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  1. Book ; Online: Controllability-Constrained Deep Network Models for Enhanced Control of Dynamical Systems

    Sharma, Suruchi / Makarenko, Volodymyr / Kumar, Gautam / Tiomkin, Stas

    2023  

    Abstract: Control of a dynamical system without the knowledge of dynamics is an important and challenging task. Modern machine learning approaches, such as deep neural networks (DNNs), allow for the estimation of a dynamics model from control inputs and ... ...

    Abstract Control of a dynamical system without the knowledge of dynamics is an important and challenging task. Modern machine learning approaches, such as deep neural networks (DNNs), allow for the estimation of a dynamics model from control inputs and corresponding state observation outputs. Such data-driven models are often utilized for the derivation of model-based controllers. However, in general, there are no guarantees that a model represented by DNNs will be controllable according to the formal control-theoretical meaning of controllability, which is crucial for the design of effective controllers. This often precludes the use of DNN-estimated models in applications, where formal controllability guarantees are required. In this proof-of-the-concept work, we propose a control-theoretical method that explicitly enhances models estimated from data with controllability. That is achieved by augmenting the model estimation objective with a controllability constraint, which penalizes models with a low degree of controllability. As a result, the models estimated with the proposed controllability constraint allow for the derivation of more efficient controllers, they are interpretable by the control-theoretical quantities and have a lower long-term prediction error. The proposed method provides new insights on the connection between the DNN-based estimation of unknown dynamics and the control-theoretical guarantees of the solution properties. We demonstrate the superiority of the proposed method in two standard classical control systems with state observation given by low resolution high-dimensional images.
    Keywords Electrical Engineering and Systems Science - Systems and Control ; Computer Science - Artificial Intelligence
    Subject code 006
    Publishing date 2023-11-10
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: AID/APOBEC–dependent somatic hypermutation and DNA rearrangements of immunoglobulin and non-immunoglobulin genes

    Kolotova T. / Makarenko V. / Sorokoumova L. / Davidenko M.

    Anali Mečnikìvsʹkogo Institutu, Iss 4, Pp 6-

    2019  Volume 19

    Abstract: Editing Ig genes by activation induced deaminase (AID) initiates the antibody diversification process in B lymphocytes. In mammalian B cells, this process includes somatic hypermutation (SHM) and class switch recombination (CSR). The activity of AID is ... ...

    Abstract Editing Ig genes by activation induced deaminase (AID) initiates the antibody diversification process in B lymphocytes. In mammalian B cells, this process includes somatic hypermutation (SHM) and class switch recombination (CSR). The activity of AID is largely confined to switch regions and Ig variable regions but now it is well established that AID/APOBEC-dependent damage and double DNA breaks leading to genome rearrangements and somatic mutagenesis are pervasive throughout the B cell genome. In this review, we focus on the molecular mechanisms that guide AID/APOBEC mutator to physiological and non-physiological targets. Epigenetic modifications, such as histone post-translational modifications and DNA methylation, cis-elements of DNA and the transcription factors that bind to it, which form regulatory clusters and superenhancers, synthesis of non-coding RNA and features of the transcription mode are involved in targeting of AID/APOBEC deaminases to Ig and non-Ig locus. However, not one of the studied factors is specific for the AID target loci. Thus, to date, there is insufficient clarity on the question of what determines the genetically programmed activity of AID in Ig loci and the genetically unprogrammed activity of AID/APOBEC family deaminases in non-Ig loci. The study of AID/APOBEC-dependent somatic hypermutation and rearrangements of Ig and non-Ig locus have both fundamental biological and applied medical significance. The fundamental significance is that the mechanisms of genetic rearrangements in somatic cells can provide a key to understanding the patterns of evolutionary variability of living organisms. The applied value is that based on the data obtained on the genomic instability of non-Ig loci, methods can be developed that suppress the instability of the genome during carcinogenesis and slow down the formation of chemotherapy resistant variants.
    Keywords aid/apobec family of deaminases ; dna editing ; ig genes somatic hypermutation ; ig class switching recombination gene ; aid/apobec off-targets ; double-stranded dna breaks ; superenhancers ; transcription factors ; histone epigenetic modifications ; non-coding rna ; Medicine (General) ; R5-920
    Subject code 572
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher Mechnikov Institute of Microbiology and immunology
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: New Technique in Assessment of Heart Chambers Remodeling in Acquired Mitral Valve Defects.

    Bokeria, Leo / Makarenko, Vladimir / Kosareva, Tatiana

    Journal of cardiovascular development and disease

    2020  Volume 7, Issue 2

    Abstract: Objective: Analysis and presentation of the capabilities of the new ultrasound technique -the index of volume remodeling (IRV), which allows comprehensive assessing of pathological remodeling of the heart as an integrated functional anatomical system.!## ...

    Abstract Objective: Analysis and presentation of the capabilities of the new ultrasound technique -the index of volume remodeling (IRV), which allows comprehensive assessing of pathological remodeling of the heart as an integrated functional anatomical system.
    Materials and methods: For this study 316 patients with acquired mitral valve disease (MVD) were examined prior to and following mitral valve replacement with bileaflet, disc-, and bioprostheses. Key parameters of the heart were measured in classical echocardiographic projections (end systolic area, end-diastolic area, end systolic volume, and end diastolic volume of ventricles, ventricular ejection fraction, atrial volume, and the ratio of ventricular to atrial volumes). The patients were examined 1-2 days prior to and following the surgery-before discharge, 6 months later, 1 year later, and then annually within next 5 years. The examination data were collected in one- and two-dimensional modes by using Philips EpiQ-7, iE33, HDI, Siemens Acuson, and HP Sonos 2500 diagnostic ultrasound machines equipped with 2.5 and 3.5 MHz transthoracic sensors.
    Results: A comprehensive study of structural geometric remodeling parameters of heart cavities in the context of acquired MVD allowed identifying new patterns in changes of the heart chambers geometry. These changes are reflected in the IRV, a digital indicator of the severity of cardiac pathological remodeling. Analysis of the dynamics of post-operative vs. pre-operative IRV-based remodeling data also showed that the index is highly sensible to the hemodynamic features of through-flows in various designs of prostheses. The IRV has a pronounced prognostic power and allows predicting the long-term outcome of surgical treatment with an accuracy of 82.35%.
    Conclusions: The IRV predictive accuracy formed the basis of the original classification of types of cardiac remodeling, which can assist both in determining the optimal timing for surgery, and in conjunction with other clinical diagnostic data, in predicting the long-term outcome of heart geometry restoration depending on the type of surgical correction. The IRV can be used in evaluation of the heart geometry for any cardiac pathology. It makes the approach to the analysis of pathological remodeling of the heart understandable, consistent, and universal, and also opens up opportunities for further expanding the diagnostic capabilities of radiology in cardiac surgery at all stages of the diagnostic process.
    Language English
    Publishing date 2020-04-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2777082-5
    ISSN 2308-3425 ; 2308-3425
    ISSN (online) 2308-3425
    ISSN 2308-3425
    DOI 10.3390/jcdd7020014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Bounding the Optimal Value Function in Compositional Reinforcement Learning

    Adamczyk, Jacob / Makarenko, Volodymyr / Arriojas, Argenis / Tiomkin, Stas / Kulkarni, Rahul V.

    2023  

    Abstract: In the field of reinforcement learning (RL), agents are often tasked with solving a variety of problems differing only in their reward functions. In order to quickly obtain solutions to unseen problems with new reward functions, a popular approach ... ...

    Abstract In the field of reinforcement learning (RL), agents are often tasked with solving a variety of problems differing only in their reward functions. In order to quickly obtain solutions to unseen problems with new reward functions, a popular approach involves functional composition of previously solved tasks. However, previous work using such functional composition has primarily focused on specific instances of composition functions whose limiting assumptions allow for exact zero-shot composition. Our work unifies these examples and provides a more general framework for compositionality in both standard and entropy-regularized RL. We find that, for a broad class of functions, the optimal solution for the composite task of interest can be related to the known primitive task solutions. Specifically, we present double-sided inequalities relating the optimal composite value function to the value functions for the primitive tasks. We also show that the regret of using a zero-shot policy can be bounded for this class of functions. The derived bounds can be used to develop clipping approaches for reducing uncertainty during training, allowing agents to quickly adapt to new tasks.

    Comment: Accepted in UAI 2023. (11+21 pages, 2+7 figures)
    Keywords Computer Science - Machine Learning
    Subject code 006
    Publishing date 2023-03-04
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: A single-institution analysis of reflector-guided localization using SAVI SCOUT® in nonpalpable breast carcinoma compared to traditional wire localization.

    Bercovici, Nicholas / Makarenko, Vladislav / Vijayaraghavan, Gopal / Larkin, Anne / Lafemina, Jennifer / Clark, Jennifer / Kandil, Dina

    The breast journal

    2021  Volume 27, Issue 9, Page(s) 737–738

    MeSH term(s) Breast Neoplasms/diagnostic imaging ; Breast Neoplasms/surgery ; Female ; Humans ; Mammography ; Mastectomy, Segmental
    Language English
    Publishing date 2021-06-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1289960-4
    ISSN 1524-4741 ; 1075-122X
    ISSN (online) 1524-4741
    ISSN 1075-122X
    DOI 10.1111/tbj.14243
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Clinical variables associated with indeterminate QuantiFERON

    Makarenko, V V / Al-Turkmani, M R / Rao, L V

    The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

    2019  Volume 22, Issue 12, Page(s) 1429–1434

    Abstract: Setting: The QuantiFERON: Objective: To evaluate clinical variables associated with lower QFT-indeterminate rates after reducing pre-incubation delay.: Design: In 2016, a new protocol of on-site incubation of QFT samples, followed by analysis at ... ...

    Abstract Setting: The QuantiFERON
    Objective: To evaluate clinical variables associated with lower QFT-indeterminate rates after reducing pre-incubation delay.
    Design: In 2016, a new protocol of on-site incubation of QFT samples, followed by analysis at the outside laboratory, was implemented, resulting in much shorter pre-incubation delay of the samples. We retrospectively identified 3583 patients who underwent QFT before and after implementation of the new protocol. Patient records were scrutinized and QFT results were evaluated with respect to associated clinical conditions.
    Results: The patients were analyzed by dividing them into two cohorts based on maximum pre-incubation time (standard vs. immediate). Monthly indeterminate results dropped from 12.7% ± 0.02 in the standard cohort to 5.5% ± 0.03 in the immediate cohort (
    Conclusion: Limiting the pre-incubation time to 1 h maximum significantly improved QFT performance, especially in patients from certain clinical categories.
    MeSH term(s) Adult ; Aged ; Female ; Humans ; Interferon-gamma Release Tests/methods ; Latent Tuberculosis/diagnosis ; Male ; Massachusetts ; Middle Aged ; Retrospective Studies ; Sensitivity and Specificity ; Specimen Handling/methods
    Language English
    Publishing date 2019-01-03
    Publishing country France
    Document type Journal Article
    ZDB-ID 1385624-8
    ISSN 1815-7920 ; 1027-3719
    ISSN (online) 1815-7920
    ISSN 1027-3719
    DOI 10.5588/ijtld.18.0914
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Deep Learning-Based Image Registration in Dynamic Myocardial Perfusion CT Imaging.

    Lara-Hernandez, A / Rienmuller, T / Juarez, I / Perez, M / Reyna, F / Baumgartner, D / Makarenko, V N / Bockeria, O L / Maksudov, M / Rienmuller, R / Baumgartner, C

    IEEE transactions on medical imaging

    2023  Volume 42, Issue 3, Page(s) 684–696

    Abstract: Registration of dynamic CT image sequences is a crucial preprocessing step for clinical evaluation of multiple physiological determinants in the heart such as global and regional myocardial perfusion. In this work, we present a deformable deep learning- ... ...

    Abstract Registration of dynamic CT image sequences is a crucial preprocessing step for clinical evaluation of multiple physiological determinants in the heart such as global and regional myocardial perfusion. In this work, we present a deformable deep learning-based image registration method for quantitative myocardial perfusion CT examinations, which in contrast to previous approaches, takes into account some unique challenges such as low image quality with less accurate anatomical landmarks, dynamic changes of contrast agent concentration in the heart chambers and tissue, and misalignment caused by cardiac stress, respiration, and patient motion. The introduced method uses a recursive cascade network with a ventricle segmentation module, and a novel loss function that accounts for local contrast changes over time. It was trained and validated on a dataset of n = 118 patients with known or suspected coronary artery disease and/or aortic valve insufficiency. Our results demonstrate that the proposed method is capable of registering dynamic cardiac perfusion sequences by reducing local tissue displacements of the left ventricle (LV), whereas contrast changes do not affect the registration and image quality, in particular the absolute CT (HU) values of the entire CT sequence. In addition, the deep learning-based approach presented reveals a short processing time of a few seconds compared to conventional image registration methods, demonstrating its application potential for quantitative CT myocardial perfusion measurements in daily clinical routine.
    MeSH term(s) Humans ; Deep Learning ; Tomography, X-Ray Computed ; Myocardium ; Heart/diagnostic imaging ; Perfusion ; Image Processing, Computer-Assisted ; Myocardial Perfusion Imaging
    Language English
    Publishing date 2023-03-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 622531-7
    ISSN 1558-254X ; 0278-0062
    ISSN (online) 1558-254X
    ISSN 0278-0062
    DOI 10.1109/TMI.2022.3214380
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Kolonializm: vzgljad iz segodnjašnego dnja

    Makarenko, V

    Obščestvo i ėkonomika : meždunarodnyj naučnyj i obščestvenno-političeskij žurnal , No. 8/9 , p. 125-182

    2002  , Issue 8, Page(s) 125–182

    Author's details V. Makarenko
    Keywords Kolonialismus ; Sowjetunion ; Welt
    Language Russian
    Publisher Izdat. Nauka
    Publishing place Moskva
    Document type Article
    Note In kyrill. Schr., russ.
    ZDB-ID 1135678-9
    Database ECONomics Information System

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  9. Article: Neural network with embedded oscillators.

    Makarenko, V

    The Biological bulletin

    1994  Volume 187, Issue 2, Page(s) 256

    MeSH term(s) Neural Networks (Computer) ; Neurons/physiology ; Periodicity
    Language English
    Publishing date 1994-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1268-3
    ISSN 1939-8697 ; 0006-3185 ; 0148-9488
    ISSN (online) 1939-8697
    ISSN 0006-3185 ; 0148-9488
    DOI 10.1086/BBLv187n2p256
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Noise Modulated Persistence of the Metastable State in a Simulated Neural Network.

    Makarenko, V

    The Biological bulletin

    1993  Volume 185, Issue 2, Page(s) 301–302

    Language English
    Publishing date 1993-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1268-3
    ISSN 1939-8697 ; 0006-3185 ; 0148-9488
    ISSN (online) 1939-8697
    ISSN 0006-3185 ; 0148-9488
    DOI 10.1086/BBLv185n2p301
    Database MEDical Literature Analysis and Retrieval System OnLINE

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