Hengzongshu/ArticleAgent huggingface dataset:
The development of high-throughput genomic sequencing coupled with chromatin immunoprecipitation technologies allows studying the binding sites of the protein transcription factors (TF) in the genome scale. The growth of data volume on the experimentally determined binding sites raises qualitatively new problems for the analysis of gene expression regulation, prediction of transcription factors target genes, and regulatory gene networks reconstruction. Genome regulation remains an insufficiently studied though plants have complex molecular regulatory mechanisms of gene expression and response to environmental stresses.

It is important to develop new software tools for the analysis of the TF binding sites location and their clustering in the plant genomes, visualization, and the following statistical estimates. This study presents application of the analysis of multiple TF binding profiles in three evolutionarily distant model plant organisms. The construction and analysis of non-random ChIP-seq binding clusters of the different TFs in mammalian embryonic stem cells were discussed earlier using similar bioinformatics approaches.

Such clusters of TF binding sites may indicate the gene regulatory regions, enhancers and gene transcription regulatory hubs. It can be used for analysis of the gene promoters as well as a background for transcription networks reconstruction. We discuss the statistical estimates of the TF binding sites clusters in the model plant genomes. The distributions of the number of different TFs per binding cluster follow same power law distribution for all the genomes studied. The binding clusters in Arabidopsis thaliana genome were discussed here in detail.
We considered a RBC shape model, corresponding to the minimal bending energy of the membrane with isotropic elasticity

We propose a method for characterization of mature red blood cells (RBCs) morphology, based on measurement of light-scattering patterns (LSPs) of individual RBCs with the scanning flow cytometer and on solution of the inverse light-scattering (ILS) problem for each LSP. We constructed an analytical approximation, which allows rapid simulation of the shape, given the diameter and minimal and maximal thicknesses. The ILS problem was solved by the nearest-neighbor interpolation using a preliminary calculated database of 250,000 theoretical LSPs.

For each RBC in blood sample we determined three abovementioned shape characteristics and refractive index, which also allows us to calculate volume, surface area, sphericity index, spontaneous curvature, hemoglobin concentration and content.
Wave steepness is presented as an extension and a valuable add-on to the conventional set of sea state parameters retrieved from satellite altimetry data.Following physical model based on recent advances of weak turbulence theory wave steepness is estimated from directly measured spatial gradient of wave height.In this way the method works with altimetry trajectories rather than with point-wise data.Moreover, in contrast to widely used parametric models this approach provides us with instantaneous values of wave steepness and period.Relevance of single-track estimates of wave steepness (period) is shown for wave climate studies and confirmed by a simple probabilistic model.The approach is verified via comparison against buoy and satellite data including crossover points for standard 1 second data of Ku-band altimeters.High quality of the physical model and robustness of the parametric ones are examined in terms of global wave statistics.Prospects and relevance of both approaches in the ocean wave climate studies are discussed.
Small supernumerary marker chromosomes can be derived from autosomes and sex chromosomes and can accompany chromosome pathologies, such as Turner syndrome.

Here, we present a case report of a patient with mosaic Turner syndrome and Dandy-Walker syndrome carrying a marker chromosome. We showed the presence of the marker chromosome in 33.8% of blood cells. FISH of the probe derived from the marker chromosome by microdissection revealed that it originated from the centromeric region of chromosome X. Additionally, we showed no telomeric sequences and no XIST sequence in the marker chromosome.

This is the first report of these two syndromes accompanied by the presence of a marker chromosome. Marker chromosome was X-derived and originated from centromeric region. Patient has mild symptoms but there is no XIST gene in marker chromosome. CPG137. Registered 03 March 2017.
Research background: This paper studies the impact of a new so-called green factor on the capitalization of petroleum companies, which is becoming highly relevant in view of the signing of the Paris agreements in 2015 and the support for clean energy. Although society, international organizations, and government authorities encourage companies to reduce their environmental impact, one of the main reasons for responsible behavior is still economic efficiency. The oil industry, on the one hand, faces one of the most volatile markets and, on the other hand, has one of the largest environmental impacts of any industry. That requires a detailed study of interconnections between market capitalization and the green factor.

Methods: Econometric analysis of panel data for Russian petroleum companies. The database includes indicators for six major Russian oil companies from 2011 to 2018. The following groups of factors are analyzed to explain the change in the companies? capitalization: macroeconomic (GDP and inflation in Russia), microeconomic (companies? revenue, net profit, tax payment, return on assets, return on equity, ratio of borrowed capital to equity), industrial (oil export, refining, production and proven reserves of the companies), and the green factor.

Findings & Value added: The selection of factors showed that the size of capitalization has been influenced most significantly by the following: the volume of the company's proven reserves, net profit, tax burden, and the green factor based on the policy of minimizing environmental damage. This result shows that investors consider companies with high environmental performance to be more valuable than companies with similar financial results but lower environmental ratings.
This work describes a new method for in situ measuring the lithium layer thickness. The method is based on the registration of the yield of 478 keV gamma-quanta of 7 Li(p,p'γ) 7 Li reaction. The results of measuring the radial distribution of the thickness of a lithium layer thermally deposited in vacuum on a cooled copper substrate are presented. The possibility of using this method for certification of lithium targets used for boron neutron capture therapy is noted.
Metamaterial formalism (MMF) approach allowing recognition of tumour areas in tissue samples

enhanced by providing an advanced technique to digitize mouse biopsy images. a colour-based segmentation technique based on the Kmeans clustering method is used allowing for a precise segmentation of the cells composing the biological tissue sample. Errors occurring at the tissue digitization steps are detected by applying MMF. The proposed methodology consists of three major steps, i.e. digitization of the biopsy image, analysis of the biopsy image, modelling of the disordered metamaterial

we end up with the robust, fully automated approach with no needs of the human intervention, ready for the clinical applications. the technique under consideration allows for the cancer stage detection. Moreover, early stage cancer diagnosis is possible by applying MMF
Factor V, encoded by the F5 gene, is a procoagulant blood clotting factor that increases the production of thrombin, the central enzyme that converts fibrinogen to fibrin, which leads to the formation of a blood clot. The F5 gene is localized to 1q24.2 chromosome and consists of 25 exons. There are various mutations in the F5 gene that lead to resistance of activated protein C (APC) (elimination of the APС cleavage site in factor V and factor Va), which can lead to arterial and venous thrombosis.

The aim of the present study was to analyze variants of the F5 gene in patients diagnosed with coronary atherosclerosis without acute coronary syndrome with stable functional class II–IV angina pectoris, confirmed by coronary angiography data, using the method of whole exome sequencing. Material and methods . The study was conducted in the framework of the Program of joint research work IIPM — branch of the ICG SB RAS and the FSBI «Research Institute of Circulation Pathology named after E.N. Meshalkin» Ministry of Health of Russian Federation. The study included 30 men aged 40–70 years with coronary angiography-verified coronary atherosclerosis, without ACS, with stable angina pectoris of the II–IV FC. Patients were admitted for coronary bypass surgery, and endarteriaectomy from the coronary artery (s) was performed during the operation according to intraoperative indications. Whole exome sequencing (SureSelectXT Human All Exon v.6+UTR) was carried out on an Illumina NextSeq 500 instrument (USA).

Results. In 30 patients, 29 single-nucleotide variants were found in the F5 gene. In patients with coronary atherosclerosis, rs9332701 of the F5 gene is 3.33 times more common, and rs6027 is 1.67 times more common than in the population. And rs184663825 was found in 3.33% of cases, while its occurrence in the population is 0.05%. For variants rs6034 and rs144979314, a possible damaging effect on the protein product is shown. Conclusion . The single-nucleotide variants rs9332701, rs6027, rs184663825, rs6034, rs144979314 of the F5 gene are of interest for inclusion in the genetic panels for the analysis of risk factors for the development of acute coronary syndrome.
The 3p26.3 microduplication involving the CNTN6 gene cause developmental delay and the intellectual disability. However, the incomplete penetrance is described for this copy number variation (CNV).

Here we describe ICAGi002-A line, which is supposed to use as a model for studying of the penetrance of the CNV in 3p26.3. The ICAGi002-A iPSCs line was obtained by the reprogramming of the skin fibroblasts from a healthy donor with 3p26.3 microduplication involving the CNTN6 gene.

The ICAGi002-A cells was pluripotent as it was shown by the expression of the pluripotency-associated markers and in vitro differentiation into the cells of three germ layers.
Using 605 fb−1 of data collected at the Υ(4S) resonance

we present a measurement of the inclusive radiative B-meson decay channel, B→Xsγ. For the lower photon energy thresholds of 1.7, 1.8, 1.9, and 2.0 GeV, as defined in the rest frame of the B meson, we measure the partial branching fraction and the mean and variance of the photon energy spectrum.

At the 1.7 GeV threshold we obtain the partial branching fraction BF(B→Xsγ)=(3.45±0.15±0.40)×10−4, where the errors are statistical and systematic.
The tumor‐suppressor gene encoding the cyclic AMP‐dependent protein kinase A type I‐α regulatory subunit PRKAR1A has been mapped to chromosome 17 (17q22–24) and is mutated in Carney complex, a familial neoplasia syndrome that is associated with thyroid tumors. Other genes implicated in cyclic nucleotide‐dependent signaling have been investigated in thyroid tumorigenesis.

We studied protein kinase A (PKA) activity in noninherited follicular thyroid adenomas and follicular, papillary, and undifferentiated (anaplastic) thyroid carcinomas. We then examined these and additional thyroid tumors for losses of the 17q22–24 PRKAR1A region, mutations of the PRKAR1A gene, and expression of its peptide product.

Total PKA activity was markedly increased in carcinomas over that in adenomas, whereas the ratio of free vs. total PKA activity was decreased in cancer. Consistent with these findings, the 17q22–24 region was frequently lost in cancer but not in benign adenomas. A novel inactivating mutation of the PRKAR1A gene (leading to premature termination of the predicted protein) was found in an aggressive thyroid cancer. The tumor with PRKAR1A gene mutation, as well as the tumors with 17q allelic losses, showed decreased PRKAR1A expression by immunostaining. We conclude that PRKAR1A, the most abundant regulatory subunit of protein kinase A and a principal cyclic AMP‐signaling modulator, acts as a tumor‐suppressor gene in sporadic thyroid cancer.
В современном мире хронический стресс и провоцирующие его состояния становятся все более социально значимыми факторами риска множества соматических заболеваний.Показано, что физиологические характеристики организма могут меняться в зависимости от формы реакции индивида на внешние раздражители.

Целью данной работы стало выявление психологических факторов патогенеза желчнокаменной болезни и поиск возможных медиаторов, опосредующих взаимосвязь психологических характеристик пациента с этим соматическим заболеванием.

По итогам обзора литературы в психологическом портрете пациента с ЖКБ были выявлены следующие тенденции: 1) забота о благополучии окружающих, что проявляется в сострадании, самопожертвовании и альтруизме; 2) трудолюбие, сосредоточенность на материальной обеспеченности, озабоченность должностными обязанностями, властность, перфекционизм, авторитарные родители; 3) склонность следовать социальным и профессиональным правилам, даже за счет ущемления собственных интересов, что становится источником недовольства и фрустрации и вызывает чувство несправедливости, мучительные раздумья, чувство тревожности и напряжения, нежелание идти на конфликт.Исследованные нами пациенты с ЖКБ имели такие черты характера как амбициозность, трудолюбие, наряду с желанием помогать другим, даже ущемляя собственные интересы.Все пациенты имели авторитарных родителей и проблемы
The results of study of hydrogeological conditions of oil and gas bearing deposit of the southern areas of Ob-Irtysh interfluves (southern regions of West Siberian basin) are presented. The hydrodynamic field is characterized by direct dependence and the presence of normal and increased pressure (formation anomalous pressure factor not exceed 1.13) is common in Apt-Alb-Cenomanian, Neokomian, Jurassic and pre-Jurassic complexes. The results of study of the reservoir properties and hydrodynamic conditions indicated that the elision water exchange play the dominant role in the modern hydrogeological structure formation. Two types of water drive system is established: elisional (lithostatical and termodehydrational) in the inner areas (southern part of Koltogor-Nyurolsky trench, Nyurolskaya megadepression, Verkhnevasyugansk anteclise and other structures) and infiltrational within the territory of Baraba-Pikhtovo monocline. Elisional system is replaced by the elisional-termodehydrational at the depth 2.0-2.2 km. Large piezo maximum zones (southern part of Koltogor-Nyurolsky trench and Nyurolskaya megadepression) become the inner regions of water pressure generation (the inner feed areas) with the maximal degree of hydrogeological closure of the interior. The region of piezo minima, tracing the structures of the Barabinsk-Pikhtovskaya megamonocline, relates to the external feed area. The hydrodynamic model of the southern areas of Ob-Irtysh interfluves is building for the first time and allow to predict the pressure change trends in the areas with poorly provided with the actual data.
The significant progress observed in the field of artificial economy opens up new possibilities for modeling economic growth. Agent-based models (ABM) allow leaving the concept of a representative agent in the past and linking investment decisions of economic agents at the micro level with long-term macroeconomic growth. Modern ABMs offer new algorithms for modeling expectations, agent interaction, technical progress, pricing, and production planning. Our article analyzes the current state of modeling investment in fixed assets in operating macroeconomic ABMs. The subject of the review is the families of models Eurace, CATS, KS, Jamel, Lagom. The authors also present the investment block of the agent-based multiregional input-output model (ABMIOM) being developed. Comparative analysis demonstrates that modern ABMs, as a rule, implement the principle of stock-flow consistency. Modeling the investment process requires detailing the commodity nomenclature, so that the initially adopted two-sector division into investment and consumer goods is replaced by more detailed structures, which gives rise to the problem of accounting for inter-sectoral relations in production and consumption. The Leontief production function copes with this problem, which is confirmed by its widespread use in ABM. The size of firms' investments is often derived from the need to expand capacity in accordance with the current production plan, so that planning turns out to be myopic, and long-term aspects in ABM are still largely unrealized. Nevertheless, already now ABMs reproduce many phenomena associated with the economic cycle. The developed ABMIOM provides horizontal consistency of cash flows between agents and analysis of results using input-output tables. ABMIOM represents a step forward in reflecting intersectoral and interregional flows. The model reproduces the growth and contraction of the economy as a result of independent investment decisions of individual firms and households, which is reflected in the sectoral and spatial structure of the economy. Further development of ABMIOM is associated with the modeling of savings, intrafirm finance, money market, innovation and technical progress.
The results of numerical studies of the interaction of a detonation wave and an electron beam with supersonic reacting flows in channel of various configurations like channel with backward-facing step, symmetrical channel with abrupt expansion and channel with a cavity are presented. A mathematical technology has been created to implement such interaction based on the ANSYS Fluent software. The flow parameters at the outlet of the channel are compared for different channel configurations and ignition initiation ways. The possibility is shown to intensify the ignition in a supersonic flow by electron beams and pulsating detonation. The possibility is identified to use a cavity for stabilizing the combustion in a supersonic combustion chamber when exposed to a detonation wave.
Neuroimaging studies have revealed a multitude of brain regions associated with self- and other-referential processing, but the question how the distinction between self, close other, and distant other is processed in the brain still remains unanswered. The default mode network (DMN) is the primary network associated with the processing of self, whereas task-positive networks (TPN) are indispensable for the processing of external objects. We hypothesize that self- and close-other-processing would engage DMN more than TPN, whereas distant-other-processing would engage TPN to a greater extent. To test this hypothesis, we used functional magnetic resonance imaging (fMRI) functional connectivity data obtained in the course of a trait adjective judgment task while subjects evaluated themselves, the best friend, a neutral stranger, and an unpleasant person. A positive association between the degree of self-relatedness and the degree of DMN dominance was revealed in cortical midline structures (CMS) and the left lateral prefrontal cortex. Relative to TPN, DMN showed greater connectivity in me than in friend, in friend than in stranger, and in stranger than in unpleasant conditions. These results show that the less the evaluated person is perceived as self-related, the more the balance of activity in the brain shifts from the DMN to the TPN.
The role of TRP ion channels in the physiological processes is far from clear.

In this work we studied the effect of the activation of the peripheral TRPM8 ion channel by its agonist menthol on the cardiovascular parameters in normotensive and hypertensive rats when animals were coming out of anesthesia.

The role of the TRPM8 ion channel in the regulation of blood pressure was clearly seen in normotensive animals: Activation of this channel by application of 1% menthol (agonist of TRPM8 ion channel) to skin significantly accelerated the increase in blood pressure and recovery of heart rate when animals come out of anesthesia. The mean rate of pressure rise increased 3 times under the menthol.
В статье представлен оригинальный подход в исследовании этнического менталитета тувинцев, который заключается в его феноменологическом описании. Подход строится на систематике соответствующих явлений, их типологии и классификации. В контексте формулируемых феноменологических теорий возможна не только индивидуализированная характеристика, но и эмпирическая диагностика менталитетов отдельных народов. В качестве фундаментальной базы для решения поставленной задачи используется творческое наследие выдающегося российско-американского социолога П. А. Сорокина, которое содержит развернутое феноменологическое учение о менталитетах культуры. Именно это учение лежит в основании анализа тувинского менталитета. Показано, что в категориях учения П. А. Сорокина социокультурная динамика менталитета тувинцев состоит в циклической смене псевдоидеационального и идеалистического менталитетов, из которых последний воспринимается как норма традиционной культуры.
South American histricognath rodents Thrichomys apereoides laurentius and Thrichomys pachyurus are natural hosts of Trypanosoma cruzi, agent of Chagas disease. We established breeding colonies of these species to serve as experimental models in various parasitological studies. Both species of Thrichomys have all the requirements necessary to become excellent laboratory models: they can be easily maintained in the standard laboratory conditions and breed throughout the year and they do not have any special dietary demands and can be fed by standard food pellets designed for laboratory mice. Both species produce precocious offspring that have their eyes and ears open, teeth erupted, fur well developed, and can eat solid food in the first week of life. T. a. laurentius has larger litter sizes and lower body masses at birth and weaning than T. pachyurus. Moreover, females of T. a. laurentius reach puberty earlier and with lower body mass than T. pachyurus.
In this paper, we consider an effect of incorrect accounting of the overburden structure and interfaces curvature on results of nonlinear AVO inversion. The research is carried out on synthetic data obtained using ray method for two- and three-layer models with convex and concave interfaces. We show that neglect of the overburden heterogeneity leads to inversion errors about 10–19 % and neglect of the reflector’s curvature to errors about 2 % for convex and 11 % for concave interfaces.
A fully-coupled 3D model of early stage of hydraulic fracture propagation is enriched by incorporating two submodels for simulation of fluid flow inside the fracture. The Herschel-Bulkley model is used to describe the flow of non-Newtonian fluid and the Reynolds equation is modified for compressible fluid flow simulation. Propagation of inclined hydraulically driven penny shaped fracture in the rock under multiaxial load is simulated. The influence of the fluid rheology and compressibility on the fluid pressure and the fracture form is shown.