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Aerosol distributions are of great relevance for air quality, especially for cities like Stuttgart, which has limited air exchange due to its location in a basin. We collected a comprehensive set of data from remote sensing and in situ methods including radiosondes for the urban background of downtown Stuttgart to determine the impact of boundary layer mixing processes on local air quality and to evaluate the simulation results of the high-resolution large eddy simulation (LES) model PALM-4U at 10 m grid spacing. Stagnant meteorological conditions caused accumulation of aerosols, and chemical composition analysis shows that ammonium nitrate (37 ± 9 %) and organic aerosol (OA; 34 ± 9 %) dominated during this winter study. Case studies show that clouds during previous nights can weaken temperature inversion and accelerate boundary layer mixing after sunrise by up to 3 h. This is important for ground-level aerosol dilution during the morning rush hour. Furthermore, our observations validate results of the LES model PALM-4U in terms of boundary layer heights and aerosol mixing for 48 h. The simulated aerosol concentrations follow the trend of our observations but are still underestimated by a factor of 4.5 ± 2.1 due to missing secondary aerosol formation processes and uncertainties of emissions and boundary conditions in the model. This paper firstly evaluates the PALM-4U model performance in simulating aerosol spatio-temporal distributions, which can help to improve the LES model and to better understand sources and sinks for air pollution as well as the role of horizontal and vertical transport.

The article examines the process of customs and logistics activities in the use of a temporary storage warehouse. The article presents the sequence of storage operations, the services of temporary storage warehouses. A logistics approach to inventory optimization of materials handling is to conduct a minimum number of inventory actions, the reduced costs for processing one ton of cargo and absolute satisfaction of the customer order.

The subject. The article is devoted to research the legal nature of international treaties.The purpose of the article is to formulate the feasibility of determining the legal status of international treaties in the composition of the sources of law in terms of its unity.The methodology. The author uses the systematic approach to research, methods of anal-ysis and synthesis, including formal legal analysis of international treaties, Russian legislation and courts’ decisions.The main results and scope of their application. The analysis of the categories of legal act, the regulatory agreement, the international treaty, describing its characteristics, legal characteristics is performed. On the basis of the main legal characteristics of the category of normative legal acts, the expediency of inclusion of an international treaty to this category is proven. It is groundless to detach international treaties on normative legal acts, thereby reducing the extent of the need for their application. This, however, does not change the fact that the source of law in each legal system may have special characteristics depending on such system and complementing the basic characteristics. The international treaty is a legal act of international law. Such a conceptual approach to this issue allows making further conclusions.Conclusions. The author highlights the circumstances of the need for reasonable use of international treaties to resolve disputes, that are significant for the process of enforcement. This position is based on the proposed definition of an international treaty including it to the normative legal acts.

The article substantiates the necessity of a system analysis of the processes of applicationof the norms of international treaties by commercial courts of the Russian Federation. Thisneed is justified, at least, by the following: an insignificant amount of special research inthis field in comparison with a similar subject within the courts of general jurisdiction, thecreation of a relatively new body of supranational control over compliance with the normsof international treaties in the field of commercial courts’ practice.The purpose of the study is to identify problems of application of international treaties ofthe Russian Federation arbitration courts of Russia.The author uses methodology of formal legal analysis of Russian legislation and courts’ decisions.The results and scope of it’s application. The author, taking into account the specifics ofcommercial proceedings and the nature of disputes heard in commercial courts, proposedlegal grounds in a concentrated form which allow to state the existence of the obligation toapply the norms of international treaties by Russian commercial courts. Two levels of suchgrounds can be stated – international and domestic.Publication of the texts of international treaties as a problematic segment of their applicability.The article highlights one of the problematic segments of the application process ofthe norms of international treaties for the purpose of more detailed reflection. The practiceof commercial courts demonstrates that in both legislative acts and acts of applying law,the concepts of "official publication" and "bringing to the public" are alternated with eachother. Despite the reform, the procedure of official publication has not acquired the characterof a systemic institution of Russian law. This significantly complicates the activity ofadministering justice with respect to the legislative acts of international law.Conclusions. From the point of view of international law, the state, independently determiningthe procedure and methods of implementing international treaties within its legalsystem, is not limited in its ability to burden itself with the need to abide by additional proceduresnot provided by the international legal system of procedures. Official publication,as a necessary procedure for the entry of a legislative act into the force, represents such anadditional procedure designed to protect more effectively human rights and freedoms andto streamline law enforcement practice. In this connection, the author formulated the provisions,the implementation of which can help in matters of systematization of the institutionof official publication of international treaties of the Russian Federation.

The article examines the process of customs and logistics activities in the use of a temporary storage warehouse. The article presents the sequence of storage operations, the services of temporary storage warehouses. A logistics approach to inventory optimization of materials handling is to conduct a minimum number of inventory actions, the reduced costs for processing one ton of cargo and absolute satisfaction of the customer order.

The influence of the support nature and electronic state of iron oxide nanoclusters on the catalytic properties of supported systems was studied for dichlorobutene isomerization. A sample with a Fe content of 2.5 wt.% on the activated silica matrix containing FeIII and FeII ions in the paramagnetic state exhibits the highest activity. The activity of iron on silica gel enhances with the appearance of magnetically ordered nanoclusters of γ-iron oxide formed at the iron content on the catalyst as high as 15 wt.%. An increase in the catalyst activity is favored by the formation of two states of iron (FeIII and FeII) that occurs under the synthesis conditions or during the action of a reactant. [ABSTRACT FROM AUTHOR]

Aim. To compare the dynamics of the clinical course of chronic adenoiditis in children and evaluate changes in the levels of products of oxidative modification of proteins in pharyngeal tonsil tissues under the influence of physical methods. Materials and methods. The study involved 84 patients with a clinical picture of chronic inflammation of the brain and hypertrophy of the adenoid vegetations of the 3rd degree, who were referred for surgical treatment as planned. All patients belonged to the age group from 3 to 15 years. The envelope method was used, patients were randomized into 3 groups. Group 1 (n=32) included children who did not receive exposure to physical methods in the preoperative period; Participants in the 2nd group (n=27) received low-frequency ultrasonic (LFU) therapy in combination with red spectrum photochromotherapy (FCT) in the preoperative period, and participants in the 3rd group (n=25) received NUS cavitation monotherapy before surgery. Statistical data were obtained using the SPSS Statistics 19.0 software package. The nonparametric Kruskal–Wallis test was used to identify differences between independent groups; for pairwise comparison of groups, the Mann–Whitney test was used. Results. Analysis of the results showed that the severity of the studied signs in the study groups was comparable to each other on the 1st day, i.e. before starting treatment. The results of endoscopic examination are graded from 0 to 3 points. the severity of nasal obstruction and difficulty nasal breathing in group 1 (control) on day 1 was 7.7 points, in group 2 – 7.4 points, in group 3 – 7.5 points. Patients underwent anterior and posterior rhinoscopy. The best result was obtained in the group using LFU cavitation in combination with FCT. There was a significant decrease in the size of the pharyngeal tonsil and the absence of discharge on the surface of the adenoid vegetations, which reflects the high clinical effectiveness of this method of treatment. Conclusion. The use of LFU cavitation in combination with FCT in the treatment of chronic adenoiditis in children leads to improved nasal breathing and a decrease in the amount of discharge in the nasal cavity.

Relevance. The new coronavirus infection (COVID-19) is still a public health problem and a threat to socio-economic well-being. Most studies have focused predominantly on humoral immunity, and there are no data on the cellular composition of blood in dynamics. Aim. To study the dynamics of changes in blood cellular composition depending on the type of immunity formed (natural, hybrid, breakthrough, postvaccinal) to SARS-CoV-2 virus. Materials and Methods. A total of 130 volunteers participated in the study. Immunophenotyping of peripheral blood leukocytes using flow cytometry was performed. The presence of specific IgG antibodies to N-protein SARS-CoV-2, total IgA and cytokines (IL-4, IL-10, IFN-γ, TNF-α) was assessed in serum by ELISA. Results and Discussion. A statistically significant increase in BL was recorded in volunteers with hybrid immunity 1 month (14,0% (12,3–16,4%)) after vaccination compared to healthy volunteers (9,1% (6,4–10,2%), p = 0,0007) and people with primary COVID-19 infection (10,2% (8,3–12,1%), p = 0,0134). In volunteers with natural and hybrid immunity, as well as in revaccinated people, an increase in B1-cells (CD3-CD19+CD5+CD27-) was observed during 3–9 months of observation. It is shown that the increase of B-lymphocytes with «switched» class of synthesized antibodies was detected in people with breakthrough immunity. Increased levels of T-lymphocytes expressing HLA-DR were recorded in all individuals during 6–9 months of follow-up. Volunteers with breakthrough immunity showed a significant increase in the positivity index when assessing the presence of specific IgG class antibodies to the coronavirus N-protein compared with volunteers with natural and hybrid immunity. Conclusions. Vaccination promotes protective immunity sufficient for timely activation of memory T- and B-cells in breakthrough immunity and maintenance of immunologic efficacy in hybrid immunity against COVID-19. The results help to assess the strain of innate and adaptive immunity in novel coronavirus infection and to fill gaps in the understanding of immunopathogenesis in COVID-19.

Relevance. COVID-19 is accompanied by high production of cytokines - immune molecules, imbalanced regulation of which leads to disruption of the immune response. Therefore, the study of cytokine status in both vaccinated and re-vaccinated patients is necessary to develop an immunoprophylaxis strategy for COVID-19. Aim. To evaluate the cytokine status in COVID-19 survivors and vaccinated employees of a health care facility against this disease. Materials and Methods. Production levels of cytokines (IL-4, IL-10, IFN-γ and TNF-α) were determined by quantitative enzyme immunoassay in serum of 144 volunteers. Results and discussion. A significant 1.5-fold increase in IL-10 and 2.0-fold increase in TNF-α was found in the group of re-invaccinated overinfected volunteers, and a 2.0-fold decrease in IL-4 compared with the vaccinated group. An inverse correlation between IL-4 and IFN-γ levels and timing after the disease was detected. A significant decrease in IL-4 in survivors (Omicron variant) and an increase in IL-10 in the survivors at the beginning of the pandemic as compared to other re-vaccinees was established. In the vaccinated group, regardless of the vaccine used, IL-10 and TNF-α decreased significantly after revaccination. No statistically significant differences were found between the cytokine status parameters in the survivors before and after vaccination. The predominance of the cellular component of immunity was established in all the examined groups, and the highest proportion of persons with a humoral immune response was detected among the vaccinated volunteers, while the highest proportion of persons with a mixed immune response was detected among the overexperienced non-vaccinated patients. Conclusions. The results obtained supplement the available data on coronavirus infection and indicate the need for further research.

Abstract. Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a multi-organ systemic damage that can lead to long-term consequences. Little is known about the possible long-term effects of COVID-19 on circulating leukocyte kinetics and functional T-cell activity after recovery. To investigate immune system changes, we designed a cohort study. Methods. Volunteer screening and sample collection were performed at the Irkutsk Research Anti-Plague Institute of Rospotrebnadzor. Sixty-four volunteers who have had COVID-19 (recovered volunteers (RVs)) between May 2020 and May 2021, 33 volunteers who had been in contact with COVID-19 patients (contact volunteers (CVs)) within the family setting but had not become ill, and 47 healthy volunteers (HVs) participated in the study. We performed immunophenotyping of peripheral blood cells using flow cytometry. Serum was tested for SARS-CoV-2 anti-nucleocapsid immunoglobulin G antibodies by enzyme-linked immunosorbent assay (Ab(+), people with specific anti-N antibodies to SARS-CoV-2; Ab(−), people without specific antibodies). Results. There were no serious disturbances in the internal environment of the body in RVs and CVs. In the evaluation of the general state of the immune system, the most informative indicator was the index of the ratio of neutrophils to blood monocytes – decreased on the 1st terms of observation (1 and 3 months post-symptom onset (PSO)/post-contact onset (PCO)), on average, 1.3 times compared with HVs (8.6% (7.5%–10.5%), P < 0.05), which recovered by the 6th month of observation. Redistribution of the cells responsible for the development of the adaptive immune response was noted only in RVs – increased B-lymphocyte content (HVs, 9.1% (6.4%–10.2%)) and immunoregulatory index ratio (HVs, 1.6% (1.2%–2.1%)) due to redistribution of T-helper and cytotoxic T cells throughout the follow-up period by an average of 1.2-fold compared with HVs (P < 0.05). However, CVs with specific antibodies to SARS-CoV-2 N-protein also had an increased proportion of CD3−CD19+ cells after 1 month PCO (Ab(+), 11.4% (10.2%–15.1%); Ab(−), 8.6% (5.7%–9.7%); P = 0.006). A significant difference between RVs and CVs is that the RVs showed significant activation of circulating T cells, which persisted up to the 6th month of the study, whereas in CVs, it persisted for 3 months PCO. The highest proportion of HLA-DR+ T-lymphocytes was recorded after 1 month PSO/PCO in Ab(+) RVs and CVs: Ab(+) volunteers, 8.1% (6.0%–11.2%) and 4.4% (2.7%–6.4%), respectively; Ab(−) volunteers, 4.2% (2.6%–5.4%) and 5.1% (3.7%–5.6%); and HVs, 3.5% (2.5%–4.7%) (P < 0.01). In CVs, natural killer cells also played a major role in preventing manifest infection (CVs, 10.8% ± 4.3%; HVs, 15.9% ± 7.6%; P < 0.05). Conclusion. In this study, we demonstrated the dynamics of returning to the initial state of health in RVs and CVs. In CVs, we observed changes in the studied immunological parameters similar to those of RVs, but which are less intense and prolonged. Complete recovery of the studied immunological parameters occurs within 6 months.

Background. Currently, the COVID-19 pandemic in the world and in Russia remains the main event. In this regard, the study of the manifestations of the epidemic process of the new coronavirus infection COVID-19 and the patterns of its development are an urgent area of research. In the fight against this viral disease, an important role is assigned to the study of the development of population immunity to the SARSCoV-2 virus, which will make it possible to assess the dynamics of seroprevalence and the formation of post-infectious humoral immunity, forecasting the development of the epidemiological situation, elucidating the characteristics of the epidemic process, and will also contribute to planning activities for specific and non-specific prevention of the disease.The aim: to determine the dynamics of population immunity to SARS-CoV-2 among the population of the Irkutsk region during the COVID-19 pandemic.Materials and methods. As a part of the Rospotrebnadzor project of assessing population immunity to SARS-CoV-2 in the population of the Russian Federation, the research has being conducted among the population of the Irkutsk region in the periods from June 23, 2020 to July 19, 2020 (Stage 1), from September 16, 2020 to September 25, 2020 (Stage 2), from December 7, 2020 to December 18, 2020 (Stage 3) and from March 8, 2021 to March 14, 2021(Stage 4), taking into account the reacted one recommended by the WHO. The content of antibodies to SARS-CoV-2 was determined by ELISA using a set of tests for human serum or plasma for specific immunoglobulins of class G to the proteins of the SARS-CoV-2 coronavirus.The results. The research of the humoral immunity of volunteers shows that during the period of an epidemic rise in the incidence of COVID-19 in the Irkutsk region, a low level of seroprevalence was formed (Stage 1 – 5.8 ± 0.5 %, Stage 2 – 12.1 ± 0.7 %), and in conditions of a long-term maximum increase in the incidence rate – 25.9 ± 1.0 % (Stage 3) and 46.2 ± 1.2 % (Stage 4). A significant proportion (Stage 1 – 82.2 ± 3.2 %, Stage 2 – 86.1 ± 2.3 %) of asymptomatic forms of infection characterizes the high intensity of the latently developing epidemic process in the first two stages. High levels of IgG in reconvalescents of COVID-19 persisted for an average of 3 to 5 months.Conclusion. The results of assessing the population immunity to the SARS-CoV-2 virus in the population of the Irkutsk region indicate that the seroprevalence level at Stage 4 of the research was 46.2 %. After the disease, on average, 49.5 % of persons did not detect antibodies. The results obtained should be taken into account when organizing preventive measures, including vaccination, and predicting morbidity.

Background. Currently, during the COVID-19 pandemic, one of the most pressing healthcare problems is to ensure the safety of the population of the Russian Federation. There is insufficient information on the duration and intensity of post-infectious immunity in relation to SARS-CoV-2, especially in case of inapparent (without clinical signs), mild or latent forms of infection.Materials and methods. The study involved 99 volunteers with a laboratory confirmed PCR diagnosis of COVID-19 who were residents of the Irkutsk Region and of other regions of the Russian Federation and arrived to work in Bodaybo on a rotational basis. Also the study included 50 conditionally healthy people living in Irkutsk who had negative PCR results for SARS-CoV-2 RNA presence.Specific IgG and IgM antibodies to SARS-CoV-2 were detected in blood serum by enzyme-linked immunosorbent assay (ELISA) using test systems “ELISA anti-SARS-CoV-2 IgG” (FBUN SSC PMB, Obolensk, Russian Federation), “SARS-CoV-2-IgG-IFA-BEST” and “SARS-CoV-2-IgM-IFA-BEST” (Vector-Best, Novosibirsk, Russian Federation).Results. The results of a study of the humoral immunity of patients with asymptomatic and clinical forms of COVID-19 are presented. The data indicate the production of specific IgG in the blood serum of people in 2–3 weeks after SARSCov-2 infection and reaching its maximum level on the 20–21st day. The seroconversion rate was 94.9 %. It was shown that the geometric mean titer of antibodies in asymptomatic and mild forms of coronavirus infection did not differ statistically and amounted to 1:512 and 1:632, respectively. Higher titers of antibodies (1:1600) were detected in the moderate form.Conclusion. The research results can serve as a basis for studying the dynamics of changes in the indicators of the humoral immune response in patients with COVID-19 and for clarifying the duration of their post- infectious immunity in order to predict the development of the epidemic situation and to ensure the planning of specific prevention.

Increasing attention has been focused on the study of protein-metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein-protein interactions, protein-metabolite interactions are still not clearly defined. Existing assays for detecting protein-metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein-metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term "interaction" to advance the field of interactomics further.

Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.

Metabolomics based on two-dimensional gas chromatography coupled with mass spectrometry is making high demands on accuracy at all stages of sample preparation, up to the storage and injection into the analytical system. In high sample flow conditions, good repeatability in peak areas and a list of detectable metabolites is sometimes challenging to obtain. In this research, we successfully obtained good repeatability for the peak areas of MSFTA-derivatives of 29 core blood plasma metabolites. Six different strategies of storage and injection were investigated and evaluated for the reproducibility of the obtained data. As the essential factors, we considered popular GC-MS syringe washing solvents (methanol and pyridine); storage conditions (freshly prepared samples and stored for 24 h in ambient temperature or in the refrigerator); scheme of injection (one injection per intact vial or three sequential injections per vial). Our GC×GC-MS results demonstrated that the usage of pyridine as a syringe wash solvent and triple injecting the sample from the same vial was the most appropriate for minimizing the coefficient of variation (CV) of the results obtained (in general, <10%). The prolonged storage of samples does not have a noticeable effect on the change in the areas of chromatographic peaks of metabolites, although it reduces CV in some cases. These storage and injection recommendations can be used in future study protocols for the GC×GC-MS analysis of blood plasma.

Background: It is relevant to study the general patterns and identify non-specific mechanisms of body protective and adaptive reactions violation, which can lead to the various pathological processes and develop principles for the correction of these disorders. One of the therapy and prevention directions is the search for new medicines. In recent years, new derivatives of pyrimidine bases have been synthesized and studied. Pyrimidine-based medicines have a membrane-stabilizing and immunomodulatory effect and can normalize metabolic disorders and increase the oxidative activity of leukocytes. Disruption of the free radical oxidation processes, the generation of reactive oxygen species and lipid peroxidation, including in whole blood and bone marrow, has gained importance in recent years., Methods: Each reaction was monitored by thin layer chromatography. 1 H, 13 C, and 15 N NMR spectra were recorded (chemical shifts were expressed as δ-values). We studied the effect of 6-methyl-3-(thietan- 3-yl)pyrimidine-2,4(1H,3H)-dione on the generation of reactive oxygen species (ROS) in the whole blood and bone marrow using the study of whole blood spontaneous and stimulated chemiluminescence (CL). CL methods make it possible to quickly and easily assess the studied material (whole blood, bone marrow) effect on free radical oxidation. Using CL methods, it is possible to reveal the presence of medicines' pro- or antioxidant properties, opening up new possibilities in the search for substances with antioxidant properties and comparing their activity., Results: Alkylation of 6-methylpyrimidine-2,4(1H,3H)-dione by 2-chloromethylthiirane in protic solvents in the presence of alkali leads to the formation of an N-thietane derivative. NMR spectroscopy showed that 6-methylpyrimidine-2,4(1H,3H)-dione was alkylated at position 3. The oxidation reactions of N-(thietan-3-yl)pyrimidine-2,4(1H,3H)-dione were studied, and it was determined that, depending on the excess of the oxidizing agent and the duration of the process, N-(1-oxothietan-3-yl)- or N-(1,1-- dioxothietan-3-yl)pyrimidine-2,4(1H,3H)-diones were formed. The effects of free radical oxidation processes of new biologically active pyrimidine-2,4(1H,3H)-diones were studied., Conclusion: New pyrimidine-2,4(1H,3H)-diones increase the general adaptive capabilities of the body and have protective effects in extreme conditions., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules' roles in living systems are not limited to traditional "building blocks" or "just fuel" for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.

Abstract: Diarrhea is one of the manifestations of the novel coronavirus disease (COVID-19), but it also develops as a complication of massive antibiotic therapy in this disease. This study aimed to compare these types of diarrhea.We included patients with COVID-19 in a cohort study and excluded patients with chronic diarrhea, laxative use, and those who died during the first day of hospitalization.There were 89 (9.3%), 161 (16.7%), and 731 (75.7%) patients with early viral, late antibiotic-associated, and without diarrhea, respectively. Late diarrhea lasted longer (6 [4-10] vs 5 [3-7] days, P < .001) and was more severe. Clostridioides difficile was found in 70.5% of tested patients with late diarrhea and in none with early diarrhea. Presence of late diarrhea was associated with an increased risk of death after 20 days of disease (P = .009; hazard ratio = 4.7). Patients with late diarrhea had a longer hospital stay and total disease duration, and a higher proportion of these patients required intensive care unit admission. Oral amoxicillin/clavulanate (odds ratio [OR] = 2.23), oral clarithromycin (OR = 3.79), and glucocorticoids (OR = 4.41) use was a risk factor for the development of late diarrhea, while ceftriaxone use (OR = 0.35) had a protective effect. Before the development of late diarrhea, decrease in C-reactive protein levels and increase in lymphocyte count stopped but the white blood cell and neutrophil count increased. An increase in neutrophils by >0.6 × 109 cells/L predicted the development of late diarrhea in the coming days (sensitivity 82.0%, specificity 70.8%, area under the curve = 0.791 [0.710-0.872]).Diarrhea in COVID-19 is heterogeneous, and different types of diarrhea require different management., Competing Interests: The authors reprot no conflicts of interest., (Copyright © 2021 the Author(s). Published by Wolters Kluwer Health, Inc.)

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., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article., (© 2021 The Author(s). Published by Elsevier Inc.)

Despite tremendous efforts in genomics, transcriptomics, and proteomics communities, there is still no comprehensive data about the exact number of protein-coding genes, translated proteoforms, and their function. In addition, by now, we lack functional annotation for 1193 genes, where expression was confirmed at the proteomic level (uPE1 proteins). We re-analyzed results of AP-MS experiments from the BioPlex 2.0 database to predict functions of uPE1 proteins and their splice forms. By building a protein-protein interaction network for 12 ths. identified proteins encoded by 11 ths. genes, we were able to predict Gene Ontology categories for a total of 387 uPE1 genes. We predicted different functions for canonical and alternatively spliced forms for four uPE1 genes. In total, functional differences were revealed for 62 proteoforms encoded by 31 genes. Based on these results, it can be carefully concluded that the dynamics and versatility of the interactome is ensured by changing the dominant splice form. Overall, we propose that analysis of large-scale AP-MS experiments performed for various cell lines and under various conditions is a key to understanding the full potential of genes role in cellular processes.

One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to catalog and annotate a myriad of heterogeneous proteoforms, produced by ca. 20 thousand genes. To achieve a detailed and personalized understanding into proteomes, we suggest using a customized RNA-seq library of potential proteoforms, which includes aberrant variants specific to certain biological samples. Two-dimensional electrophoresis coupled with high-performance liquid chromatography allowed us to downgrade the difficulty of biological mixing following shotgun mass spectrometry. To benchmark the proposed pipeline, we examined heterogeneity of the HepG2 hepatoblastoma cell line proteome. Data are available via ProteomeXchange with identifier PXD018450., Competing Interests: The authors declare no conflict of interest.

Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a stage when more attention and curiosity need to be exerted in the identification of every novel protein in order to expand the unusual types of biomaterials and/or conditions. It seems that we have exhausted the current conventional approaches to the discovery of missing proteins and may need to investigate alternatives. Here, we present an approach to deciphering missing proteins based on the use of non-standard methodological solutions and encompassing diverse MS/MS data, obtained for rare types of biological samples by members of the Russian Proteomic community in the last five years. These data were re-analyzed in a uniform manner by three search engines, which are part of the SearchGUI package. The study resulted in the identification of two missing and five uncertain proteins detected with two peptides. Moreover, 149 proteins were detected with a single proteotypic peptide. Finally, we analyzed the gene expression levels to suggest feasible targets for further validation of missing and uncertain protein observations, which will fully meet the requirements of the international consortium. The MS data are available on the ProteomeXchange platform (PXD014300).

This work on solving the mystery of words encoded by amino acids in peptides was derived by the YPIC-EuPA Challenge. We received a dry synthetic peptide sample and performed a mass spectrometric analysis followed by de novo peptide sequencing. As a result, a part of "Rays of positive electricity and their application to chemical analyses" by J.J.Tomson was found to be encoded in the peptides of the sample. The words were first revealed from the peptides, that matched by Google search to find the answer. After that, the answer was validated using a standard proteomic search against a database constructed from the quotation found., (© 2019 The Authors.)

Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the "speed" of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF[Formula: see text], MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI ( http://searchgui.googlecode.com ) into total result of proteoforms identification and optimized set of engines working simultaneously. We also compared the results of our search combination with Mascot results using protein kit UPS2, containing 48 human proteins. We selected combination of X!Tandem, MS-GF[Formula: see text] and OMMSA as the most time-efficient and productive combination of search. We added homemade java-script to automatize pipeline from file picking to report generation. These settings resulted in rise of the efficiency of our customized pipeline unobtainable by manual scouting: the analysis of 192 files searched against human proteome (42153 entries) downloaded from UniProt took 11[Formula: see text]h.