Vestnik (series: physical-mathematical and natural sciences), №1/2024

Manukyan A. The Moore-Penrose Inverse of Tridiagonal Skew-Hermitian Matrices with Zero Diagonal Elements

ABSTRACT. The present paper is devoted to deriving closed form expressions for the Moore-Penrose inverse of tridiagonal skew-Hermitian matrices with zero diagonal elements. Using the formulas obtained, a numerical algorithm with optimal computational efforts is constructe.
Keywords:  Moore-Penrose inverse, skew-Hermitian matrix, tridiagonal matrix.

Aramyan R., Apinyan L. Reconstruction of an Ellipse from the Distributions of Chords in Directions

ABSTRACT. The problem of finding information or completely reconstructing convex bodies from the distributions of characteristics of k-dimensional sections is one of the main problems of stochastic tomography. This work is devoted to the reconstruction of an ellipse on a plane through the distribution of random chords in directions. A reconstruction algorithm is proposed.
Keywords: ellipse, convexity, distribution function, support function, ellipse restoration.

Altunyan V. Comparative Analysis of Symmetry Corrected RMSD Calculation Tools in Molecular Docking

ABSTRACT. The accurate calculation of RMSD, especially with symmetry correction, is vital for reliable molecular comparisons in computational chemistry. This study conducts a comparative analysis of three advanced RMSD calculation tools to assess their accuracy, failure rates, and computational efficiency across varied molecular scenarios. Utilizing two large datasets, each comprising approximately 2000 molecular structures, the tools are evaluated in the context of molecular docking simulations. These datasets are sourced from well-established molecular databases and include a range of complexities to challenge the tools under test. The research extends to include special molecular cases, designed to expose strengths and weaknesses of each tool, providing a comprehensive overview of their performance. This analysis aims to guide computational chemists in selecting the most appropriate RMSD calculation tools for their research needs, enhancing the accuracy and reliability of molecular modeling studies.
Keywords: symmetry corrected RMSD, molecular docking.

Fahradyan A., Baghdasaryan T., Melkonyan V., Sahakyan V., Kirakosyan
L., Hovhannisyan O., Sargsyan S., Darbinyan A. Comparing and Improving Change Detection Method

ABSTRACT. This paper delves into a comparative analysis of various Change Detection (CD) methods on aerial image pairs known for their promising outcomes. By incorporating adjustments, like Image Matching, Sliding Window, and our proposed method, the Gaussian Sliding Window, these methods were trained on distinct CD datasets to attain the most effective solution for the proposed problem.
Keywords: Change Detection, Transformers, Image Matching, UAV, Aerial Images.

Melentevа D., Zernov N., Ghamaryan V., Hunanyan L., Popugaeva E. Effect of TRPC6 Modulators on Actin Cytoskeleton in vitro

ABSTRACT. During experiments, the effect of TRPC6 plasma membrane channel modulators on cellular actin was evaluated. Compounds GSK1702934A, C20, Z12-30 were used as agonists of TRPC6, and SKF96365 were used as blocker. Experiments were performed on primary tip tail fibroblasts culture, as well as on primary hippocampal culture. 
Keywords:  TRPC6, neurodegeneration, actin cytoskeleton, neuron.

Paronyan А. A Comparative Analysis of Protein Structure Prediction Programs Using the Example of 14-3-3

ABSTRACT. Identifying the tertiary structures of proteins is very important for understanding the molecular mechanisms of action, especially if a given protein plays a key role in disease pathogenesis. A wide range of software packages and servers are currently available to model the full-length structures of proteins based on the amino acid sequence. In this paper, we reviewed the three most common programs for predicting protein structures: AlphaFold2, Rosetta, and I-TASSER. 
Keywords:  protein structure modeling, in silico, prediction methods, AlphaFold2, Rosetta, I-TASSER.

Davitavyan S. Multi-omics portrayal of breast cancers

ABSTRACT. The factors that influence tumor development are diverse and ambiguous. Consequently, there is a necessity for the development of new data-mining approaches that will contribute to efficient disease diagnostics, prognostics, and monitoring of disease courses. This study is aimed to identify patterns of genetic changes that provide changes in expression in tumor samples. Multiomics data for analyzing the main manifestations of genetic shifts were obtained from the GDC database. We used a multilayer self-organizing map (ML-SOM) algorithm for clustering and dimension reduction. This approach allows for distinguishing the sets of factors associated with cancer, and on the other hand, it provides information on the distribution of multilayer genetic data among tumor samples..
Keywords: breast cancer, multi-omics data, self-organizing maps.

Kotlov N.Yu. Lymphoma Microenvironment Subtypes Prognostic power Validation in frontline Obinutuzumab treated patients
with Diffuse large B-cell Lymphoma

ABSTRACT. The standard treatment for diffuse large B-cell lymphoma still remains the combination of immunochemotherapy agents R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone). However, up to 40% of patients do not achieve stable remission. Obinutuzumab – a monoclonal antibody against the B-cell receptor CD20, is being tested in clinical trials as an alternative to rituximab in the form of the combination GCHOP. The microenvironment of lymphomas plays a significant prognostic role in the treatment with R-CHOP in the first line. In this study, the association of the LME-GC and LME-MS subtypes with a better prognosis was confirmed compared to the LME-DE subtype when treated with the combination of G-CHOP in the first line based on data from the clinical trial GOYA.
Keywords:  Diffuse large B-cell lymphoma – lymphoma microenvironment – prognostic biomarkers.