Hengzongshu/ArticleAgent huggingface dataset:
Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only some operons, primarily those that encode physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. Nevertheless, even the limited conservation of operon organisation that is observed provides valuable evolutionary and functional clues through multiple genome comparisons. With the rapid growth in the number and diversity of sequenced prokaryotic genomes, functional inferences for uncharacterized genes located in the same conserved gene neighborhood with well-studied genes are becoming increasingly important. In this review, we discuss various computational approaches for identification of conserved gene strings and construction of local alignments of gene orders in prokaryotic genomes.
Globodera rostochiensis belongs to major potato pathogens with a sophisticated mechanism of interaction with roots of the host plants. Resistance of commercial varieties is commonly based on specific R genes introgressed from natural populations of related wild species and from native potato varieties grown in the Andean highlands. Investigation of molecular resistance mechanisms and screening the natural populations for novel R genes are important for both fundamental knowledge on plant pathogen interactions and breeding for durable resistance.

Here we exploited the Solanum phureja accessions collected in South America with contrasting resistance to G. rostochiensis.The infestation of S. phureja with G. rostochiensis juveniles resulted in wounding stress followed by activation of cell division and tissue regeneration processes. Unlike the susceptible S. phureja genotype, the resistant accession reacted by rapid induction of variety of stress response related genes. Transcriptomic analysis also revealed considerable differences between the analyzed S. phureja genotypes and the reference genome.

This chain of molecular events accompanies the hypersensitive response at the juveniles' invasion sites and provides high-level resistance. The molecular processes in plant roots associated with changes in gene expression patterns in response to G. rostochiensis infestation and establishment of either resistant or susceptible phenotypes are discussed. De novo transcriptome assembling is considered as an important tool for discovery of novel resistance traits in S. phureja accessions.
In the paper, an experimental investigation of the turbulent structure of bubbly free and impinging jets was carried out by means of PIV and PFBI techniques. PIV was applied to measure velocity distributions and turbulent characteristics in the continuous phase, while the PFBI approach was applied to visualize bubbles in the flow and evaluate their sizes. The flow was studied at the Reynolds number of 12,500 and three void fractions β = 0, 1 and 2%. The mean air bubble diameter was estimated to be roughly 0.8 mm for all β. It was revealed that, in the free jet, the air bubbles reduce the jet core size by more than 30% at the distance of a half of the nozzle diameter. In the two-phase jet, the radial velocity fluctuations rise faster in the mixing layer in the initial jet region between the nozzle edge and the downstream position of 40% of the nozzle diameter but further downstream they are suppressed about two times by the bubbles. In the impinging jet, the bubbles produce a high peak of the radial component of turbulent fluctuations near the wall at the distance of 70% of the nozzle diameter from the jet axis.
A new test facility for experimental simulation of transient heat load expected in the ITER divertor during unmitigated events is developed.

Application of a long-pulse (0.1–0.3 ms) wide-aperture (up to 2 cm2) electron beam as a heating device provides powerful energy loads at a tungsten target with FHF> 250 MJ m−2 s−0.5. Dynamics of tungsten particles in the ablation plume is investigated with a novel for PSI experiments small-angle laser light scattering technique.

The threshold of intense droplet generation and dynamics of particles sizes are estimated.
The new code for numerical simulation of magnetic hydrodynamical astrophysical flows with consideration of chemical reactions is given in the paper.

At the heart of the code – the new original low-dissipation numerical method based on a combination of operator splitting approach and piecewise-parabolic method on the local stencil.

The chemodynamics of the hydrogen while the turbulent formation of molecular clouds is modeled.
Purpose. This article introduces three samples of spearheads of long-shafted weapons from the collection of the Nizhny Novgorod State Historical and Architectural Museum-Reserve (Nizhny Novgorod, Russia). Long-range weapons being of a certain scientific interest, the samples of spearheads considered are important as they have not been described yet. In the course of our research, we have analyzed the features of their design in order to clarify the origin and time of their creation. Results. Two spearheads from the collection of the Nizhny Novgorod State Historical and Architectural Museum-Reserve came from a private collection of A. O. Karelin (1837–1906), and the third one from the funds of the Museum of Lyskovo. Their origin in those collections is unknown; however, museum workers have managed to date them to the 17th century. All the spearheads considered are in a good condition, with barely noticeable spots of rust. Obviously, they have new shafts, two of which are broken. All spearheads were manufactured from iron; belong to the sleeved type according to the method of planting on the shaft and to the group of lenticular according to the cross-section of the pen. The pens of the spearheads are of two types – elongated rhombic and elongated triangular. The spearheads’ feathers are decorated with rows of holes along the edge and two curls (sprouts) below the shoulders. All the spearheads have another decorative element, a so called “apple” on the neck of the pen, which was not a mandatory element of this type of spearheads. The elongated rhombic pens belong to the spearheads from the collection of the museum in Lyskovo and Karelin’s collection (spearheads No. 1–2). The spearhead No. 1 (inventory number GOM 11943. IM 1512) has the total length of 28.4 cm; the blade is 11 cm long and 4.7 cm wide at most. The biggest diameter of the sleeves measures 3.8 cm with the length of 13.6 cm. The spearhead No. 2 (inventory number GOM 7274-13. OR 451) has the total length of 34 cm; the blade is 17 cm long and 5.4 cm wide at most. The biggest diameter of the sleeves measures 3.8 cm with the length of 12.4 cm. The elongated triangular pen is from Karelin’s collection. The spearhead No. 3 (inventory number GOM 7274-10.OR 382) has the total length of 37 cm; the blade is 28.5 cm long and 5.5 cm wide at most. The biggest diameter of the sleeves measures 3.8 cm with the length of 12.3 cm. Conclusion. Three previously unknown spearheads have been introduced into scientific circulation. The analysis of the design features of these weapons allowed us to date them to the 17th century. The spearheads are attributed to the type “rogatina”, which was widespread in the Russian state being massive and big. Such long-range weapons were known as “bear-spear” and initially were used for hunting large animals. Such items are widely found in the European part of Russia and in Siberia, where they were brought by Russian pioneers.
The {\it prime graph} $Γ(G)$ of a finite group $G$ is the graph whose vertex set is the set of prime divisors of $|G|$ and in which two distinct vertices $r$ and $s$ are adjacent if and only if there exists an element of $G$ of order $rs$. Let $A_n$ ($S_n$) denote the alternating (symmetric) group of degree $n$. We prove that if $G$ is a finite group with $Γ(G)=Γ(A_n)$ or $Γ(G)=Γ(S_n)$, where $n\geq19$, then there exists a normal subgroup $K$ of $G$ and an integer $t$ such that $A_t\leq G/K\leq S_t$ and $|K|$ is divisible by at most one prime greater than $n/2$.
This paper is a reply to the criticism of our work on particle production in modified gravity by D. Gorbunov and A. Tokareva.

We show that their arguments against efficient particle production are invalid.

$F(R)$ theories can lead to an efficient generation of high energy cosmic rays in contracting systems.
The most effective method of treating allergic diseases, aimed not at relieving symptoms, but at eliminating the cause of the disease, is allergen-specific immunotherapy (AIT). To reduce the risk of side effects and improve the delivery of allergens to the mucosa, various delivery systems, such as liposomes, dendrimers, nanoparticles, etc., can be used. To date, there are data on the creation of delivery systems based on glycyrrhizic acid (GA) and its derivatives, but such a delivery system has not been used for allergen-specific therapy until now. At the same time, it is known that GA has an anti-inflammatory effect, shifts the balance towards Th1, and increases the number of Treg cells, which means that in the future it can enhance the anti-allergic effect of AIT and reduce the risk of unwanted side effects. Thus, the study of the immunomodulatory effect of supramolecular complexes (micelles) of GA with extracts of allergens seems to be very promising for the development of new drugs for AIT.
TOWN AND GOWN» 1 : УНИВЕРСИТЕТ В ГОРОДСКОМ СОЦИАЛЬНО-ЭКОНОМИЧЕСКОМ И КУЛЬТУРНО-ИСТОРИЧЕСКОМ ПРОСТРАНСТВЕ ЕВРОПЫ (НА ПРИМЕРЕ ВЕЛИКОБРИТАНИИ, ГЕРМАНИИ, ФРАНЦИИ И ПОЛЬШИ) Статья подготовлена в
We present a theoretical formalism for scattering of twisted neutrons by nuclei in a kinematic regime where interference between the Coulomb interaction and the strong interaction is essential.

Twisted neutrons have definite quantized values of an angular momentum projection along the direction of propagation, and we show that this results in novel observable effects for the scattering cross section, spin asymmetries, and polarization of the scattered neutrons. We demonstrate that additional capabilities provided by a beam's orbital angular momentum enable new techniques for measuring both real and imaginary parts of the scattering amplitude. Several possible observables are considered, for which the targets may be either well localized with respect to the spatial beam profile or the scattering occurs incoherently on nuclei in a bulk target.

The developed approach can be applied to other nuclear reactions with strongly interacting twisted particles.
The serotonergic system is one of the most important neurotransmitter systems that take part in the regulation of vital CNS functions. The understanding of its mechanisms will help scientists create new therapeutic approaches to the treatment of mental and neurodegenerative diseases and find out how this neurotransmitter system interacts with other parts of the brain and regulates their activity. Since the serotonergic system anatomy and functionality are heterogeneous and complex, the best tools for studying them are based on manipulation of individual types of neurons without affecting neurons of other neurotransmitter systems. The selective cell control is possible due to the genetic determinism of their functions. Proteins that determine the uniqueness of the cell type are expressed under the regulation of cell-specific promoters. By using promoters that are specific for genes of the serotonin system, one can control the expression of a gene of interest in serotonergic neurons. Here we review approaches based on such promoters. The genetic models to be discussed in the article have already shed the light on the role of the serotonergic system in modulating behavior and processing sensory information. In particular, genetic knockouts of serotonin genes sert , pet1 , and tph2 promoted the determination of their contribution to the development and functioning of the brain. In addition, the review describes inducible models that allow gene expression to be controlled at various developmental stages. Finally, the application of these genetic approaches in optogenetics and chemogenetics provided a new resource for studying the functions, discharge activity, and signal transduction of serotonergic neurons. Nevertheless, the advantages and limitations of the discussed genetic approaches should be taken into consideration in the course of creating models of pathological conditions and developing pharmacological treatments for their correction.
In this study, we collected and systemized diverse information related to depressive and anxiety disorders as the first step on the way to investigate the associations between molecular genetics, electrophysiological, behavioral, and psychological characteristics of people.

Keeping that in mind, we developed an internet resource including a database and tools for primary presentation of the collected data of genetic factors, the results of electroencephalography (EEG) tests, and psychological questionnaires. The sample of our study was 1010 people from different regions of Russia. We created the integrated ICBrainDB database that enables users to easily access, download, and further process information about individual behavioral characteristics and psychophysiological responses along with inherited trait data.

The data obtained can be useful in training neural networks and in machine learning construction processes in Big Data analysis. We believe that the existence of such a resource will play an important role in the further search for associations of genetic factors and EEG markers of depression.
Inhibition of DNA repair enzymes tyrosyl-DNA phosphodiesterase 1 and poly(ADP-ribose)polymerases 1 and 2 in the presence of pyrimidine nucleoside derivatives was studied here. New effective Tdp1 inhibitors were found in a series of nucleoside derivatives possessing 2′,3′,5′-tri-O-benzoyl-d-ribofuranose and 5-substituted uracil moieties and have half-maximal inhibitory concentrations (IC50) in the lower micromolar and submicromolar range. 2′,3′,5′-Tri-O-benzoyl-5-iodouridine manifested the strongest inhibitory effect on Tdp1 (IC50 = 0.6 μM). A decrease in the number of benzoic acid residues led to a marked decline in the inhibitory activity, and pyrimidine nucleosides lacking lipophilic groups (uridine, 5-fluorouridine, 5-chlorouridine, 5-bromouridine, 5-iodouridine, and ribothymidine) did not cause noticeable inhibition of Tdp1 (IC50 > 50 μM). No PARP1/2 inhibitors were found among the studied compounds (residual activity in the presence of 1 mM substances was 50–100%). Several O-benzoylated uridine and cytidine derivatives strengthened the action of topotecan on HeLa cervical cancer cells.
Tables 2 and 3 in the paper by Tumanov et al. [(2010), Acta Cryst. B 66 , 458–471]

are corrected.
Ecological and climatic factors have an impact on the health, productivity and reproduction of the cattle.

The goal of this work is the study of physiological status of servicing bulls reared under ecological and climate conditions of the Altai region, by defining the differences between Red-Steppe, Simmental and Black-and-White breeds in spermatogenic, hormonal, biochemical and hematological parameters. Samples of peripheral blood and ejaculates were taken from 48 grown-up servicing bulls (average age 5.6±0.3 years) in autumn period.

It was established that Red-Steppe bulls have higher concentrations of nonorganic phosphorus, leucocytes, erythrocytes, hemoglobin, hematocrit and erythrocyte sedimentation rate in comparison with animals of Simmental breed, and the hemoglobin concentration and hematocrit are also higher in comparison with Black-and-White breed. It was noted that bulls of Black-and-White breed have a higher level of cortisol in comparison with the other breeds. The lowest level of serum urea and total protein and increased serum activity of creatine kinase and γ-glutamyl transferase, as well as the heaviest body weight were observed in Simmental breed bulls. The differences between breeds in a wide spectrum of physiological measures reflect not only genetically determined peculiarities of homeostatic mechanism, but also may reflect different ability to adapt to local ecological and climate conditions of the Altai region. Spermatogenic, biochemical and hematological measures in bull sires reared in the Altai region were similar to those in bulls bred in other Russian regions and some other countries. The measures reported could serve as reference values and therefore represent 'normal' values of physiological status for these bull sires reared in this ecological and climatic zone, but could be utilized in further studies for comprehensive monitoring of cattle breeding stock in other ecological and climatic zones of the Siberian region of Russia.
A random walk based stochastic simulation algorithm for solving a nonlinear system of transient drift-diffusion-Poisson equations for semiconductors with random doping profile is developed. The method is then applied to simulate and analyze the stochastic dynamics of the transport of electrons and holes in doped semiconductor material. This analysis has a theoretical but also a practical interest since an addition even of a small concentration of foreign atoms to the regular semiconductor material produces dramatic changes in the electrical properties. The nonlinear drift-diffusion-Poisson system is solved by the iteration procedure including alternating simulation of the drift-diffusion processes and solving the Poisson equation. Here, we extend the iteration algorithm to solve the drift-diffusion-Poisson system with additional term governing the random inputs in the system like the stochastic doping, random distribution of quantum dots, and an irregular family of defects. Impact of these random entries on the stochastic dynamics of the drift velocity and electron and hole concentrations is studied.
In this paper, we developed a new dip-pen nanolithography (DPN) method. Using this method, we fabricated conductive nanowires with diameters of 30–50 nm on silicon substrates. To accomplish this, indium was transferred from an atomic force microscopy tip to the surface by applying a potential difference between the tip and substrate. The fabricated indium nanowires were several micrometers in length. Unlike thermal DPN, our DPN method hardly oxidized the indium, producing nanowires with conductivities from 5.7 × 10−3 to 4 × 10−2 Ω cm.
Auto-completion is an essential feature of any popular text editor for some language. It allows users to avoid the process of annoying typing of long expressions in their projects. There are a lot of different works in this direction in scientific research and commercial products. These works are very different and either use some special features and heuristics to improve code completion or use machine learning techniques. Most of these approaches rely on synthetic data and do not take into account the behavior of real users.

The article proposes an approach to improve the automatic code completion mechanism for the Python language by collecting information about usage of this mechanism by real users. The obtained data is used to train the model to rank completion variants with machine learning algorithms. To train the model, two types of features are used: contextual and elemental. Contextual features describe information about the code next to the cursor position in a text editor. Elemental features describe the characteristics of the proposed variant, for example, the length of the matching prefix.

When building a model, it is important to take into account the limits of the response time of the model and its size. Also, in the paper, various approaches of assessing the quality of the final model are considered.
For two series of catalysts based on praseodymium ferrite

their structural and redox properties as well as performance in ethanol steam reforming have been studied

The first series was PrFe
Stable free radicals are widely used as molecular probes and labels in various biophysical and biomedical research applications of magnetic resonance spectroscopy and imaging. Among these radicals, sterically shielded nitroxides of pyrrolidine series demonstrate the highest stability in biological systems.

Here, we suggest new convenient procedure for preparation of 3-carboxy-2,2,5,5-tetraethylpyrrolidine-1-oxyl, a reduction-resistant analog of widely used carboxy-Proxyl, from cheap commercially available reagents with the yield exceeding the most optimistic literature data.

Several new spin labels and probes of 2,2,5,5-tetraethylpyrrolidine-1-oxyl series were prepared and reduction of these radicals in ascorbate solutions, mice blood and tissue homogenates was studied.
The creation of problem-oriented monitoring strategies for the study of natural processes in the atmosphere-Earth system based on use of mathematical models in combination with observational data is discussed. Major objects of a modeling system are described. These are: a model of processes of transport and transformation of substances in the gas and aerosol state, data and models of observations.

We develop a variational approach that provides formulation, construction, and implementation of solutions to direct and inverse problems. To formulate the variational principle, some target functionals are defined. They serve for forecasting, assimilating observational data, controlling atmospheric quality, etc. Data assimilation techniques play a significant role in successful management of environmental objectives.

The result of the study is a version of the so-called 'seamless' modeling technology in which five classes of the required functions are calculated. These are state functions, adjoint functions, uncertainty functions, and two functions of sensitivity with respect to variations of model parameters and monitoring data. We can solve inverse problems of strategic operational assessments of hazardous situations and identification of sources of intensive technogenic impacts to organize the targeted monitoring.
Embryo production is a routine procedure in several species. However, in felids, the effectiveness of this approach is far behind that in the majority of laboratory species. The development of a suitable environment starts with the proper composition of culture media. Therefore, for the improvement of assisted reproduction techniques and their outcome in cats, this is an urgent task. As the addition of insulin-like growth factors (IGF-I, IGF-II) or granulocyte-macrophage colony-stimulating factor (GM-CSF) was beneficial in other mammalian species, this study aims to check whether these components, combined with other factors (such as type of fertilisation or type of culture) can provide a benefit in the felid culture system in current use. Thus, these supplements, in different concentrations and combinations, were merged with the use of two fertilisation techniques and randomly assigned to single or group culturing. The results showed that the addition of IGF-I and/or GM-CSF produced an increase in morula and blastocyst rate in a single culture system. In particular, the supplementation with 20 ng/mL of IGF-I incremented the maturation rate by 10% and significantly increased the morula and blastocyst rates in single culturing. This result is especially remarkable for wild felids, where only a few oocytes and/or embryos are available.