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  1. Article ; Online: Kinetics of Ca

    Emelyanenko, Victor I / Vologzhannikova, Alisa A / Kazakov, Alexey S / Borisova, Nadezhda I / Permyakov, Eugene A

    Protein and peptide letters

    2023  Volume 30, Issue 2, Page(s) 108–115

    Abstract: Background: Small Ca: Objective: Intrinsic protein fluorescence of cod parvalbumin can be used for elucidating the mechanism of Ca: Methods: Steady-state fluorescence spectra of cod parvalbumin were measured using Cary Eclipse spectrofluorimeter. ... ...

    Abstract Background: Small Ca
    Objective: Intrinsic protein fluorescence of cod parvalbumin can be used for elucidating the mechanism of Ca
    Methods: Steady-state fluorescence spectra of cod parvalbumin were measured using Cary Eclipse spectrofluorimeter. Stopped-flow accessories in combination with a novel high-speed spectrofluorimeter were used for measurements of kinetics of Ca
    Results: The fluorescent phase plots (fluorescence intensity at a fixed wavelength plotted against a fluorescence intensity at another fixed wavelength), constructed from steady state and kinetical data, shows a break at [Ca
    Conclusion: The results of the present spectral study showed that the binding of Ca
    MeSH term(s) Binding Sites ; Calcium/chemistry ; Cations ; Cations, Divalent ; Kinetics ; Parvalbumins/chemistry ; Parvalbumins/metabolism ; Protein Binding ; Spectrometry, Fluorescence ; Gadiformes
    Chemical Substances Calcium (SY7Q814VUP) ; Cations ; Cations, Divalent ; Parvalbumins
    Language English
    Publishing date 2023-01-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1280776-x
    ISSN 1875-5305 ; 0929-8665
    ISSN (online) 1875-5305
    ISSN 0929-8665
    DOI 10.2174/0929866530666230109123224
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4452: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article: CCR5/CXCR3 antagonist TAK-779 prevents diffuse alveolar damage of the lung in the murine model of the acute respiratory distress syndrome.

    Chernov, Aleksandr S / Rodionov, Maksim V / Kazakov, Vitaly A / Ivanova, Karina A / Meshcheryakov, Fedor A / Kudriaeva, Anna A / Gabibov, Alexander G / Telegin, Georgii B / Belogurov, Alexey A

    Frontiers in pharmacology

    2024  Volume 15, Page(s) 1351655

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2024-02-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2024.1351655
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  3. Article: Machine learning-based detection of cardiovascular disease using ECG signals: performance vs. complexity.

    Pham, Huy / Egorov, Konstantin / Kazakov, Alexey / Budennyy, Semen

    Frontiers in cardiovascular medicine

    2023  Volume 10, Page(s) 1229743

    Abstract: Introduction: Cardiovascular disease remains a significant problem in modern society. Among non-invasive techniques, the electrocardiogram (ECG) is one of the most reliable methods for detecting cardiac abnormalities. However, ECG interpretation ... ...

    Abstract Introduction: Cardiovascular disease remains a significant problem in modern society. Among non-invasive techniques, the electrocardiogram (ECG) is one of the most reliable methods for detecting cardiac abnormalities. However, ECG interpretation requires expert knowledge and it is time-consuming. Developing a novel method to detect the disease early improves the quality and efficiency of medical care.
    Methods: The paper presents various modern approaches for classifying cardiac diseases from ECG recordings. The first approach suggests the Poincaré representation of ECG signal and deep-learning-based image classifiers. Additionally, the raw signals were processed with the one-dimensional convolutional model while the XGBoost model was facilitated to predict based on the time-series features.
    Results: The Poincaré-based methods showed decent performance in predicting AF (atrial fibrillation) but not other types of arrhythmia. XGBoost model gave an acceptable performance in long-term data but had a long inference time due to highly-consuming calculations within the pre-processing phase. Finally, the 1D convolutional model, specifically the 1D ResNet, showed the best results in both studied CinC 2017 and CinC 2020 datasets, reaching the F1 score of 85% and 71%, respectively, and they were superior to the first-ranking solution of each challenge. The 1D models also presented high specificity. Additionally, our paper investigated efficiency metrics including power consumption and equivalent CO
    Discussion: Despite the under-performed results, the Poincaré diagrams are still worth studying further because of the accessibility and inexpensive procedure. In the 1D convolutional models, the residual connections are useful to keep the model simple but not decrease the performance. Our approach in power measurement and model interpretation helped understand the numerical complexity and mechanism behind the model decision.
    Language English
    Publishing date 2023-07-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2781496-8
    ISSN 2297-055X
    ISSN 2297-055X
    DOI 10.3389/fcvm.2023.1229743
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  4. Article ; Online: New drugs and stock market: a machine learning framework for predicting pharma market reaction to clinical trial announcements.

    Budennyy, Semen / Kazakov, Alexey / Kovtun, Elizaveta / Zhukov, Leonid

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 12817

    Abstract: Pharmaceutical companies operate in a strictly regulated and highly risky environment in which a single slip can lead to serious financial implications. Accordingly, the announcements of clinical trial results tend to determine the future course of ... ...

    Abstract Pharmaceutical companies operate in a strictly regulated and highly risky environment in which a single slip can lead to serious financial implications. Accordingly, the announcements of clinical trial results tend to determine the future course of events, hence being closely monitored by the public. Most works focus on retrospective analysis of announcement impact on company stock prices, bypassing the consideration of the problem in the predictive paradigm. In this work, we aim to close this gap by proposing a framework that allows predicting the numerical values of announcement-induced changes in stock prices. In fact, it is a problem of the impact prediction of the specific event on the corresponding time series. Our framework includes a BERT model for extracting the sentiment polarity of announcements, a Temporal Fusion Transformer for forecasting the expected return, a graph convolution network for capturing event relationships, and gradient boosting for predicting the price change. We operate with one of the biggest FDA (the Food and Drug Administration) datasets, consisting of 5436 clinical trial announcements from 681 companies for the years 2018-2022. During the study, we get several significant outcomes and domain-specific insights. Firstly, we obtain statistical evidence for the clinical result promulgation influence on the public pharma market value. Secondly, we witness inherently different patterns of responses to positive and negative announcements, reflected in a stronger and more pronounced reaction to negative clinical news. Thirdly, we discover two factors that play a crucial role in a predictive framework: (1) the drug portfolio size of the company, indicating the greater susceptibility to an announcement in the case of low diversification among drug products and (2) the announcement network effect, manifesting through an increase in predictive power when exploiting interdependencies of events belonging to the same company or nosology. Finally, we prove the viability of the forecast setting by getting ROC AUC scores predominantly greater than 0.7 for the classification of price change on historical data. We emphasize the transferability and generalizability of the developed framework on other datasets and domains but on the condition of the presence of two key entities: events and the associated time series.
    MeSH term(s) Retrospective Studies ; Pharmaceutical Preparations ; Machine Learning
    Chemical Substances Pharmaceutical Preparations
    Language English
    Publishing date 2023-08-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-39301-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Recognition of granulocyte-macrophage colony-stimulating factor by specific S100 proteins.

    Kazakov, Alexey S / Rastrygina, Victoria A / Vologzhannikova, Alisa A / Zemskova, Marina Y / Bobrova, Lolita A / Deryusheva, Evgenia I / Permyakova, Maria E / Sokolov, Andrey S / Litus, Ekaterina A / Shevelyova, Marina P / Uversky, Vladimir N / Permyakov, Eugene A / Permyakov, Sergei E

    Cell calcium

    2024  Volume 119, Page(s) 102869

    Abstract: Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a pleiotropic myelopoietic growth factor and proinflammatory cytokine, clinically used for multiple indications and serving as a promising target for treatment of many disorders, including ... ...

    Abstract Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a pleiotropic myelopoietic growth factor and proinflammatory cytokine, clinically used for multiple indications and serving as a promising target for treatment of many disorders, including cancer, multiple sclerosis, rheumatoid arthritis, psoriasis, asthma, COVID-19. We have previously shown that dimeric Ca
    MeSH term(s) Humans ; Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology ; Granulocyte-Macrophage Colony-Stimulating Factor/metabolism ; S100 Proteins/metabolism ; Recombinant Proteins/metabolism ; Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/chemistry ; Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/metabolism ; Protein Binding ; Binding Sites
    Chemical Substances Granulocyte-Macrophage Colony-Stimulating Factor (83869-56-1) ; S100 Proteins ; Recombinant Proteins ; Receptors, Granulocyte-Macrophage Colony-Stimulating Factor
    Language English
    Publishing date 2024-03-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 757687-0
    ISSN 1532-1991 ; 0143-4160
    ISSN (online) 1532-1991
    ISSN 0143-4160
    DOI 10.1016/j.ceca.2024.102869
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1596: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Nonspecific Amyloid Aggregation of Chicken Smooth-Muscle Titin: In Vitro Investigations.

    Bobylev, Alexander G / Yakupova, Elmira I / Bobyleva, Liya G / Molochkov, Nikolay V / Timchenko, Alexander A / Timchenko, Maria A / Kihara, Hiroshi / Nikulin, Alexey D / Gabdulkhakov, Azat G / Melnik, Tatiana N / Penkov, Nikita V / Lobanov, Michail Y / Kazakov, Alexey S / Kellermayer, Miklós / Mártonfalvi, Zsolt / Galzitskaya, Oxana V / Vikhlyantsev, Ivan M

    International journal of molecular sciences

    2023  Volume 24, Issue 2

    Abstract: A giant multidomain protein of striated and smooth vertebrate muscles, titin, consists of tandems of immunoglobulin (Ig)- and fibronectin type III (FnIII)-like domains representing β-sandwiches, as well as of disordered segments. Chicken smooth muscles ... ...

    Abstract A giant multidomain protein of striated and smooth vertebrate muscles, titin, consists of tandems of immunoglobulin (Ig)- and fibronectin type III (FnIII)-like domains representing β-sandwiches, as well as of disordered segments. Chicken smooth muscles express several titin isoforms of ~500-1500 kDa. Using various structural-analysis methods, we investigated in vitro nonspecific amyloid aggregation of the high-molecular-weight isoform of chicken smooth-muscle titin (SMT
    MeSH term(s) Animals ; Amyloid/metabolism ; Amyloidogenic Proteins/metabolism ; Chickens/metabolism ; Connectin/metabolism ; Muscle, Smooth/metabolism ; Avian Proteins/metabolism
    Chemical Substances Amyloid ; Amyloidogenic Proteins ; Connectin ; Avian Proteins
    Language English
    Publishing date 2023-01-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24021056
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  7. Article ; Online: Calcium-Bound S100P Protein Is a Promiscuous Binding Partner of the Four-Helical Cytokines.

    Kazakov, Alexey S / Deryusheva, Evgenia I / Permyakova, Maria E / Sokolov, Andrey S / Rastrygina, Victoria A / Uversky, Vladimir N / Permyakov, Eugene A / Permyakov, Sergei E

    International journal of molecular sciences

    2022  Volume 23, Issue 19

    Abstract: S100 proteins are multifunctional calcium-binding proteins of vertebrates that act intracellularly, extracellularly, or both, and are engaged in the progression of many socially significant diseases. Their extracellular action is typically mediated by ... ...

    Abstract S100 proteins are multifunctional calcium-binding proteins of vertebrates that act intracellularly, extracellularly, or both, and are engaged in the progression of many socially significant diseases. Their extracellular action is typically mediated by the recognition of specific receptor proteins. Recent studies indicate the ability of some S100 proteins to affect cytokine signaling through direct interaction with cytokines. S100P was shown to be the S100 protein most actively involved in interactions with some four-helical cytokines. To assess the selectivity of the S100P protein binding to four-helical cytokines, we have probed the interaction of Ca
    MeSH term(s) Calcium/metabolism ; Calcium, Dietary ; Calcium-Binding Proteins/metabolism ; Carrier Proteins/metabolism ; Cytokines/metabolism ; Humans ; Immunologic Factors ; Molecular Docking Simulation ; Neoplasm Proteins/metabolism ; Protein Binding ; Receptor for Advanced Glycation End Products/metabolism ; S100 Proteins/metabolism
    Chemical Substances Calcium, Dietary ; Calcium-Binding Proteins ; Carrier Proteins ; Cytokines ; Immunologic Factors ; Neoplasm Proteins ; Receptor for Advanced Glycation End Products ; S100 Proteins ; S100P protein, human ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2022-10-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms231912000
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  8. Article ; Online: Interaction of S100A6 Protein with the Four-Helical Cytokines.

    Kazakov, Alexey S / Deryusheva, Evgenia I / Rastrygina, Victoria A / Sokolov, Andrey S / Permyakova, Maria E / Litus, Ekaterina A / Uversky, Vladimir N / Permyakov, Eugene A / Permyakov, Sergei E

    Biomolecules

    2023  Volume 13, Issue 9

    Abstract: S100 is a family of over 20 structurally homologous, but functionally diverse regulatory (calcium/zinc)-binding proteins of vertebrates. The involvement of S100 proteins in numerous vital (patho)physiological processes is mediated by their interaction ... ...

    Abstract S100 is a family of over 20 structurally homologous, but functionally diverse regulatory (calcium/zinc)-binding proteins of vertebrates. The involvement of S100 proteins in numerous vital (patho)physiological processes is mediated by their interaction with various (intra/extra)cellular protein partners, including cell surface receptors. Furthermore, recent studies have revealed the ability of specific S100 proteins to modulate cell signaling via direct interaction with cytokines. Previously, we revealed the binding of ca. 71% of the four-helical cytokines via the S100P protein, due to the presence in its molecule of a cytokine-binding site overlapping with the binding site for the S100P receptor. Here, we show that another S100 protein, S100A6 (that has a pairwise sequence identity with S100P of 35%), specifically binds numerous four-helical cytokines. We have studied the affinity of the recombinant forms of 35 human four-helical cytokines from all structural families of this fold to Ca
    MeSH term(s) Humans ; Animals ; S100 Calcium Binding Protein A6 ; Molecular Docking Simulation ; Immunologic Factors ; S100 Proteins ; Binding Sites ; Cell Cycle Proteins
    Chemical Substances S100 Calcium Binding Protein A6 ; Immunologic Factors ; S100 Proteins ; S100A6 protein, human (105504-00-5) ; Cell Cycle Proteins
    Language English
    Publishing date 2023-09-04
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom13091345
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  9. Article ; Online: Leonid Shilnikov and mathematical theory of dynamical chaos.

    Gonchenko, Sergey / Kazakov, Alexey / Turaev, Dmitry / Shilnikov, Andrey L

    Chaos (Woodbury, N.Y.)

    2022  Volume 32, Issue 1, Page(s) 10402

    Language English
    Publishing date 2022-02-01
    Publishing country United States
    Document type Editorial
    ZDB-ID 1472677-4
    ISSN 1089-7682 ; 1054-1500
    ISSN (online) 1089-7682
    ISSN 1054-1500
    DOI 10.1063/5.0080836
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: On discrete Lorenz-like attractors.

    Gonchenko, Sergey / Gonchenko, Alexander / Kazakov, Alexey / Samylina, Evgeniya

    Chaos (Woodbury, N.Y.)

    2021  Volume 31, Issue 2, Page(s) 23117

    Abstract: We study geometrical and dynamical properties of the so-called discrete Lorenz-like attractors. We show that such robustly chaotic (pseudohyperbolic) attractors can appear as a result of universal bifurcation scenarios, for which we give a ... ...

    Abstract We study geometrical and dynamical properties of the so-called discrete Lorenz-like attractors. We show that such robustly chaotic (pseudohyperbolic) attractors can appear as a result of universal bifurcation scenarios, for which we give a phenomenological description and demonstrate certain examples of their implementation in one-parameter families of three-dimensional Hénon-like maps. We pay special attention to such scenarios that can lead to period-2 Lorenz-like attractors. These attractors have very interesting dynamical properties and we show that their crises can lead, in turn, to the emergence of discrete Lorenz shape attractors of new types.
    Language English
    Publishing date 2021-03-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1472677-4
    ISSN 1089-7682 ; 1054-1500
    ISSN (online) 1089-7682
    ISSN 1054-1500
    DOI 10.1063/5.0037621
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