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Article: Quality Assessment of Processed Graphene Chips for Biosensor Application.

Shmidt, Natalia M / Shabunina, Evgeniya I / Gushchina, Ekaterina V / Petrov, Vasiliy N / Eliseyev, Ilya A / Lebedev, Sergey P / Priobrazhenskii, Sergei Iu / Tanklevskaya, Elena M / Puzyk, Mikhail V / Roenkov, Alexander D / Usikov, Alexander S / Lebedev, Alexander A

Materials (Basel, Switzerland)

2023 Volume 16, Issue 16

Abstract: The quality of graphene intended for use in biosensors was assessed on manufactured chips using a set of methods including atomic force microscopy (AFM), Raman spectroscopy, and low-frequency noise investigation. It is shown that local areas of residues ... ...

Abstract	The quality of graphene intended for use in biosensors was assessed on manufactured chips using a set of methods including atomic force microscopy (AFM), Raman spectroscopy, and low-frequency noise investigation. It is shown that local areas of residues on the graphene surface, formed as a result of the interaction of graphene with a photoresist at the initial stage of chip development, led to a spread of chip resistance (R) in the range of 1-10 kOhm and to an increase in the root mean square (RMS) roughness up to 10 times, which can significantly worsen the reproducibility of the parameters of graphene chips for biosensor applications. It was observed that the control of the photoresist residues after photolithography (PLG) using AFM and subsequent additional cleaning reduced the spread of R values in chips to 1-1.6 kOhm and obtained an RMS roughness similar to the roughness in the graphene film before PLG. Monitoring of the spectral density of low-frequency voltage fluctuation (S
Language	English
Publishing date	2023-08-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma16165628
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Article ; Online: Receptions of mechanical equipment used to stimulate the memory process in the department of medical biology and genetics UGMU

Vasiliy M. Petrov / Elena A. Shorikova / Olga V. Kostromina / Daria A. Proshchenko

Развитие образования, Vol , Iss 1 (3), Pp 14-

2019 Volume 17

Abstract: The article is devoted to the problem of finding productive pedagogical and psychological techniques that help to structure a large amount of information in a short time. As a solution to this issue, it is proposed to use methods of mnemotechnics for ... ...

Abstract	The article is devoted to the problem of finding productive pedagogical and psychological techniques that help to structure a large amount of information in a short time. As a solution to this issue, it is proposed to use methods of mnemotechnics for students to master complex biological material. The paper presents the results of a study by the authors, which showed that the most difficult for students of the course of cytology are associated with a large amount of memorization units, and the most effective technique used to study this topic is the letter code.
Keywords	letter code ; memorization process ; mnemotechnical methods ; molecular biology ; асра тыту процесӗ ; буквенный код ; Education (General) ; L7-991 ; Theory and practice of education ; LB5-3640 ; Special aspects of education ; LC8-6691
Language	Chuvash
Publishing date	2019-02-01T00:00:00Z
Publisher	Publishing house "Sreda"
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: AI-Based Approach to One-Click Chronic Subdural Hematoma Segmentation Using Computed Tomography Images.

Petrov, Andrey / Kashevnik, Alexey / Haleev, Mikhail / Ali, Ammar / Ivanov, Arkady / Samochernykh, Konstantin / Rozhchenko, Larisa / Bobinov, Vasiliy

Sensors (Basel, Switzerland)

2024 Volume 24, Issue 3

Abstract: This paper presents a computer vision-based approach to chronic subdural hematoma segmentation that can be performed by one click. Chronic subdural hematoma is estimated to occur in 0.002-0.02% of the general population each year and the risk increases ... ...

Abstract	This paper presents a computer vision-based approach to chronic subdural hematoma segmentation that can be performed by one click. Chronic subdural hematoma is estimated to occur in 0.002-0.02% of the general population each year and the risk increases with age, with a high frequency of about 0.05-0.06% in people aged 70 years and above. In our research, we developed our own dataset, which includes 53 series of CT scans collected from 21 patients with one or two hematomas. Based on the dataset, we trained two neural network models based on U-Net architecture to automate the manual segmentation process. One of the models performed segmentation based only on the current frame, while the other additionally processed multiple adjacent images to provide context, a technique that is more similar to the behavior of a doctor. We used a 10-fold cross-validation technique to better estimate the developed models' efficiency. We used the Dice metric for segmentation accuracy estimation, which was 0.77. Also, for testing our approach, we used scans from five additional patients who did not form part of the dataset, and created a scenario in which three medical experts carried out a hematoma segmentation before we carried out segmentation using our best model. We developed the OsiriX DICOM Viewer plugin to implement our solution into the segmentation process. We compared the segmentation time, which was more than seven times faster using the one-click approach, and the experts agreed that the segmentation quality was acceptable for clinical usage.
MeSH term(s)	Humans ; Aged ; Hematoma, Subdural, Chronic/diagnostic imaging ; Tomography, X-Ray Computed ; Neural Networks, Computer ; Research Design ; Image Processing, Computer-Assisted/methods
Language	English
Publishing date	2024-01-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s24030721
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Article ; Online: Hybrid (Bovine Serum Albumin)/Poly(

Estifeeva, Tatyana M / Barmin, Roman A / Rudakovskaya, Polina G / Nechaeva, Anna M / Luss, Anna L / Mezhuev, Yaroslav O / Chernyshev, Vasiliy S / Krivoborodov, Efrem G / Klimenko, Oleg A / Sindeeva, Olga A / Demina, Polina A / Petrov, Kirill S / Chuprov-Netochin, Roman N / Fedotkina, Elena P / Korotchenko, Olga E / Sencha, Ekaterina A / Sencha, Alexander N / Shtilman, Mikhail I / Gorin, Dmitry A

ACS applied bio materials

2022 Volume 5, Issue 7, Page(s) 3338–3348

Abstract: Microbubbles are routinely used ultrasound contrast agents in the clinic. While a soft protein shell is commercially preferable for imaging purposes, a rigid polymer shell demonstrates prolonged agent stability. Hence, combining polymers and proteins in ... ...

Abstract	Microbubbles are routinely used ultrasound contrast agents in the clinic. While a soft protein shell is commercially preferable for imaging purposes, a rigid polymer shell demonstrates prolonged agent stability. Hence, combining polymers and proteins in one shell composition can advance microbubble properties. We formulated the hybrid "protein-copolymer" microbubble shell with a complex of bovine serum albumin and an amphiphilic copolymer of
MeSH term(s)	Acrylates ; Acrylic Resins ; Contrast Media/chemistry ; Microbubbles ; Polymers/chemistry ; Povidone/analogs & derivatives ; Serum Albumin, Bovine
Chemical Substances	Acrylates ; Acrylic Resins ; Contrast Media ; Polymers ; poly(N-vinyl-2-pyrrolidone-co-acrylic acid) ; Serum Albumin, Bovine (27432CM55Q) ; Povidone (FZ989GH94E) ; acrylic acid (J94PBK7X8S)
Language	English
Publishing date	2022-07-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2576-6422
ISSN (online)	2576-6422
DOI	10.1021/acsabm.2c00331
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Article ; Online: Clinical Case Report of Non-Diabetic Hypoglycemia Due to a Combination of Germline Mutations in the

Yukina, Marina / Solodovnikova, Ekaterina / Popov, Sergey / Zakharova, Victorya / Utkina, Marina / Petrov, Vasiliy / Troshina, Ekaterina / Mokrysheva, Natalia

Genes

2023 Volume 14, Issue 10

Abstract: Introduction: Non-diabetic hypoglycemia (NDH) is a collective term including the multiple causes of hypoglycemic syndrome not due to diabetes mellitus. NDH may result from insulinoma, IGF-2-omas, hypocorticism, Hirata's disease, genital disorders of ... ...

Abstract	Introduction: Non-diabetic hypoglycemia (NDH) is a collective term including the multiple causes of hypoglycemic syndrome not due to diabetes mellitus. NDH may result from insulinoma, IGF-2-omas, hypocorticism, Hirata's disease, genital disorders of glucose metabolism, etc. One of the most common causes of NDH faced by an endocrinologist is insulinoma, which in turn can be part of the hereditary syndrome of multiple endocrine neoplasia type 1 (MEN1). Congenital disorders of glucose metabolism in adult patients, on the contrary, are diagnosed extremely rarely, since they usually manifest in childhood. This article presents a unique clinical case of a patient with NDH and genetically verified MEN1 in combination with congenital hyperinsulinism due to an ABCC8 gene mutation. Case report: A 43-year-old patient with hypoglycemic symptoms from childhood is presented, in whom multiple pancreatic tumors and fluctuations in glycemia from 38.7 mg/dL to 329.7 mg/dL (2.15 to 18.3 mmol/L) were detected in adulthood, but a mild course of hypoglycemic syndrome was noted. Numerous examinations that were performed to establish an accurate diagnosis are described, signs that served as a reason for expanding the complex of studies are indicated, possible pathogenetic mechanisms of the mild course of hypoglycemic syndrome and hyperglycemic conditions are discussed. Conclusion: This case report is original and highlights that we must always remain intolerant of the inexplicable. Conducting an extended gene study can help perform a correct diagnosis in complex cases.
MeSH term(s)	Adult ; Humans ; Multiple Endocrine Neoplasia Type 1/genetics ; Insulinoma/genetics ; Insulinoma/pathology ; Germ-Line Mutation ; Congenital Hyperinsulinism ; Hypoglycemic Agents ; Glucose ; Sulfonylurea Receptors/genetics
Chemical Substances	Hypoglycemic Agents ; Glucose (IY9XDZ35W2) ; ABCC8 protein, human ; Sulfonylurea Receptors
Language	English
Publishing date	2023-10-17
Publishing country	Switzerland
Document type	Case Reports ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14101952
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Article ; Online: A Tribute to Sergey Odinokov

Olga I. Odinokova / Vasiliy Ya. Kolyuchkin / Artem B. Solomashenko / Maria V. Shishova / Evgenii Yu. Zlokazov / Rostislav S. Starikov / Nikolay N. Evtikhiev / Nikolay V. Nikonorov / Sergey A. Shoydin / Leonid V. Tanin / Gennadiy A. Gavrilov / Nina M. Ganzherli / Anatoliy V. Lukin / Andrei N. Melnikov / Rosalia Kh. Makaeva / Nadezhda K. Pavlycheva / Elena N. Bogachevskaya / Alkis Lembessis / Rajan Thomas /

Michel Grosmann / Michael K. Shevtsov / Yves Gentet / Sergey G. Kalenkov / Olga F. Tikhomirova / Natalia L. Istomina / Olga V. Andreeva / Vladimir Yu. Venediktov / Nikolay V. Petrov

Applied Sciences, Vol 12, Iss 2892, p

2022 Volume 2892

Abstract: My main goal was to point out new phenomena and spread the ideas, which will become the starting points for new research” [.] ...

Abstract	“My main goal was to point out new phenomena and spread the ideas, which will become the starting points for new research” [.]
Keywords	n/a ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Genetic insertions and diversification of the PolB-type DNA polymerase (gp43) of T4-related phages.

Petrov, Vasiliy M / Ratnayaka, Swarnamala / Karam, Jim D

Journal of molecular biology

2010 Volume 395, Issue 3, Page(s) 457–474

Abstract: In Escherichia coli phage T4 and many of its phylogenetic relatives, gene 43 consists of a single cistron that encodes a PolB family (PolB-type) DNA polymerase. We describe the divergence of this phage gene and its protein product (gp43) (gene product 43) ...

Abstract	In Escherichia coli phage T4 and many of its phylogenetic relatives, gene 43 consists of a single cistron that encodes a PolB family (PolB-type) DNA polymerase. We describe the divergence of this phage gene and its protein product (gp43) (gene product 43) among 26 phylogenetic relatives of T4 and discuss our observations in the context of diversity among the widely distributed PolB enzymes in nature. In two T4 relatives that grow in Aeromonas salmonicida phages 44RR and 25, gene 43 is fragmented by different combinations of three distinct types of DNA insertion elements: (a) a short intercistronic untranslated sequence (IC-UTS) that splits the polymerase gene into two cistrons, 43A and 43B, corresponding to N-terminal (gp43A) and C-terminal (gp43B) protein products; (b) a freestanding homing endonuclease gene (HEG) inserted between the IC-UTS and the 43B cistron; and (c) a group I intron in the 43B cistron. Phage 25 has all three elements, whereas phage 44RR has only the IC-UTS. We present evidence that (a) the split gene of phage 44RR encodes a split DNA polymerase consisting of a complex between gp43A and gp43B subunits; (b) the putative HEG encodes a double-stranded DNA endonuclease that specifically cleaves intron-free homologues of the intron-bearing 43B site; and (c) the group I intron is a self-splicing RNA. Our results suggest that some freestanding HEGs can mediate the homing of introns that do not encode their own homing enzymes. The results also suggest that different insertion elements can converge on a polB gene and evolve into a single integrated system for lateral transfer of polB genetic material. We discuss the possible pathways for the importation of such insertion elements into the genomes of T4-related phages.
MeSH term(s)	Aeromonas salmonicida/virology ; Amino Acid Sequence ; Bacteriophage T4/classification ; Bacteriophage T4/enzymology ; Bacteriophage T4/genetics ; Base Sequence ; DNA Transposable Elements ; DNA, Viral/genetics ; DNA-Directed DNA Polymerase/biosynthesis ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/genetics ; Evolution, Molecular ; Genes, Viral ; Genetic Variation ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymorphism, Genetic ; Protein Conformation ; RNA Splicing ; RNA, Viral/chemistry ; RNA, Viral/genetics ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Species Specificity ; Viral Proteins/biosynthesis ; Viral Proteins/chemistry ; Viral Proteins/genetics
Chemical Substances	DNA Transposable Elements ; DNA, Viral ; RNA, Viral ; Recombinant Proteins ; Viral Proteins ; gene 43 protein, Enterobacteria phage T4 ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2010-01-22
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2009.10.054
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Article ; Online: RNA determinants of translational operator recognition by the DNA polymerases of bacteriophages T4 and RB69.

Petrov, Vasiliy M / Karam, Jim D

Nucleic acids research

2001 Volume 30, Issue 15, Page(s) 3341–3348

Abstract: The DNA polymerases (gp43s) of the two related phages T4 and RB69 are DNA-binding proteins that also function as mRNA-binding autogenous translational repressors. As repressors, T4 gp43 is narrowly specific to its own mRNA whereas RB69 gp43 is equally ... ...

Abstract	The DNA polymerases (gp43s) of the two related phages T4 and RB69 are DNA-binding proteins that also function as mRNA-binding autogenous translational repressors. As repressors, T4 gp43 is narrowly specific to its own mRNA whereas RB69 gp43 is equally effective against mRNA for either protein. We used in vitro RNase-sensitivity and RNA footprinting assays to identify features of the non-identical T4 and RB69 mRNA targets (translational operators) that allow for their identical binding affinities and biological responses to RB69 gp43. We observed that T4 gp43 and RB69 gp43 produce identical footprints on RNA substrates bearing the T4-derived operator, suggesting that the two gp43s make identical contacts with this operator. In contrast, the footprint produced by RB69 gp43 on its autogenous RNA target was shorter than its footprint on operator RNA from T4. As expected, we also observed only weak protection of RB69-derived operator RNA from RNase by T4 gp43; however, photocross-linking studies suggested that T4 gp43 recognizes structural features of the RB69-derived operator that are not detected by RNase- sensitivity assays. The results suggest that RB69 gp43 and T4 gp43 differ in their abilities to use RNA-sequence-independent interactions to configure potential RNA targets for translational repression.
MeSH term(s)	Bacteriophages/enzymology ; Base Sequence ; Binding Sites ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Biosynthesis ; RNA/chemistry ; RNA/metabolism ; RNA-Binding Proteins/metabolism ; Repressor Proteins/metabolism ; Ribonucleases/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	RNA-Binding Proteins ; Repressor Proteins ; Viral Proteins ; gene 43 protein, Enterobacteria phage T4 ; RNA (63231-63-0) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; bacteriophage RB69 DNA polymerase (EC 2.7.7.7) ; Ribonucleases (EC 3.1.-)
Language	English
Publishing date	2001-02-06
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkf447
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Article: Genomes of the T4-related bacteriophages as windows on microbial genome evolution

Petrov, Vasiliy M / Ratnayaka, Swarnamala / Nolan, James M / Miller, Eric S / Karam, Jim D

Virology journal. 2010 Dec., v. 7, no. 1

2010

Abstract: The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined ... ...

Abstract	The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature.
Keywords	DNA ; coliphages ; evolution ; genetic heterogeneity ; genome ; morphogenesis ; protein content ; proteome ; virology
Language	English
Dates of publication	2010-12
Size	p. 292.
Publishing place	BioMed Central
Document type	Article
Note	Review
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/1743-422X-7-292
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Article ; Online: Genomes of the T4-related bacteriophages as windows on microbial genome evolution.

Petrov, Vasiliy M / Ratnayaka, Swarnamala / Nolan, James M / Miller, Eric S / Karam, Jim D

Virology journal

2010 Volume 7, Page(s) 292

Abstract	The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature.
MeSH term(s)	Bacteriophages/genetics ; Biological Evolution ; DNA, Viral/chemistry ; DNA, Viral/genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Molecular Sequence Data ; Sequence Analysis, DNA
Chemical Substances	DNA, Viral
Language	English
Publishing date	2010-10-28
Publishing country	England
Document type	Journal Article ; Review
ISSN	1743-422X
ISSN (online)	1743-422X
DOI	10.1186/1743-422X-7-292
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