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The aim of the study is to present an analysis of the lexical and grammatical means of expression of dominant assessment in the speech behavior of the Russian-speaking and English-speaking virtual language personality in blogs, depending on belonging to a particular gender. The research material is a card index of more than 200 posts of beauty bloggers on the social network in 2021. There were used 15 accounts of the Russian-speaking and 15 accounts of the English-speaking addressers. All blogger’s virtual language personalities position themselves on the Internet as men, transgender people (mtf – male-to-female) and women. In total more than 3,800 small syntactic groups have been analyzed. The following research methods were used in the work: the lexico-semantic, lexico-grammatical, and stylistic analyses, method of objective pragmalinguistic analysis combining modified content analysis and the comparison method. When studying the differences in the media speeches among the English- and Russian-speaking virtual communicative personalities, several lexical differences in the speeches of the women, men and transgender people were identified. Thus, among the Russian-speaking bloggers the highest percentage of negative attitudes and in general the brightest emotional coloring of lexis and grammar constructions was observed in the men’s media speech despite the widespread stereotype about the greater emotional intensity of women’s media speech. The women in their media speech tend to prevail in the formation of positive assessment. For the transgender people in blogs, all three indicators of the formation of assessment using lexical and grammatical means occupy a middle position between the media speech of the women and the men, which indicates the presence of female and male traits in the media speech of the transgender people. For the English-speaking virtual communicative personalities in the media speeches of the women and the men, all three indicators are approximately equal, while for the transgender people the index of the formation of a negative attitude using lexical and grammatical means is twice exceeded, and the indicator of the formation of a positive attitude through vocabulary is twice reduced. In general, the media speech of the English-speaking transgender people in blogs is characterized by a more open and more emotionally colored lexical and grammatical constructions in media speech. The transgender bloggers share all the events from their lives, regardless of whether they are positive or negative, which indicates maximum self-presentation and maximum attention of Internet users to their language personality and lifestyle among Internet users. It seems promising to consider the linguopragmatic aspect of gender self-presentation of virtual language personalities in blogs, to identify the main tactics of their self-presentation in media space.

Dermal fibroblast cell culture is a convenient model for studying various effects on cells, including hypoxia. Fibroblasts, in addition to collagen production, are able to synthesize biogenic amines, hormones, neuropeptides, and neurotransmitters identical to those in the central nervous and endocrine systems, which allows them to be used to study cellular disorders in various diseases. The purpose of the study was to evaluate the functional changes in the culture of dermal fibroblasts under hypoxic conditions using biochemical and molecular biological methods. In cells of fibroblast culture under normoxia (air and 5% CO2 in an incubator) and hypoxic exposure (a mixture of gases - 95% N2 and 5% CO2) at 1 and 3 hours, biochemical methods were used to determine the activity of aspartate aminotransferase (AsAT), alanine aminotransferase (AlAT), gamma-glutamyl transferase (GGT), lactate dehydrogenase (LDH), glucose levels, concentrations of ATP, ADP, AMP, as well as the level of mRNA expression of the hypoxia-induced factor Hif-1a and the nuclear factor Nf-κb by polymerase chain reaction. It was shown that under hypoxic exposure at 1 hour in fibroblast culture, cell viability, glucose levels and activity of LDH, AlAT, AsAT decrease, the amount of ATP decreases, after 3 hours there is a tendency to normalize all indicators. Adaptive mechanisms make it possible to normalize the functioning of cells under hypoxic conditions from 1 to 3 hours. The results obtained in the evaluation of metabolic changes at different times of hypoxic exposure (1 and 3 hours) in the culture of rat fibroblasts indicate a high adaptive capacity of connective tissue cells - fibroblasts at a lack of oxygen. The study of intracellular parameters during hypoxia, the determination of critical points depending on the time of exposure will determine the directions for further study of the mechanisms of cell adaptation, which, perhaps, will complement the tactics of compensatory effects in ischemia of tissues of various genesis. The revealed changes reflect the adaptive response of the fibroblast culture in response to hypoxic exposure.

The article for the fi rst time carried out a comprehensive analysis of the architecture of rural houses of clergymen in the middle Volga region and the Southern Urals in the 19th - early 20th century. The materials of construction, planning, composition and stylistic features of the architecture of these buildings in the region have been studied. Houses made by local carpenters and designed in St. Petersburg are considered. Changes in the architecture of such buildings over time have been revealed. Examples and descriptions of the architecture of diff erent types of wooden houses of clergymen are given. The most detailed complex of buildings at the church of Nicholas the Wonderworker in the village of Epifanovka. The features of the interweaving of “red-brick” and neo-Russian architectural styles in the decoration of the buildings of this complex have been analyzed.

A study done at the expense of the State program of the Russian Federation “Science and technology” in the framework of the plan of basic scientifi c research Ministry of Russia and the RUSSIAN. In the article, an att empt has been made to the analysis of a wide range of issues related to the formation of the rural architecture of Orthodox churches in the territory of the Middle Volga region in the 19th century. Considered layout, composition and stylistic features of the architecture of Orthodox churches in the region. Peculiarities of regional religious architecture of the Middle Volga region. Provides extensive material fi eld surveys.

Multicultural mentality, formed in the Republic of North Ossetia-Alania, reflects the vectors of the state language policy of the Russian Federation, carried out in conditions of ethno cultural diversity. Philosophical understanding of bilingualism allows you to show the axiological and value-oriented functions of the native and second languages in the territory of compact residence of various ethnic groups. The study is carried out in an interdisciplinary manner, based on the achievements of the philosophy of language, political linguistics, and theoretical developments in the fields of cognitive and sociolinguistics, linguoculturology, bi- and polylingualism. A multifaceted Ossetian and Russian-language material, including data from parliamentary and government sites of North and South Ossetia, the results of a blitz survey of the population and the texts of genres of official congratulations, information messages and slogans, is at the heart of the search. The article is aimed at demonstrating the established conceptual field of ethnic community within the multicultural communicative space in the republics of ethnic Ossetians – North and South Ossetia, developed because of the application of a common humanitarian strategy for the preservation and development of all languages and cultures.

This article analyses linguistic, cultural, and cognitive aspects of the image “businesswoman” in the French language. The target of this article is to study the features of the concept “business woman” in French media discourse and the representation of this concept in French linguistic culture. The linguistic units that verbalize the concept “businesswoman” in French media discourse are described. The representative and axiological characteristics of the concept of businesswoman in the French language are defined. The article presents a multi-faceted analysis of the concept “businesswoman”. The main modes of verbal exteriorization of the concept “businesswoman” with the help of the French language means are studied. The most important cognitive stereotypes are identified. These cognitive stereotypes serve as the reproduction base for the analyzed concept in the French language. It has been proved that the structures of the verbal exteriorization of the concept reflect the main model of a businesswoman in French cultural linguistics.

The article examines the materials of the beginning of the Migration period from the Biklyan’ settlement, located in the Lower Kama region. The area of 100 m2 was excavated in 2018, where a rectangular structure slightly deepened into subsoil loam with a large pit in the central part was revealed. The finds are mainly represented by fragments of ceramics, as well as an iron sickle, spinning whorls, a fragment of a crucible and ceramic objects of unknown purpose. The artifacts from the Biklyan’ settlement have close analogies in the materials of the sites dated to the beginning of the Migration period in the Middle Volga region (3rd–4th centuries CE) and reflect the traditions of several different population groups. The bulk of the ceramics collection is similar to the vessels of the Middle Volga variant of the Kiev culture; there are also fragments that find analogies in the assemblages of the forest-steppe peripheral sites of the Late Sarmatian world and in the simultaneous cultures of the Kama region. Stratigraphic records and radiocarbon dating testify in favor of the relatively short-term functioning of the site in the late 3rd – early 4th centuries.

The Beganchik locality is a stratigraphic sequence of loessic deposits, pedogenic horizons and Paleolithic occupations located at the Kama-Volga confluence. The sequence is exposed on a bluff formed on the west side of an erosional remnant between the Kuybyshev Reservoir and the former channel of the Aktay River. Although the site is known for its Terminal Paleolithic-Mesolithic occupations of the Pleistocene-Holocene transition, evidence of older occupations and remains of fauna has been identified. Our research team identified evidence of human presence associated with a pedogenic horizon of MIS 3 age. Two AMS radiocarbon ages from a hearth produced ages around 47 000 years BP. Pollen and phytoliths from two soils horizons, including the one associated with the hearths indicate a steppe environment coincident with the formation of correlative soils elsewhere in the Russian Plain.

The article establishes the linguacultural gender specifics of the British song slang. All languages are constantly changing, slang invades the vocabulary of people (male and female). Of research, interest is the definition of slang, its origin, the vital need for human communication. The purpose of the study is to identify the gender characteristics of British song slang. Slang as a language system of modern linguistics is considered. In the article, main features and gender characteristics of British slang are described. The authors analyze the song slang of female and male performers and compare the song slang of performers of both sexes. The methods of research are descriptive method, comparative analysis, definitional analysis, lexical and semantic analysis, lexical and grammatical analysis, stylistic analysis, interpretive analysis, quantitative analysis, involving a continuous sample. The material of the study was songs by modern British male and female performers. The theoretical significance of the study is to identify the features of modern British song slang. Research results contribute to the development of lexicology and stylistics of the English language, to contrastive linguistics, linguoculturology. The establishment of the gender specificity of British musical slang contributes to the development of linguistic gender studies. The practical application of the research results is revealed in the possibility of teaching courses in English lexicology, stylistics, and gender linguistics, as well as compiling a linguistic dictionary of modern musical culture.

Using human chromosome 18 (Ch18) genes as an example, a PCR analysis of the interindividual variability of gene expression in liver tissue was performed. Although the quantitative profiles of the Ch18 transcriptome, expressed in the number of cDNA copies per single cell, showed a high degree of correlation between donors (Pearson correlation coefficients ranged from 0.963 to 0.966), the expression of the significant number of genes (from 13% to 19%, depending on the method of experimental data normalization) varied by more than 4-fold when comparing donors pairwise. At the same time, the proportion of differentially expressed genes increased with a decrease in the level of their expression. It is shown that the higher quantitative variability of low-abundance transcripts is mainly not technical, but biological. Bioinformatic analysis of the interindividual variability of the differential expression of chromosome 18 genes in human liver tissue did not reveal any statistically significant groups of genes related to certain biological processes that indicated a rather transient nature of the interindividual variability of their expression, probably reflecting the response of cells of an individual to specific external stimuli.Na primere khromosomy 18 cheloveka proveden PTsR-analiz mezhindividual'noĭ variabel'nosti ékspressii 244 genov v tkani pecheni. V tselom kolichestvennye profili transkriptoma khromosomy 18, vyrazhennye v kolichestve kopiĭ kDNK na edinichnuiu kletku, pokazyvaiut vysokuiu stepen' korreliatsii (rp=0,963-0,966). Odnako pri poparnom sravnenii donorov ékspressiia sushchestvennogo kolichestva genov (ot 13% do 19% v zavisimosti ot sposoba normirovki éksperimental'nykh dannykh) razlichaetsia bolee chem 4-kratno. Pri étom dolia differentsial'no ékspressirovannykh genov vozrastaet s ponizheniem urovnia ikh ékspressii. Bolee vysokaia kolichestvennaia variabel'nost' nizkopredstavlennykh transkriptov imeet v osnovnom ne tekhnicheskuiu, a biologicheskuiu prichinu. Bioinformaticheskiĭ analiz mezhindividual'noĭ variabel'nosti differentsial'noĭ ékspressii genov khromosomy 18 v tkani pecheni cheloveka ne vyiavil kakikh-libo statisticheski znachimykh grupp genov, otnosiashchikhsia k opredelennym biologicheskim protsessam. Éto, po-vidimomu, ukazyvaet na vremennuiu prirodu mezhindividual'noĭ variabel'nosti ikh ékspressii, veroiatno, otrazhaiushchuiu reaktsiiu kletok dannogo individuuma na konkretnye vneshnie stimuly.

The study was carried out at the expense of the State Program of the Russian Federation “Development of Science and Technology” for 2013-2020 in the framework of the Plan of Basic Scientifi c Research of the Ministry of Construction of Russia and the RAASN, topic 1.2.14. The article att empts to analyze a wide range of issues related to the formation of the architecture of rural Orthodox churches in the middle Volga region in the 18th century. The layout, composition and stylistic features of the architecture of the region’s Orthodox churches are considered. The features of the regional religious architecture of the Middle Volga region are revealed. The extensive material of fi eld surveys is presented.

This article examines the ideological and aesthetic peculiarities of autobiographical writing in “La Place” by Annie Ernaux, a well-known contemporary French writer. We argue that Annie Ernaux 's “flat writing” is close to a sociological or ethnographic study and nearly devoid of any autobiographical subjectivity. Autobiographical writing is approached through the concept of symbolic violence, borrowed from the sociologist P. Bourdieu. Ernaux indeed replaces event history, a feature of autobiography, by the study of socio-historical causes of “class distancing” between father and daughter. The analysis of key concepts of the Ernaux's poetics makes it possible, on the one hand, to grasp the appearance of social and cultural alienation and, on the other hand, to achieve a social criticism of reality.

The growth in the role of the military sector of certain Soviet states in the overall structure of the national economy, to the detriment of other sectors, along with providing military assistance ...

Within the Human Proteome Project initiative framework for creating functional annotations of uPE1 proteins, the neXt-CP50 Challenge was launched in 2018. In analogy with the missing-protein challenge, each command deciphers the functional features of the proteins in the chromosome-centric mode. However, the neXt-CP50 Challenge is more complicated than the missing-protein challenge: the approaches and methods for solving the problem are clear, but neither the concept of protein function nor specific experimental and/or bioinformatics protocols have been standardized to address it. We proposed using a retrospective analysis of the key HPP repository, the neXtProt database, to identify the most frequently used experimental and bioinformatic methods for analyzing protein functions, and the dynamics of accumulation of functional annotations. It has been shown that the dynamics of the increase in the number of proteins with known functions are greater than the progress made in the experimental confirmation of the existence of questionable proteins in the framework of the missing-protein challenge. At the same time, the functional annotation is based on the guilty-by-association postulate, according to which, based on large-scale experiments on API-MS and Y2H, proteins with unknown functions are most likely mapped through “handshakes” to biochemical processes.

The beginning of the twenty-first century witnessed novel breakthrough research directions in the life sciences, such as genomics, transcriptomics, translatomics, proteomics, metabolomics, and bioinformatics. A newly developed single-molecule approach addresses the physical and chemical properties and the functional activity of single (individual) biomacromolecules and viral particles. Within the alternative approach, the combination of “single-molecule approaches” is opposed to “omics approaches”. This new approach is fundamentally unique in terms of its research object (a single biomacromolecule). Most studies are currently performed using postgenomic technologies that allow the properties of several hundreds of millions or even billions of biomacromolecules to be analyzed. This paper discusses the relevance and theoretical, methodological, and practical issues related to the development potential of a single-molecule approach using methods based on molecular detectors.

In metabolomics, many metabolites are measured simultaneously in a single run. Such analytical performance opens up prospects for clinical laboratory diagnostics. In this work, a mass spectrometric metabogram was developed as a simplified and clinically applicable way of measuring the blood plasma metabolome. To develop the metabogram, blood plasma samples from healthy male volunteers (n = 48) of approximately the same age, direct infusion mass spectrometry (DIMS) of the low molecular fraction of samples, and principal component analysis (PCA) of the mass spectra were used. The seven components of the metabogram defined by PCA, which cover ~70% of blood plasma metabolome variability, were characterized using a metabolite set enrichment analysis (MSEA) and clinical test results of participating volunteers. It has been established that the components of the metabogram are functionally related groups of the blood metabolome associated with regulation, lipid–carbohydrate, and lipid–amine blood components, eicosanoids, lipid intake into the organism, and liver function thereby providing a lot of clinically relevant information. Therefore, metabogram provides the possibility to apply the metabolomics performance in the clinic. The features of the metabogram are also discussed in comparison with the thin-layer chromatography and with the analysis of blood metabolome by liquid chromatography combined with mass spectrometry.

A meta-analysis of the results of targeted quantitative screening of human blood plasma was performed to generate a reference standard kit that can be used for health analytics. The panel included 53 of the 296 proteins that form a “stable” part of the proteome of a healthy individual; these proteins were found in at least 70% of samples and were characterized by an interindividual coefficient of variation

The main goal of the Russian part of C-HPP is to detect and functionally annotate missing proteins (PE2-PE4) encoded by human chromosome 18. However, identifying such proteins in a complex biological mixture using mass spectrometry (MS)-based methods is difficult due to the insufficient sensitivity of proteomic analysis methods. In this study, we determined the proteomic technology sensitivity using a standard set of UPS1 proteins as an example. The results revealed that 100% of proteins in a mixture could only be identified at a concentration of at least 10−9 M. The decrease in concentration leads to protein losses associated with technology sensitivity, and no UPS1 protein is detected at a concentration of 10−13 M. Therefore, two-dimensional fractionation of samples was applied to improve sensitivity. The human liver tissue was examined by selected reaction monitoring and shotgun methods of MS analysis using one-dimensional and two-dimensional fractionation to identify the proteins encoded by human chromosome 18. A total of 134 proteins were identified. The overlap between proteomic and transcriptomic data in human liver tissue was ~50%. This weak convergence is due to the low sensitivity of proteomic technology compared to transcriptomic approaches. Data is available via ProteomeXchange with identifier PXD026997.

Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a. single gene often have different functions, which implies different protein partners. By interacting with each other, proteoforms create a. network reflecting the dynamics of cellular processes in an organism. Perturbations of protein-protein interactions change the network topology, which often triggers pathological processes. Studying proteoforms is a. relatively new research area in proteomics, and this is why there are comparatively few experimental studies on the interaction of proteoforms. Bioinformatics tools can facilitate such studies by providing valuable complementary information to the experimental data and, in particular, expanding the possibilities of the studies of proteoform interactions.

There is a fierce competitive fight for innovation and talent all over the world. As we know, talented and competent personnel appear in higher education and scientific research. Now, the country’s competitiveness depends both on its ability to realize the innovative potential, and on the ability to respond to global challenges – environmental, social, epidemiological, etc. In this regard, the experience of France, associated with its ambitious goals, to take a leading position in the field of R&D, to update the formation mechanism within the country and attract talented researchers, to strengthen research potential, to develop institutional forms of support for innovation and to attract public and private investment, looks quite interesting. The most important thing for us is a specific toolkit for resolving the contradictions of accumulated problems in French society to develop the processes of research and innovation as a whole. At present, serious discussions are underway on the government’s draft Law on the long-term programming of scientific research, and in this article, we present the results of these disputes.

This paper proposes a method of comparative analysis of scientific trajectories based on bibliographic profiles. The bibliographic profile ("meshprint") is a list of MeSH terms (key terms used to index articles in the PubMed), indicating the relative frequency of occurrence of each term in the scientist's articles. Comparison of personalized bibliographic profiles can be represented in the form of a semantic network, where the nodes are the names of scientists, and the relationships are proportional to the calculated measures of similarity of bibliographic profiles. The proposed method was used to analyze the semantic network of scientists united by the academic school of the academician A.I. Archakov. The results of the work allowed us to show the relationship between the scientific trajectories of one scientific school and to correlate the results with world trends.Predlozhen metod sravnitel'nogo analiza nauchnykh traektoriĭ uchenykh na osnove bibliograficheskogo profilia (t.n. “meshprint”), kotoryĭ predstavliaet soboĭ perechen' terminov MeSH (kliuchevye terminy, ispol'zuemye dlia indeksatsii stateĭ v biblioteke biomeditsinskikh tekstov PubMed) s ukazaniem otnositel'noĭ chastoty vstrechaemosti kazhdogo termina v stat'iakh uchenogo. Sopostavlenie personalizirovannykh bibliograficheskikh profileĭ mozhno predstavit' v vide semanticheskoĭ seti, gde uzlami iavliaiutsia familii uchenykh, a sviazi proportsional'ny rasschitannym meram skhodstva bibliograficheskikh profileĭ. Dannyĭ metod byl ispol'zovan dlia analiza semanticheskoĭ seti uchenykh, ob"edinennykh nauchnoĭ shkoloĭ akademika A.I. Archakova. Rezul'taty raboty pozvolili pokazat' vzaimosviazi mezhdu nauchnymi traektoriiami odnoĭ nauchnoĭ shkoly i sootnesti rezul'taty s mirovymi trendami razvitiia nauchnykh napravleniĭ.

The Chromosome-centric Human Proteome Project aims at characterizing the expression of proteins encoded in each chromosome at the tissue, cell, and subcellular levels. The proteomic profiling of a particular tissue or cell line commonly results in a substantial portion of proteins that are not observed (the "missing" proteome). The concurrent transcriptome profiling of the analyzed tissue/cells samples may help define the set of untranscribed genes in a given type of tissue or cell, thus narrowing the size of the "missing" proteome and allowing us to focus on defining the reasons behind undetected proteins, namely, whether they are technical (insufficient sensitivity of protein detection) or biological (correspond to not-translated transcripts). We believe that the quantitative polymerase chain reaction (qPCR) can provide an efficient approach to studying low-abundant transcripts related to undetected proteins due to its high sensitivity and the possibility of ensuring the specificity of detection via the simple Sanger sequencing of PCR products. Here we illustrated the feasibility of such an approach on a set of low-abundant transcripts. Although inapplicable to the analysis of whole transcriptome, qPCR can successfully be utilized to profile a limited cohort of transcripts encoded on a particular chromosome, as we previously demonstrated for human chromosome 18.

This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the "dark part" of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.

The paper features the results of a comprehensive study of the fortifications of the Troitskii-Urai I hillfort. An analysis of a rampart section using the archaeological, geomorphological, palynological and soil science methods has made it possible to draw the following conclusions. The hillfort was built at the site of a community of the Bronze Age – the beginning of the Early Iron Age (12th – 9th centuries B.C.), and the rampart is connected to a saddle, which became an additional element of fortification. Two stages of the rampart’s construction were identified, which was completed by the population of the Post-Maklasheevka culture of Ananyino cultural and historical area. The early rampart is dated the 8th – 5th centuries B.C., and the late rampart was constructed in late 5th – 3rd/2nd centuries B.C. No information on the participation of representatives of the Imenkovo and Bolgar pre-Mongol cultures in the construction of the rampart has been revealed in this section. Throughout the entire period of the hillfort’s existence in the Early Iron Age, its inhabitants were engaged in agriculture, and the predominant consumed food items at its initial and late stages were fish and meat, respectively. The Troitskii-Urai II hillfort was built to the west of the Troitskii-Urai I hillfort in the Imenkovo period (4th –6th centuries).The second one significantly differs in terms of rampart morphology.

An experimental slash-and-burn (SABC) site and a site included in the cycle of SABC in 19th century were used as a reference to describe a signature of this cultivation method in sandy soils. Documented slash-and-burn layers were compared to pyrogenic layers from other sites and time periods in attempt to differentiate between results of slash-and-burn cultivation and wild fires. The swidden layers in sandy soils appeared as 5 to 10- cm thick, dark-coloured “humus” layers with a characteristic scalloped lower boundary, formed by numerous constructions of fossorial insects, predominantly sweat bees. The dark coloration originates from high concentrations of charcoal fragments with a median length of 4 to 5 mm, pebbly shape and silt coating, uniformly distributed within the swidden layers. A low proportion of bark and presence of foliage (buds and needles) in charcoal assemblages are characteristic for SABC layers. The phytolith content of SABC layers varied from tens to hundreds of thousands per gram of soil, with up to 50% of phytoliths being charred. The SABC layers contained dendritic and/or panicoid phytoliths and cereal glumes and paleas indicative of in situ cultivation of crops. The palynological signature of swiddens is a pollen spectrum of forest ecosystem with a proportion of fire-dependant taxa, such as Onagraceae pollen and Marshantia spores.

The article presents the results of the study of the hillfort at Bolshie Algashi village (Chuvashia, Russia) conducted in 2016–17. The study provides new data on the cultural and economic dynamics in the region during the Bronze and Early Iron Ages. A mixed group of Khula-Syuch and Chirki population can be identified as pastoralists and, probably, also farmers, who developed floodplains and forestless landscapes of the elevated riverbanks. Our research, therefore, provides evidence of almost the oldest farming activity episode in the lower reaches of the Sura River. The Early Iron Age occupation of the site is associated with the Andreevka-Piseraly population, who used the site mostly for its military functions.

The existing clinical laboratory practice has limitations in terms of specificity and sensitivity of diagnosis, making the introduction of new methods in medicine more topical. Application of ‘omics’ technologies, especially metabolomics, allows overcoming these limitations. The composition of blood metabolites reflects the physical state of an organism at the molecular level. The analysis of blood metabolome can serve as effective means of diagnosis, implementation of which in healthcare is timely and relevant. This paper demonstrates the versatility of metabolomic diagnostics, its applicability to various diseases. We discussed the standard of human digital image, which includes the metabolomic data sufficient to make an accurate assessment of general health and carry out precision diagnostics of a wide range of diseases.

The paper describes a scheme for the comparative analysis of the sets of Pubmed publications. The proposed analysis is based on the comparison of the frequencies of occurrence of keywords-MeSH terms. The purpose of the analysis is to identify MeSH terms that characterize research areas specific to each group of articles, as well as to identify trends-topics on which the number of published works has changed significantly in recent years. The proposed approach was tested by comparing a set of medical publications and a group of articles in the field of personalized medicine. We analyzed about 700 thousand abstracts published in the period 2009-2021 and indexed them with MeSH terms. Topics with increasing research interest have been identified both in the field of medicine in general and specific to personalized medicine. Retrospective analysis of the keywords frequency of occurrence changes has shown the shift of the scientific priorities in this area over the past 10 years. The revealed patterns can be used to predict the relevance and significance of the scientific work direction in the horizon of 3-5 years. The proposed analysis can be scaled in the future for a larger number of groups of publications, as well as adjusted by introducing filters at the stage of sampling (scientific centers, journals, availability of full texts, etc.) or selecting a list of keywords (frequency threshold, use of qualifiers, category of generalizations).The online version contains supplementary material available at 10.1007/s11192-022-04292-y.

The cutoff level applied in sequencing analysis varies according to the sequencing technology, sample type, and study purpose, which can largely affect the coverage and reliability of the data obtained. In this study, we aimed to determine the optimal combination of parameters for reliable RNA transcriptome data analysis. Toward this end, we compared the results obtained from different transcriptome analysis platforms (quantitative polymerase chain reaction, Illumina RNASeq, and Oxford Nanopore Technologies MinION) for the transcriptome encoded by human chromosome 18 (Chr 18) using the same sample types (HepG2 cells and liver tissue). A total of 275 protein-coding genes encoded by Chr 18 was taken as the gene set for evaluation. The combination of Illumina RNASeq and MinION nanopore technologies enabled the detection of at least one transcript for each protein-coding gene encoded by Chr 18. This combination also reduced the probability of false-positive detection of low-copy transcripts due to the simultaneous confirmation of the presence of a transcript by the two fundamentally different technologies: short reads essential for reliable detection (Illumina RNASeq) and long-read sequencing data (MinION). The combination of these technologies achieved complete coverage of all 275 protein-coding genes on Chr 18, identifying transcripts with non-zero expression levels. This approach can improve distinguishing the biological and technical reasons for the absence of mRNA detection for a given gene in transcriptomics.

The chromosome-centric dataset was created by applying several technologies of transcriptome profiling. The described dataset is available at NCBI repository (BioProject ID PRJNA635536). The dataset referred to the same type of tissue, cell lines, transcriptome sequencing technologies, and was accomplished in a period of 8 years (the first data were obtained in 2013 while the last ones - in 2020). The high-throughput sequencing technologies were employed along with the quantitative PCR (qPCR) approach, for data generation using the gene expression level assessment. qPCR was performed for a limited group of genes, encoded on human chromosome 18, for the Russian part of the Chromosome-Centric Human Proteome Project. The data of high-throughput sequencing are provided as Excel spreadsheets, where the data on FPKM and TMP values were evaluated for the whole transcriptome with both Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing.

Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of proteins encoded by human Chr18 genes. Within half a year, since the January 2020 version of NextProt, the number of entries in the MP+uPE1 datasets changed, mainly due to the achievements of antibody-based proteomics. Assuming that the proteome is closely related to the transcriptome scaffold, quantitative PCR, Illumina HiSeq, and Oxford Nanopore Technology were applied to characterize the liver samples of three male donors in comparison with the HepG2 cell line. The data mining of the Expression Atlas (EMBL-EBI) and the profiling of biopsy samples by using orthogonal methods of transcriptome analysis have shown that in HepG2 cells and the liver, the genes encoding functionally uncharacterized proteins (uPE1) are expressed as low as for the missing proteins (less than 1 copy per cell), except the selected cases of HSBP1L1, TMEM241, C18orf21, and KLHL14. The initial expectation that uPE1 genes might be expressed at higher levels than MP genes, was compromised by severe discrepancies in our semi-quantitative gene expression data and in public databanks. Such discrepancy forced us to revisit the transcriptome of Chr18, the target of the Russian C-HPP Consortium. Tanglegram of highly expressed genes and further correlation analysis have shown the severe dependencies on the mRNA extraction method and the analytical platform. Targeted gene expression analysis by quantitative PCR (qPCR) and high-throughput transcriptome profiling (Illumina HiSeq and ONT MinION) for the same set of samples from normal liver tissue and HepG2 cells revealed the detectable expression of 250+ (92%) protein-coding genes of Chr18 (at least one method). The expression of slightly more than 50% protein-coding genes was detected simultaneously by all three methods. Correlation analysis of the gene expression profiles showed that the grouping of the datasets depended almost equally on both the type of biological material and the experimental method, particularly cDNA/mRNA isolation and library preparation., Отсутствующие белки и функционально не охарактеризованные белки (в англоязычной литературе обозначенные как missing (MP) и functionally uncharacterized proteins (uPE1), соответственно) составляют менее 5% от общего числа белков, кодируемых генами 18 хромосомы человека. В течение полугода, начиная с января 2020 года, в версии NextProt выросло количество записей в наборах данных MP+uPE1. Подобные изменения обусловлены преимущественно достижениями протеомики на основе антител. В данной работе количественная ПЦР, технологии секвенирования Illumina HiSeq и Oxford Nanopore Technologies были применены для сравнительного анализа транскриптомного профиля образцов печени трех доноров мужского пола и клеточной линии HepG2. Анализ данных атласа экспрессии (Expression Atlas, EMBL-EBI) и полученных результатов по биологическим образцам с использованием ортогональных методов анализа транскриптома показал, что в клетках печени и HepG2 уровень экспрессии генов, кодирующих функционально не охарактеризованные белки (uPE1), находится на таком же низком уровне, как и в случае генов MP (в количестве менее 1 копии на клетку). Исключение составили несколько генов: HSBP1L1, TMEM241, C18orf21 и KLHL14. Согласно существенным расхождениям в ранее полученных полуколичественных данных по экспрессии генов и данным в открытых базах данных, изначально предполагалось, что экспрессия генов uPE1 может быть выше, чем генов MP. Подобное расхождение побудило обратиться к транскриптому 18 хромосомы человека, являющейся целевой для России в проекте «Протеом человека». Полученные результаты о наиболее экспрессируемых генах и дальнейший корреляционный анализ показал существование зависимости от метода экстракции мРНК и аналитической платформы. Анализ экспрессии целевых генов 18 хромосомы с применением количественной ПЦР (qPCR) и методов высокопроизводительного профилирования транскриптома (Illumina HiSeq и ONT MinION) для одинаковых наборов образцов нормальной ткани печени и клеточной линии HepG2 выявил более 250 (92%) белок-кодирующих генов, детектируемых хотя бы одним методом. Экспрессия более чем 50% белок-кодирующих генов была детектирована всеми тремя методами. Корреляционный анализ профилей экспрессии генов показал, что результаты «группируются» в зависимости от типа биологического материала и экспериментальных методов, в частности от способа подготовки библиотеки (выделения кДНК, мРНК). Зависимость от выбора способа биоинформатической обработки была отмечена в значительно меньшей степени.

We used automatic text-mining of PubMed abstracts of papers related to obesity, with the aim of revealing that the information used in abstracts reflects the current understanding and key concepts of this widely explored problem. We compared expert data from DisGeNET to the results of an automated MeSH (Medical Subject Heading) search, which was performed by the ScanBious web tool. The analysis provided an overview of the obesity field, highlighting major trends such as physiological conditions, age, and diet, as well as key well-studied genes, such as adiponectin and its receptor. By intersecting the DisGeNET knowledge with the ScanBious results, we deciphered four clusters of obesity-related genes. An initial set of 100+ thousand abstracts and 622 genes was reduced to 19 genes, distributed among just a few groups: heredity, inflammation, intercellular signaling, and cancer. Rapid profiling of articles could drive personalized medicine: if the disease signs of a particular person were superimposed on a general network, then it would be possible to understand which are non-specific (observed in cohorts and, therefore, most likely have known treatment solutions) and which are less investigated, and probably represent a personalized case.

One of the main goals of the Chromosome-Centric Human Proteome Project (C-HPP) is detection of "missing proteins" (PE2-PE4). Using the UPS2 (Universal proteomics standard 2) set as a model to simulate the range of protein concentrations in the cell, we have previously shown that 2D fractionation enables the detection of more than 95% of UPS2 proteins in a complex biological mixture. In this study, we propose a novel experimental workflow for protein detection during the analysis of biological samples. This approach is extremely important in the context of the C-HPP and the neXt-MP50 Challenge, which can be solved by increasing the sensitivity and the coverage of the proteome encoded by a particular human chromosome. In this study, we used 2D fractionation for in-depth analysis of the proteins encoded by human chromosome 18 (Chr 18) in the HepG2 cell line. Use of 2D fractionation increased the sensitivity of the SRM SIS method by 1.3-fold (68 and 88 proteins were identified by 1D fractionation and 2D fractionation, respectively) and the shotgun MS/MS method by 2.5-fold (21 and 53 proteins encoded by Chr 18 were detected by 1D fractionation and 2D fractionation, respectively). The results of all experiments indicate that 111 proteins encoded by human Chr 18 have been identified; this list includes 42% of the Chr 18 protein-coding genes and 67% of the Chr 18 transcriptome species (Illumina RNaseq) in the HepG2 cell line obtained using a single sample. Corresponding mRNAs were not registered for 13 of the detected proteins. The combination of 2D fractionation technology with SRM SIS and shotgun mass spectrometric analysis did not achieve full coverage, i.e., identification of at least one protein product for each of the 265 protein-coding genes of the selected chromosome. To further increase the sensitivity of the method, we plan to use 5-10 crude synthetic peptides for each protein to identify the proteins and select one of the peptides based on the obtained mass spectra for the synthesis of an isotopically labeled standard for subsequent quantitative analysis. Data are available via ProteomeXchange with the identifier PXD019263.

Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of human Chr18 genes. Within half a year, since the January 2020 version of NextProt, the number of entries in the MP+uPE1 datasets has changed, mainly due to the achievements of antibody-based proteomics. Assuming that the proteome is closely related to the transcriptome scaffold, quantitative PCR, Illumina HiSeq, and Oxford Nanopore Technology were applied to characterize the liver samples of three male donors compared with the HepG2 cell line. The data mining of Expression Atlas (EMBL-EBI) and the profiling of our biospecimens using orthogonal methods of transcriptome analysis have shown that in HepG2 cells and the liver, the genes encoding functionally uncharacterized proteins (uPE1) are expressed as low as for the missing proteins (less than 1 copy per cell), except for selected cases of HSBP1L1, TMEM241, C18orf21, and KLHL14. The initial expectation that uPE1 genes might be expressed at higher levels than MP genes, was compromised by severe discrepancies in our semi-quantitative gene expression data and in public databanks. Such discrepancy forced us to revisit the transcriptome of Chr18, the target of Russian C-HPP Consortia. Tanglegram of highly expressed genes and further correlation analysis have shown the severe dependencies on the mRNA extraction method and analytical platform.Targeted gene expression analysis by quantitative PCR (qPCR) and high-throughput transcriptome profiling (Illumina HiSeq and ONT MinION) for the same set of samples from normal liver tissue and HepG2 cells revealed the detectable expression of 250+ (92%) protein-coding genes of Chr18 (at least one method). The expression of slightly more than 50% protein-coding genes was detected simultaneously by all three methods. Correlation analysis of the gene expression profiles showed that the grouping of the datasets depended almost equally on both the type of biological material and the experimental method, particularly cDNA/mRNA isolation and library preparation. The dependence on the choice of bioinformatics analysis pipeline was also noticeable but significantly less. Furthermore, the combination of Illumina HiSeq and ONT MinION sequencing to validate proteotypic peptides of missing and uPE1 proteins was performed for the heat-shock factor binding protein HSBP1L1 (missing protein, recently transferred to PE1 category) and uncharacterized protein C18orf21 (uPE1). We observed that a nonsynonymous SNP led to the loss of the site of trypsinolysis in HSBP1L1. The modified version of HSBP1L1 was included in the sequence database and searched against the MS/MS dataset from Kulak, Geyer & Mann (2017), but delivered no significant identification. Thus, HSBP1L1 is still missing for the MS-pillar of C-HPP, although its existence at the protein level has been confirmed.

In the frame of the work, data on the implementation of metabolomics tests in medicine have been systematized. Based on the obtained data, a set of protocols was proposed, the sequential realization of which makes it possible to conduct a blood metabolome analysis for medical purposes. Using this analysis and the number of blood samples from healthy volunteers, a prototype of a healthy person's metabolomic image has been developed; it allows visually and digitally to assess the compliance of the human blood metabolome with the norm. At the same time, 99% of the metabolic processes reflected in the blood plasma are estimated. If abnormalities are detected, the metabolomic image allows to get the value of these deviations of metabolic processes in digital terms.Sistematizirovany dannye po vnedreniiu metabolomnykh testov v meditsinu. Osnovyvaias' na poluchennykh dannykh, predlozhena sovokupnost' protokolov, posledovatel'naia realizatsiia kotorykh pozvoliaet provesti metabolomnyĭ analiz krovi dlia meditsinskikh tseleĭ. Ispol'zuia dannyĭ analiz i vyborku obraztsov krovi zdorovykh dobrovol'tsev, razrabotan prototip metabolomnogo obraza zdorovogo cheloveka, pozvoliaiushchiĭ nagliadno i v tsifrovom vyrazhenii otsenit' sootvetstvie metaboloma krovi cheloveka norme. Pri étom otsenivaetsia 99% metabolicheskikh protsessov, otrazhennykh v plazme krovi. V sluchae vyiavleniia otkloneniĭ metabolomnyĭ obraz pozvoliaet poluchit' v tsifrovom vyrazhenii velichinu étikh otkloneniĭ metabolicheskikh protsessov.