GPU-accelerated Kendall distance computation for large or sparse data.

Background: Current experimental practices typically produce large multidimensional datasets. Distance matrix calculation between elements (e.g.

scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting.

Single-cell ATAC-seq (scATAC-seq) is a recently developed approach that provides means to investigate open chromatin at single cell level, to assess epigenetic regulation and transcription factors binding landscapes. The sparsity of the scATAC-seq data calls for imputation. Similarly, preprocessing (filtering) may be required to reduce computational load due to the large number of open regions.

Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms.

Differential methylation (DM) is actively recruited in different types of fundamental and translational studies. Currently, microarray- and NGS-based approaches for methylation analysis are the most widely used with multiple statistical models designed to extract differential methylation signatures. The benchmarking of DM models is challenging due to the absence of gold standard data.

Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking.

Expression analysis of small noncoding RNA (sRNA), including microRNA, piwi-interacting RNA, small rRNA-derived RNA, and tRNA-derived small RNA, is a novel and quickly developing field. Despite a range of proposed approaches, selecting and adapting a particular pipeline for transcriptomic analysis of sRNA remains a challenge. This paper focuses on the identification of the optimal pipeline configurations for each step of human sRNA analysis, including reads trimming, filtering, mapping, transcript abundance quantification and differential expression analysis.

In Silico Drug Repurposing in Multiple Sclerosis Using scRNA-Seq Data.

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system still lacking a cure. Treatment typically focuses on slowing the progression and managing MS symptoms. Single-cell transcriptomics allows the investigation of the immune system-the key player in MS onset and development-in great detail increasing our understanding of MS mechanisms and stimulating the discovery of the targets for potential therapies.

Hobotnica: exploring molecular signature quality.

A Molecular Features Set (MFS), is a result of a vast diversity of bioinformatics pipelines. The lack of a "gold standard" for most experimental data modalities makes it difficult to provide valid estimation for a particular MFS's quality. Yet, this goal can partially be achieved by analyzing inner-sample Distance Matrices (DM) and their power to distinguish between phenotypes.

ITAS: Integrated Transcript Annotation for Small RNA.

Transcriptomics analysis of various small RNA (sRNA) biotypes is a new and rapidly developing field. Annotations for microRNAs, tRNAs, piRNAs and rRNAs contain information on transcript sequences and loci that is vital for downstream analyses. Several databases have been established to provide this type of data for specific RNA biotypes.

Star-Shaped Polydimethylsiloxanes with Organocyclotetrasilsesquioxane Branching-Out Centers: Synthesis and Properties.

New non-crystallizable low-dispersity star-shaped polydimethylsiloxanes (PDMS) containing stereoregular -tetra(organo)(dimethylsiloxy)cyclotetrasiloxanes containing methyl-, tolyl- and phenyl-substituents at silicon atoms and the mixture of four stereoisomers of tetra[phenyl(dimethylsiloxy)]cyclotetrasiloxane as the cores were synthesized. Their thermal and viscous properties were studied. All synthesized compounds were characterized by a complex of physicochemical analysis methods: nuclear magnetic resonance (NMR), FT-IR spectroscopy, gel permeation chromatography (GPC), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), viscometry in solution, rheometry, and Langmuir trough study.

Robustness of differential gene expression analysis of RNA-seq.

RNA-sequencing (RNA-seq) is a relatively new technology that lacks standardisation. RNA-seq can be used for Differential Gene Expression (DGE) analysis, however, no consensus exists as to which methodology ensures robust and reproducible results. Indeed, it is broadly acknowledged that DGE methods provide disparate results.

Clinically Actionable Insights into Initial and Matched Recurrent Glioblastomas to Inform Novel Treatment Approaches.

Glioblastoma is the most common primary adult brain tumour, and despite optimal treatment, the median survival is 12-15 months. Patients with matched recurrent glioblastomas were investigated to try to find actionable mutations. Tumours were profiled using a validated DNA-based gene panel.

Recounting the FANTOM CAGE-Associated Transcriptome.

Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes, including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study.

Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients.

Background: Deciphering the meaning of the human DNA is an outstanding goal which would revolutionize medicine and our way for treating diseases. In recent years, non-coding RNAs have attracted much attention and shown to be functional in part. Yet the importance of these RNAs especially for higher biological functions remains under investigation.

NUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free Methods.

Longitudinal next-generation sequencing of cancer patient samples has enhanced our understanding of the evolution and progression of various cancers. As a result, and due to our increasing knowledge of heterogeneity, such sampling is becoming increasingly common in research and clinical trial sample collections. Traditionally, the evolutionary analysis of these cohorts involves the use of an aligner followed by subsequent stringent downstream analyses.

[Diagnostic criteria for the transition from occlusal splints to non-removable orthopedic appliances in patients with TMJ dysfunction with disc disorders].

The aim of the study was to elaborate Diagnostic criteria for the transition from occlusal splints to non-removable orthopedic appliances in patients with TMJ dysfunction with disc disorders. The study involved 95 patients with the clinics of TMJ dysfunction. An examination included electrovibrography and computerized electromyography in order to assess diagnostic value of the methods.

Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression.

Purpose: Gene expression profiling can uncover biologic mechanisms underlying disease and is important in drug development. RNA sequencing (RNA-seq) is routinely used to assess gene expression, but costs remain high. Sample multiplexing reduces RNAseq costs; however, multiplexed samples have lower cDNA sequencing depth, which can hinder accurate differential gene expression detection.

Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid .

is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration-rehydration transcriptomes, together with the genome of (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes during anhydrobiosis, as well as a developmental series, we show that the TCTAGAA DNA motif, which closely resembles the binding motif of the heat shock transcription activator (Hsf), is significantly enriched in the promoter regions of desiccation-induced genes in , such as genes encoding late embryogenesis abundant (LEA) proteins, thioredoxins, or trehalose metabolism-related genes, but not in Unlike , has double TCTAGAA sites upstream of the Hsf gene itself, which is probably responsible for the stronger activation of Hsf in during desiccation compared with To confirm the role of Hsf in desiccation-induced gene activation, we used the Pv11 cell line, derived from embryo.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files.

Motivation: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (i) a cost efficient and (ii) an optimal experimental design leading to a compromise, e.

Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients.

Background: Data from RNA-seq experiments provide a wealth of information about the transcriptome of an organism. However, the analysis of such data is very demanding. In this study, we aimed to establish robust analysis procedures that can be used in clinical practice.

[Use of functional packages of medical stuff by military level of medical service of the Armed Forces].

Authors submitted results of recent developments made by The Kirov Military-Medical Academy and OOO "Special medical equipment" in accordance with State defence order in the area of modernization of the system of organizational equipment of military level of medical service of the Armed Forces of the Russian Federation. Along with other samples of organizational equipment, new functional equipment of medical stuff was developed and approved as supply. New equipment of medical stuff meets modern requirements and is highly valuated by medical services of foreign countries.

[Use of modern first-aid kits in the Armed Forces of the Russian Federation].

Taken to supply of the Armed Forces of the Russian Federation, individual and group first aid kits include a range of innovative pharmaceuticals and medical devices, which ensures effective implementation of measures of first aid to servicemen injured and wounded in the performance of combat training missions, the conduct of hostilities with conventional weapons and weapons of mass destruction, as well as the occurrence of natural and man-made disasters (catastrophes).

[Development of the rationing of medical equipment for troops in the modern world].

Specification of new legal document of medical service of Armed Forces of Russian Federation is presented. It is the calculate norms of medical equipment for delivery of health care and treatment for the wounded. This document was developed for the purpose of development the rationing of medical equipment in the design of measures of the military medical arrangement instead of identical norm of the 1995 edition.

[Organization of support and quality control of medicaments in Russian Federation Armed Forces medical service].

The article presents the chronological analysis of formation of the system for providing the medicament quality control in the medical service of Russian Federation Armed Forces. The role of Centers of medicament quality control and certification in the State system for providing medicament quality is demonstrated. The aims of these Centers are to prevent the getting of poor and falsified medicaments into the troops.