perform barrier-trophic, informational, and antiinvasive functions results in a decreased mitotic and proliferative activity of chondroblasts. The spine kyphotic deformity develops in association with an active osteogenesis.
The paper demonstrates an algorithm for using physics-informed neural networks in workflow of processing microseismic data regarding the problem of localization of microseismic events. The proposed algorithm involves the use of a physics-informed neural network solution to the eikonal equation to calculate the traveltimes of the first arrivals. As a result, the network solution is compared with the observed arrival times to solve the inverse kinematic problem to determine the coordinates of the event locations. Using a synthetic 3D example, it was shown that the average absolute error of the arrival time misfit was less than 0.25 ms, and the average localization error did not exceed 4.5 meters.
Using the standard Balitsky-Fadin-Kuraev-Lipatov (BFKL) approach, with partial inclusion of next-to-leading order effects, we propose the inclusive hadroproduction of a Higgs boson and of a jet, featuring large transverse momenta and well separated in rapidity, as a new channel to probe the BFKL dynamics. Predictions are presented for cross-sections and azimuthal angle correlations in different kinematics configurations for the final-state transverse momenta. We find that the large energy scales provided by the emission of a Higgs boson stabilize the BFKL series.