Ontogenetic Structure of Ceоnopopulations of Tulipa korolkowii Regel in Uzbekistan

Ontogenetic structure of eight coenopopulations of Tulipa korolkowii Regel were studied in Uzbekistan. Resistance mechanisms of Tulipa korolkowii coenopopulations are shown: seed and vegetative methods of self-maintenance of coenopopulations. Coenopopulations (CP) of T. korolkovii studied in normal. CP 1, 2, 6, 7,8 complete, and the rest (3, 4, 5) are incomplete, no senile individuals. Absence of old specimens in coenopopulation connected with die-off great number plants in generative period of ontogenesis

Dynamics of Endovascular Therapy Department’s work of Scientific Research Institute of Heart Surgery and Organ Transplantation, Bishkek, Kyrgyzstan

In recent years, high medical-social importance of most nosological types of cardiovascular diseases reflects an increase of surgery activity in this medical field. The enlargement of endovascular procedures is obvious and logical process. Today Endovascular therapy department of Scientific Research Institute of Heart Surgery and Organ Transplantation is one of the medical facility, where conducted scientific researches and new methods of diagnostics and treatment of vascular and cardiac diseases are being introduced

Соотношение изменений гемодинамики малого круга кровообращения и сократимости желудочков сердца у больных с дилатационной кардиомиопатией

In 32 patients with acute dilatational cardiomyopathy (ACMP) the relation between left and right section of lesser circulation with and without high pulmonary hypertension (PH) was studied. In the patients with the low stroke volume of the right ventricle it was not found significant differences in PH level in comparison with the subgroup with the more higher stroke volume. This fact testifies that in patients with ACMP the level of PH depends in general on the relationship between impairments of left and right ventricles.У 32 больных острой дилатационной кардиомиопатией (ОКМП) изучено соотношение нарушений гемодинамики левых и правых отделов сердца малого круга кровообращения с высокой легочной артериальной гипертензией (ЛАГ) и без нее. У больных ОКМП с низкой фракцией выброса правого желудочка не было получено достоверных отличий в величине ЛАГ по сравнению с подгруппой с более высокой фракцией выброса правого желудочка. Это свидетельствует о том, что у больных ОКМП ЛАГ в основном зависит от соотношения левого и правого желудочковых нарушений

Treatment of cryptorchidism in pediatric surgical practice: a multicenter study

Introduction. Cryptorchidism is a common disease in pediatric urological and andrological practice since the issues of tactical approaches and its optimal treatment remain extremely relevant. Cryptorchidism makes a significant contribution to the structure of male infertility.Objective. To conduct a retrospective analysis of treatment results in children and adolescents with cryptorchidism.Materials & methods. This study summarises the treatment results of 8308 patients with cryptorchidism aged from 6 months to 17 years who underwent inpatient treatment in the Russian Federation and the Republic of Uzbekistan.Results. It was revealed that from 2015 to 2019, patients were admitted for surgical treatment evenly over the years. The ratio of right-sided / left-sided / bilateral cryptorchidism was 4.6 : 4.4 : 1 The inguinal form prevailed more than 6 times over the abdominal location. At the same time, 26.1% of the patients underwent surgery at the optimal time, and 9.8% were older than 10 years. More often, children are operated from an open inguinal access (95.0%), much less often — laparoscopically and percutaneously. Stage-by-stage treatment was carried out in 6.0% of patients.Conclusion. Thus, the approach presented in the study in the surgical treatment of cryptorchidism provided good treatment results. The number of disease relapses was 1.9% (mainly among children over 7 years old). Most surgeons are very reserved about primary orchidectomies (only 3.8% were performed)

Membrane Efficiency and Diffusive Tortuosity of a Dense Prehydrated Geosynthetic Clay Liner

In this study, a series of membrane/diffusion tests were conducted on specimens of a dense prehydrated geosynthetic clay liner (DPH GCL) subjected to KCl solutions (source concentration, Co = 8.7-160 mM) in rigid-wall cells. The source KCl solutions and de-ionized water (DIW) were circulated across the top and bottom specimen boundaries, respectively, and membrane efficiency coefficients, w, were measured based on the differential pressures induced across the specimens due to prevention of liquid flux. Also, effective salt-diffusion coefficients, Ds*, and apparent tortuosity factors, ta, were determined for each specimen based on the steady-state diffusive Cl- flux measured at the exit (bottom) boundary. The DPH GCL specimens exhibited higher w and lower Ds* (and, likewise, lower ta) relative to conventional (granular, non-prehydrated) GCL specimens tested under similar conditions. The results were consistent with the lower hydraulic conductivities, k, measured for the DPH GCL specimens and are attributed primarily to the higher bentonite dry densities in the DPH GCL specimens (1.1 Mg/m3) relative to the conventional GCL specimens (~0.4 Mg/m3), although differences in bentonite texture (powdered versus granular), bentonite type (treated versus untreated), and testing apparatus (rigid wall versus flexible wall) may have been contributing factors. Both the DPH GCL and the conventional GCL exhibited similar trends of decreasing ta with increasing w. The ta values are considered to be a function of both a matrix tortuosity factor, tm, that accounts for the geometry of the interconnected pores, and a restrictive tortuosity factor, tr, that accounts for solute exclusion due to membrane behavior. Whereas the DPH GCL exhibited a lower tm relative to the conventional GCL, both GCLs exhibited similar trends of decreasing tr with increasing w. The relationship between tr and w for both GCLs is reasonably well represented by tr = 1 – w, an expression that has been proposed for clay membranes in previous theoretical and experimental studies

LAUNCH OF Q-SYMPHONY BIOINFORMATICS COMPUTING SYSTEM: A HIGH-PERFORMANCE CLUSTER FOR ANALYSIS OF LARGE-SCALE GENOMIC DATASETS

Introduction: One whole human genome, provided by next generation sequencing platforms, in raw format takes 20 to 50 GB. In the course of bioinformatics analysis and data analysis, the data volume increases to 300-500 GB per genome. with an increase in the number of samples, the occupied volume increases. Such a large amount of data required for the analysis of whole genomes demands powerful computing power in the form of servers and data warehouses combined into clusters. We at Laboratory of Bioinformatics and Systems Biology have developed and launched Q-Symphony bioinformatics computing system called (“Qazaq Symphony of Bioinformatics”) for bioinformatics analyses of solving large scale genomic datasets. Materials and methods: The Q-Symphony bioinformatics computing system consists 12high-performance HPE servers: 1control node, 8 compute nodes, 1fat-memory compute node, and 2storage nodes. The system runs on Red Hat Enterprise Linux. The management node controls access to user profiles, data warehouse and Moab Workload Manager. The total number of processing cores is 172, the total amount of RAM is 3072GB, and the total storage capacity is 198 TB, a peak performance of the system of 7.3 TFlops. All nodes use high-speed Infiniband network connections, which allow the data exchange between nodes at 100 Gbps speed. The computational capabilities of the Q-symphony system allow us to evenly distribute resources for each task performed, monitor the load on processor and memory resources in real time, and queue and execute sequentially large lists of tasks. Results: Benchmark measurements performed on Q-symphony system showed an increase of subtasks execution from 15 to 54 times compared to standard solutions built on similar computational processors. Conclusion: The presence of Q-Symphony, well-established and proven bioinformatics methods will make it possible to successfully analyze large-scale human genomic data and determine structural genomic variants and carry out complex comparative and population analysis

IDENTIFICATION OF KAZAKH SPECIFIC GENOMIC VARIANTS USING COMPARATIVE GENOMICS ANALYSIS

Introduction: The modern development of high-performance genomic technologies opens up new possibilities for studying the human genome. Large-scale genomic research generates huge amounts of data, the active development of bioinformatics with the availability of modern methods and approaches of analysis makes it possible to create detailed databases and comprehensively study genomic data. One of contemporary task is to study and identify specific genomic variants of population by detailed analysis of complete genome and complete exome data comparison with open large-scale population datasets. Materials and methods: Materials of the study are 14 complete genomes and 125 complete exomes of Kazakhstani individuals. Our dataset was replenished with data from large whole genome population datasets (SGDP, PRJEB26349, HGDP and 1000 Genomes) for comparative population genomics and to search and identify specific genomic variants. The data in the raw format was mapped and aligned on a single reference genome hg19, then genomic variants were searched and an individual map of the found variants was formed for each dataset in the VCF format. For replenished datasets formed a general map of all variants, which were then excluded from the total number variants found for of Kazakh sampling to search for specific genomic variants. Then the filtered variants were annotated and interpreted. Results: For Kazakр whole exomes were found 9 heterozygous or mutant variants unique among formed genomic databases. 7 variants located on the intron region, 1on the upstream and the last variant frameshift deletion on exonic region. For the Kazakh whole genomes were found 4732heterozygous or mutant variants, 517 variants presented among all Kazakh samples and 144 variants were completely mutant. Only 8 SNVs are located at exonic region: 4 synonymous SNV, 3 nonsynonymous SNV, and 1frameshift deletion. Conclusion: We have discovered unique several genomic variants specific for now to the kazakh individuals. These results can serve as a basis for the creation of a Kazakh reference genome, subsequent research and comparative analysis of Kazakh individuals with various populations of the world. Grant references: AP05135430; MES RK

META-ANALYSIS OF CANCER TRANSCRIPTOMES USING INDEPENDENT COMPONENT ANALYSIS

Introduction: Independent Component Analysis (ICA) is a matrix factorization method for data dimension reduction. ICA has been widely applied for the analysis of transcriptomic data for blind separation of biological, environmental and technical factors affecting gene expression. This study aimed to analyze cancer data using the ICA for identification and comprehensive analysis of reproducible signaling pathways and molecular signatures in cancer. Materials and Methods: In this study, four independent cancer transcriptomic datasets GSE26886, GSE69925, GSE32701and GSE21293 (Affymetrix) from GEO databases were used. R Bioconductor and Matlab have been used for normalization. A bioinformatics tool «BiODICA - Independent Component Analysis of Big Omics Data» was applied to compute independent components (ICs). Gene Set Enrichment Analysis (GSEA) and ToppGene uncovered the most significantly enriched pathways. Construction and visualization of gene networks and graphs were performed using the OFTEN method, Cytoscape and HPRD database. Results: The correlation graph between decompositions into 30 ICs was built with absolute correlation values exceeding 0.15. Clusters of components - pseudocliques were observed in the structure of the correlation graph. Top 500 most contributing genes of each ICs in pseudocliques were mapped to the PPI network to construct signaling pathways for gene interaction. Some cliques were composed of densely interconnected nodes and included components common to most cancer types, while others were common to some of them. Conclusion: The results of this investigation may reveal potential biomarkers of carcinogenesis, functional subsystems in the tumor cells, and helpful in predicting the early development of a tumor

MULTIDRUG-RESISTANT TUBERCULOSIS: WHOLE-GENOME SEQUENCING AND BIOINFORMATICS ANALYSIS

Introduction:Tuberculosis (TB) remains a serious public health threat worldwide. It is estimated that approximately one-third of the world’s population has been infected with multidrug-resistant tuberculosis (MDR-TB), and 1.8 million people die of this disease annually. It is extremely important to determinate susceptible and resistant strains with different mutations in genes encoding drug metabolism of Mycobacterium tuberculosis (MTB) strains in Kazakhstan. Materials and Methods: The whole genome sequencing of 8 MDR-TB clinical isolates using next-generation sequencing platform were examined. Results: Both missense and splice mutations, known pathogenic and novel variants were found. Genomic variants (SNPs and indels) in de novo assembled and annotated whole-genomes and specific/ novel variants in drug-resistant genes of MDR strains from Kazakhstan were observed. We identified 1933 non repetitive single nucleotide variations (SNVs), among which a common pool of 1037 SNPs were shared by the 8 isolates. We found several mutations that are known to confer resistance to drugs. The majority of MTB isolates were the Beijing-type strain (lineage 2- East-Asian lineage) and their complete genomes were studied for the first time in Kazakhstan. The most frequent resistance mutations were observed in the katG and rpoB genes, conferring resistance to isoniazid and rifampicin respectively. In addition, WGS analysis allowed the detection of heteroresistance to multiple drugs. Conclusion: These findings may provide a basis for expansion of the reference MTB database, and further investigation of virulence and transmissibility patterns in MDR strains. This study may provide a basis for creation of the reference database, the subsequent study, and comparison with the different drug-resistant MTB isolates circulating in Kazakhstan. Grant references: AP05134737; MES RK