A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a benchmark containing mosaic variants in the Genome in a Bottle Consortium (GIAB) HG002 reference material DNA from a large batch of a normal lymphoblastoid cell line. First, we used a somatic variant caller with high coverage (300x) Illumina whole genome sequencing data from the Ashkenazi Jewish trio to detect variants in HG002 not detected in at least 5% of cells from the combined parental data.

Build-a-Bio-Strip: An Online Platform for Rapid Toxicity Assessment in Chemical Synthesis.

The increasing need to understand and control the environmental impact of chemical processes has revealed the challenge in efficient evaluation of toxicity of the vast number of chemical compounds and their varying effects on biological systems. In this study, we introduce "Build-a-bio-Strip", a novel online service designed to carry out a quick initial analysis of the toxic impact of chemical processes. This platform enables users to automatically generate toxicity characteristics of chemical reactions using their own data on cytotoxicity or median lethal doses of the substances involved or computational predictions based on SMILES strings.

Kinetics of Adsorption-Induced Deformation of Microporous Carbons.

Equilibrium and kinetic behavior of adsorption-induced deformation have attracted a lot of attention in the last few decades. The theoretical and experimental works cover activated carbons, coals, zeolites, glasses, etc. However, most of the theoretical works describe only the equilibrium part of the deformation process or focus on the time evolution of the adsorption process.

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.

Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms of repeat mapping and variant phasing. We present DeepSomatic, a deep learning method for detecting somatic SNVs and insertions and deletions (indels) from both short-read and long-read data, with modes for whole-genome and exome sequencing, and able to run on tumor-normal, tumor-only, and with FFPE-prepared samples.

Ecological condition and invasiveness of Fraxinus pennsylvanica in different ecotopes of the arid Caspian region.

The study investigated ash development in an arid region, focusing on its invasive spread mechanisms at organismic and ecosystem levels under varying moisture conditions. Conducted in the Northern Caspian region's Volga-Urals interfluve, it examined the effects of arid climate, soil salinity, and limited moisture on plant communities. The features of ash functioning at the organismal and ecosystem levels with permanent and partial deficiency of productive moisture in the soil, as well as with its optimal availability, were investigated.

What Drives Deformation of Smart Nanoporous Materials During Adsorption and Electrosorption?

Nanoporous solids have high surface area, so processes at the surface affect the sample as a whole. When guest species adsorb in nanopores, be they molecules adsorbing from the gas phase, or ions adsorbing from solution, they cause material deformation. While often undesired, adsorption- or electrosorption-induced deformation provides a potential for nanoporous materials to be used as actuators.

A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models.

Inherited retinopathies are devastating diseases that in most cases lack treatment options. Disease-modifying therapies that mitigate pathophysiology regardless of the underlying genetic lesion are desirable due to the diversity of mutations found in such diseases. We tested a systems pharmacology-based strategy that suppresses intracellular cAMP and Ca2+ activity via G protein-coupled receptor (GPCR) modulation using tamsulosin, metoprolol, and bromocriptine coadministration.

Polyunsaturated Fatty Acid - mediated Cellular Rejuvenation for Reversing Age-related Vision Decline.

The retina is uniquely enriched in polyunsaturated fatty acids (PUFAs), which are primarily localized in cell membranes, where they govern membrane biophysical properties such as diffusion, permeability, domain formation, and curvature generation. During aging, alterations in lipid metabolism lead to reduced content of very long-chain PUFAs (VLC-PUFAs) in the retina, and this decline is associated with normal age-related visual decline and pathological age-related macular degeneration (AMD). (Elongation of very-long-chain fatty acids-like 2) encodes a transmembrane protein that produces precursors to docosahexaenoic acid (DHA) and VLC-PUFAs, and methylation level of its promoter is currently the best predictor of chronological age.

Local read haplotagging enables accurate long-read small variant calling.

Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy.

PROTECTION OF CONFIDENTIAL MEDICAL INFORMATION IN UKRAINE: PROBLEMS OF LEGAL REGULATION.

The aim of the article is to analyze the legal aspects and mechanisms of confidential medical information protection about an individual in the health care sphere in Ukraine. During the scientific research, various methods of cognition of legal phenomena were used. Among the general scientific approaches, the dialectical method was primarily used, which allowed to identify trends in the development of patient information rights and formulate proposals for improving legislation in the field of medical data protection.

The effect of lactoferin on the free radical and cytokine status of cornea in the experimental thermal burn.

The free radical and cytokine statuses of the cornea during its thermal burn and the possibility of its correction by lactoferrin have been studied in Soviet Chinchilla rabbits. The development of a corneal thermal burn was accompanied by the development of oxidative stress (increased levels of TBA-reactive substances and carbonyl derivatives of proteins, decreased activity of SOD and GPx enzymes) and a pronounced inflammatory reaction with increased levels of TNF-1α, IL-10, TGF-1β. The use of lactoferrin had a pronounced therapeutic effect, which was manifested by accelerated healing, prevention of the development of complications (corneal perforations), a decrease in the severity of oxidative stress, an increase in the concentrations of TNF-1α (in the early stages), IL-10 (in the later stages), TGF-1β (throughout the experiment).

Pyridyl-Substituted Nitronyl Nitroxides: Comprehensive Magnetochemical and Quantum Chemical Study.

A series of pyridyl-substituted nitronyl nitroxides was synthesized and structurally characterized. A comprehensive magnetochemical and quantum chemical study of extended raw of the nitroxides with different substituents R in the pyridine fragment was performed. It was shown, that temperature-dependent magnetic properties are determined by the short contacts between nitroxide groups of adjacent molecules as well as between nitroxide group and methyl substituents in the pseudo axial positions of imidazoline fragments.

Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition.

Vibrational spectroscopy allows us to understand complex physical and chemical interactions of molecular crystals and liquids such as ammonia, which has recently emerged as a strong hydrogen fuel candidate to support a sustainable society. We report inelastic neutron scattering measurement of vibrational properties of ammonia along the solid-to-liquid phase transition with high enough resolution for direct comparisons to ab-initio simulations. Theoretical analysis reveals the essential role of nuclear quantum effects (NQEs) for correctly describing the intermolecular spectrum as well as high energy intramolecular N-H stretching modes.

Neutron Instruments for Research in Coordination Chemistry.

Neutron diffraction and spectroscopy offer unique insight into structures and properties of solids and molecular materials. All neutron instruments located at the various neutron sources are distinct, even if their designs are based on similar principles, and thus, they are usually less familiar to the community than commercial X-ray diffractometers and optical spectrometers. Major neutron instruments in the USA, which are open to scientists around the world, and examples of their use in coordination chemistry research are presented here, along with a list of similar instruments at main neutron facilities in other countries.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads.

Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy.

Germline knockout of protects photoreceptors in three distinct mouse models of retinal degeneration.

Retinitis pigmentosa (RP) is a common form of retinal dystrophy that can be caused by mutations in any one of dozens of rod photoreceptor genes. The genetic heterogeneity of RP represents a significant challenge for the development of effective therapies. Here, we present evidence for a potential gene-independent therapeutic strategy based on targeting , a transcription factor required for the normal differentiation of rod photoreceptors.

Temperature Evolution of Sorbonorit-4 Methane-Induced Deformation through the Eyes of Classical Density Functional Theory.

Activated carbons are widely used industrial adsorbents due to their attractive sorption properties. Although extensive research on activated carbon has been carried out for several centuries, some aspects of the adsorption-induced deformation of activated carbon remain unclear. The puzzling temperature dependence of the methane-induced deformation of activated carbon is investigated in the present work.

Dataset for Automatic Region-based Coronary Artery Disease Diagnostics Using X-Ray Angiography Images.

X-ray coronary angiography is the most common tool for the diagnosis and treatment of coronary artery disease. It involves the injection of contrast agents into coronary vessels using a catheter to highlight the coronary vessel structure. Typically, multiple 2D X-ray projections are recorded from different angles to improve visualization.

Novel pyridyl-substituted nitronyl nitroxides as potential antiarrhythmic and hypotensive agents with low toxicity and enhanced stability in aqueous solutions.

This study explores the antiarrhythmic and hypotensive potential of pyridyl-substituted nitronyl nitroxides derivatives, uncovering the crucial role of a single carbon moiety of the pyridine cycle alongside radical and charged oxygen centers of the imidazoline fragment. Notably, the introduction of fluorine atoms diminished the antiarrhythmic effect, while the most potent derivatives featured the nitronyl nitroxide pattern positioned at the third site of the pyridine cycle. Gender-dependent responses were observed in lead compounds L and L, with L inducing temporary bradycardia and hypotension specifically in female rats, and L causing significant blood pressure reduction followed by rebound in females compared to milder effects in males.