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Article: [Destabilization of the DNA Duplex of Actively Replicating Promoters of T7-Like Bacteriophages].

Orlov, M A / Ryasik, A A / Sorokin, A A

2018 Volume 52, Issue 5, Page(s) 793–800

Abstract: The relation between the processes of replication and transcription has been actively studied over several decades, but detailed mechanisms for their interaction have not been established reliably. Among the initiating transcription promoters of bacteria ...

Abstract	The relation between the processes of replication and transcription has been actively studied over several decades, but detailed mechanisms for their interaction have not been established reliably. Among the initiating transcription promoters of bacteria and bacteriophages, there are both promoters having an additional function of the secondary origin of replication (OR) and promoters not participating in this process. In this paper, we describe the stability of DNA by Stress-Induced Duplex Destabilization (SIDD) profiles for a complete set of promoters and the primary OR of the bacteriophage T7 genome. It has been shown that, among the native T7 promoters, only those that have an additional function of secondary OR are characterized by high destabilization. These include the phiOL and phiOR promoters adjoining the 5' and 3' terminal repeats of bacteriophage T7, and of six other T7 group phages. In each case, these two promoters are located in the regions of DNA with high destabilization of the duplex. Additionally, the genomes of seven representatives of the T7 group without annotated phiOL and phiOR have been considered. For three of them, high peaks of SIDD profiles have been found near the ends of the genomic DNA that may be due to the presence of similar phiOL and phiOR promoters. Probably, such promoters can be found in the genomes of other bacteriophages. Thus, for the promoters of bacteriophages, we have a confirmation of the relationship of SIDD as a DNA duplex parameter and the DNA replication initiation on promoters, serving as secondary OR.
MeSH term(s)	Bacteriophages/genetics ; DNA Replication ; DNA, Viral/genetics ; Promoter Regions, Genetic
Chemical Substances	DNA, Viral
Language	Russian
Publishing date	2018-11-16
Publishing country	Russia (Federation)
Document type	Journal Article
ZDB-ID	213542-5
ISSN	0026-8984
ISSN	0026-8984
DOI	10.1134/S0026898418050117
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Article ; Online: Implementation of rapid microwave sintering using a 24 GHz gyrotron system.

Egorov, S V / Eremeev, A G / Kholoptsev, V V / Plotnikov, I V / Rybakov, K I / Sorokin, A A

The Review of scientific instruments

2022 Volume 93, Issue 6, Page(s) 64708

Abstract: Rapid microwave sintering of different oxide ceramics with heating rates up to 300 °C/min and zero hold time has been implemented using a 24 GHz gyrotron-based system for high-temperature processing of materials. The design of the system, principle of ... ...

Abstract	Rapid microwave sintering of different oxide ceramics with heating rates up to 300 °C/min and zero hold time has been implemented using a 24 GHz gyrotron-based system for high-temperature processing of materials. The design of the system, principle of operation, and process control are described. Particular attention is given to the design of thermal insulation assemblies and the implementation of temperature measurement in an environment with intense electromagnetic fields. A description of an optical system for dilatometry and temperature measurement is presented. The interrelation between the automatically regulated output power of the gyrotron and the microwave power absorbed volumetrically in the sample is analyzed on the basis of energy balance considerations. The analysis is illustrated by considering examples of rapid sintering processes with ZnO-based and BaTiO
Language	English
Publishing date	2022-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/5.0093341
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Book ; Online: Comparison of Three Job Mapping Algorithms for Supercomputer Resource Managers

Baranov, A. V. / Kiselev, E. A. / Shabanov, B. M. / Sorokin, A. A. / Telegin, P. N.

2022

Abstract: Performance of supercomputer depends on the quality of resource manager, one of its functions is assignment of jobs to the nodes of clusters or MPP computers. Parts of parallel programs interact with each other with different intensity, and mapping of ... ...

Abstract	Performance of supercomputer depends on the quality of resource manager, one of its functions is assignment of jobs to the nodes of clusters or MPP computers. Parts of parallel programs interact with each other with different intensity, and mapping of program to supercomputer nodes influence efficiency of the run. At each program run graph representing application program is to be mapped onto graph of nodes representing a subset of computer system. The both graphs are not known beforehand, hence the mapping must be done in reasonable time while scheduling resources. Three mapping algorithms were explored: parallel versions of simulated annealing, genetic and composite algorithms. A set of experimental runs with different algorithms parameters was performed, comparison of mapping quality and runtime was made, and suggestions on applicability of algorithms for resource managers were provided.
Keywords	Computer Science - Performance ; 68W10 ; F.2.0
Publishing date	2022-12-22
Publishing country	us
Document type	Book ; Online
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Article: Late Jurassic to early Early Cretaceous tectonic nature on the NE Asian continental margin: Constraints from Mesozoic accretionary complexes

Li, Yu / Ge, Wen-Chun / Sorokin, A.A / Wang, Feng / Xu, Wen-Liang / Zhu, Ri-Xiang

Earth-science reviews. 2020 Jan., v. 200

2020

Abstract: It is widely accepted that subduction of the Paleo-Pacific Plate beneath Eurasia began in the early Mesozoic. However, the tectonic nature and processes of the NE Asian continental margin in the Late Jurassic to early Early Cretaceous remain unclear. In ... ...

Abstract	It is widely accepted that subduction of the Paleo-Pacific Plate beneath Eurasia began in the early Mesozoic. However, the tectonic nature and processes of the NE Asian continental margin in the Late Jurassic to early Early Cretaceous remain unclear. In this contribution, lithological, provenance, and metamorphic–deformation data are used to constrain the formation of Mesozoic accretionary complexes (AC) along the NE Asian continental margin and determine the tectonic relationship between the NE Asian continental margin and the Paleo-Pacific Plate in the Late Jurassic to early Early Cretaceous. The Mesozoic AC formed during the Late Jurassic (including the Raohe AC in NE China; the Khabarovsk, Samarka, and Taukha ACs in the Russian Far East; and the Mino–Tamba AC in Japan) and Early Cretaceous (including the Shimanto AC in Japan and the Kiselevka–Manoma AC in the Russian Far East). The Jurassic AC underwent a complex evolution, including the formation of seamounts, Middle–Late Jurassic terrigenous clastic sedimentation adjacent to the trench, collision of seamounts with Eurasia, northward migration of the AC, early Early Cretaceous terrigenous clastic sedimentation, a second period of accretion, and final emplacement. The earliest Mesozoic AC arrived at the trench at ca. 195 Ma. Combined with the occurrence of early Mesozoic calc-alkaline igneous rocks along the NE Asian continental margin, we suggest that subduction of the Paleo-Pacific Plate beneath Eurasia began in the Early Jurassic. Jurassic AC in Japan was affected by a regional high-P/T metamorphic event at 160 Ma, which might have been related to subduction–collision of seamounts with Eurasia at the trench. Ages and Hf isotopic compositions of detrital zircon grains from the Middle–Upper Jurassic and Cretaceous AC sandstones, together with paleontological and paleomagnetic data, indicate that Jurassic clastic sediments were sourced mainly from the South China Block (SCB), whereas the Lower Cretaceous sandstones were sourced from the eastern Central Asian Orogenic Belt (CAOB). The inferred northward migration of Jurassic AC in the Late Jurassic to early Early Cretaceous indicates that the boundary between the NE Asian continental margin and the Paleo-Pacific Plate was characterized by strike-slip tectonics at this time, likely due to a small angle of obliquity in the subduction of the Paleo-Pacific Plate beneath Eurasia. In the late Early Cretaceous, westward subduction of the Paleo-Pacific Plate beneath Eurasia resulted in the emplacement of the Raohe and Khabarovsk ACs at 137–130 Ma and the formation of ACs in the Russian Far East and Japan.
Keywords	Early Cretaceous epoch ; Early Jurassic epoch ; igneous rocks ; Late Jurassic epoch ; provenance ; sandstone ; seamounts ; sediments ; subduction ; tectonics ; zircon ; China ; Eurasia ; Japan ; Russia
Language	English
Dates of publication	2020-01
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1792-9
ISSN	0012-8252
ISSN	0012-8252
DOI	10.1016/j.earscirev.2019.103042
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Article ; Online: The software for interactive evaluation of mass spectra stability and reproducibility.

Zhvansky, E S / Sorokin, A A / Bormotov, D S / Bocharov, K V / Zavorotnyuk, D S / Ivanov, D G / Nikolaev, E N / Popov, I A

Bioinformatics (Oxford, England)

2020 Volume 37, Issue 1, Page(s) 140–142

Abstract: Summary: Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of ... ...

Abstract	Summary: Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here, we present spectra similarity matrix (SSM) Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra. Availability and implementation: Source code, example datasets, binaries and other information are available at https://github.com/EvgenyZhvansky/R_matrix. Supplementary information: Supplementary data are available at Bioinformatics online.
Language	English
Publishing date	2020-12-25
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa1072
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Article ; Online: Metrics for evaluating the stability and reproducibility of mass spectra.

Zhvansky, E S / Pekov, S I / Sorokin, A A / Shurkhay, V A / Eliferov, V A / Potapov, A A / Nikolaev, E N / Popov, I A

Scientific reports

2019 Volume 9, Issue 1, Page(s) 914

Abstract: In this work, we demonstrate a new approach for assessing the stability and reproducibility of mass spectra obtained via ambient ionization methods. This method is suitable for both comparing experiments during which only one mass spectrum is measured ... ...

Abstract	In this work, we demonstrate a new approach for assessing the stability and reproducibility of mass spectra obtained via ambient ionization methods. This method is suitable for both comparing experiments during which only one mass spectrum is measured and for evaluating the internal homogeneity of mass spectra collected over a period of time. The approach uses Pearson's r coefficient and the cosine measure to compare the spectra. It is based on the visualization of dissimilarities between measurements, thus leading to the analysis of dissimilarity patterns. The cosine measure and correlations are compared to obtain better metrics for spectra homogeneity. The method filters out unreliable scans to prevent the analyzed sample from being wrongly characterized. The applicability of the method is demonstrated on a set of brain tumor samples. The developed method could be employed in neurosurgical applications, where mass spectrometry is used to monitor the intraoperative tumor border.
Language	English
Publishing date	2019-01-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-37560-0
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Article: Analiz izmeneniĭ sostava fosfatidilkholinov v glioblastomakh cheloveka ex vivo.

Pekov, S I / Sorokin, A A / Kuzin, A A / Bocharov, K V / Bormotov, D S / Shivalin, A S / Shurkhay, V A / Potapov, A A / Nikolaev, E N / Popov, I A

Biomeditsinskaia khimiia

2021 Volume 67, Issue 1, Page(s) 81–87

Abstract: Significant metabolism alteration is accompanying the cell malignization process. Energy metabolism disturbance leads to the activation of de novo synthesis and beta-oxidation processes of lipids and fatty acids in a cancer cell, which becomes an ... ...

Title translation	Analysis of phosphatidylcholines alterations in human glioblastoma multiform tissues ex vivo.
Abstract	Significant metabolism alteration is accompanying the cell malignization process. Energy metabolism disturbance leads to the activation of de novo synthesis and beta-oxidation processes of lipids and fatty acids in a cancer cell, which becomes an indicator of pathological processes inside the cell. The majority of studies dealing with lipid metabolism alterations in glial tumors are performed using the cell lines in vitro or animal models. However, such conditions do not entirely represent the physiological conditions of cell growth or possible cells natural variability. This work presents the results of the data obtained by applying ambient mass spectrometry to human glioblastoma multiform tissues. By analyzing a relatively large cohort of primary and secondary glioblastoma samples, we identify the alterations in cells lipid composition, which accompanied the development of grade IV brain tumors. We demonstrate that primary glioblastomas, as well as ones developed from astrocytomas, are enriched with mono- and diunsaturated phosphatidylcholines (PC 26:1, 30:2, 32:1, 32:2, 34:1, 34:2). Simultaneously, the saturated and polyunsaturated phosphatidylcholines and phosphatidylethanolamines decrease. These alterations are obviously linked to the availability of the polyunsaturated fatty acids and activation of the de novo lipid synthesis and beta-oxidation pathways under the anaerobic conditions in the tumor core.
MeSH term(s)	Animals ; Astrocytoma ; Brain Neoplasms ; Glioblastoma ; Humans ; Lipid Metabolism ; Phosphatidylcholines
Chemical Substances	Phosphatidylcholines
Language	Russian
Publishing date	2021-02-28
Publishing country	Russia (Federation)
Document type	Journal Article
ZDB-ID	2130758-1
ISSN	2310-6905 ; 2310-6972 ; 0042-8809
ISSN (online)	2310-6905
ISSN	2310-6972 ; 0042-8809
DOI	10.18097/PBMC20216701081
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Article ; Online: 37 Spatial organisation of electrostatic interactions between T7 specific RNA polymerase and its native promoters.

Sorokin, A A / Temlyakova, E A / Dzhelyadin, T R / Kamzolova, S G

Journal of biomolecular structure & dynamics

2015 Volume 33 Suppl 1, Page(s) 25–26

Language	English
Publishing date	2015
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2015.1032586
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Article: Rol' lipidov pri klassifikatsii astrotsitomy i glioblastomy pri pomoshchi mass-spektrometricheskogo profilirovaniia opukholeĭ.

Eliferov, V A / Zhvansky, E S / Sorokin, A A / Shurkhay, V A / Bormotov, D S / Pekov, S I / Nikitin, P V / Ryzhova, M V / Kulikov, E E / Potapov, A A / Nikolaev, E N / Popov, I A

Biomeditsinskaia khimiia

2020 Volume 66, Issue 4, Page(s) 317–325

Abstract: Express MS identification of biological tissues has become a much more accessible research method due to the application of direct specimen ionization at atmospheric pressure. In contrast to traditional methods of analysis employing GC-MS methods for ... ...

Title translation	The role of lipids in the classification of astrocytoma and glioblastoma using MS tumor profiling.
Abstract	Express MS identification of biological tissues has become a much more accessible research method due to the application of direct specimen ionization at atmospheric pressure. In contrast to traditional methods of analysis employing GC-MS methods for determining the molecular composition of the analyzed objects it eliminates the influence of mutual ion suppression. Despite significant progress in the field of direct MS of biological tissues, the question of mass spectrometric profile attribution to a certain type of tissue still remains open. The use of modern machine learning methods and protocols (e.g., "random forests") enables us to trace possible relationships between the components of the sample MS profile and the result of brain tumor tissue classification (astrocytoma or glioblastoma). It has been shown that the most pronounced differences in the mass spectrometric profiles of these tumors are due to their lipid composition. Detection of statistically significant differences in lipid profiles of astrocytoma and glioblastoma may be used to perform an express test during surgery and inform the neurosurgeon what type of malignant tissue he is working with. The ability to accurately determine the boundaries of the neoplastic growth significantly improves the quality of both surgical intervention and postoperative rehabilitation, as well as the duration and quality of life of patients.
MeSH term(s)	Astrocytoma ; Biomarkers, Tumor/analysis ; Brain Neoplasms/diagnosis ; Glioblastoma/diagnosis ; Humans ; Lipids/analysis ; Male ; Quality of Life
Chemical Substances	Biomarkers, Tumor ; Lipids
Language	Russian
Publishing date	2020-09-06
Publishing country	Russia (Federation)
Document type	Journal Article
ZDB-ID	2130758-1
ISSN	2310-6905 ; 2310-6972 ; 0042-8809
ISSN (online)	2310-6905
ISSN	2310-6972 ; 0042-8809
DOI	10.18097/PBMC20206604317
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Article: High-resolution mass spectra processing for the identification of different pathological tissue types of brain tumors.

Zhvansky, E S / Sorokin, A A / Popov, I A / Shurkhay, V A / Potapov, A A / Nikolaev, E N

European journal of mass spectrometry (Chichester, England)

2017 Volume 23, Issue 4, Page(s) 213–216

Abstract: The purpose of the work is to demonstrate the possibilities of identifying the different types of pathological tissue identification directly through tissue mass spectrometry. Glioblastoma parts dissected during neurosurgical operation were investigated. ...

Abstract	The purpose of the work is to demonstrate the possibilities of identifying the different types of pathological tissue identification directly through tissue mass spectrometry. Glioblastoma parts dissected during neurosurgical operation were investigated. Tumor fragments were investigated by the immunohistochemistry method and were identified as necrotic tissue with necrotized vessels, necrotic tissue with tumor stain, tumor with necrosis (tumor tissue as major), tumor, necrotized tumor (necrotic tissues as major), parts of tumor cells, boundary brain tissue, and brain tissue hyperplasia. The technique of classification of tumor tissues based on mass spectrometric profile data processing is suggested in this paper. Classifiers dividing the researched sample to the corresponding tissue type were created as a result of the processing. Classifiers of necrotic and tumor tissues are shown to yield a combined result when the tissue is heterogeneous and consists of both tumor cells and necrotic tissue.
Language	English
Publishing date	2017
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1469-0667
ISSN	1469-0667
DOI	10.1177/1469066717721484
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