VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.

The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities.

Top-down and bottom-up control of phytoplankton communities by zebra mussels Dreissena polymorpha (Pallas, 1771).

Zebra mussels (ZM), Dreissena polymorpha (Pallas, 1771), are one of the most aggressive invasive species. ZM have a strong bidirectional impact on phytoplankton because of their high nutrient excretion rates and high grazing pressure. Furthermore, the interactions between excretion and selective grazing are related to the trophic status of a waterbody and could cause unpredictable changes in phytoplankton.

MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.

An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes.

MGnify: the microbiome sequence data analysis resource in 2023.

The MGnify platform (https://www.ebi.ac.

Aquacobalamin Accelerates Orange II Destruction by Peroxymonosulfate via the Transient Formation of Secocorrinoid: A Mechanistic Study.

Besides its use in medicine, vitamin B (cobalamin) and its derivatives have found in numerous applications as catalysts. However, studies related to the activation of oxidants via cobalamin are scant. In this work, we showed how the addition of aquacobalamin (HOCbl) accelerates the destruction of azo-dye Orange II by peroxymonosulfate (HSO) in aqueous solutions.

A unified catalog of 204,938 reference genomes from the human gut microbiome.

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog.

MGnify: the microbiome analysis resource in 2020.

MGnify (http://www.ebi.ac.

svist4get: a simple visualization tool for genomic tracks from sequencing experiments.

Background: High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track constructed by short read mapping to a particular genome assembly. There are many software tools to visualize genomic tracks in a web browser or with a stand-alone graphical user interface.

[The interaction effect of ANKK1/DRD2 TaqIA and HTR2C Cys23Ser on approach motivation in schizophrenic patients and normals].

Aim: To evaluate the association of the DRD2 gene and DRD2 x HTR2C interaction with hedonic and activational aspects of approach motivation in schizophrenia.

Material And Methods: Genotypes at polymorphic loci DRD2 rs1800497 and HTR2C rs6318 (Cys23Ser) were identified in a sample that included 174 patients with schizophrenic spectrum disorders and 268 healthy subjects without a family history of psychoses. The participants completed the BIS/BAS and Temporal Experience of Pleasure Scale (TEPS).

[The evaluation of the effectiveness of electrophoresis in the form of Polymineral wipes on the basis of iodine- bromine natural water in the young children suffering from the consequences of perinatal lesions in the central nervous system].

Unlabelled: The background: the increased frequency of serious consequences of perinatal lesions in the central nervous system of the young children dictates the necessity to develop the effective methods of physiotherapy for the early-stage rehabilitation of such patients on the basis of an objective assessment of the adaptive reserves of the organism.

Material And Methods: The present study involved 53 children at the age from 1 to 12 months presenting with the consequences of perinatal lesions to the central nervous system. Thirty of the children were treated with the use of electrophoresis in the form of Polymineral wipes on the basis of natural iodine-bromine water.

[Correlation between the receptor specificity of pandemic influenza A (H1N1)pdm09 virus strains isolated in 2009-2011 and the structure of the receptor-binding site and the probability of fatal primary viral pneumonia].

The receptor specificity (RS) of pandemic influenza A(H1N1) pdm09 virus strains deposited into the State Collection of Viruses of the Russian Federation, D. I. Ivanovsky Research Institute of Virology, Ministry of Health and Social Development of Russia, in the 2009-2010 and 2010-2011 epidemic seasons to a panel of 9 sialoglycopolymers (SGP).

[A possible association of fatal pneumonia with mutations of pandemic influenza A/H1N1 sw1 virus in the receptor-binding site of the HA1 subunit].

The paper gives the results of sequence analysis of 150 positive samples in real-time RT-PCR, including 47 autopsy materials from patients (including 10 pregnant women), who died from fatal pneumonia mainly in November-December 2009, in whom the lifetime etiological diagnosis had not been made and hence no early etiotropic therapy performed. 70% of the primary materials from the deceased patients were found to have pandemic influenza A(H1N1) v mutants in the lung tissue with D222G (15%), D222N (15%), D222E (2%) substitutions, as well as a mixture of mutants (38%). Nasopharyngeal lavages from 3 Chukotka deceased patients exhibited only consensus (nonmutant) D222 virus variants; there was a mixture of consensus and mutant virus variants in the trachea and a mixture of mutant ones in the lung.

[Detection of the virus of hepatitis E isolates and elucidation of the possibility of their replication in vitro].

Blood serum samples collected from patients with acute hepatitis symptoms admitted to Infectious Disease Hospitals of Novosibirsk, Barnaul, and Irkutsk were studied. The serum samples were tested for the IgM and IgG antibodies to HEV using ELISA. Seropositive samples were tested using RT-PCR for HEV RNA.

[Role of starch preparations in the intraoperative correction of hypovolemia in patients with large-size uterine myomas].

The course of anesthesia during uterine extirpation for large and giant myomas depends on the efficiency of blood loss compensation and relative hypovolemia after rapid decompensation when a mass is removed. Thirty-five patients with a uterine myoma with the size corresponding to 18-40-week gestation were examined. Dextrans and voluven (hydroxyethylstarch 130/0.

[Quantitative evaluation of blood loss severity in surgical practice].

Aim: To develop a quantitative method of evaluation of the volume and degree of intraoperative blood loss.

Material And Methods: Blood loss quantitation is based on maximal collection of the lost blood and its measurement by lost globular volume (GV), i.e.

Is replication of hepatitis C virus a marker of activity of infectious process? (Findings of polymerase chain reaction and morphological analysis of liver biopsy specimens).

Comparative study of replication markers of hepatitis C virus in various biological substrates and evaluation of activity of chronic HCV infection in liver biopsy specimens showed that replication of hepatitis C virus and the number of HCV-infected hepatocytes did not promote liver damage in chronic hepatitis C. These findings indicate that the expression of antiviral reactions by liver parenchyma cells plays the key role in the morphogenesis of HCV infection.

Immunohistochemical, molecular, and pathomorphological study of liver biopsy specimens during chronic hepatitis C.

We carried out a comparative study of replication markers of hepatitis C virus (HCV RNA) in some biological substrates and NS3-antigen in liver biopsy specimens. It was found that 82% liver specimens contained RNA HCV, in 44% cases HCV RNA was present in the serum, mononuclear blood cells, and liver. The presence of NS3-antigen in hepatocytes can be considered as a structural marker of HCV replication, which is confirmed by positive correlation with the results of PCR for viral RNA in tissue specimens.

[Markers of hepatitis C and its various genotypes in patients from Novosibirsk].

Study of the prevalence of hepatitis C virus (HCV) markers in 153 patients of Municipal Infectious Diseases Clinical Hospital No. 1 in Novosibirsk revealed anti-HCV in 88.2% patients and viral RNA in 69.

[Certification of oral hygiene agents from a microbiological viewpoint].

The authors validate the necessity of hygienic certification including microbiological control of perfumes and cosmetics, to which oral hygiene means belong. They consider that the absence of sanitary regulations for some goods, toothpastes included, is one of the causes, responsible for the absence of a proper sanitary control on the part of State Epidemiological Survey of the Russian Federation. In accordance with the resolution "On Certification of Perfumes and Cosmetics" issued in 1994, Central Research Institute of Stomatology is appointed the central institution responsible for certification of means of oral hygiene, and at present its main task is development of sanitary regulations, standards, methods of investigation, and training of personnel for institutions which are to carry out certification.

[The local immunity of the oral cavity in dental caries].

Functional activity of local immunity with regard to dental caries in children is liable to appreciable individual fluctuations which depend on sex, age, and season. In children aged 4 to 5 no association between the titer of antibodies to cariogenic Streptococcus and number of carious lesions was observed, whereas in those aged 9 to 19 these parameters were in inverse relationship. In children aged 11-12 and 14-16 this association is inverse.