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Article ; Online: Determination of Pair Interaction Parameters of Multicomponent Polymer Systems.

Chalykh, Anatoly E / Gerasimov, Vladimir K / Petrova, Tatiana F / Shcherbina, Anna A

2023 Volume 16, Issue 1

Abstract: From the examples of three and four-component polymer-polymer systems characterized by amorphous separation, an original technique for determining the pair parameters of interaction between components based on the sorption isotherms of common solvent ... ...

Abstract	From the examples of three and four-component polymer-polymer systems characterized by amorphous separation, an original technique for determining the pair parameters of interaction between components based on the sorption isotherms of common solvent vapor, particularly water vapor, has been developed. The possibility of calculating thermodynamic characteristics of multicomponent polymer compositions with specific interactions of functional groups from experimentally obtained sorption isotherms is shown. An algorithm for calculating pair interaction parameters, estimating concentration dependences of chemical potential and Gibbs free energy of mixing, and predicting the phase state of polymer mixtures was presented for the first time for such systems. The technique was tested on the example of systems poly(N-vinylpyrrolidone) (PNVP)-polyethylene glycol (PEG), PNVP-PEG-Poly(acrylic acid) (PAA), poly(N-vinylcaprolactam) (PNVCL)-PEG, and polyvinyl alcohol (PVA)-PEG.
Language	English
Publishing date	2023-12-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527146-5
ISSN	2073-4360 ; 2073-4360
ISSN (online)	2073-4360
ISSN	2073-4360
DOI	10.3390/polym16010068
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Article ; Online: The Energy Characteristics of the Surface of Statistical Copolymers.

Chalykh, Anatoly E / Stepanenko, Valentina Y / Petrova, Tatiana F / Shcherbina, Anna A

Polymers

2023 Volume 15, Issue 8

Abstract: The results of systematic studies on the surface ... ...

Abstract	The results of systematic studies on the surface energy
Language	English
Publishing date	2023-04-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527146-5
ISSN	2073-4360 ; 2073-4360
ISSN (online)	2073-4360
ISSN	2073-4360
DOI	10.3390/polym15081939
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Article ; Online: FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets.

Shcherbina, Anna

BMC research notes

2014 Volume 7, Page(s) 533

Abstract: Background: High-throughput next generation sequencing technologies have enabled rapid characterization of clinical and environmental samples. Consequently, the largest bottleneck to actionable data has become sample processing and bioinformatics ... ...

Abstract	Background: High-throughput next generation sequencing technologies have enabled rapid characterization of clinical and environmental samples. Consequently, the largest bottleneck to actionable data has become sample processing and bioinformatics analysis, creating a need for accurate and rapid algorithms to process genetic data. Perfectly characterized in silico datasets are a useful tool for evaluating the performance of such algorithms. Background contaminating organisms are observed in sequenced mixtures of organisms. In silico samples provide exact truth. To create the best value for evaluating algorithms, in silico data should mimic actual sequencer data as closely as possible. Results: FASTQSim is a tool that provides the dual functionality of NGS dataset characterization and metagenomic data generation. FASTQSim is sequencing platform-independent, and computes distributions of read length, quality scores, indel rates, single point mutation rates, indel size, and similar statistics for any sequencing platform. To create training or testing datasets, FASTQSim has the ability to convert target sequences into in silico reads with specific error profiles obtained in the characterization step. Conclusions: FASTQSim enables users to assess the quality of NGS datasets. The tool provides information about read length, read quality, repetitive and non-repetitive indel profiles, and single base pair substitutions. FASTQSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software. In this regard, in silico datasets generated with the FASTQsim tool hold several advantages over natural datasets: they are sequencing platform independent, extremely well characterized, and less expensive to generate. Such datasets are valuable in a number of applications, including the training of assemblers for multiple platforms, benchmarking bioinformatics algorithm performance, and creating challenge datasets for detecting genetic engineering toolmarks, etc.
MeSH term(s)	Algorithms ; Computer Simulation ; High-Throughput Nucleotide Sequencing/methods ; Humans
Language	English
Publishing date	2014-08-15
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/1756-0500-7-533
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Article ; Online: The Kinetic Study of the Influence of Common Modifiers on the Curing Process of Epoxy Vitrimers.

Korotkov, Roman / Shutov, Vyacheslav / Orlov, Alexey / Bornosuz, Natalia / Kulemza, Daria / Onuchin, Denis / Shcherbina, Anna / Gorbunova, Irina / Sirotin, Igor

Polymers

2024 Volume 16, Issue 3

Abstract: An analysis of the influence of common modifiers on the kinetics of the curing process of epoxy-anhydride vitrimers was carried out. As common modifiers to enhance the "vitrimeric" nature of the material, zinc acetylacetonate as a transesterification ... ...

Abstract	An analysis of the influence of common modifiers on the kinetics of the curing process of epoxy-anhydride vitrimers was carried out. As common modifiers to enhance the "vitrimeric" nature of the material, zinc acetylacetonate as a transesterification catalyst and glycerol as a modifier of hydroxyl group content were chosen. The curing process of all obtained compositions was studied by differential scanning calorimetry (DSC) followed by the application of the isoconversional approach. It was shown that additives significantly affect the curing process. The resulting cured polymers were shown to be chemically recyclable by dissolution in the mixture of ethylene glycol and N-methylpirrolidone in a volume ratio of nine to one. The introduction of both zinc acethylacetonate and glycerol to the neat formulation led to a decrease in the dissolution time by 85.7% (from 35 h for the neat epoxy-anhydride formulation to 5 h for the modified formulation). In order to show the opportunity of the secondary use of recyclates, the mixtures based on the basic composition containing 10 wt. % of secondary polymers were also studied. The introduction of a recycled material to neat composition led to the same curing behavior as glycerol-containing systems.
Language	English
Publishing date	2024-01-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527146-5
ISSN	2073-4360 ; 2073-4360
ISSN (online)	2073-4360
ISSN	2073-4360
DOI	10.3390/polym16030392
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Article ; Online: Variations and expression features of CYP2D6 contribute to schizophrenia risk.

Ma, Liang / Shcherbina, Anna / Chetty, Sundari

Molecular psychiatry

2020 Volume 26, Issue 6, Page(s) 2605–2615

Abstract: Genome-wide association studies (GWAS) have successfully identified 145 loci implicated in schizophrenia (SCZ). However, the underlying mechanisms remain largely unknown. Here, we analyze 1497 RNA-seq data in combination with their genotype data and ... ...

Abstract	Genome-wide association studies (GWAS) have successfully identified 145 loci implicated in schizophrenia (SCZ). However, the underlying mechanisms remain largely unknown. Here, we analyze 1497 RNA-seq data in combination with their genotype data and identify SNPs that are associated with expression throughout the genome by dissecting expression features to genes (eGene) and exon-exon junctions (eJunction). Then, we colocalize eGene and eJunction with SCZ GWAS using SMR and fine mapping. Multiple ChIP-seq data and DNA methylation data generated from brain were used for identifying the causal variants. Finally, we used a hypothesis-free (no SCZ risk loci considered) enrichment analysis to determine implicated pathways. We identified 171 genes and eight splicing junctions located within four genes (SNX19, ARL6IP4, APOPT1, and CYP2D6) that potentially contribute to SCZ susceptibility. Among the genes, CYP2D6 is significantly associated with SCZ SNPs in eGene and eJunction. In-depth examination of the CYP2D6 region revealed that a nonsynonymous single nucleotide variant rs16947 is strongly associated with a higher abundance of CYP2D6 exon 3 skipping junctions. While we found rs133377 and other functional SNPs in high linkage disequilibrium with rs16947 (r
MeSH term(s)	Cytochrome P-450 CYP2D6/genetics ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Humans ; Polymorphism, Single Nucleotide/genetics ; Schizophrenia/genetics
Chemical Substances	Cytochrome P-450 CYP2D6 (EC 1.14.14.1)
Language	English
Publishing date	2020-02-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-020-0675-y
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Article ; Online: Cancer-causing MAP2K1 mutation in a mosaic patient with cardio-facio-cutaneous syndrome and immunodeficiency.

Zakharova, Victorya / Raykina, Elena / Mersiyanova, Irina / Deordieva, Ekaterina / Pershin, Dmitry / Vedmedskia, Victorya / Rodina, Yulia / Kuzmenko, Natalia / Maschan, Michael / Shcherbina, Anna

Human mutation

2022 Volume 43, Issue 12, Page(s) 1852–1855

Abstract: RASopathies are disorders caused by germline mutations in genes that encode components of the RAS/mitogen-activated protein kinase (MAPK) pathway. These syndromes share features of developmental delay, facial dysmorphisms, and defects in various organs, ... ...

Abstract	RASopathies are disorders caused by germline mutations in genes that encode components of the RAS/mitogen-activated protein kinase (MAPK) pathway. These syndromes share features of developmental delay, facial dysmorphisms, and defects in various organs, as well as cancer predisposition. Somatic mutations of the same pathway are one of the primary causes of cancer. It is thought that germline cancer-causing mutations would be embryonic lethal, as a more severe phenotype was shown in Drosophila and zebrafish embryos with cancer MAP2K1 mutations than in those with RASopathy mutations. Here we report the case of a patient with RASopathy caused by a cancer-associated MAP2K1 p.Phe53Leu mutation. The postzygotic mosaic nature of this mutation could explain the patient's survival.
MeSH term(s)	Animals ; Humans ; Zebrafish/genetics ; Failure to Thrive/genetics ; Ectodermal Dysplasia/diagnosis ; Ectodermal Dysplasia/genetics ; Facies ; Heart Defects, Congenital/genetics ; Mutation ; Immunologic Deficiency Syndromes ; Neoplasms ; MAP Kinase Kinase 1/genetics
Chemical Substances	MAP2K1 protein, human (EC 2.7.12.2) ; MAP Kinase Kinase 1 (EC 2.7.12.2)
Language	English
Publishing date	2022-09-12
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.24463
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Zs.A 3586: Show issues

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Article: Serious Hemorrhagic Complications After Successful Treatment of Hematopoietic Stem Cell Transplantation-Associated Thrombotic Microangiopathy With Defibrotide in Pediatric Patient With Myelodysplastic Syndrome.

Laberko, Alexandra / Aksenova, Marina / Shipitsina, Irina / Khamin, Igor / Shcherbina, Anna / Balashov, Dmitry / Maschan, Alexei

Frontiers in pediatrics

2020 Volume 8, Page(s) 155

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2020-05-05
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2711999-3
ISSN	2296-2360
ISSN	2296-2360
DOI	10.3389/fped.2020.00155
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Article: Manipulation of the nucleoscaffold potentiates cellular reprogramming kinetics.

Yang, Benjamin A / da Rocha, André Monteiro / Newton, Isabel / Shcherbina, Anna / Wong, Sing-Wan / Fraczek, Paula M / Larouche, Jacqueline A / Hiraki, Harrison L / Baker, Brendon M / Shin, Jae-Won / Takayama, Shuichi / Thouless, M D / Aguilar, Carlos A

bioRxiv : the preprint server for biology

2023

Abstract: Somatic cell fate is an outcome set by the activities of specific transcription factors and the chromatin landscape and is maintained by gene silencing of alternate cell fates through physical interactions with the nuclear scaffold. Here, we evaluate the ...

Abstract	Somatic cell fate is an outcome set by the activities of specific transcription factors and the chromatin landscape and is maintained by gene silencing of alternate cell fates through physical interactions with the nuclear scaffold. Here, we evaluate the role of the nuclear scaffold as a guardian of cell fate in human fibroblasts by comparing the effects of transient loss (knockdown) and mutation (progeria) of functional Lamin A/C, a core component of the nuclear scaffold. We observed that Lamin A/C deficiency or mutation disrupts nuclear morphology, heterochromatin levels, and increases access to DNA in lamina-associated domains. Changes in Lamin A/C were also found to impact the mechanical properties of the nucleus when measured by a microfluidic cellular squeezing device. We also show that transient loss of Lamin A/C accelerates the kinetics of cellular reprogramming to pluripotency through opening of previously silenced heterochromatin domains while genetic mutation of Lamin A/C into progerin induces a senescent phenotype that inhibits the induction of reprogramming genes. Our results highlight the physical role of the nuclear scaffold in safeguarding cellular fate.
Language	English
Publishing date	2023-03-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.12.532246
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Article ; Online: Allogeneic Hematopoietic Stem Cell Transplantation Activity in Inborn Errors of Immunity in Russian Federation.

Laberko, Alexandra / Mukhinа, Anna / Machneva, Elena / Pashchenko, Olga / Bykova, Tatiana / Vahonina, Larisa / Bronin, Gleb / Skvortsova, Yulia / Skorobogatova, Elena / Kondratenko, Irina / Fechina, Larisa / Shcherbina, Anna / Zubarovskaya, Ludmila / Balashov, Dmitry / Rumiantsev, Alexander

Journal of clinical immunology

2023 Volume 43, Issue 6, Page(s) 1241–1249

Abstract: Purpose: Allogeneic hematopoietic stem cell transplantation (HSCT) is an established therapy for many inborn errors of immunity (IEI). The indications for HSCT have expanded over the last decade. The study aimed to collect and analyze the data on HSCT ... ...

Abstract	Purpose: Allogeneic hematopoietic stem cell transplantation (HSCT) is an established therapy for many inborn errors of immunity (IEI). The indications for HSCT have expanded over the last decade. The study aimed to collect and analyze the data on HSCT activity in IEI in Russia. Methods: The data were collected from the Russian Primary Immunodeficiency Registry and complemented with information from five Russian pediatric transplant centers. Patients diagnosed with IEI by the age of 18 years and who received allogeneic HSCT by the end of 2020 were included. Results: From 1997 to 2020, 454 patients with IEI received 514 allogeneic HSCT. The median number of HSCTs per year has risen from 3 in 1997-2009 to 60 in 2015-2020. The most common groups of IEI were immunodeficiency affecting cellular and humoral immunity (26%), combined immunodeficiency with associated/syndromic features (28%), phagocyte defects (21%), and diseases of immune dysregulation (17%). The distribution of IEI diagnosis has changed: before 2012, the majority (65%) had severe combined immunodeficiency (SCID) and hemophagocytic lymphohistiocytosis (HLH), and after 2012, only 24% had SCID and HLH. Of 513 HSCTs, 48.5% were performed from matched-unrelated, 36.5% from mismatched-related (MMRD), and 15% from matched-related donors. In 349 transplants T-cell depletion was used: 325 TCRαβ/CD19+ depletion, 39 post-transplant cyclophosphamide, and 27 other. The proportion of MMRD has risen over the recent years. Conclusion: The practice of HSCT in IEI has been changing in Russia. Expanding indications to HSCT and SCID newborn screening implementation may necessitate additional transplant beds for IEI in Russia.
MeSH term(s)	Child ; Infant, Newborn ; Humans ; Adolescent ; Hematopoietic Stem Cell Transplantation ; Immunologic Deficiency Syndromes/diagnosis ; Immunologic Deficiency Syndromes/epidemiology ; Immunologic Deficiency Syndromes/therapy ; Receptors, Antigen, T-Cell, alpha-beta ; Severe Combined Immunodeficiency/therapy ; Lymphohistiocytosis, Hemophagocytic/diagnosis
Chemical Substances	Receptors, Antigen, T-Cell, alpha-beta
Language	English
Publishing date	2023-04-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	779361-3
ISSN	1573-2592 ; 0271-9142
ISSN (online)	1573-2592
ISSN	0271-9142
DOI	10.1007/s10875-023-01476-w
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Article ; Online: Accelerated death of megakaryocytes from Wiskott-Aldrich syndrome patients.

Obydennyi, Sergei I / Kuznetsova, Sofya A / Fedyanina, Olga S / Khoreva, Anna / Voronin, Kirill / Mazurov, Alexey V / Glukhova, Anna A / Artemenko, Elena O / Ataullakhanov, Fazoil I / Maschan, Alexey A / Novichkova, Galina A / Shcherbina, Anna / Panteleev, Mikhail A

British journal of haematology

2023 Volume 202, Issue 3, Page(s) 645–656

Abstract: Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disorder caused by WAS gene mutations resulting in haematopoietic/immune cell defects. Recent studies report accelerated death of WAS platelets and lymphocytes. Data on megakaryocyte (MK) maturation, ...

Abstract	Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disorder caused by WAS gene mutations resulting in haematopoietic/immune cell defects. Recent studies report accelerated death of WAS platelets and lymphocytes. Data on megakaryocyte (MK) maturation, viability and their possible role in thrombocytopenia development in WAS are limited. In this study we evaluate the MK viability and morphology in untreated, romiplostim-treated WAS patients compared with normal controls. The study included 32 WAS patients and 17 healthy donors. MKs were captured from bone marrow aspirates by surface-immobilized anti-GPIIb-IIIa antibody. Viability (by phosphatidylserine [PS] externalization), distribution by maturation stages and size of MK were determined by light microscopy. MK distribution by maturation stages in patients differed from controls. 40 ± 22% of WAS MKs versus 23 ± 11% of normal MKs were at maturation stage 3 (p = 0.02), whereas 24 ± 20% in WAS and 39 ± 14% in controls had megakaryoblast morphology (p = 0.05). Romiplostim treatment changed the MK maturation stages distribution close to normal. PS-positive (PS+) MK in WAS was significantly higher (21 ± 21%) than in healthy controls (2 ± 4%, p < 0.01). WAS patients with more damaging truncating mutations and higher disease score had higher PS+ MK fraction (Spearman r = 0.6, p < 0.003). We conclude that WAS MKs have increased cell death tendency and changes in maturation pattern. Both could contribute to thrombocytopenia in WAS patients.
MeSH term(s)	Humans ; Megakaryocytes ; Wiskott-Aldrich Syndrome/genetics ; Blood Platelets/metabolism ; Thrombocytopenia/genetics ; Hematopoiesis
Language	English
Publishing date	2023-05-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80077-6
ISSN	1365-2141 ; 0007-1048
ISSN (online)	1365-2141
ISSN	0007-1048
DOI	10.1111/bjh.18875
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