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Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia
Komissarov A. B., Safina K. R., Garushyants S. K., Fadeev A. V., Sergeeva M. V., Ivanova A. A., Danilenko D. M., Lioznov D., Shneider O. V., Shvyrev Nikita, Spirin V., Glyzin D., Shchur V., Bazykin G. A.
The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions came from non-Chinese sources, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-4) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.7 (2.5-5.0).
Priority areas:
IT and mathematics
Language:
English
Publication based on the results of:
Slivnitsin P., Mylnikov L., Engineering Applications of Artificial Intelligence 2026 Vol. 179 Article 115185
The paper describes a applied artificial intelligence task of recognition-by-components method of real objects based on the recognition of a limited set of primitives or components. The recognition-by-components makes it possible to determine the components, that compose an object, and increase the number of recognizable objects without degrading the recognition quality. Training is performed on ...
Added: May 29, 2026
Kazantseva A. V., A.V. Toropova, Khusnutdinova E. K. et al., ВАВИЛОВСКИЙ ЖУРНАЛ ГЕНЕТИКИ И СЕЛЕКЦИИ, Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук» (ИЦиГ СО РАН) (Новосибирск) 2025 Vol. 30 No. 3 P. 470–481
The development of musical abilities, including absolute pitch, musical memory, rhythm sense, and musicality, at a high degree is determined by a hereditary component (up to 68 %). The studies implementing a genome-wide linkage and association approach to musical aptitude have revealed more than 100 genetic loci. This spectrum is comprised of the genes encoding ...
Added: May 29, 2026
Gorbounov Vassily, Kazakov A., Data Analytics and Topology 2025 Vol. 1 No. 1 P. 33–45
A classic problem in data analysis is studying the systems of subsets defined by either a similarity or a dissimilarity function on X which is either observed directly or derived from a data set.
For an electrical network there are two functions on the set of the nodes defined by the resistance matrix and the response ...
Added: May 28, 2026
Mokienko O., Zisman M. A., Bobrov P. et al., American Journal of Physical Medicine and Rehabilitation 2026 Vol. 105 No. 6 P. 555–563
Brain-computer interfaces (BCIs) represent a promising technology for restoring lower limb motor functions and gait after stroke. The application of BCIs in this field is supported by a limited number of studies. The objective of the review was to systematically and critically evaluate the current evidence on the use of BCIs for lower limb function ...
Added: May 28, 2026
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Background:
Delay discounting refers to the tendency to choose sooner, smaller rewards over larger, later rewards. Many previous studies link this tendency positively to reward sensitivity, yet the specific mechanisms behind this association remain poorly understood. Reward sensitivity may relate to delay discounting through at least three possible pathways: increased sensitivity to reward size, increased sensitivity ...
Added: May 27, 2026
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В сборник вошли материалы VIII Международной научной конференции «Информационные технологии и технические средства управления» (ICCT-2024). На конференции были рассмотрены вопросы, касающиеся перспектив развития научного приборостроения в телекоммуникационных и управляющих системах, биомедицинской информатики, аппаратного и программного обеспечения информационнокоммуникационных систем, надежности, диагностики и неразрушающего контроля, систем управления и автоматизации, цифровых экосистем, управления производством и логистикой, методов математического ...
Added: May 27, 2026
Degtyarev A., Bakhurin S., Yudin N., DSPA 2026 P. 1–6
This paper investigates one possible solution to the problem of self-interference cancellation (SIC) arising in the design of in-band full-duplex (IBFD) communication systems. Self-interference cancellation is performed in the digital domain using multilayer nonlinear models adapted via gradient-based optimization. The presence of local minima and saddle points during the adaptation of multilayer models limits the ...
Added: May 26, 2026
Ilyashenko Y., Shilin I., Stanislav Minkov, Russian Journal of Mathematical Physics 2026 Vol. 33 No. 1 P. 89–106
In this paper, new numerical invariants of structurally unstable vector fields in the plane
are found. One of the main tools is an improved asymptotics of sparkling saddle connections that
occur when a separatrix loop of a hyperbolic saddle breaks. Another main tool is a new topological
invariant of two arithmetic progressions, both perturbed and unperturbed, on the ...
Added: May 26, 2026
Androsov I., Proceedings of the Institute for System Programming of the RAS 2026 Vol. 38 No. 3 P. 87–114
This paper examines echo state networks (ESNs), one of the most prevalent approaches to
implementing reservoir computing. An ESN consists of a recurrent neural network with fixed (untrained)
weights and a readout layer that is typically linear and trainable. This approach enables the creation of energyefficient and computationally efficient neural networks capable of real-time learning. However, since ...
Added: May 26, 2026
Gusev I., Maksaev A., Promyslov V., Journal of Mathematical Sciences 2025 Vol. 299 No. 6
The regular graph of the space of n × m matrices over a field F is defined as the undirected graph whose vertices are matrices of rank min(n, m), and distinct matrices A and B are connected by an edge if and only if rk(A + B) < min(n, m). In this paper, for |F| ...
Added: May 25, 2026
Kochetkova E., Kostanian D., Martynova O. et al., Brain Topography 2026 Vol. 39 No. 4 Article 51
Letter recognition is assumed to involve several levels of analysis, including coarse tuning for category and novelty and more fine tuning for specific features, related to letter orientation. We employed an oddball fast periodic visual stimulation (FPVS) paradigm with magnetoencephalography (Elekta VectorView, 306 sensors) to study neural discrimination responses in the source space. Using contrasts ...
Added: May 24, 2026
Караваева Е. А., Кулигин Л. А., Rezunik L. et al., Труды Института системного программирования РАН 2026 Т. 38 № 3 С. 67–94
В статье представлен метод рефакторинга исходного кода на основе интеграции большой языковой модели (LLM) и расширенной UML-модели программного кода. Предложенный подход позволяет выявлять проблемные участки кода с использованием функций тревожности и структурных метрик классов, а затем выполнять автоматизированный рефакторинг. Ключевой особенностью метода является использование LLM для генерации формальных спецификаций на языке OCL (Object Constraint Language), ...
Added: May 24, 2026
Tyukin I., Tyukina T., van Helden D. P. et al., Information Sciences 2024 Vol. 678 Article 120856
AI errors pose a significant challenge, hindering real-world applications. This work introduces a novel approach to cope with AI errors using weakly supervised error correctors that guarantee a specific level of error reduction. Our correctors have low computational cost and can be used to decide whether to abstain from making an unsafe classification. We provide ...
Added: May 23, 2026
Zaikin A., Sviridov I., Sosedka A. et al., Technologies 2026 Vol. 14 No. 2 Article 84
High-dimensional tabular data are common in biomedical and clinical research, yet conventional machine learning methods often struggle in such settings due to data scarcity, feature redundancy, and limited generalization. In this study, we systematically evaluate Synolitic Graph Neural Networks (SGNNs), a framework that transforms high-dimensional samples into sample-specific graphs by training ensembles of low-dimensional pairwise ...
Added: May 23, 2026
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A fast simulation of the detector response is a vital task in high-energy physics (HEP). Traditional Monte-Carlo methods form the backbone of modern particle physics simulation software but are computationally expensive. We present a machine-learning-based approach to fast simulation of the Focusing Aerogel Ring Imaging Cherenkov (FARICH) detector response. Given a particle track and momentum, ...
Added: May 19, 2026
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Comprehensive data on natural hazards and their consequences are crucial for effective for risk assessment, adaptation planning, and emergency response. However, many countries face challenges with fragmented, inconsistent, and inaccessible data, particularly regarding local-scale events. To address this data gap in Russia, we developed an end-to-end processing pipeline that scrapes news from various online sources, ...
Added: April 28, 2026
Dvoynikova A., Маркитантов М. В., Рюмина Е. В. et al., Информатика и автоматизация (Труды СПИИРАН) 2021 Т. 20 № 5 С. 1116–1152
Начиная с 2019 года все страны мира столкнулись со стремительным распространением пандемии, вызванной коронавирусной инфекцией COVID-19, борьба с которой продолжается мировым сообществом и по настоящее время. Несмотря на очевидную эффективность средств индивидуальной защиты органов дыхания от заражения коронавирусной инфекцией, многие люди пренебрегают использованием защитных масок для лица в общественных местах. Поэтому для контроля и своевременного ...
Added: April 24, 2026
Pilé I., Deng Y., Shchur L., / Series arXiv "math". 2026. No. 2604.10254.
We investigate the spatial overlap of successive spin configurations in Markov chain Monte Carlo simulations using the local Metropolis algorithm and the Svendsen-Wang and Wolff cluster algorithms. We examine the dynamics of these algorithms for two models in different universality classes: the Ising model and the Potts model with three components. The overlap of two ...
Added: April 20, 2026
Салагай О. О., Сахарова Г. М., Антонов Н. С. et al., Общественное здоровье 2024 Т. 4 № 4 С. 4–15
Introduction. The study is devoted to the analysis of the dynamics of the tobacco and alcohol use prevalence among the adult population during the COVID-19 pandemic.
The purpose of the study: to analyze the impact of the COVID-19 pandemic on the prevalence of tobacco and nicotine-containing products consumption among the adult population of the Russian Federation, men and ...
Added: April 9, 2026
Салагай О. О., Сахарова Г. М., Антонов Н. С. et al., Общественное здоровье 2022 Т. 2 № 2 С. 29–39
The fight against the COVID‑19 pandemic has led to the implementation of unprecedented measures in countries, including self-isolation, which have had a significant impact on people’s behavior and could lead to a change in the consumption of tobacco and nicotine-containing products. This article provides an overview of studies evaluating smoking behavior change and its impact ...
Added: April 9, 2026
Gabdullin N., Androsov I., / Series Computer Science "arxiv.org". 2026.
Label prediction in neural networks (NNs) has O(n) complexity proportional to the number of classes. This holds true for classification using fully connected layers and cosine similarity with some set of class prototypes. In this paper we show that if NN latent space (LS) geometry is known and possesses specific properties, label prediction complexity can ...
Added: April 2, 2026
Islentyeva Anna, Scheffler T., Discourse and Communication 2024 Vol. 18 No. 2 P. 216–243
This paper represents a comparative study that explores the governmental vaccine advertising campaigns that were authorised by two English-speaking and two German-speaking countries – namely Australia, Britain, Austria and Germany – within the context of the global SARS-CoV-2 pandemic. The data set in question comprises 40 vaccination posters issued by each country’s respective government between ...
Added: March 9, 2026
Bilqis L. C., Shishkina A., Journal of Globalization Studies 2025 Vol. 16 No. 2 P. 169–179
This article is devoted to the study of the phenomenon of digital nomadism in the period after the onset of the COVID-19 pandemic, which has accelerated the trend on transformation of many aspects of life, including labor market, due to digitalization. The authors discuss the significance of this phenomenon in the context of the intensified ...
Added: February 25, 2026