Geometric algorithms for input constrained systems with application to flight control.

In this thesis novel numerical algorithms are developed to solve some problems of analysis and control design for unstable linear dynamical systems having their input constrained by maximum amplitude and rate of the control signals. Although the results obtained are of a general nature, all the problems considered are induced by flight control applications. Moreover, all these problems are stated in terms of geometry, and because of this their solution in the thesis was effectively achieved by geometrically-oriented methods. The problems considered are mainly connected with the notions of the controllable and stability regions. The controllable region is defined as the set of states of an unstable dynamical system that can be stabilized by some realizable control action. This region is bounded due to input constraints and its size can serve as a controllability measure for the control design problem. A numerical algorithm for the computation of two-dimensional slices of the region is proposed. Moreover, the stability region design is also considered. The stability region of the closed-loop system is the set of states that can be stabilized by a particular controller. This region generally utilizes only a part of the controllable region. Therefore, the controller design objective may be formulated as maximizing this region. A controller that is optimal in this sense is proposed for the case of one and two exponentially unstable open-loop eigenvalues. In the final part of the thesis a linear control allocation problem is considered for overactuated systems and its real-time solution is suggested. Using the control allocation, the actuator selection task is separated from the regulation task in the control design. All fault detection and reconfiguration capabilities are concentrated in one special unit called the control allocator, while a general control algorithm, which produces 'virtual' input for the system, remains intact. In the case of an actuator fault, only the control allocation unit needs to be reconfigured and in many cases it can generate the same 'virtual' input using a different set of control effectors. A novel control allocation algorithm, which is proposed in the thesis, is based on multidimensional interval bisection techniques

Bifurcation control of aeroelastic limit cycle oscillations

An active flutter suppression using linear saturated control is investigated for a 2dof wing section with nonlinear torsional stiffness and limited deflection amplitude of its single control effector. The suppression of limit cycle oscillations in the nonlinear closed-loop system is achieved through maximization of the stability region of the linearized system. A bifurcation sequence leading to limit cycle disappearance is revealed. With increase of the maximum control input amplitude, the closed-loop limit cycle is transformed into a stable torus, which disappears at higher control amplitude through a nonlocal bifurcation similar to a boundary crisis in chaotic systems. Finally, a saddle-node bifurcation of the limit cycle gives necessary conditions for global stability in the closed-loop system

Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature

Saik, Olga V, Demenkov PS, Ivanisenko, Timofey V, et al. Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature. JOURNAL OF INTEGRATIVE BIOINFORMATICS. 2018;15(4): 20180054.Comorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including ILIA, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes

Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature

Comorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including IL1A, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes

No forest without management

Criterion 1 results. (XLSX 59 kb

Additional file 1: Table S2. of Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

Results of gene ontology enrichment analysis. (XLSX 280 kb

Additional file 6: Table S6. of Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

Criteria 4 and 5 results. (XLSX 36 kb

Additional file 4: Table S4. of Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

Criterion 2 results. (XLSX 41 kb

Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

Abstract Background Hypertension and bronchial asthma are a major issue for people’s health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235–330 million people globally have been affected by asthma and approximately 250,000–345,000 people have died each year from the disease. The development of the effective treatment therapies against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and their treatment. Hence, in this study the bioinformatical methodology for the analysis of the comorbidity of these two diseases have been developed. As such, the search for candidate genes related to the comorbid conditions of asthma and hypertension can help in elucidating the molecular mechanisms underlying the comorbid condition of these two diseases, and can also be useful for genotyping and identifying new drug targets. Results Using ANDSystem, the reconstruction and analysis of gene networks associated with asthma and hypertension was carried out. The gene network of asthma included 755 genes/proteins and 62,603 interactions, while the gene network of hypertension - 713 genes/proteins and 45,479 interactions. Two hundred and five genes/proteins and 9638 interactions were shared between asthma and hypertension. An approach for ranking genes implicated in the comorbid condition of two diseases was proposed. The approach is based on nine criteria for ranking genes by their importance, including standard methods of gene prioritization (Endeavor, ToppGene) as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analysed genes. According to the proposed approach, the genes IL10, TLR4, and CAT had the highest priority in the development of comorbidity of these two diseases. Additionally, it was revealed that the list of top genes is enriched with apoptotic genes and genes involved in biological processes related to the functioning of central nervous system. Conclusions The application of methods of reconstruction and analysis of gene networks is a productive tool for studying the molecular mechanisms of comorbid conditions. The method put forth to rank genes by their importance to the comorbid condition of asthma and hypertension was employed that resulted in prediction of 10 genes, playing the key role in the development of the comorbid condition. The results can be utilised to plan experiments for identification of novel candidate genes along with searching for novel pharmacological targets