A pipeline for processing hyperspectral images, with a case of melanin-containing barley grains as an example.

Analysis of hyperspectral images is of great interest in plant studies. Nowadays, this analysis is used more and more widely, so the development of hyperspectral image processing methods is an urgent task. This paper presents a hyperspectral image processing pipeline that includes: preprocessing, basic statistical analysis, visualization of a multichannel hyperspectral image, and solving classification and clustering problems using machine learning methods. The current version of the package implements the following methods: construction of a confidence interval of an arbitrary level for the difference of sample averages; verification of the similarity of intensity distributions of spectral lines for two sets of hyperspectral images on the basis of the Mann-Whitney U-criterion and Pearson's criterion of agreement; visualization in two-dimensional space using dimensionality reduction methods PCA, ISOMAP and UMAP; classification using linear or ridge regression, random forest and catboost; clustering of samples using the EM-algorithm. The software pipeline is implemented in Python using the Pandas, NumPy, OpenCV, SciPy, Sklearn, Umap, CatBoost and Plotly libraries. The source code is available at: https://github.com/igor2704/Hyperspectral_images. The pipeline was applied to identify melanin pigment in the shell of barley grains based on hyperspectral data. Visualization based on PCA, UMAP and ISOMAP methods, as well as the use of clustering algorithms, showed that a linear separation of grain samples with and without pigmentation could be performed with high accuracy based on hyperspectral data. The analysis revealed statistically significant differences in the distribution of median intensities for samples of images of grains with and without pigmentation. Thus, it was demonstrated that hyperspectral images can be used to determine the presence or absence of melanin in barley grains with great accuracy. The flexible and convenient tool created in this work will significantly increase the efficiency of hyperspectral image analysis.

Analysis of T-cell and Humoral Immune Response to SARS-CoV-2 Antigens in Rituximab-Treated Patients with Rheumatoid Arthritis Vaccinated with Combined Vector Vaccine Gam-COVID-Vac.

The COVID-19 pandemic has brought significant changes in managing of patients with rheumatoid arthritis. Rituximab-treated patients were more susceptible to severe infection. This required a "switch" to another genetically engineered drug in the patients with high risk of adverse COVID-19. In this study, we assessed the severity of immune response to SARS-CoV-2 antigens in rituximab-treated patients with rheumatoid arthritis vaccinated with the combined vector vaccine Gam-COVID-Vac. Insufficient formation of the humoral response and a high level of T-cell response to SARS-CoV-2 antigens in this group of patients were revealed. An imbalance of cellular and humoral response may play a role in more severe COVID-19 in rituximab-treated patients with rheumatoid arthritis.

Phytoestrogens decorated nanocapsules for therapeutic methionine γ-lyase targeted delivery.

The main task of targeted therapy is the selective destruction of cancer cells without affecting normal ones. For these purposes, small molecules and antibodies are used that target specific receptors and proteins or block signaling pathways in tumor cells. The natural phytoestrogens daidzein (Dz) and genistein (Gn) possess binding capacity to estrogen receptors (ER). Methionine γ-lyase (MGL) is promising in two strategies of antitumor therapy: for the elimination of l-methionine, which is necessary for the proliferation of tumor cells, and for the production of cytotoxic dialkyl thiosulfinates in situ. For delivery of MGL-loaded nanocapsules (nanoreactors) to the surface of cancer cells a technique for Dz or Gn incorporation into the shell of polyionic vesicles (PICsomes) was developed. The nanoreactors were characterized by dynamic light scattering and transmission electron microscopy. The enzyme retained its catalytic efficiency inside the decorated PICsomes. The binding of Dz/Gn-nanoreactors to the surface of ER + MCF7 breast adenocarcinoma cells was demonstrated. For the first time an influence of enzyme-loaded PICsomes and their individual components on embryos development was evaluated. The high rate of blastocysts formation (>80%) was observed for all tested components and nanoreactors themselves. A strong inhibitory effect on the early embryonic development of MGL-loaded PICsomes in the presence of S-alkyl-l-cysteine sulfoxide substrates was showed. This proves that the substrates can freely penetrate through the polymer shell of the polyionic vesicle and are cleaved by MGL to form cytotoxic thiosulfinates. The data obtained for phytoestrogens decorated PICsomes may be applied in enzyme therapy of malignant tumors.

Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods.

The pigment composition of plant seed coat affects important properties such as resistance to pathogens, pre-harvest sprouting, and mechanical hardness. The dark color of barley (Hordeum vulgare L.) grain can be attributed to the synthesis and accumulation of two groups of pigments. Blue and purple grain color is associated with the biosynthesis of anthocyanins. Gray and black grain color is caused by melanin. These pigments may accumulate in the grain shells both individually and together. Therefore, it is difficult to visually distinguish which pigments are responsible for the dark color of the grain. Chemical methods are used to accurately determine the presence/ absence of pigments; however, they are expensive and labor-intensive. Therefore, the development of a new method for quickly assessing the presence of pigments in the grain would help in investigating the mechanisms of genetic control of the pigment composition of barley grains. In this work, we developed a method for assessing the presence or absence of anthocyanins and melanin in the barley grain shell based on digital image analysis using computer vision and machine learning algorithms. A protocol was developed to obtain digital RGB images of barley grains. Using this protocol, a total of 972 images were acquired for 108 barley accessions. Seed coat from these accessions may contain anthocyanins, melanins, or pigments of both types. Chemical methods were used to accurately determine the pigment content of the grains. Four models based on computer vision techniques and convolutional neural networks of different architectures were developed to predict grain pigment composition from images. The U-Net network model based on the EfficientNetB0 topology showed the best performance in the holdout set (the value of the "accuracy" parameter was 0.821).

Daidzein-directed methionine γ-lyase in enzyme prodrug therapy against breast cancer.

Thiosulfinates in situ formed by "pharmacological pair" C115H methionine γ-lyase/S-(allyl/alkyl)-l-cysteine sulfoxides possess cytotoxic activity against various malignant cell lines. To investigate in vivo antitumor activity of thiosulfinates generated directly at the surface of tumor cells, a chemical conjugate between Clostridium novyi C115H methionine γ-lyase (C115H MGL) and isoflavone daidzein was prepared. The binding of conjugate (C115H-Dz) to various breast cancer cell lines was demonstrated, as well as its cytotoxicity in the presence of S-(allyl/alkyl)-l-cysteine sulfoxides. The most promising among thiosulfinates was dipropyl thiosulfinate (IC50 < 0.53 µM). The pharmacokinetic parameters of C115H MGL and C115H-Dz were obtained. Plasma half-lives of the enzyme and conjugated enzyme were 4.4 and 7.2 h, respectively. In vivo antitumor effect of pharmacological pairs on SKBR-3 xenografts was demonstrated. Treatment of tumor-bearing mice with a pair of C115H-Dz/propiin inhibited tumor growth by 85%.

Prompt gamma activation analysis for determining the elemental composition of archaeological ceramics.

The first experiments were carried out to study the elemental composition of archaeological ceramics using prompt gamma activation analysis (PGAA) at the pulsed reactor IBR-2, Frank Laboratory of Neutron Physics (FLNP) - Joint Institute for Nuclear Research (JINR). A radiation-resistant n-type High Purity Germanium (HPGe) detector was used to measure the radioactivity. The concentrations of 14 elements were determined namely; Al, C, Ca, Fe, Gd, H, K, Mn, Na, P, S, Si, Sm, and Ti. The obtained results were compared with those analyzed by other analytical techniques INAA (Instrumental Neutron Activation Analysis) and portable X-ray fluorescence (XRF) for the same archaeological batches. The results revealed a good agreement within a range of 1-30%. These insights will contribute to the discussion of improving the PGAA installation and automation of the data obtained, which in turn will improve the quality of analysis and increase the number of determined elements. In this work results are presented, and the analytical merits are compared.

10 W-level sub-100 ps 1 MHz MOPA laser with a microchip master oscillator.

A 10 W level master oscillator power amplifier (MOPA) laser with pulse repetition rate up to 1 MHz and 75-95 ps pulse duration was developed based on a passively Q-switched Nd:YVO4 microchip 1064 nm laser as a master oscillator. A double-rod double-end-pumping configuration of two-pass Nd:YAG ring power amplifier was used to achieve high gain, near-Fourier-transform-limited pulses, and laser beam quality factor M2=1.27 along both the horizontal and vertical directions.

Conjugates of methionine γ-lyase with polysialic acid: Two approaches to antitumor therapy.

The methionine dependence is a well known phenomenon in metabolism of cancer cells. Methionine γ-lyase (EC 4.4.1.11, MGL) catalyzes the γ-elimination reaction of L-methionine and thus could effectively inhibit the growth of malignant cells. Recently we have demonstrated that the mutant form of the enzyme C115H MGL can be used as a component of the pharmacological pair enzyme/S-(allyl/alkyl)-L-cysteine sulfoxides to yield thiosulfinates in situ. Thiosulfinates were shown to be toxic to various cancer cell lines. Therefore the application of the enzyme in enzyme pro-drug therapy may be promising. The conjugates of MGL and C115H MGL with polysialic acid were obtained and their kinetic and pharmacokinetic parameters were determined. The formation of polysialic shell around the enzyme was confirmed by atomic force microscopy. The half-life of conjugated enzymes increased 3-6 times compared to the native enzyme. The cytotoxic effect of conjugated MGL against methionine dependent cancer cell lines was increased two times compared to the values for the native enzymes. The anticancer efficiency of thiosulfinates produced by pharmacological pair C115H MGL/S-(allyl/alkyl)-L-cysteine sulfoxides was demonstrated in vitro. The results indicate that the conjugates of MGL with polysialic acid could be new antitumor drugs.

Assessment of the Phenylketonuria (PKU)-Associated Mutation p.R155H Biochemical Manifestations by Mass Spectrometry-Based Blood Metabolite Profiling.

Homozygous siblings with different treatment histories represent an excellent model to study both the phenotypic manifestation of mutations and the efficacy of therapy. We compared phenylketonuria (PKU) manifestations in two different gender siblings who were homozygous carriers of a rare phenylalanine hydroxylase (PAH) mutation, p.R155H, subjected to different treatments. PKU caused by mild mutations may be easily underdiagnosed if the diagnosis is based solely on the phenylalanine (Phe) blood concentration. One of the described patients is an example of this diagnostic error. For reducing diagnostic errors, we suggest the use of more elaborate methods in screening practice, in particular mass spectrometric analysis of blood metabolites, the efficiency of which is demonstrated in the present study.

Antibacterial Effect of Thiosulfinates on Multiresistant Strains of Bacteria Isolated from Patients with Cystic Fibrosis.

The multiresistance of A. ruhlandii 155B, B. cenocepacia 122, and P. aeruginosa 48B strains isolated from patients with cystic fibrosis was established. The antibacterial effect of allicin, dimethyl thiosulfinate, and dipropyl thiosulfinate on multidrug-resistant strains was shown. Thiosulfinates can have both bacteriostatic and bactericidal effects depending on the microorganism and the concentration. The studied thiosulfinates may be candidates for the development of alternative antibiotic drugs to treat infections caused by multidrug-resistant pathogens.

Global DNA dynamics of 8-oxoguanine repair by human OGG1 revealed by stopped-flow kinetics and molecular dynamics simulation.

The toxic action of different endogenous and exogenous agents leads to damage in genomic DNA. 8-Oxoguanine is one of the most often generated and highly mutagenic oxidative forms of damage in DNA. Normally, in human cells it is promptly removed by 8-oxoguanine-DNA-glycosylase hOGG1, the key DNA-repair enzyme. An association between the accumulation of oxidized guanine and an increased risk of harmful processes in organisms was already found. However, the detailed mechanism of damaged base recognition and removal is still unclear. To clarify the role of active site amino acids in the damaged base coordination and to reveal the elementary steps in the overall enzymatic process we investigated hOGG1 mutant forms with substituted amino acid residues in the enzyme base-binding pocket. Replacing the functional groups of the enzyme active site allowed us to change the rates of the individual steps of the enzymatic reaction. To gain further insight into the mechanism of hOGG1 catalysis a detailed pre-steady state kinetic study of this enzymatic process was carried out using the stopped-flow approach. The changes in the DNA structure after mixing with enzymes were followed by recording the FRET signal using Cy3/Cy5 labels in DNA substrates in the time range from milliseconds to hundreds of seconds. DNA duplexes containing non-damaged DNA, 8-oxoG, or an AP-site or its unreactive synthetic analogue were used as DNA-substrates. The kinetic parameters of DNA binding and damage processing were obtained for the mutant forms and for WT hOGG1. The analyses of fluorescence traces provided information about the DNA dynamics during damage recognition and removal. The kinetic study for the mutant forms revealed that all introduced substitutions reduced the efficiency of the hOGG1 activity; however, they played pivotal roles at certain elementary stages identified during the study. Taken together, our results gave the opportunity to restore the role of substituted amino acids and main "damaged base-amino acid" contacts, which provide an important link in the understanding the mechanism of the DNA repair process catalyzed by hOGG1.

[Dimeric bisbenzimidazoles suppress the herpes simplex virus and human cytomegalovirus infections in cell сultures].

Antiviral activity of new AТ-specific fluorescent symmetric dimeric bisbenzimidazoles of DBА(n) series was assessed in the cell models of infections caused by type 1 herpes simplex virus (HSV1) and human cytomegalovirus (CMV). In DBA(n) molecules bisbenzimidazole fragments are bound to an oligomethylene liner with varied number of methylene groups in the linker (n = 1, 3, 5, 7, 9, 11). In contrast to DB(n) dimeric bisbenzimidazoles, in DBA(n) series terminal fragments of macromolecules contain N-dimethylaminopropylcarboxamide groups instead of N-methylpiperazine groups. DBА(n) compounds better dissolve in water, pass across plasma and nuclear membrane, and stain DNA in living cells. DBA(1) and DBA(7) produced therapeutic effects in HSV1 infection; DBA(7) completely suppressed the infection. DBA(11) displayed in vitro therapeutic activity in HSV1 and CMV infections. In addition, DBA(7) and DBA(1) showed microbicidal activity. Thus, DBA(11), which is active against two viruses causing severe diseases with serious health consequences for immunodeficient individuals, should be further investigated. High antiviral activity of DBA(7) in all test models indicates that this compound is a promising active agent for innovative antiviral drugs.

[EFFICIENCY OF CONCOMITANT USE OF POLICOSANOL AND ROSUVASTATIN IN PATIENTS WITH STABLE CORONARY ARTERY DISEASE AND MODERATE HEPATIC DYSFUNCTION].

The article presents the results for the study of lipid correction capacity and safety of concomitant use of policosanol and rosuvastatin compared with rosuvastatin monotherapy in patients with stable coronary artery disease and moderate hepatic dysfunction. Fifty-seven subjects aged 37 to 72 years (mean age 54.4 years +/- 6.5 years) have been enrolled into the study with the following inclusion criteria: therapy with statins for more than 8 weeks, failure to achieve target LDL cholesterol levels and moderately elevated liver enzymes. The following laboratory tests were performed at baseline and after 12 weeks of follow-up: blood lipid profile (total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), very low density lipoprotein cholesterol (VLDL-C), high density lipoprotein cholesterol (HDL-C) and triglycerides (TG), lipid peroxidation (ma- Ionic dialdehyde (MDA), glycosylated hemoglobin HbAlc (%) and liver function tests (gamma-glutamyl transpeptidase-gamma-GTP) and alanine aminotransferase (ALT). Concomitant use of policosanol with rosuvastatin was superior to rosuvastatin monotherapy in terms of reduction of pro-aterogenicity of lipid metabolism by decreasing serum TC, LDL-C and TG, increasing serum HDL-C and decreasing the pro-oxidative activity (MDA) with simultaneous substantial improvement of hepatic function. Concomitant use of policosanol at the dose of 20 mg/day and rosuvastatin at 10-20 mg/day was favorably tolerated. None of the subjects had any discontinuations of therapy due to adverse events.

[Tactics and results of treatment of acute hemorrhage in gastroduodenal erosive ulcers due to application of gastro-aggressive preparations].

Results of treatment of 238 patients, suffering an acute gastrointestinal hemorrhage, occurring on background of application of medicinal preparations, were adduced. The incidence rate for an acute medicinal ulcers of foregut was analyzed, as well as possibilities for their treatment.

Structural Features of the Interaction between Human 8-Oxoguanine DNA Glycosylase hOGG1 and DNA.

The purpose of the present review is to summarize the data related with the structural features of interaction between the human repair enzyme 8-oxoguanine DNA glycosylase (hOGG1) and DNA. The review covers the questions concerning the role of individual amino acids of hOGG1 in the specific recognition of the oxidized DNA bases, formation of the enzyme-substrate complex, and excision of the lesion bases from DNA. Attention is also focused upon conformational changes in the enzyme active site and disruption of enzyme activity as a result of amino acid mutations. The mechanism of damaged bases release from DNA induced by hOGG1 is discussed in the context of structural dynamics.

[Estimation of efficiency of anti-helicobacter therapy in patients with a chronic pancreatitis combined with an erosive gastropathy].

SUMMARY Eradikacion therapy at patients with chronic pancreatitis and combined with Helicobacter associated erosive gastropathy in a month after treatment appeared successful at 75% patients which accepted therapy of the first line--pantoprazol, amoksicillin, klaritromicin. Inclusion in antihelicobakter therapy of seknidazol in place of klaritromicin rendered a positive antihelicobakter effect at 85% patients with a chronic pancreatitis. Therapy with the use of seknidazole was better tolerated. Application of synbiotik laktiale on a background antihelicobakter therapy helped normalizations of chair and was comfortable in application, which is important in the treatment of patients. Application of synbiotika laktiale on a background antigelikobakter therapy is helped in the improvement of clinical effect.

[Chymotripsin-like activity and subunit composition of proteasomes in human cancers].

Activity of the proteasome, polyfunctional enzymatic complex, is known to undergo changes during cancer development. This phenomenon is, probably, caused by the changes in subunit composition of proteasomes. In present work, we studied chymotrypsin-like activity of proteasomes, subunit composition and their association in breast cancer, head and neck squamous cell carcinoma, endometrial cancer, renal cancer, bladder cancer, stomach cancer and colorectal cancer. The increase of proteasome activity was revealed in most cancer tissues compared with adjacent tissues except for the renal cell carcinoma. Changes in proteasome activity in cancer tissues compared with correspondent normal tissues were accompanied by modification of its subunit composition. High proteasome activity was observed in combination with an increased expression of immune subunits and/or proteasome activator PA28, associated with activity of 20S proteasome. In breast cancer, head and neck squamous cell carcinoma, bladder cancer, stomach cancer and colorectal cancer we additionally found higher expression of Rpt6 subunit of 26S proteasome. Correlations between chymotrypsin like proteasome activity and subunit expressions were found in human cancer tissues. In summary, we suggest that proteasome ac- tivation and changes in its subunit composition plays an important role in cancer pathogenesis.

[Relationship between the expression levels of PAPP-A metalloproteinase and growth and transcriptional factors in endometrial cancer].

We have examined for the first time the relationship between the expression of PAPP-A metalloproteinase and insulin-like growth factors (IGF-I, IGF-II, VEGF) and transcription factors (NF-kappaB, HIF-1) playing an important role in pathogenesis of cancer. We also demonstrated a positive association between the level of PAPP-A metalloproteinase and the level of growth (VEGF and IGF-I) and transcription factors (NF-kappaB p50, NF-kappaB p65, HIF-1alpha). The current findings suggest an important role of PAPP-A in regulation of bioavailability of IGF-I, VEGF, activated forms of NF-kappaB, and alpha-subunits of HIF-1 in endometrial tumors.

Kinetic mechanism of the interaction of Saccharomyces cerevisiae AP-endonuclease 1 with DNA substrates.

The apurinic/apyrimidinic endonuclease from Saccharomyces cerevisiae Apn1 is one of the key enzymes involved in base excision repair of DNA lesions. A major function of the enzyme is to cleave the upstream phosphodiester bond of an apurinic/apyrimidinic site (AP-site), leading to the formation of a single-strand break with 3'-hydroxyl (OH) and 5'-deoxyribose phosphate (dRP) termini. In this study, the pre-steady-state kinetics and conformational dynamics of DNA substrates during their interaction with Apn1 were investigated. A stopped-flow method with detection of the fluorescence intensity of 2-aminopurine and pyrrolocytosine located adjacent or opposite to the damage was used. It was found that upon interaction with Apn1, both DNA strands undergo a number of rapid changes. The location of fluorescent analogs of heterocyclic bases in DNA does not influence the catalytic step of the reaction. Comparison of data obtained for yeast Apn1 and reported data (Kanazhevskaya, L. Yu., Koval, V. V., Vorobjev, Yu. N., and Fedorova, O. S. (2012) Biochemistry, 51, 1306-1321) for human Ape1 revealed some differences in their interaction with DNA substrates.

[Synthesis and properties of methylene carboxamide mimetics of nucleic acids based on morpholine nucleosides].

Uracyl and adenine containing oligocarboxamide mimetics of nucleic acids based on morpholine nucleosides (MorGly) are synthesized using peptide chemistry methods. Conditions for an analysis of homogeneity of protonated at physiological pH oligomers using a capillary electrophoresis are proposed. Studies of thermostability of complementary complexes formed by MorGly oligomers revealed that melting temperature dramatically depends on heterocyclic base composition (uracyl or adenine). Cooperative interactions realized at junctions in tandem complexes give more contribution to the thermostability in the case of complexes formed by modified oligomers than native oligodeoxyriboadenilates. Adenine containing MorGly oligomers form more stable complexes with poly(U) than native oligodeoxyriboadenilate of the same length. Complexes formed by modified oligomers with polyribonucleotides are more stable in compare with polydeoxyribonucleotide.