Understanding the 3D structure of RNA is key to understanding RNA function. RNA 3D structure is modular and can be seen as a composition of building blocks of various sizes called tertiary motifs. Currently, long-range motifs formed between distant loops and helical regions are largely less studied than the local motifs determined by the RNA secondary structure. We surveyed long-range tertiary interactions and motifs in a non-redundant set of non-coding RNA 3D structures. A new dataset of annotated LOng-RAnge RNA 3D modules (LORA) was built using an approach that does not rely on the automatic annotations of non-canonical interactions. An original algorithm, ARTEM, was developed for annotation-, sequence- and topology-independent superposition of two arbitrary RNA 3D modules. The proposed methods allowed us to identify and describe the most common long-range RNA tertiary motifs. Along with the prevalent canonical A-minor interactions, a large number of previously undescribed staple interactions were observed. The most frequent long-range motifs were found to belong to three main motif families: planar staples, tilted staples, and helical packing motifs.

Data analysis in the context of the features of the problem domain and the dynamics of processes are significant in various industries. Uncertainty modeling based on fuzzy logic allows building approximators for solving a large class of problems. In some cases, type-2 fuzzy sets in the model are used. The article describes constructing fuzzy time series models of the analyzed processes within the context of the problem domain. An algorithm for fuzzy modeling of the time series was developed. A new time series forecasting scheme is proposed. An illustrative example of the time series modeling is presented. The benefits of contextual modeling are demonstrated.

The development of the economy and the transition to industry 4.0 creates new challenges for artificial intelligence methods. Such challenges include the processing of large volumes of data, the analysis of various dynamic indicators, the discovery of complex dependencies in the accumulated data, and the forecasting of the state of processes. The main point of this study is the development of a set of analytical and prognostic methods. The methods described in this article based on fuzzy logic, statistic, and time series data mining, because data extracted from dynamic systems are initially incomplete and have a high degree of uncertainty. The ultimate goal of the study is to improve the quality of data analysis in industrial and economic systems. The advantages of the proposed methods are flexibility and orientation to the high interpretability of dynamic data. The high level of the interpretability and interoperability of dynamic data is achieved due to a combination of time series data mining and knowledge base engineering methods. The merging of a set of rules extracted from the time series and knowledge base rules allow for making a forecast in case of insufficiency of the length and nature of the time series. The proposed methods are also based on the summarization of the results of processes modeling for diagnosing technical systems, forecasting of the economic condition of enterprises, and approaches to the technological preparation of production in a multi-productive production program with the application of type 2 fuzzy sets for time series modeling. Intelligent systems based on the proposed methods demonstrate an increase in the quality and stability of their functioning. This article contains a set of experiments to approve this statement.

Understanding the 3D structure of RNA is key to understanding RNA function. RNA 3D structure is modular and can be seen as a composition of building blocks of various sizes called tertiary motifs. Currently, long-range motifs formed between distant loops and helical regions are largely less studied than the local motifs determined by the RNA secondary structure. We surveyed long-range tertiary interactions and motifs in a non-redundant set of non-coding RNA 3D structures. A new dataset of annotated LOng-RAnge RNA 3D modules (LORA) was built using an approach that does not rely on the automatic annotations of non-canonical interactions. An original algorithm, ARTEM, was developed for annotation-, sequence- and topology-independent superposition of two arbitrary RNA 3D modules. The proposed methods allowed us to identify and describe the most common long-range RNA tertiary motifs. Three basic interaction types were identified to be recurrent in the long-range RNA 3D modules: ribose-ribose interactions, canonical Type I and Type II A-minor interactions, and previously undescribed staple interactions. These three interaction types were found to be different building blocks of the same complex staple motifs common to non-coding RNA 3D structures.