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Lopina OD, Sidorenko SV, Fedorov DA, Klimanova EA. G-Quadruplexes as Sensors of Intracellular Na+/K + Ratio: Potential Role in Regulation of Transcription and Translation. Biochemistry (Mosc) 2024; 89:S262-S277. [PMID: 38621755 DOI: 10.1134/s0006297924140153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 04/17/2024]
Abstract
Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.
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Affiliation(s)
- Olga D Lopina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | | | - Dmitry A Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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Varfolomeeva LA, Klimanova EA, Sidorenko SV, Fedorov DA, Lopina OD. [Identification of Melittin-Like Proteins with a Molecular Weight of 67 κDa that Interact with Na^(+)/K^(+)-ATPase]. Mol Biol (Mosk) 2023; 57:1077-1083. [PMID: 38062961 DOI: 10.31857/s0026898423060216, edn: qlkrwl] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/30/2023] [Indexed: 12/18/2023]
Abstract
Melittin, a peptide from bee venom, was found to be able to interact with many proteins, including calmodulin target proteins and ion-transporting P-type ATPases. It is assumed that melittin mimics a protein module involved in protein-protein interactions within cells. Previously, a Na^(+)/K^(+)-ATPase containing the α1 isoform of the catalytic subunit was found to co-precipitate with a protein with a molecular weight of about 70 κDa that interacts with antibodies against melittin by cross immunoprecipitation. In the presence of a specific Na^(+)/K^(+)-ATPase inhibitor (ouabain), the amount of protein with a molecular weight of 70 κDa interacting with Na^(+)/K^(+)-ATPase increases. In order to identify melittin-like protein from murine kidney homogenate, a fraction of melittin-like proteins with a molecular weight of approximately 70 κDa was obtained using affinity chromatography with immobilized antibodies specific to melittin. By mass spectrometry analysis, the obtained protein fraction was found to contain three molecular chaperones of Hsp70 superfamily: mitochondrial mtHsp70 (mortalin), Hsp73, Grp78 (BiP) of endoplasmic reticulum. These data suggest that chaperones from the HSP-70 superfamily contain a melittin-like module.
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Affiliation(s)
- L A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071 Russia
| | - E A Klimanova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - S V Sidorenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - D A Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - O D Lopina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
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Arkhipov VI, Chernomorets IY, Zhuikova NS, Fedorov DA, Pershina EV. The Role of NMDA Receptor Subunits in the Effect of Memantine on the Brain of Healthy Animals. Bull Exp Biol Med 2023; 175:446-449. [PMID: 37768458 DOI: 10.1007/s10517-023-05882-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 09/29/2023]
Abstract
The non-competitive NMDA glutamate receptor antagonist memantine has neuroprotective properties and is the first non-cholinergic drug approved for the treatment of Alzheimer's disease. The purpose of this work was to test the hypothesis that injections of memantine to healthy animals can affect the subunit composition of NMDA receptors in the brain, which may explain the effects of its chronic administration. For this, the expression of subunits GluN1, GluN2A, GluN2B, and GluN2C was studied in the hippocampus and prefrontal cortex of rats after single or five subchronic injections of memantine. The results showed that the GluN2C subunit (GRIN2C) plays an important role in the effects of memantine; against the background of memantine treatment, the expression of this subunit markedly decreased in the prefrontal cortex, but not in the hippocampus, which significantly affected the excitation/inhibition balance in cortical structures.
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Affiliation(s)
- V I Arkhipov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, Russia.
| | - I Yu Chernomorets
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - N S Zhuikova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - D A Fedorov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - E V Pershina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, Russia
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Mosoyan MS, Shelipanov DA, Fedotov PA, Fedorov DA, Simonenko MA. [Experience in performing robot-assisted radical prostatectomy in patients after heart transplan- tation]. Urologiia 2023:92-97. [PMID: 37417416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
INTRODUCTION Prostate cancer (PCa) occupies a leading position in the structure of oncological morbidity and mortality and is an urgent problem of modern oncourology. In recipients after organ transplantation, due to the intake of immunosuppressants, the risk of aggressive forms of cancer increases, which necessitates active treatment. In the world, there is not enough data on the radical treatment of PCa in patients after heart transplantation (HT), especially on surgical treatment. We present the first experience in Russia and Eastern Europe of 3 robot-assisted radical prostatectomy for localized PCa in patients after HT. MATERIALS AND METHODS The procedures were performed from February 2021 to November 2021 at the FGBU NMRC named after V.A. Almazov. Preoperative preparation, as well as postoperative management of patients was carried out jointly by urologists and transplant cardiologists. RESULTS The main demographic, perioperative indicators, as well as oncological and non-oncological outcomes are presented. All patients were discharged from the hospital in a satisfactory condition. During the follow-up period, there were no biochemical recurrences of PCa. Early urinary continence in all three patients was satisfactory. CONCLUSION Thus, robot-assisted radical prostatectomy in patients after HT is a technically feasible, effective, and safe treatment for PCa. The comparative studies with prolonged follow-up are needed.
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Affiliation(s)
- M S Mosoyan
- FGBU NMRC named after V.A. Almazov of the Ministry of Health of the Russian Federation, Saint Petersburg, Russia
| | - D A Shelipanov
- FGBU NMRC named after V.A. Almazov of the Ministry of Health of the Russian Federation, Saint Petersburg, Russia
| | - P A Fedotov
- FGBU NMRC named after V.A. Almazov of the Ministry of Health of the Russian Federation, Saint Petersburg, Russia
| | - D A Fedorov
- FGBU NMRC named after V.A. Almazov of the Ministry of Health of the Russian Federation, Saint Petersburg, Russia
| | - M A Simonenko
- FGBU NMRC named after V.A. Almazov of the Ministry of Health of the Russian Federation, Saint Petersburg, Russia
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Pershina EV, Chernomorets IY, Fedorov DA, Arkhipov VI. Pharmacological Modulation of Excitotoxicity through the Combined Use of NMDA Receptor Inhibition and Group III mGlu Activation Reduces TMT-Induced Neurodegeneration in the Rat Hippocampus. Int J Mol Sci 2023; 24:ijms24098249. [PMID: 37175959 PMCID: PMC10179112 DOI: 10.3390/ijms24098249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
We studied the neuroprotective properties of the non-competitive NMDA receptor antagonist memantine, in combination with a positive allosteric modulator of metabotropic glutamate receptors of Group III, VU 0422288. The treatment was started 48 h after the injection of neurotoxic agent trimethyltin (TMT) at 7.5 mg/kg. Three weeks after TMT injection, functional and morphological changes in a rat hippocampus were evaluated, including the expression level of genes characterizing glutamate transmission and neuroinflammation, animal behavior, and hippocampal cell morphology. Significant neuronal cell death occurred in the CA3 and CA4 regions, and to a lesser extent, in the CA1 and CA2 regions. The death of neurons in the CA1 field was significantly reduced in animals with a combined use of memantine and VU 0422288. In the hippocampus of these animals, the level of expression of genes characterizing glutamatergic synaptic transmission (Grin2b, Gria1, EAAT2) did not differ from the level in control animals, as well as the expression of genes characterizing neuroinflammation (IL1b, TGF beta 1, Aif1, and GFAP). However, the expression of genes characterizing neuroinflammation was markedly increased in the hippocampus of animals treated with memantine or VU 0422288 alone after TMT. The results of immunohistochemical studies confirmed a significant activation of microglia in the hippocampus three weeks after TMT injection. In contrast to the hilus, microglia in the CA1 region had an increase in rod-like cells. Moreover, in the CA1 field of the hippocampus of the animals of the MEM + VU group, the amount of such microglia was close to the control. Thus, the short-term modulation of glutamatergic synaptic transmission by memantine and subsequent activation of Group III mGluR significantly affected the dynamics of neurodegeneration in the hippocampus.
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Affiliation(s)
- Ekaterina V Pershina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Irina Yu Chernomorets
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Dmitry A Fedorov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Vladimir I Arkhipov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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Fedorov DA, Sidorenko SV, Yusipovich AI, Bukach OV, Gorbunov AM, Lopina OD, Klimanova EA. Increased Extracellular Sodium Concentration as a Factor Regulating Gene Expression in Endothelium. Biochemistry (Mosc) 2022; 87:489-499. [PMID: 35790409 DOI: 10.1134/s0006297922060013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Hyperosmotic stimulation of endothelial cells often leads to its dysfunction accompanied, among other things, by proinflammatory response. The mechanisms of this phenomenon are not fully understood. It may arise due to increase in the plasma Na+ concentration, due to increase in the extracellular osmolarity, increase in the intracellular Na+i/K+i ratio, and/or change in the cell stiffness. In the present study we investigated the effects of short-term increase in osmolarity of extracellular medium on the mRNA content of some genes important for endothelial function (including Na+i/K+i-sensitive ones) and the equivalent elasticity constant of human umbilical vein endothelial cells membranes. Hyperosmotic stimulation of these cells with NaCl but not mannitol resulted in accumulation of Na+ ions inside the cells despite the Na,K-ATPase activation, and was also accompanied by the decrease in their equivalent elasticity constant. The amount of IL1α mRNA decreased with increasing osmolarity of the extracellular medium, whereas the amount of ATF3, PAR2, and PTGS2 mRNAs increased only in response to the increasing NaCl concentration. At the same time, under the conditions of our experiments, we did not detect changes in the expression of the osmoprotective transcription factor NFAT5. The obtained data indicate that the increase of extracellular Na+ concentration in the physiological range is an independent factor that affects intracellular Na+i/K+i ratio and regulates expression of some genes (in particular, ATF3, PAR2, PTGS2) in endothelial cells.
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Affiliation(s)
- Dmitry A Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | | | | | - Olesya V Bukach
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Andrey M Gorbunov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Olga D Lopina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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Abstract
Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann-Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems.
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Affiliation(s)
- Dmitry A Fedorov
- Oak Ridge Associated Universities, 100 Orau Way, Oak Ridge, Tennessee 37830, USA
| | - Matthew J Otten
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Stephen K Gray
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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Abstract
In this article, we review nonadiabatic molecular dynamics (NAMD) methods for modeling spin-crossover transitions. First, we discuss different representations of electronic states employed in the grid-based and direct NAMD simulations. The nature of interstate couplings in different representations is highlighted, with the main focus on nonadiabatic and spin-orbit couplings. Second, we describe three NAMD methods that have been used to simulate spin-crossover dynamics, including trajectory surface hopping, ab initio multiple spawning, and multiconfiguration time-dependent Hartree. Some aspects of employing different electronic structure methods to obtain information about potential energy surfaces and interstate couplings for NAMD simulations are also discussed. Third, representative applications of NAMD to spin crossovers in molecular systems of different sizes and complexities are highlighted. Finally, we pose several fundamental questions related to spin-dependent processes. These questions should be possible to address with future methodological developments in NAMD.
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Affiliation(s)
- Saikat Mukherjee
- Institut de Chimie Radicalaire, CNRS 7273, Aix-Marseille University, 13013 Marseille, France;
| | - Dmitry A Fedorov
- Oak Ridge Associated Universities, Oak Ridge, Tennessee 37830, USA;
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, USA;
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Abstract
The ab initio multiple spawning (AIMS) method enables nonadiabatic quantum molecular dynamics simulations in an arbitrary number of dimensions, with potential energy surfaces provided by electronic structure calculations performed on-the-fly. However, the intricacy of the AIMS algorithm complicates software development, deployment on modern shared computer resources, and postsimulation data analysis. PySpawn is a nonadiabatic molecular dynamics software package that addresses these issues. The program is designed to be easily interfaced with electronic structure software, and an interface to the TeraChem software package is described here. PySpawn introduces a task-based reorganization of the AIMS algorithm, allowing fine-grained restart capability and setting the stage for efficient parallelization in a future release. PySpawn includes a user-friendly and interactive Python analysis module that will enable novice users to painlessly adopt AIMS. As a demonstration of PySpawn's simulation capability and analysis module, we report complete active space self-consistent field-based AIMS simulations of the 1,2-dithienyl-1,2-dicyanoethene molecule, a promising molecular photoswitch.
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Affiliation(s)
- Dmitry A Fedorov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Stefan Seritan
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94305, United States
| | - B Scott Fales
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94305, United States
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94305, United States
| | - Benjamin G Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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Klimanova EA, Fedorov DA, Sidorenko SV, Abramicheva PA, Lopina OD, Orlov SN. Ouabain and Marinobufagenin: Physiological Effects on Human Epithelial and Endothelial Cells. Biochemistry (Mosc) 2020; 85:507-515. [PMID: 32569558 DOI: 10.1134/s0006297920040112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Long-term study on the identification of Na,K-ATPase endogenous inhibitors in mammalian tissues has resulted in the discovery of ouabain, marinobufagenin (MBG), and other cardiotonic steroids (CTS) in the blood plasma. Production of ouabain and MBG is increased in essential hypertension and other diseases associated with hypervolemia. Here, we compared the effects of ouabain and MBG on the Na,K-ATPase activity (measured as the transport of Na+, K+, and Rb+ ions) and proliferation and death of human renal epithelial cells (HRECs) and human umbilical vein endothelial cells (HUVEC) expressing α1-Na,K-ATPase. Ouabain concentration that provided the half-maximal inhibition of the Rb+ influx (IC50) into HRECs and HUVECs was 0.07 μM. In both types of cells, the IC50 values for MBG were 10 times higher than for ouabain. Incubation of HREC and HUVEC with 0.001-0.01 μM ouabain for 30 h resulted in 40% increase in the [3H]thymidine incorporation into DNA; further elevation of ouabain concentration to 0.1 μM completely suppressed DNA synthesis. MBG at the concentration of 0.1 μM activated DNA synthesis by 25% in HRECs, but not in HUVECs; 1 μM MBG completely inhibited DNA synthesis in HRECs and by 50% in HUVECs. In contrast to HRECs, incubation of HUVECs in the serum-free medium induced apoptosis, which was almost completely suppressed by ouabain and MBG at the concentrations of 0.1 and 3 μM, respectively. Based on these data, we can conclude that (i) the effect of MBG at the concentrations detected in the blood plasma (<0.01 μM) on HRECs and HUVECs was not due to the changes in the [Na+]i/[K+]i ratio; (ii) the effect of physiological concentrations of ouabain on these cells might be mediated by the activation of Na,K-ATPase, leading to cell proliferation.
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Affiliation(s)
- E A Klimanova
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia.
| | - D A Fedorov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - S V Sidorenko
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - P A Abramicheva
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - O D Lopina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - S N Orlov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
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Abstract
Most nonadiabatic molecular dynamics methods require the determination of a basis of adiabatic or diabatic electronic states at every time step, but in dense manifolds of electronic states, such approaches become intractable. A notable exception is Ehrenfest molecular dynamics, which can be implemented without explicit determination of such a basis but suffers from unphysical behavior when propagation on a mean-field potential energy surface (PES) does not accurately reflect the true dynamics on multiple electronic states. Here we introduce the multiple cloning for dense manifolds of states (MCDMS) method, a systematically improvable approximation to the multiple cloning method. MCDMS avoids both the mean-field PES problem and the need to compute the full electronic spectrum. This is achieved by reformulating multiple cloning to use a subspace of approximate eigenstates constructed from the time-dependent Ehrenfest electronic wave function. By application to model systems, we show that this approach allows a substantial reduction in the size of the required electronic basis without significant loss in accuracy.
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Affiliation(s)
- Dmitry A Fedorov
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Benjamin G Levine
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
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13
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Fedorov DA, Levine BG. A discontinuous basis enables numerically exact solution of the Schrödinger equation around conical intersections in the adiabatic representation. J Chem Phys 2019; 150:054102. [PMID: 30736673 DOI: 10.1063/1.5058268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Solving the vibrational Schrödinger equation in the neighborhood of conical intersections in the adiabatic representation is a challenge. At the intersection point, first- and second-derivative nonadiabatic coupling matrix elements become singular, with the singularity in the second-derivative coupling (diagonal Born-Oppenheimer correction) being non-integrable. These singularities result from discontinuities in the vibronic functions associated with the individual adiabatic states, and our group has recently argued that these divergent matrix elements cancel when discontinuous adiabatic vibronic functions sum to a continuous total nonadiabatic wave function. Here we describe the realization of this concept: a novel scheme for the numerically exact solution of the Schrödinger equation in the adiabatic representation. Our approach is based on a basis containing functions that are discontinuous at the intersection point. We demonstrate that the individual adiabatic nuclear wave functions are themselves discontinuous at the intersection point. This proves that discontinuous basis functions are essential to any tractable method that solves the Schrödinger equation around conical intersections in the adiabatic representation with high numerical precision. We establish that our method provides numerically exact results by comparison to reference calculations performed in the diabatic representation. In addition, we quantify the energetic error associated with constraining the density to be zero at the intersection point, a natural approximation. Prospects for extending the present treatment of a two-dimensional model to systems of higher dimensionality are discussed.
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Affiliation(s)
- Dmitry A Fedorov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Benjamin G Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Affiliation(s)
- Dmitry A. Fedorov
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
| | - Aleksandr O. Lykhin
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
- Department of Chemistry, Siberian Federal University, 79 Svobodny Prospect, Krasnoyarsk, Krasnoyarsk krai, 660041, Russia
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
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15
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Fedorov DA, Derevianko A, Varganov SA. Erratum: “Accurate potential energy, dipole moment curves, and lifetimes of vibrational states of heteronuclear alkali dimers” [J. Chem. Phys. 140, 184315 (2014)]. J Chem Phys 2017; 147:209901. [DOI: 10.1063/1.5004718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dmitry A. Fedorov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0216, USA
| | - Andrei Derevianko
- Department of Physics, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0220, USA
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0216, USA
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16
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Wefers AK, Haberlandt C, Tekin NB, Fedorov DA, Timmermann A, van der Want JJL, Chaudhry FA, Steinhäuser C, Schilling K, Jabs R. Synaptic input as a directional cue for migrating interneuron precursors. Development 2017; 144:4125-4136. [PMID: 29061636 DOI: 10.1242/dev.154096] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/11/2017] [Indexed: 02/02/2023]
Abstract
During CNS development, interneuron precursors have to migrate extensively before they integrate in specific microcircuits. Known regulators of neuronal motility include classical neurotransmitters, yet the mechanisms that assure interneuron dispersal and interneuron/projection neuron matching during histogenesis remain largely elusive. We combined time-lapse video microscopy and electrophysiological analysis of the nascent cerebellum of transgenic Pax2-EGFP mice to address this issue. We found that cerebellar interneuronal precursors regularly show spontaneous postsynaptic currents, indicative of synaptic innervation, well before settling in the molecular layer. In keeping with the sensitivity of these cells to neurotransmitters, ablation of synaptic communication by blocking vesicular release in acute slices of developing cerebella slows migration. Significantly, abrogation of exocytosis primarily impedes the directional persistence of migratory interneuronal precursors. These results establish an unprecedented function of the early synaptic innervation of migrating neuronal precursors and demonstrate a role for synapses in the regulation of migration and pathfinding.
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Affiliation(s)
- Annika K Wefers
- Anatomisches Institut, Anatomie & Zellbiologie, Medizinische Fakultät, University of Bonn, 53115 Bonn, Germany.,Institut für Zelluläre Neurowissenschaften, Medizinische Fakultät, University of Bonn, 53105 Bonn, Germany
| | - Christian Haberlandt
- Institut für Zelluläre Neurowissenschaften, Medizinische Fakultät, University of Bonn, 53105 Bonn, Germany
| | - Nuriye B Tekin
- Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Dmitry A Fedorov
- Institut für Zelluläre Neurowissenschaften, Medizinische Fakultät, University of Bonn, 53105 Bonn, Germany
| | - Aline Timmermann
- Institut für Zelluläre Neurowissenschaften, Medizinische Fakultät, University of Bonn, 53105 Bonn, Germany
| | - Johannes J L van der Want
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Farrukh A Chaudhry
- Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Christian Steinhäuser
- Institut für Zelluläre Neurowissenschaften, Medizinische Fakultät, University of Bonn, 53105 Bonn, Germany
| | - Karl Schilling
- Anatomisches Institut, Anatomie & Zellbiologie, Medizinische Fakultät, University of Bonn, 53115 Bonn, Germany
| | - Ronald Jabs
- Institut für Zelluläre Neurowissenschaften, Medizinische Fakultät, University of Bonn, 53105 Bonn, Germany
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Fedorov DA, Barnes DK, Varganov SA. Ab initio calculations of spectroscopic constants and vibrational state lifetimes of diatomic alkali-alkaline-earth cations. J Chem Phys 2017; 147:124304. [PMID: 28964028 DOI: 10.1063/1.4986818] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We investigate the lifetimes of vibrational states of diatomic alkali-alkaline-earth cations to determine their suitability for ultracold experiments where long decoherence time and controllability by an external electric field are desirable. The potential energy and permanent dipole moment curves for the ground electronic states of LiBe+, LiMg+, NaBe+, and NaMg+ are obtained using the coupled cluster with singles doubles and triples and multireference configuration interaction methods in combination with large all-electron cc-pCVQZ and aug-cc-pCV5Z basis sets. The energies and wave functions of all vibrational states are obtained by solving the Schrödinger equation for nuclei with the B-spline basis set method. To predict the lifetimes of vibrational states, the transition dipole moments, as well as the Einstein coefficients describing spontaneous emission, and the stimulated absorption and emission induced by black body radiation are calculated. Surprisingly, in all studied ions, the lifetimes of the highest excited vibrational states are similar to the lifetimes of the ground vibrational states indicating that highly vibrationally excited ions could be useful for the ultracold experiments requiring long decoherence time.
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Affiliation(s)
- Dmitry A Fedorov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0216, USA
| | - Dustin K Barnes
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0216, USA
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0216, USA
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18
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Fedorov DA, Pruitt SR, Keipert K, Gordon MS, Varganov SA. Ab Initio Multiple Spawning Method for Intersystem Crossing Dynamics: Spin-Forbidden Transitions between 3B1 and 1A1 States of GeH2. J Phys Chem A 2016; 120:2911-9. [DOI: 10.1021/acs.jpca.6b01406] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dmitry A. Fedorov
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
| | - Spencer R. Pruitt
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 South
Cass Avenue, Lemont, Illinois 60439, United States
| | - Kristopher Keipert
- Ames
Laboratory, Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Mark S. Gordon
- Ames
Laboratory, Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Sergey A. Varganov
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
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19
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Kotenko OG, Kondratyuk VA, Fedorov DA, Grinenko AV, Korshak AA, Gusev AV, Popov AO, Grigoryan MS. [ROENTGEN-ENDOVASCULAR EMBOLIZATION OF THE PORTAL VEIN BRANCHES AS A PATIENTS CONDITIONING FOR EXTENSIVE HEPATIC RESECTION]. Klin Khir 2015:5-8. [PMID: 26263633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The results of surgical treatment of 316 patients, suffering focal hepatic diseases, in whom for preoperative preparation a portal vein embolization (PVE) was performed, were analyzed. PVE was applied in a small planned hepatic residual volume. The patients have aged from 21 to 77 yrs, (57 ± 10.6) yrs at average. During (22 ± 7) days after the procedure a hypertrophy of a planned postresectional hepatic volume by 58.6% was observed, while a hypertrophy degree have depended on the embolization volume performed: 57.3%--after embolization of branches of C(V)-C(VIII) hepatic segments, 66%--the segments C(V)-C(VIII) + C(IV). In 281 (89%) patients the extensive hepatic resection was performed, a fatal postresection hepatic insufficiency was not observed. A three-year and five-year disease-free survival have constituted 43.8 and 16.4% accordingly. Thus, a PVE constitutes a miniinvasive intervention, permitting to achieve a planned residual hepatic volume, to expand a diapazon of application of radical extensive hepatic resection in patients, suffering focal hepatic diseases while a small planned residual hepatic volume.
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20
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Kotenko OG, Kondratiuk VA, Fedorov DA, Grinenko AV, Korshak AA, Gusev AV, Popov AO, Grigorian MS. [Results of preoperative embolization of portal vein in patients with biliary hepatic tumors]. Klin Khir 2014:5-7. [PMID: 25675733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The results of preoperative embolization of portal vein (EPV) in 90 patients, operated on for biliary hepatic tumors, were analyzed. In 47 patients Klatskin tumor was revealed, in 29--peripheral cholangiocarcinoma, in 14--tumor of a gallbladder. In all the patients a radical major hepatic resection was planned, a checking hepatic volume (CHHV) did not exceed 40% of a noninvolved parenchyma. The EPV volume have corresponded generally to the planned resection volume. After performance of EPV a pressure in a portal vein have risen by 75%, and later it have had lowered step by step during 24 h. The CHHV index have raised from (354 +/- 72) up to (462 +/- 118) cm3, or from (33 +/- 7) up to (45 +/- 11)%, permitting to perform radical hepatic resection in 79 (87.8%) patients. Thus, application of EPV in patients, suffering biliary hepatic tumors, have permitted to increase the CHHV index after radical resection, and to raise resectability of such tumors.
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21
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Kotenko OG, Kondratiuk VA, Fedorov DA, Grinenko AV, Korshak AA, Gusev AV, Popov AO, Grigorian MS. [Preoperative portal vein embolization: dynamics of portal pressure]. Klin Khir 2014:37-39. [PMID: 25252551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The pressure dynamics was studied in a portal vein (PV) in patients, suffering focal hepatic pathology, to whom portal vein embolization (PVE) was performed as a stage of preparation to radical hepatic resection. In 236 patients the immediate measurement of pressure in a PV was performed intraoperatively before and after PVE, in 26 - catheter for control portography and monitoring of pressure in a PV was left in its trunk for 24 h postoperatively. There was noted a pressure rising in a PV immediately after its embolization by 86.7%, positive correlation was established between PVE volume and pressure gradient in a PV before and after it. While doing monitoring during 24 h there was observed the pressure rising in a PV during 3 h after its embolization with subsequent lowering down to initial. Application of PVE as a preparation procedure for performance of extended hepatic resection, together with enhancement of residual liver minimizes sharp postresectional pressure rising in PV, what constitutes essential factor of the hepatocytes damage of residual hepatic part in immediate postoperative period.
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22
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Fedorov DA, Derevianko A, Varganov SA. Accurate potential energy, dipole moment curves, and lifetimes of vibrational states of heteronuclear alkali dimers. J Chem Phys 2014; 140:184315. [PMID: 24832278 DOI: 10.1063/1.4875038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We calculate the potential energy curves, the permanent dipole moment curves, and the lifetimes of the ground and excited vibrational states of the heteronuclear alkali dimers XY (X, Y = Li, Na, K, Rb, Cs) in the X(1)Σ(+) electronic state using the coupled cluster with singles doubles and triples method. All-electron quadruple-ζ basis sets with additional core functions are used for Li and Na, and small-core relativistic effective core potentials with quadruple-ζ quality basis sets are used for K, Rb, and Cs. The inclusion of the coupled cluster non-perturbative triple excitations is shown to be crucial for obtaining the accurate potential energy curves. A large one-electron basis set with additional core functions is needed for the accurate prediction of permanent dipole moments. The dissociation energies are overestimated by only 14 cm(-1) for LiNa and by no more than 114 cm(-1) for the other molecules. The discrepancies between the experimental and calculated harmonic vibrational frequencies are less than 1.7 cm(-1), and the discrepancies for the anharmonic correction are less than 0.1 cm(-1). We show that correlation between atomic electronegativity differences and permanent dipole moment of heteronuclear alkali dimers is not perfect. To obtain the vibrational energies and wave functions the vibrational Schrödinger equation is solved with the B-spline basis set method. The transition dipole moments between all vibrational states, the Einstein coefficients, and the lifetimes of the vibrational states are calculated. We analyze the decay rates of the vibrational states in terms of spontaneous emission, and stimulated emission and absorption induced by black body radiation. In all studied heteronuclear alkali dimers the ground vibrational states have much longer lifetimes than any excited states.
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Affiliation(s)
- Dmitry A Fedorov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0216, USA
| | - Andrei Derevianko
- Department of Physics, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0220, USA
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557-0216, USA
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Kotenko OG, Popov AO, Gusev AV, Grinenko AV, Grigorian MS, Korshak AA, Fedorov DA, Moshkovskiĭ GI, Furkalo SN. [The treatment of hepatic artery stenosis after orthotopic transplantation of hepatic right lobe from a live relative donor]. Klin Khir 2012:65-67. [PMID: 23610826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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24
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Fedorov AS, Fedorov DA, Kuzubov AA, Avramov PV, Nishimura Y, Irle S, Witek HA. Relative isomer abundance of fullerenes and carbon nanotubes correlates with kinetic stability. Phys Rev Lett 2011; 107:175506. [PMID: 22107538 DOI: 10.1103/physrevlett.107.175506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Indexed: 05/31/2023]
Abstract
A methodology to evaluate the kinetic stability of carbon nanostructures is presented based on the assumption of the independent and random nature of thermal vibrations. The kinetic stability is directly correlated to the cleavage probability for the weakest bond of a given nanostructure. The application of the presented method to fullerenes and carbon nanotubes yields clear correlation to their experimentally observed relative isomer abundances. The general and simple formulation of the method ensures its applicability to other nanostructures for which formation is controlled by kinetic factors.
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Affiliation(s)
- A S Fedorov
- Kirensky Institute of Physics, Akademgorodok 50, Krasnoyarsk, 660036, Russia.
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25
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Kotenko OG, Furkalo SN, Kondratiuk VA, Fedorov DA. [A portal vein branch embolization as a method of preparation for liver resection]. Klin Khir 2011:5-9. [PMID: 22295541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The results of preoperative transcutaneous transhepatic embolization of portal vein (PTTEPV) were analyzed in 86 patients, suffering malignant hepatic tumors. Depending on a planned hepatic resection (HR) volume there was conducted embolization of a right lobar portal vein (in 45 patients), right vein with a vein of C(IV) segment (in 32), lobar portal vein with anterior right vein (in 9). In 3-4 weeks after PTTEPV there was noted the enhancement of ratio of a planned residual hepatic volume/total hepatic volume from 16.3 to 27.5%, permitting to perform HR successfully in these patients. In 4 (4.7%) patients HR was not performed because of progressing of the tumor development or a total thrombosis of portal vein. The data obtained witness, that PTTEPV constitute an effective method of the patients preparation for HR while presence of a planned small residual hepatic volume.
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26
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Kotenko OG, Grinenko AV, Popov AO, Korshak AA, Gusev AV, Fedorov DA. [The portal vein reconstruction during operations for hepatocellular carcinoma]. Klin Khir 2011:5-13. [PMID: 22168017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
There was the objective to improve the results of treatment in patients, suffering hepatocellular carcinoma (HCC) with vena cava invasion by the tumor. In the main group a hepatic resection with the portal vein resection and portoplasty was performed in 21 patients, suffering HCC with vena cava invasion by the tumor of second-third degree (according to J. Shi, 2007); in a control group in 61 patients, suffering the portal vein tumoral invasion of first degree, the hepatic resection only was done. The mortality have constituted 9.5% in the main group and 8.1%--in a control one. The 5-year survival index have constituted 11.5%--in the main group and 25.3%--in a control one. The aggressive surgical tactics application for HCC with portal vein tumoral invasion permits to enhance the indices of the patients far-remote survival.
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Kotenko OG, Gusev AV, Korshak AA, Popov AO, Grinenko AV, Fedorov DA, Grigorian MS, Petrishche II. [Antibacterial therapy in surgical treatment of chronic hepatic abscess]. Klin Khir 2010:13-17. [PMID: 20469689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The results of surgical treatment of 58 patients for chronic hepatic abscess were presented. In patients of the main group hepatic resection was performed and in a control one--sanation and drainage of the abscess cavity. Antibacterial therapy was conducted in patients of both groups before and after operative treatment. The peculiarities and common efficacy of antibacterial therapy depending on the operative treatment kind were noted.
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Kotenko OG, Fedorov DA, Popov AO, Gusev AV, Korshak AA, Grinenko AV. [Peculiarities of the venous bed vessels reconstruction while performing liver transplantation from live relative donor in children]. Klin Khir 2008:40-46. [PMID: 19405403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The rate of hepatic transplantation from live relative donor in children is increasing in all over the world and in Ukraine as well. Significant incidence of the pathology together with necessity of technically complex intervention performance causes the need for surgical technique improvement, a new methods elaboration and clinical introduction, permitting to lower the postoperative complications rate. Technical complexity constitutes the main peculiarity of transplantation operation of liver, obtained from live relative donor, in children, it is caused by the vessels small diameter, pathological changes of the recipient portal vein and lack of plastic material for reconstruction of vessels. There are proposed various plastic methods for the transplant portal inflow and venous outflow guaranteeing to achieve a success while performing left lateral hepatic section transplantation, permitting to improve the results of hepatic transplantation from live relative donor in children.
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Kotenko OG, Kalita NI, Popov AO, Korshak AA, Grinenko AV, Gusev AV, Fedorov DA, Vasil'ev OV, Andreeshchev SA. [Scientific and practical legacy of the academician A.A. Shalimov in the modern liver surgery]. Klin Khir 2007:16-20. [PMID: 17515061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
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30
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Kotenko OG, Grinenko AV, Popov AO, Korshak AA, Gusev AV, Fedorov DA, Andreeshchev SA. [Hepatic and the portal vein resection in the surgical treatment of hepatocellular carcinoma]. Klin Khir 2007:5-11. [PMID: 17438716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Modern problems of the portal vein resection while hepatectomy performance are enlighted. Indications for resection of the portal vein bifurcation zone are adduced, various methods of portoplasty are depicted. New methods of the portal vein passability restoration in disparity of its sutured parts diameters are proposed. The results of hepatectomy combined with portal vein resection are studied.
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Kalita NI, Kotenko OG, Gusev AV, Moshkovskiĭ GI, Vasil'ev OV, Popov AO, Korshak AA, Grinenko AV, Khokhlov AV, Fedorov DA. [Caroli's disease]. Klin Khir 2006:60-2. [PMID: 16826820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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